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Sample records for opportunistic pathogens enriched

  1. Environmental Variation Generates Environmental Opportunist Pathogen Outbreaks.

    Science.gov (United States)

    Anttila, Jani; Kaitala, Veijo; Laakso, Jouni; Ruokolainen, Lasse

    2015-01-01

    Many socio-economically important pathogens persist and grow in the outside host environment and opportunistically invade host individuals. The environmental growth and opportunistic nature of these pathogens has received only little attention in epidemiology. Environmental reservoirs are, however, an important source of novel diseases. Thus, attempts to control these diseases require different approaches than in traditional epidemiology focusing on obligatory parasites. Conditions in the outside-host environment are prone to fluctuate over time. This variation is a potentially important driver of epidemiological dynamics and affect the evolution of novel diseases. Using a modelling approach combining the traditional SIRS models to environmental opportunist pathogens and environmental variability, we show that epidemiological dynamics of opportunist diseases are profoundly driven by the quality of environmental variability, such as the long-term predictability and magnitude of fluctuations. When comparing periodic and stochastic environmental factors, for a given variance, stochastic variation is more likely to cause outbreaks than periodic variation. This is due to the extreme values being further away from the mean. Moreover, the effects of variability depend on the underlying biology of the epidemiological system, and which part of the system is being affected. Variation in host susceptibility leads to more severe pathogen outbreaks than variation in pathogen growth rate in the environment. Positive correlation in variation on both targets can cancel the effect of variation altogether. Moreover, the severity of outbreaks is significantly reduced by increase in the duration of immunity. Uncovering these issues helps in understanding and controlling diseases caused by environmental pathogens.

  2. Common features of opportunistic premise plumbing pathogens.

    Science.gov (United States)

    Falkinham, Joseph O

    2015-04-24

    Recently it has been estimated that the annual cost of diseases caused by the waterborne pathogens Legionella pneumonia, Mycobacterium avium, and Pseudomonas aeruginosa is $500 million. For the period 2001-2012, the estimated cost of hospital admissions for nontuberculous mycobacterial pulmonary disease, the majority caused by M. avium, was almost $1 billion. These three waterborne opportunistic pathogens are normal inhabitants of drinking water--not contaminants--that share a number of key characteristics that predispose them to survival, persistence, and growth in drinking water distribution systems and premise plumbing. Herein, I list and describe these shared characteristics that include: disinfectant-resistance, biofilm-formation, growth in amoebae, growth at low organic carbon concentrations (oligotrophic), and growth under conditions of stagnation. This review is intended to increase awareness of OPPPs, identify emerging OPPPs, and challenge the drinking water industry to develop novel approaches toward their control.

  3. Cultivation of Pathogenic and Opportunistic Free-Living Amebas

    Science.gov (United States)

    Schuster, Frederick L.

    2002-01-01

    Free-living amebas are widely distributed in soil and water, particularly members of the genera Acanthamoeba and Naegleria. Since the early 1960s, they have been recognized as opportunistic human pathogens, capable of causing infections of the central nervous system (CNS) in both immunocompetent and immunocompromised hosts. Naegleria is the causal agent of a fulminant CNS condition, primary amebic meningoencephalitis; Acanthamoeba is responsible for a more chronic and insidious infection of the CNS termed granulomatous amebic encephalitis, as well as amebic keratitis. Balamuthia sp. has been recognized in the past decade as another ameba implicated in CNS infections. Cultivation of these organisms in vitro provides the basis for a better understanding of the biology of these amebas, as well as an important means of isolating and identifying them from clinical samples. Naegleria and Acanthamoeba can be cultured axenically in cell-free media or on tissue culture cells as feeder layers and in cultures with bacteria as a food source. Balamuthia, which has yet to be isolated from the environment, will not grow on bacteria. Instead, it requires tissue culture cells as feeder layers or an enriched cell-free medium. The recent identification of another ameba, Sappinia diploidea, suggests that other free-living forms may also be involved as causal agents of human infections. PMID:12097243

  4. Morganella morganii, a non-negligent opportunistic pathogen.

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    Liu, Hui; Zhu, Junmin; Hu, Qiwen; Rao, Xiancai

    2016-09-01

    Morganella morganii belongs to the tribe Proteeae of the Enterobacteriaceae family. This species is considered as an unusual opportunistic pathogen that mainly causes post-operative wound and urinary tract infections. However, certain clinical M. morganii isolates present resistance to multiple antibiotics by carrying various resistant genes (such as blaNDM-1, and qnrD1), thereby posing a serious challenge for clinical infection control. Moreover, virulence evolution makes M. morganii an important pathogen. Accumulated data have demonstrated that M. morganii can cause various infections, such as sepsis, abscess, purple urine bag syndrome, chorioamnionitis, and cellulitis. This bacterium often results in a high mortality rate in patients with some infections. M. morganii is considered as a non-negligent opportunistic pathogen because of the increased levels of resistance and virulence. In this review, we summarized the epidemiology of M. morganii, particularly on its resistance profile and resistant genes, as well as the disease spectrum and risk factors for its infection.

  5. Relationship between lactobacilli and opportunistic bacterial pathogens associated with vaginitis

    OpenAIRE

    Razzak, Mohammad Sabri A.; Alaa H. Al-Charrakh; Bara Hamid AL-Greitty

    2011-01-01

    Background: Vaginitis, is an infectious inflammation of the vaginal mucosa, which sometimes involves the vulva. The balance of the vaginal flora is maintained by the Lactobacilli and its protective and probiotic role in treating and preventing vaginal infection by producing antagonizing compounds which are regarded as safe for humans. Aim: The aim of this study was to evaluate the protective role of Lactobacilli against common bacterial opportunistic pathogens in vaginitis and study the effec...

  6. Relationship between lactobacilli and opportunistic bacterial pathogens associated with vaginitis

    Science.gov (United States)

    Razzak, Mohammad Sabri A.; Al-Charrakh, Alaa H.; AL-Greitty, Bara Hamid

    2011-01-01

    Background: Vaginitis, is an infectious inflammation of the vaginal mucosa, which sometimes involves the vulva. The balance of the vaginal flora is maintained by the Lactobacilli and its protective and probiotic role in treating and preventing vaginal infection by producing antagonizing compounds which are regarded as safe for humans. Aim: The aim of this study was to evaluate the protective role of Lactobacilli against common bacterial opportunistic pathogens in vaginitis and study the effects of some antibiotics on Lactobacilli isolates. Materials and Methods: In this study (110) vaginal swabs were obtained from women suffering from vaginitis who admitted to Babylon Hospital of Maternity and Paediatrics in Babylon province, Iraq. The study involved the role of intrauterine device among married women with vaginitis and also involved isolation of opportunistic bacterial isolates among pregnant and non pregnant women. This study also involved studying probiotic role of Lactobacilli by production of some defense factors like hydrogen peroxide, bacteriocin, and lactic acid. Results: Results revealed that a total of 130 bacterial isolates were obtained. Intrauterine device was a predisposing factor for vaginitis. The most common opportunistic bacterial isolates were Staphylococcus aureus, Escherichia coli, Streptococcus agalactiae, and Klebsiella pneumoniae. All Lactobacilli were hydrogen peroxide producers while some isolates were bacteriocin producers that inhibited some of opportunistic pathogens (S. aureus, E. coli). Lactobacilli were sensitive to erythromycin while 93.3% of them were resistant to ciprofloxacin and (40%, 53.3%) of them were resistant to amoxicillin and gentamycin respectively. Results revealed that there was an inverse relationship between Lactobacilli presence and organisms causing vaginitis. This may be attributed to the production of defense factors by Lactobacilli. Conclusion: The types of antibiotics used to treat vaginitis must be very

  7. Relationship between lactobacilli and opportunistic bacterial pathogens associated with vaginitis.

    Science.gov (United States)

    Razzak, Mohammad Sabri A; Al-Charrakh, Alaa H; Al-Greitty, Bara Hamid

    2011-04-01

    Vaginitis, is an infectious inflammation of the vaginal mucosa, which sometimes involves the vulva. The balance of the vaginal flora is maintained by the Lactobacilli and its protective and probiotic role in treating and preventing vaginal infection by producing antagonizing compounds which are regarded as safe for humans. The aim of this study was to evaluate the protective role of Lactobacilli against common bacterial opportunistic pathogens in vaginitis and study the effects of some antibiotics on Lactobacilli isolates. In this study (110) vaginal swabs were obtained from women suffering from vaginitis who admitted to Babylon Hospital of Maternity and Paediatrics in Babylon province, Iraq. The study involved the role of intrauterine device among married women with vaginitis and also involved isolation of opportunistic bacterial isolates among pregnant and non pregnant women. This study also involved studying probiotic role of Lactobacilli by production of some defense factors like hydrogen peroxide, bacteriocin, and lactic acid. Results revealed that a total of 130 bacterial isolates were obtained. Intrauterine device was a predisposing factor for vaginitis. The most common opportunistic bacterial isolates were Staphylococcus aureus, Escherichia coli, Streptococcus agalactiae, and Klebsiella pneumoniae. All Lactobacilli were hydrogen peroxide producers while some isolates were bacteriocin producers that inhibited some of opportunistic pathogens (S. aureus, E. coli). Lactobacilli were sensitive to erythromycin while 93.3% of them were resistant to ciprofloxacin and (40%, 53.3%) of them were resistant to amoxicillin and gentamycin respectively. Results revealed that there was an inverse relationship between Lactobacilli presence and organisms causing vaginitis. This may be attributed to the production of defense factors by Lactobacilli. The types of antibiotics used to treat vaginitis must be very selective in order not to kill the beneficial bacteria

  8. Secondary metabolite arsenal of an opportunistic pathogenic fungus.

    Science.gov (United States)

    Bignell, Elaine; Cairns, Timothy C; Throckmorton, Kurt; Nierman, William C; Keller, Nancy P

    2016-12-05

    Aspergillus fumigatus is a versatile fungus able to successfully exploit diverse environments from mammalian lungs to agricultural waste products. Among its many fitness attributes are dozens of genetic loci containing biosynthetic gene clusters (BGCs) producing bioactive small molecules (often referred to as secondary metabolites or natural products) that provide growth advantages to the fungus dependent on environment. Here we summarize the current knowledge of these BGCs-18 of which can be named to product-their expression profiles in vivo, and which BGCs may enhance virulence of this opportunistic human pathogen. Furthermore, we find extensive evidence for the presence of many of these BGCs, or similar BGCs, in distantly related genera including the emerging pathogen Pseudogymnoascus destructans, the causative agent of white-nose syndrome in bats, and suggest such BGCs may be predictive of pathogenic potential in other fungi.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

  9. Morganella morganii, a non-negligent opportunistic pathogen

    Directory of Open Access Journals (Sweden)

    Hui Liu

    2016-09-01

    Full Text Available Morganella morganii belongs to the tribe Proteeae of the Enterobacteriaceae family. This species is considered as an unusual opportunistic pathogen that mainly causes post-operative wound and urinary tract infections. However, certain clinical M. morganii isolates present resistance to multiple antibiotics by carrying various resistant genes (such as blaNDM-1, and qnrD1, thereby posing a serious challenge for clinical infection control. Moreover, virulence evolution makes M. morganii an important pathogen. Accumulated data have demonstrated that M. morganii can cause various infections, such as sepsis, abscess, purple urine bag syndrome, chorioamnionitis, and cellulitis. This bacterium often results in a high mortality rate in patients with some infections. M. morganii is considered as a non-negligent opportunistic pathogen because of the increased levels of resistance and virulence. In this review, we summarized the epidemiology of M. morganii, particularly on its resistance profile and resistant genes, as well as the disease spectrum and risk factors for its infection.

  10. Hospital Water Supply as a Potential Source of Opportunistic Pathogens

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    H. T. El-Zanfaly

    2012-01-01

    Full Text Available In Egypt as well as in many other developing countries, there are no specific standards for hospital water. Even water is free from the traditional bacterial indicators, it may represent a source of health hazards especially for elderly, children and patients under dialysis due to the presence of opportunistic pathogenic bacteria. The study was carried out on the bacteriological water quality at the intakes as well as the end of water treatment train of two water treatment plants that supplying three hospitals located in Greater Cairo, Egypt with water that used for different purposes. Samples of the raw water supply for the two water treatment plants (Nile River water showed ranges of 102-105 cfu mL-1, 102-104 MPN 100 mL-1, 102-104 MPN 100 mL-1 and 102-103 MPN 100 mL-1 for Heterotrophic Plate Count (HPC bacteria, Total Coliforms (TC, Fecal Coliforms (FC and Fecal Streptococci (FS, respectively. Treated water showed considerable reduction in HPC while the other bacterial indicators reached the undetectable level. The distribution system impact on treated water quality was limited to causing an increase in HPC bacteria. A study was carried out to determine the presence of Pseudomonas aeuginosa, Aeromonas spp. and Staphylococcus aureus in hospitals tap water, water reservoirs, as well as water for preparation of hemodialysis fluids. Although the post-chlorinated water in both water treatment plants was free from bacterial indicators, it still contaminated with the three studied opportunistic pathogenic bacteria. The detected opportunistic pathogens may be attributed to the distribution system condition and/or the presence of storage tanks. Hemodialysis water samples showed the higher percentage of P. aeruginosa isolates which represent a major source of health risk to patient’s attending dialysis process in hospitals and clinics. The presence of opportunistic bacteria in drinking water and dialysate with absence of coliform and low HPC

  11. Opportunistic pathogens relative to physicochemical factors in water storage tanks.

    Science.gov (United States)

    Al-Bahry, S N; Elshafie, A E; Victor, R; Mahmoud, I Y; Al-Hinai, J A

    2011-06-01

    Household water in Oman, as well as in other countries in the region, is stored in tanks placed on house roofs that can be subjected to physicochemical factors which can promote microbial growth, including pathogens and opportunistic pathogens which pose health risks. Water samples were collected from 30 houses in a heavily populated suburb of Muscat. The tanks used were either glass reinforced plastic (GRP), polyethylene or galvanised iron (GI). Heterotrophic bacteria, coliforms, faecal coliforms and iron sulphur bacteria varied significantly in the three tanks. Yeast and mould count showed significant variations. Isolation of Aeromonas spp., fluorogenic and pathogenic Pseudomonas, Pasteurella, Salmonella, Serratia and Tatumella, and Yersinia and Legionella in biofilms varied in the three tanks. The fungi isolates in the three tanks were Penicillium, Cladosporium and Aspergillus. Nephelometric turbidity unit, threshold odour number and free chlorine varied significantly in the three tanks. True colour unit values did not show a significant difference; however, GRP tanks had algae, autotrophic and pigmented microorganisms. In addition, GI tanks had sediments and corrosion. The results of this investigation are important to evaluate the status of the present household water tanks in countries with high annual temperatures, which may affect public health.

  12. OPPORTUNISTIC ASPERGILLUS PATHOGENS MEASURED IN HOME AND HOSPITAL TAP WATER BY MOLD SPECIFIC QUANTITATIVE PCR (MSQPCR)

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    Opportunistic fungal pathogens are a concern because of the increasing number of immunocompromised patients. The goal of this research was to test a simple extraction method and rapid quantitative PCR (QPCR) measurement of the occurrence of potential pathogens, Aspergillus fumiga...

  13. ANTIBIOTIC RESISTANCE IN THE OPPORTUNISTIC PATHOGEN STENOTROPHOMONAS MALTOPHILIA

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    María Blanca Sánchez

    2015-06-01

    Full Text Available Stenotrophomonas maltophilia is an environmental bacterium found in the soil, associated with plants and animals, and in aquatic environments. It is also an opportunistic pathogen now causing an increasing number of nosocomial infections. The treatment of S. maltophilia is quite difficult given its intrinsic resistance to a number of antibiotics, and because it is able to acquire new resistances via horizontal gene transfer and mutations. Certainly, strains resistant to quinolones, cotrimoxale and/or cephalosporins - antibiotics commonly used to treat S. maltophilia infections - have emerged. The increasing number of available S. maltophilia genomes has allowed the identification and annotation of a large number of antimicrobial and heavy metal resistance genes. Most encode inactivating enzymes and efflux pumps, but information on their role in intrinsic and acquired resistance is limited. Non-typical antibiotic resistance mechanisms that also form part of the intrinsic resistome have been identified via mutant library screening. These include non-typical antibiotic resistance genes, such as bacterial metabolism genes, and non-inheritable resistant phenotypes, such as biofilm formation and persistence. Their relationships with resistance are complex and require further study.

  14. Epidemiology and Ecology of Opportunistic Premise Plumbing Pathogens: Legionella pneumophila, Mycobacterium avium, and Pseudomonas aeruginosa

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    BACKGROUND: Legionella pneumophila, Mycobacterium avium, and Pseudomonas aeruginosa are opportunistic premise plumbing pathogens (OPPPs) that persist and grow in household plumbing, habitats they share with humans. Infections caused by these OPPPs involve individuals with preexis...

  15. Occurrence of Opportunistic Pathogens Legionella pneumophila and non-tuberculous mycobacteria in hospital plumbing systems

    Science.gov (United States)

    Occurrence of Opportunistic Pathogens Legionella pneumophila and non-tuberculous mycobacteria in hospital plumbing systems Jill Hoelle, Michael Coughlin, Elizabeth Sotkiewicz, Jingrang Lu, Stacy Pfaller, Mark Rodgers, and Hodon Ryu U.S. Environmental Protection Agency, Cincinnati...

  16. Epidemiology and Ecology of Opportunistic Premise Plumbing Pathogens: Legionella pneumophila, Mycobacterium avium, and Pseudomonas aeruginosa

    Science.gov (United States)

    BACKGROUND: Legionella pneumophila, Mycobacterium avium, and Pseudomonas aeruginosa are opportunistic premise plumbing pathogens (OPPPs) that persist and grow in household plumbing, habitats they share with humans. Infections caused by these OPPPs involve individuals with preexis...

  17. Free-living amoebae as opportunistic and non-opportunistic pathogens of humans and animals.

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    Schuster, Frederick L; Visvesvara, Govinda S

    2004-08-01

    Knowledge that free-living amoebae are capable of causing human disease dates back some 50 years, prior to which time they were regarded as harmless soil organisms or, at most, commensals of mammals. First Naegleria fowleri, then Acanthamoeba spp. and Balamuthia mandrillaris, and finally Sappinia diploidea have been recognised as etiologic agents of encephalitis; Acanthamoeba spp. are also responsible for amoebic keratitis. Some of the infections are opportunistic, occurring mainly in immunocompromised hosts (Acanthamoeba and Balamuthia encephalitides), while others are non-opportunistic (Acanthamoeba keratitis, Naegleria meningoencephalitis, and cases of Balamuthia encephalitis occurring in immunocompetent humans). The amoebae have a cosmopolitan distribution in soil and water, providing multiple opportunities for contacts with humans and animals, as evidenced by antibody titers in surveyed human populations. Although, the numbers of infections caused by these amoebae are low in comparison to other protozoal parasitoses (trypanosomiasis, toxoplasmosis, malaria, etc.), the difficulty in diagnosing them, the challenge of finding optimal antimicrobial treatments and the morbidity and relatively high mortality associated with, in particular, the encephalitides have been a cause for concern for clinical and laboratory personnel and parasitologists. This review presents information about the individual amoebae: their morphologies and life-cycles, laboratory cultivation, ecology, epidemiology, nature of the infections and appropriate antimicrobial therapies, the immune response, and molecular diagnostic procedures that have been developed for identification of the amoebae in the environment and in clinical specimens.

  18. Identification of quorum-sensing regulated proteins in the opportunistic pathogen Pseudomonas aeruginosa by proteomics

    DEFF Research Database (Denmark)

    Arevalo-Ferro, C.; Hentzer, Morten; Reil, G.

    2003-01-01

    The Gram-negative bacterium Pseudomonas aeruginosa is an opportunistic human pathogen which is responsible for severe nosocomial infections in immunocompromised patients and is the major pathogen in cystic fibrosis. The bacterium utilizes two interrelated quorum-sensing (QS) systems, which rely...

  19. Loss of competition in the outside host environment generates outbreaks of environmental opportunist pathogens.

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    Jani Anttila

    Full Text Available Environmentally transmitted pathogens face ecological interactions (e.g., competition, predation, parasitism in the outside-host environment and host immune system during infection. Despite the ubiquitousness of environmental opportunist pathogens, traditional epidemiology focuses on obligatory pathogens incapable of environmental growth. Here we ask how competitive interactions in the outside-host environment affect the dynamics of an opportunist pathogen. We present a model coupling the classical SI and Lotka-Volterra competition models. In this model we compare a linear infectivity response and a sigmoidal infectivity response. An important assumption is that pathogen virulence is traded off with competitive ability in the environment. Removing this trade-off easily results in host extinction. The sigmoidal response is associated with catastrophic appearances of disease outbreaks when outside-host species richness, or overall competition pressure, decreases. This indicates that alleviating outside-host competition with antibacterial substances that also target the competitors can have unexpected outcomes by providing benefits for opportunist pathogens. These findings may help in developing alternative ways of controlling environmental opportunist pathogens.

  20. Plumbing of hospital premises is a reservoir for opportunistically pathogenic microorganisms: a review.

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    Williams, Margaret M; Armbruster, Catherine R; Arduino, Matthew J

    2013-01-01

    Several bacterial species that are natural inhabitants of potable water distribution system biofilms are opportunistic pathogens important to sensitive patients in healthcare facilities. Waterborne healthcare-associated infections (HAI) may occur during the many uses of potable water in the healthcare environment. Prevention of infection is made more challenging by lack of data on infection rate and gaps in understanding of the ecology, virulence, and infectious dose of these opportunistic pathogens. Some healthcare facilities have been successful in reducing infections by following current water safety guidelines. This review describes several infections, and remediation steps that have been implemented to reduce waterborne HAIs.

  1. Public health implications of Acanthamoeba and multiple potential opportunistic pathogens in roof-harvested rainwater tanks.

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    Hamilton, K A; Ahmed, W; Palmer, A; Sidhu, J P S; Hodgers, L; Toze, S; Haas, C N

    2016-10-01

    A study of six potential opportunistic pathogens (Acanthamoeba spp., Legionella spp., Legionella longbeachae, Pseudomonas aeruginosa, Mycobacterium avium and Mycobacterium intracellulare) and an accidental human pathogen (Legionella pneumophila) in 134 roof-harvested rainwater (RHRW) tank samples was conducted using quantitative PCR (qPCR). All five opportunistic pathogens and accidental pathogen L. pneumophila were detected in rainwater tanks except Legionella longbeachae. Concentrations ranged up to 3.1×10(6) gene copies per L rainwater for Legionella spp., 9.6×10(5) gene copies per L for P. aeruginosa, 6.8×10(5) gene copies per L for M. intracellulare, 6.6×10(5) gene copies per L for Acanthamoeba spp., 1.1×10(5) gene copies per L for M. avium, and 9.8×10(3) gene copies per L for L. pneumophila. Among the organisms tested, Legionella spp. (99% tanks) were the most prevalent followed by M. intracellulare (78%). A survey of tank-owners provided data on rainwater end-uses. Fecal indicator bacteria (FIB) Escherichia coli and Enterococcus spp. were enumerated using culture-based methods, and assessed for correlations with opportunistic pathogens and L. pneumophila tested in this study. Opportunistic pathogens did not correlate well with FIB except E. coli vs. Legionella spp. (tau=0.151, P=0.009) and E. coli vs. M. intracellulare (tau=0.14, P=0.015). However, M. avium weakly correlated with both L. pneumophila (Kendall's tau=0.017, P=0.006) and M. intracellulare (tau=0.088, P=0.027), and Legionella spp. also weakly correlated with M. intracellulare (tau=0.128, P=0.028). The presence of these potential opportunistic pathogens in tank water may present health risks from both the potable and non-potable uses documented from the current survey data.

  2. Draft Genome Sequence of the Rodent Opportunistic Pathogen Pasteurella pneumotropica ATCC 35149T.

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    Sasaki, Hiraku; Ishikawa, Hiroki; Asano, Ryoki; Ueshiba, Hidehiro; Matsumoto, Tetsuya; Boot, Ron; Kawamoto, Eiichi

    2014-08-07

    Pasteurella pneumotropica is an opportunistic pathogen in rodents that is commonly isolated from upper respiratory tracts in laboratory rodents. Here, we report the draft genome sequence of the P. pneumotropica type strain ATCC 35149, which was first isolated and characterized as biotype Jawetz. Copyright © 2014 Sasaki et al.

  3. Draft Genome Sequence of the Rodent Opportunistic Pathogen Pasteurella pneumotropica ATCC 35149T

    OpenAIRE

    Sasaki, Hiraku; Ishikawa, Hiroki; Asano, Ryoki; Ueshiba, Hidehiro; Matsumoto, Tetsuya; Boot, Ron; Kawamoto, Eiichi

    2014-01-01

    Pasteurella pneumotropica is an opportunistic pathogen in rodents that is commonly isolated from upper respiratory tracts in laboratory rodents. Here, we report the draft genome sequence of the P. pneumotropica type strain ATCC 35149, which was first isolated and characterized as biotype Jawetz.

  4. Opportunistic Aspergillus pathogens measured in home and hospital tap water by quantitative PCR (QPCR).

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    Vesper, S J; Haugland, R A; Rogers, M E; Neely, A N

    2007-09-01

    Opportunistic fungal pathogens are a concern because of the increasing number of immunocompromised patients. The goal of this research was to test a simple extraction method and rapid quantitative PCR (QPCR) measurement of the occurrence of potential pathogens, Aspergillus fumigatus, A. flavus, A. terreus and A. niger, in home tap water and a hospital water supply. Water samples were taken from the kitchen tap in the homes of 60 patients who were diagnosed with legionellosis. Water samples were also taken from three locations in a hospital that generated all of its hot water by flash heating. Opportunistic infectious agents Aspergillus fumigatus, A. flavus, A. terreus and A. niger were measured using QPCR. Aspergillus terreus DNA was found in 16.7% and A. fumigatus DNA in 1.7% of the samples taken from the kitchen tap. None of the Aspergillus species were found in any of the hospital water samples.The development of a simple DNA extraction method along with QPCR analysis is suitable for rapid screening of tap water for opportunistic fungal pathogens. This simple method can be used to obtain pathogen occurrence results in about 3 h, instead of waiting days to weeks for culture data. Obtaining pathogen occurrence data in a timely manner could promote the elimination of the pathogens from the water supply of immunocompromised patients.

  5. Cutaneous Aspergillus ustus in a lung transplant recipient: emergence of a new opportunistic fungal pathogen.

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    Vagefi, Parsia A; Cosimi, A Benedict; Ginns, Leo C; Kotton, Camille N

    2008-01-01

    Opportunistic fungal infections remain a significant complication in immunosuppressed patients, especially those having undergone solid-organ transplantation. We report a 39-year-old patient who represents the second case of cutaneous Aspergillus ustus infection in a solid-organ transplant recipient, and the first documented case after lung transplantation. The patient's cutaneous lower extremity aspergillosis responded to a combination of intravenous liposomal amphotericin B, caspofungin and topical terbinafine cream, with a concomitant reduction in immunosuppression. A. ustus is an emerging opportunistic fungal pathogen in transplant recipients.

  6. Characterization and Identification of Two Opportunistic Human Bacterial Pathogens in Rice

    Institute of Scientific and Technical Information of China (English)

    LUO Yuan-chan; XIE Guan-lin; ZHANG Li-xin; AN Gilmyong; FANG Yuan; LUO Jin-yan; HAO Xiao-juan; ZHAO Si-feng

    2006-01-01

    Burkholderia cepacia (Bc) and Pseudomonas aeruginosa (Pa) are both biocontrol agents in agriculture and opportunistic human pathogens in hospitals. Effective management and utilization practice is needed to understand their characteristics and distribution in rice. During the last decade, the two opportunistic human pathogens were detected in 631 samples of rice seed and 117 samples of rice plant in plain, highland and mountainous rice growing areas of China. Bc and Pa were primarily differentiated by common bacteriological characteristics and pathogenic tests and then identified into species by Biolog and FAME tests. However,the genotypes of Bc still could not be distinguished. It has been noted that the Bc and Pa mainly existed in rice root with the highest distribution frequency in plain areas ( 6.1% and 16.1%) and lowest in the mountainous areas (1.0% and 7.8%).

  7. Stress responses in the opportunistic pathogen Acinetobacter baumannii.

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    Fiester, Steven E; Actis, Luis A

    2013-03-01

    Acinetobacter baumannii causes a wide range of severe infections among compromised and injured patients worldwide. The relevance of these infections are, in part, due to the ability of this pathogen to sense and react to environmental and host stress signals, allowing it to persist and disseminate in medical settings and the human host. This review summarizes current knowledge on the roles that environmental and cellular stressors play in the ability of A. baumannii to resist nutrient deprivation, oxidative and nitrosative injury, and even the presence of the commonly used antiseptic ethanol, which could serve as a nutrient- and virulence-enhancing signal rather than just being a convenient disinfectant. Emerging experimental evidence supports the role of some of these responses in the pathogenesis of the infections A. baumannii causes in humans and its capacity to resist antibiotics and host response effectors.

  8. Shewanella putrefaciens – a new opportunistic pathogen of freshwater fish

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    Paździor Ewa

    2016-12-01

    Full Text Available In recent years, Shewanella putrefaciens, commonly known as a halophilic bacteria, has been associated with serious health disorders in freshwater fish. Therefore, it has been described as a new aetiological agent of the disease, named shewanellosis. S. putrefaciens is a heterogeneous group of microorganisms, belonging to the Alteromonadaceae family. Based on different criteria, three biovars and biogroups as well as four genomic groups have been distinguished. The first infections of S. putrefaciens in fish were reported in rabbitfish (Siganus rivulatus and European sea bass (Dicentrarchus labrax L.. Outbreaks in farmed fish were reported in Poland for the first time in 2004. The disease causes skin disorders and haemorrhages in internal organs. It should be noted that S. putrefaciens could also be associated with different infections in humans, such as skin and tissue infections, bacteraemia, otitis. Investigations on pathogenic mechanisms of S. putrefaciens infections are very limited. Enzymatic activity, cytotoxin secretion, adhesion ability, lipopolysaccharide (LPS, and the presence of siderophores are potential virulence factors of S. putrefaciens. Antimicrobial resistance of S. putrefaciens is different and depends on the isolates. In general, these bacteria are sensitive to antimicrobial drugs commonly used in aquaculture.

  9. Interactions between the tropical sea anemone Aiptasia pallida and Serratia marcescens, an opportunistic pathogen of corals.

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    Krediet, Cory J; Meyer, Julie L; Gimbrone, Nicholas; Yanong, Roy; Berzins, Ilze; Alagely, Ali; Castro, Herman; Ritchie, Kim B; Paul, Valerie J; Teplitski, Max

    2014-06-01

    Coral reefs are under increasing stress caused by global and local environmental changes, which are thought to increase the susceptibility of corals to opportunistic pathogens. In the absence of an easily culturable model animal, the understanding of the mechanisms of disease progression in corals remains fairly limited. In the present study, we tested the susceptibility of the tropical sea anemone Aiptasia pallida to an opportunistic coral pathogen (Serratia marcescens). A. pallida was susceptible to S. marcescens PDL100 and responded to this opportunistic coral pathogen with darkening of the tissues and retraction of tentacles, followed by complete disintegration of polyp tissues. Histological observations revealed loss of zooxanthellae and structural changes in eosinophilic granular cells in response to pathogen infection. A screen of S. marcescens mutants identified a motility and tetrathionate reductase mutants as defective in virulence in the A. pallida infection model. In co-infections with the wild-type strain, the tetrathionate reductase mutant was less fit within the surface mucopolysaccharide layer of the host coral Acropora palmata.

  10. The Black Yeast Exophiala dermatitidis and Other Selected Opportunistic Human Fungal Pathogens Spread from Dishwashers to Kitchens.

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    Jerneja Zupančič

    dishwashers. We conclude that dishwashers represent a reservoir of enriched opportunistic pathogenic species that can spread from the dishwasher into the indoor biome.

  11. The Black Yeast Exophiala dermatitidis and Other Selected Opportunistic Human Fungal Pathogens Spread from Dishwashers to Kitchens.

    Science.gov (United States)

    Zupančič, Jerneja; Novak Babič, Monika; Zalar, Polona; Gunde-Cimerman, Nina

    2016-01-01

    conclude that dishwashers represent a reservoir of enriched opportunistic pathogenic species that can spread from the dishwasher into the indoor biome.

  12. From Environment to Man: Genome Evolution and Adaptation of Human Opportunistic Bacterial Pathogens

    Science.gov (United States)

    Aujoulat, Fabien; Roger, Frédéric; Bourdier, Alice; Lotthé, Anne; Lamy, Brigitte; Marchandin, Hélène; Jumas-Bilak, Estelle

    2012-01-01

    Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. The versatility of bacterial life-style involves adaptation to various niches. Adaptation to both open environment and human specific niches is a major challenge that involves intermediate organisms allowing pre-adaptation to humans. The aim of this review is to analyze genomic features of environmental bacteria in order to explain their adaptation to human beings. The genera Pseudomonas, Aeromonas and Ochrobactrum provide valuable examples of opportunistic behavior associated to particular genomic structure and evolution. Particularly, we performed original genomic comparisons among aeromonads and between the strictly intracellular pathogens Brucella spp. and the mild opportunistic pathogens Ochrobactrum spp. We conclude that the adaptation to human could coincide with a speciation in action revealed by modifications in both genomic and population structures. This adaptation-driven speciation could be a major mechanism for the emergence of true pathogens besides the acquisition of specialized virulence factors. PMID:24704914

  13. Opportunistic pathogens and elements of the resistome that are common in bottled mineral water support the need for continuous surveillance

    OpenAIRE

    Maria Fernanda Falcone-Dias; Daniela Centrón; Fernando Pavan; Adriana Candido da Silva Moura; Felipe Gomes Naveca; Victor Costa de Souza; Adalberto Farache Filho; Clarice Queico Fujimura Leite

    2015-01-01

    Several differences concerning bacterial species, opportunistic pathogens, elements of the resistome as well as variations concerning the CFU/mL counts were identified in some of the five most marketed bottled mineral water from Araraquara city, São Paulo, Brazil. Two out of five brands tested were confirmed as potential source of opportunistic pathogens, including Mycobacterium gordonae, Ralstonia picketti and Burkholderia cepacia complex (Bcc). A total of one hundred and six isolates were r...

  14. [Genetic determinants of pathogenicity of opportunistic enterobacteria isolated from children with acute intestinal infections].

    Science.gov (United States)

    Anganova, E V; Dukhanina, A V; Savilov, E D

    2012-01-01

    Detection of nucleotide sequences of genes controlling synthesis of pathogenicity factors in clinical strains of opportunistic enterobacteria isolated from children with acute intestinal infections (AII), as well as their association with resistance to antibiotics and the course of the infectious process. 175 clinical strains obtained from children with AII undergoing treatment in Irkutsk state infectious diseases hospital (2007-2010) were studied. Primers to a number of genes detected in Escherichia coli pathogenicity islands, controlling type S and type 1 adhesion; formation of hemolysins; iron-regulatory protein synthesis; capsule formation were used in the study. PCR products analysis was performed by agar gel electrophoresis. Genetic determinants of pathogenicity were detected in bacteria genera Klebsiella, Citrobacter, Enterobacter, Proteus, Kluyvera, Morganella, Pantoea, Serratia. Fragments of hlyA and hlyB genes (hemolysin production) were detected more frequently; less frequently--sfaA, sfaG, fimA (adhesion), as well as irp-2 gene (synthesis of iron-regulatory protein). The largest set of genetic determinants of pathogenicity was noted in clinical strains of Klebsiella spp. Cultures with DNA fragments specific to genes of E. coli pathogenicity clusters were obtained predominately from children aged up to 3 years, had multiple antibiotic resistance and were isolated significantly more frequently in severe forms of AII when compared with strains in which these determinants were not detected. The studies performed showed that clinical strains of opportunistic bacteria isolated from patients with AII have a certain pathogenic potential, as evidenced by the presence of genetic pathogenicity markers in them.

  15. Insights on the Horizontal Gene Transfer of Carbapenemase Determinants in the Opportunistic Pathogen Acinetobacter baumannii

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    Gabriela Jorge Da Silva

    2016-08-01

    Full Text Available Horizontal gene transfer (HGT is a driving force to the evolution of bacteria. The fast emergence of antimicrobial resistance reflects the ability of genetic adaptation of pathogens. Acinetobacter baumannii has emerged in the last few decades as an important opportunistic nosocomial pathogen, in part due to its high capacity of acquiring resistance to diverse antibiotic families, including to the so-called last line drugs such as carbapenems. The rampant selective pressure and genetic exchange of resistance genes hinder the effective treatment of resistant infections. A. baumannii uses all the resistance mechanisms to survive against carbapenems but production of carbapenemases are the major mechanism, which may act in synergy with others. A. baumannii appears to use all the mechanisms of gene dissemination. Beyond conjugation, the mostly reported recent studies point to natural transformation, transduction and outer membrane vesicles-mediated transfer as mechanisms that may play a role in carbapenemase determinants spread. Understanding the genetic mobilization of carbapenemase genes is paramount in preventing their dissemination. Here we review the carbapenemases found in A. baumannii and present an overview of the current knowledge of contributions of the various HGT mechanisms to the molecular epidemiology of carbapenem resistance in this relevant opportunistic pathogen.

  16. Regrowth of potential opportunistic pathogens and algae in reclaimed-water distribution systems.

    Science.gov (United States)

    Jjemba, Patrick K; Weinrich, Lauren A; Cheng, Wei; Giraldo, Eugenio; Lechevallier, Mark W

    2010-07-01

    A study of the quality of reclaimed water in treated effluent, after storage, and at three points in the distribution system of four plants in California, Florida, Massachusetts, and New York was conducted for 1 year. The plants had different treatment processes (conventional versus membrane bioreactor), production capacities, and methods for storage of the water, and the intended end uses of the water were different. The analysis focused on the occurrence of indicator bacteria (heterotrophic bacteria, coliforms, Escherichia coli, and enterococci) and opportunistic pathogens (Aeromonas spp., enteropathogenic E. coli O157:H7, Legionella spp., Mycobacterium spp., and Pseudomonas spp.), as well as algae. Using immunological methods, E. coli O157:H7 was detected in the effluent of only one system, but it was not detected at the sampling points, suggesting that its survival in the system was poor. Although all of the treatment systems effectively reduced the levels of bacteria in the effluent, bacteria regrew in the reservoir and distribution systems because of the loss of residual disinfectant and high assimilable organic carbon levels. In the systems with open reservoirs, algal growth reduced the water quality by increasing the turbidity and accumulating at the end of the distribution system. Opportunistic pathogens, notably Aeromonas, Legionella, Mycobacterium, and Pseudomonas, occurred more frequently than indicator bacteria (enterococci, coliforms, and E. coli). The Mycobacterium spp. were very diverse and occurred most frequently in membrane bioreactor systems, and Mycobacterium cookii was identified more often than the other species. The public health risk associated with these opportunistic pathogens in reclaimed water is unknown. Collectively, our results show the need to develop best management practices for reclaimed water to control bacterial regrowth and degradation of water before it is utilized at the point of use.

  17. Draft Genome Sequences of Vibrio alginolyticus Strains V1 and V2, Opportunistic Marine Pathogens.

    Science.gov (United States)

    Castillo, Daniel; D'Alvise, Paul; Kalatzis, Panos G; Kokkari, Constantina; Middelboe, Mathias; Gram, Lone; Liu, Siyang; Katharios, Pantelis

    2015-07-02

    We announce the draft genome sequences of Vibrio alginolyticus strains V1 and V2, isolated from juvenile Sparus aurata and Dentex dentex, respectively, during outbreaks of vibriosis. The genome sequences are 5,257,950 bp with a G+C content of 44.5% for V. alginolyticus V1 and 5,068,299 bp with a G+C content of 44.8% for strain V2. These genomes provide further insights into the putative virulence factors, prophage carriage, and evolution of this opportunistic marine pathogen. Copyright © 2015 Castillo et al.

  18. The role and regulation of catalase in respiratory tract opportunistic bacterial pathogens.

    Science.gov (United States)

    Eason, Mia M; Fan, Xin

    2014-09-01

    Respiratory tract bacterial pathogens are the etiologic agents of a variety of illnesses. The ability of these bacteria to cause disease is imparted through survival within the host and avoidance of pathogen clearance by the immune system. Respiratory tract pathogens are continually bombarded by reactive oxygen species (ROS), which may be produced by competing bacteria, normal metabolic function, or host immunological responses. In order to survive and proliferate, bacteria have adapted defense mechanisms to circumvent the effects of ROS. Bacteria employ the use of anti-oxidant enzymes, catalases and catalase-peroxidases, to relieve the effects of the oxidative stressors to which they are continually exposed. The decomposition of ROS has been shown to provide favorable conditions in which respiratory tract opportunistic bacterial pathogens such as Haemophilus influenzae, Mycobacterium tuberculosis, Legionella pneumophila, and Neisseria meningitidis are able to withstand exposure to highly reactive molecules and yet survive. Bacteria possessing mutations in the catalase gene have a decreased survival rate, yet may be able to compensate for the lack of catalatic activity if peroxidatic activity is present. An incomplete knowledge of the mechanisms by which catalase and catalase-peroxidases are regulated still persists, however, in some bacterial species, a regulatory factor known as OxyR has been shown to either up-regulate or down-regulate catalase gene expression. Yet, more research is still needed to increase the knowledge base in relation to this enzyme class. As with this review, we focus on major respiratory tract opportunistic bacterial pathogens in order to elucidate the function and regulation of catalases. The importance of the research could lead to the development of novel treatments against respiratory bacterial infections.

  19. Draft Genome Sequences of Biosafety Level 2 Opportunistic Pathogens Isolated from the Environmental Surfaces of the International Space Station.

    Science.gov (United States)

    Checinska Sielaff, Aleksandra; Singh, Nitin K; Allen, Jonathan E; Thissen, James; Jaing, Crystal; Venkateswaran, Kasthuri

    2016-12-29

    The draft genome sequences of 20 biosafety level 2 (BSL-2) opportunistic pathogens isolated from the environmental surfaces of the International Space Station (ISS) were presented. These genomic sequences will help in understanding the influence of microgravity on the pathogenicity and virulence of these strains when compared with Earth strains.

  20. Hiding in Fresh Fruits and Vegetables: Opportunistic Pathogens May Cross Geographical Barriers

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    Zahra S. Al-Kharousi

    2016-01-01

    Full Text Available Different microbial groups of the microbiome of fresh produce can have diverse effects on human health. This study was aimed at identifying some microbial communities of fresh produce by analyzing 105 samples of imported fresh fruits and vegetables originated from different countries in the world including local samples (Oman for aerobic plate count and the counts of Enterobacteriaceae, Enterococcus, and Staphylococcus aureus. The isolated bacteria were identified by molecular (PCR and biochemical methods (VITEK 2. Enterobacteriaceae occurred in 60% of fruits and 91% of vegetables. Enterococcus was isolated from 20% of fruits and 42% of vegetables. E. coli and S. aureus were isolated from 22% and 7% of vegetables, respectively. Ninety-seven bacteria comprising 21 species were similarly identified by VITEK 2 and PCR to species level. E. coli, Klebsiella pneumoniae, Enterococcus casseliflavus, and Enterobacter cloacae were the most abundant species; many are known as opportunistic pathogens which may raise concern to improve the microbial quality of fresh produce. Phylogenetic trees showed no relationship between clustering of the isolates based on the 16S rRNA gene and the original countries of fresh produce. Intercountry passage of opportunistic pathogens in fresh produce cannot be ruled out, which requires better management.

  1. Acanthamoeba polyphaga, a potential environmental vector for the transmission of food-borne and opportunistic pathogens.

    Science.gov (United States)

    Anacarso, Immacolata; de Niederhäusern, Simona; Messi, Patrizia; Guerrieri, Elisa; Iseppi, Ramona; Sabia, Carla; Bondi, Moreno

    2012-06-01

    The endosymbiotic relationship could represent for many bacteria an important condition favouring their spread in the environment and in foods. For this purpose we studied the behaviour of some food-borne and opportunistic pathogens (Listeria monocytogenes, Staphylococcus aureus, Enterococcus faecalis, Salmonella enterica serovar Enteritidis, Aeromonas hydrophila, Yersinia enterocolitica) when internalized in Acanthamoeba polyphaga. Our results confirm the capability of the bacteria tested to grow within amoebal hosts. We can observe two types of interactions of the bacteria internalized in A. polyphaga. The first type, showed by Y. enterocolitica and A. hydrophila, was characterized by an early replication, probably followed by the killing and digestion of the bacteria. The second type, showed by E. faecalis and S. aureus was characterized by the persistence and grow inside the host without lysis. Lastly, when amoebae were co-cultured with L. monocytogenes and S. Enteritidis, an eclipse phase followed by an active intracellular growth was observed, suggesting a third type of predator-prey trend. The extracellular count in presence of A. polyphaga, as a result of an intracellular multiplication and subsequent release, was characterized by an increase of E. faecalis, S. aureus, L. monocytogenes and S. Enteritidis, and by a low or absent cell count for Y. enterocolitica and A. hydrophila. Our study suggests that the investigated food-borne and opportunistic pathogens are, in most cases, able to interact with A. polyphaga, to intracellularly replicate and, lastly, to be potentially spread in the environment, underlining the possible role of this protozoan in food contamination.

  2. The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis

    Science.gov (United States)

    Pryszcz, Leszek P.; Németh, Tibor; Saus, Ester; Ksiezopolska, Ewa; Hegedűsová, Eva; Nosek, Jozef; Wolfe, Kenneth H.; Gacser, Attila; Gabaldón, Toni

    2015-01-01

    Candida metapsilosis is a rarely-isolated, opportunistic pathogen that belongs to a clade of pathogenic yeasts known as the C. parapsilosis sensu lato species complex. To gain insight into the recent evolution of C. metapsilosis and the genetic basis of its virulence, we sequenced the genome of 11 clinical isolates from various locations, which we compared to each other and to the available genomes of the two remaining members of the complex: C. orthopsilosis and C. parapsilosis. Unexpectedly, we found compelling genomic evidence that C. metapsilosis is a highly heterozygous hybrid species, with all sequenced clinical strains resulting from the same past hybridization event involving two parental lineages that were approximately 4.5% divergent in sequence. This result indicates that the parental species are non-pathogenic, but that hybridization between them formed a new opportunistic pathogen, C. metapsilosis, that has achieved a worldwide distribution. We show that these hybrids are diploid and we identified strains carrying loci for both alternative mating types, which supports mating as the initial mechanism for hybrid formation. We trace the aftermath of this hybridization at the genomic level, and reconstruct the evolutionary relationships among the different strains. Recombination and introgression -resulting in loss of heterozygosis- between the two subgenomes have been rampant, and includes the partial overwriting of the MTLa mating locus in all strains. Collectively, our results shed light on the recent genomic evolution within the C. parapsilosis sensu lato complex, and argue for a re-definition of species within this clade, with at least five distinct homozygous lineages, some of which having the ability to form hybrids. PMID:26517373

  3. The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis.

    Directory of Open Access Journals (Sweden)

    Leszek P Pryszcz

    2015-10-01

    Full Text Available Candida metapsilosis is a rarely-isolated, opportunistic pathogen that belongs to a clade of pathogenic yeasts known as the C. parapsilosis sensu lato species complex. To gain insight into the recent evolution of C. metapsilosis and the genetic basis of its virulence, we sequenced the genome of 11 clinical isolates from various locations, which we compared to each other and to the available genomes of the two remaining members of the complex: C. orthopsilosis and C. parapsilosis. Unexpectedly, we found compelling genomic evidence that C. metapsilosis is a highly heterozygous hybrid species, with all sequenced clinical strains resulting from the same past hybridization event involving two parental lineages that were approximately 4.5% divergent in sequence. This result indicates that the parental species are non-pathogenic, but that hybridization between them formed a new opportunistic pathogen, C. metapsilosis, that has achieved a worldwide distribution. We show that these hybrids are diploid and we identified strains carrying loci for both alternative mating types, which supports mating as the initial mechanism for hybrid formation. We trace the aftermath of this hybridization at the genomic level, and reconstruct the evolutionary relationships among the different strains. Recombination and introgression -resulting in loss of heterozygosis- between the two subgenomes have been rampant, and includes the partial overwriting of the MTLa mating locus in all strains. Collectively, our results shed light on the recent genomic evolution within the C. parapsilosis sensu lato complex, and argue for a re-definition of species within this clade, with at least five distinct homozygous lineages, some of which having the ability to form hybrids.

  4. The distribution of Aspergillus spp. opportunistic parasites in hives and their pathogenicity to honey bees.

    Science.gov (United States)

    Foley, Kirsten; Fazio, Géraldine; Jensen, Annette B; Hughes, William O H

    2014-03-14

    Stonebrood is a disease of honey bee larvae caused by fungi from the genus Aspergillus. As very few studies have focused on the epidemiological aspects of stonebrood and diseased brood may be rapidly discarded by worker bees, it is possible that a high number of cases go undetected. Aspergillus spp. fungi are ubiquitous and associated with disease in many insects, plants, animals and man. They are regarded as opportunistic pathogens that require immunocompromised hosts to establish infection. Microbiological studies have shown high prevalences of Aspergillus spp. in apiaries which occur saprophytically on hive substrates. However, the specific conditions required for pathogenicity to develop remain unknown. In this study, an apiary was screened to determine the prevalence and diversity of Aspergillus spp. fungi. A series of dose-response tests were then conducted using laboratory reared larvae to determine the pathogenicity and virulence of frequently occurring isolates. The susceptibility of adult worker bees to Aspergillus flavus was also tested. Three isolates (A. flavus, Aspergillus nomius and Aspergillus phoenicis) of the ten species identified were pathogenic to honey bee larvae. Moreover, adult honey bees were also confirmed to be highly susceptible to A. flavus infection when they ingested conidia. Neither of the two Aspergillus fumigatus strains used in dose-response tests induced mortality in larvae and were the least pathogenic of the isolates tested. These results confirm the ubiquity of Aspergillus spp. in the apiary environment and highlight their potential to infect both larvae and adult bees.

  5. Genomics of adaptation during experimental evolution of the opportunistic pathogen Pseudomonas aeruginosa.

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    Alex Wong

    2012-09-01

    Full Text Available Adaptation is likely to be an important determinant of the success of many pathogens, for example when colonizing a new host species, when challenged by antibiotic treatment, or in governing the establishment and progress of long-term chronic infection. Yet, the genomic basis of adaptation is poorly understood in general, and for pathogens in particular. We investigated the genetics of adaptation to cystic fibrosis-like culture conditions in the presence and absence of fluoroquinolone antibiotics using the opportunistic pathogen Pseudomonas aeruginosa. Whole-genome sequencing of experimentally evolved isolates revealed parallel evolution at a handful of known antibiotic resistance genes. While the level of antibiotic resistance was largely determined by these known resistance genes, the costs of resistance were instead attributable to a number of mutations that were specific to individual experimental isolates. Notably, stereotypical quinolone resistance mutations in DNA gyrase often co-occurred with other mutations that, together, conferred high levels of resistance but no consistent cost of resistance. This result may explain why these mutations are so prevalent in clinical quinolone-resistant isolates. In addition, genes involved in cyclic-di-GMP signalling were repeatedly mutated in populations evolved in viscous culture media, suggesting a shared mechanism of adaptation to this CF-like growth environment. Experimental evolutionary approaches to understanding pathogen adaptation should provide an important complement to studies of the evolution of clinical isolates.

  6. Proteomic profiling of Cronobacter turicensis 3032, a food-borne opportunistic pathogen.

    Science.gov (United States)

    Carranza, Paula; Hartmann, Isabel; Lehner, Angelika; Stephan, Roger; Gehrig, Peter; Grossmann, Jonas; Barkow-Oesterreicher, Simon; Roschitzki, Bernd; Eberl, Leo; Riedel, Kathrin

    2009-07-01

    Members of the genus Cronobacter are opportunistic pathogens for neonates and are often associated with contaminated milk powder formulas. At present little is known about the virulence mechanisms or the natural reservoir of these organisms. The proteome of Cronobacter turicensis 3032, which has recently caused two deaths, was mapped aiming at a better understanding of physiology and putative pathogenic traits of this clinical isolate. Our analyses of extracellular, surface-associated and whole-cell proteins by two complementary proteomics approaches, 1D-SDS-PAGE combined with LC-ESI-MS/MS and 2D-LC-MALDI-TOF/TOF MS, lead to the identification of 832 proteins corresponding to a remarkable 19% of the theoretically expressed protein complement of C. turicensis. The majority of the identified proteins are involved in central metabolic pathways, translation, protein folding and stability. Several putative virulence factors, whose expressions were confirmed by phenotypic assays, could be identified: a macrophage infectivity potentiator involved in C. turicensis persistence in host cells, a superoxide dismutase protecting the pathogen against reactive oxygen species and an enterobactin-receptor protein for the uptake of siderophore-bound iron. Most interestingly, a chitinase and a metalloprotease that might act against insects and fungi but no casein hydrolysing enzymes were found, suggesting that there is an environmental natural habitat of C. turicensis 3032.

  7. Effective but costly, evolved mechanisms of defense against a virulent opportunistic pathogen in Drosophila melanogaster.

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    Yixin H Ye

    2009-04-01

    Full Text Available Drosophila harbor substantial genetic variation for antibacterial defense, and investment in immunity is thought to involve a costly trade-off with life history traits, including development, life span, and reproduction. To understand the way in which insects invest in fighting bacterial infection, we selected for survival following systemic infection with the opportunistic pathogen Pseudomonas aeruginosa in wild-caught Drosophila melanogaster over 10 generations. We then examined genome-wide changes in expression in the selected flies relative to unselected controls, both of which had been infected with the pathogen. This powerful combination of techniques allowed us to specifically identify the genetic basis of the evolved immune response. In response to selection, population-level survivorship to infection increased from 15% to 70%. The evolved capacity for defense was costly, however, as evidenced by reduced longevity and larval viability and a rapid loss of the trait once selection pressure was removed. Counter to expectation, we observed more rapid developmental rates in the selected flies. Selection-associated changes in expression of genes with dual involvement in developmental and immune pathways suggest pleiotropy as a possible mechanism for the positive correlation. We also found that both the Toll and the Imd pathways work synergistically to limit infectivity and that cellular immunity plays a more critical role in overcoming P. aeruginosa infection than previously reported. This work reveals novel pathways by which Drosophila can survive infection with a virulent pathogen that may be rare in wild populations, however, due to their cost.

  8. Oxidative stress response to menadione and cumene hydroperoxide in the opportunistic fungal pathogen Candida glabrata

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    Mayra Cuéllar-Cruz

    2009-07-01

    Full Text Available Candida glabrata is an opportunistic fungal pathogen that can cause severe invasive infections and can evade phagocytic cell clearance. We are interested in understanding the virulence of this fungal pathogen, in particular its oxidative stress response. Here we investigated C. glabrata, Saccharomyces cerevisiae and Candida albicans responses to two different oxidants: menadione and cumene hydroperoxide (CHP. In log-phase, in the presence of menadione, C. glabrata requires Cta1p (catalase, while in a stationary phase (SP, Cta1p is dispensable. In addition, C. glabrata is less resistant to menadione than C. albicans in SP. The S. cerevisiae laboratory reference strain is less resistant to menadione than C. glabrata and C. albicans; however S. cerevisiaeclinical isolates (CIs are more resistant than the lab reference strain. Furthermore, S. cerevisiae CIs showed an increased catalase activity. Interestingly, in SP C. glabrata and S. cerevisiae are more resistant to CHP than C. albicans and Cta1p plays no apparent role in detoxifying this oxidant.

  9. Oxidative stress response to menadione and cumene hydroperoxide in the opportunistic fungal pathogen Candida glabrata.

    Science.gov (United States)

    Cuéllar-Cruz, Mayra; Castaño, Irene; Arroyo-Helguera, Omar; De Las Peñas, Alejandro

    2009-07-01

    Candida glabrata is an opportunistic fungal pathogen that can cause severe invasive infections and can evade phagocytic cell clearance. We are interested in understanding the virulence of this fungal pathogen, in particular its oxidative stress response. Here we investigated C. glabrata, Saccharomyces cerevisiae and Candida albicans responses to two different oxidants: menadione and cumene hydroperoxide (CHP). In log-phase, in the presence of menadione, C. glabrata requires Cta1p (catalase), while in a stationary phase (SP), Cta1p is dispensable. In addition, C. glabrata is less resistant to menadione than C. albicans in SP. The S. cerevisiae laboratory reference strain is less resistant to menadione than C. glabrata and C. albicans; however S. cerevisiaeclinical isolates (CIs) are more resistant than the lab reference strain. Furthermore, S. cerevisiae CIs showed an increased catalase activity. Interestingly, in SP C. glabrata and S. cerevisiae are more resistant to CHP than C. albicans and Cta1p plays no apparent role in detoxifying this oxidant.

  10. The opportunistic human pathogen Acinetobacter baumannii senses and responds to light.

    Science.gov (United States)

    Mussi, María A; Gaddy, Jennifer A; Cabruja, Matías; Arivett, Brock A; Viale, Alejandro M; Rasia, Rodolfo; Actis, Luis A

    2010-12-01

    Light is a ubiquitous environmental signal that many organisms sense and respond to by modulating their physiological responses accordingly. While this is an expected response among phototrophic microorganisms, the ability of chemotrophic prokaryotes to sense and react to light has become a puzzling and novel issue in bacterial physiology, particularly among bacterial pathogens. In this work, we show that the opportunistic pathogen Acinetobacter baumannii senses and responds to blue light. Motility and formation of biofilms and pellicles were observed only when bacterial cells were incubated in darkness. In contrast, the killing of Candida albicans filaments was enhanced when they were cocultured with bacteria under light. These bacterial responses depend on the expression of the A. baumannii ATCC 17978 A1S_2225 gene, which codes for an 18.6-kDa protein that contains an N-terminal blue-light-sensing-using flavin (BLUF) domain and lacks a detectable output domain(s). Spectral analyses of the purified recombinant protein showed its ability to sense light by a red shift upon illumination. Therefore, the A1S_2225 gene, which is present in several members of the Acinetobacter genus, was named blue-light-sensing A (blsA). Interestingly, temperature plays a role in the ability of A. baumannii to sense and respond to light via the BlsA photoreceptor protein.

  11. Genome-wide identification of small RNAs in the opportunistic pathogen Enterococcus faecalis V583.

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    Kouki Shioya

    Full Text Available Small RNA molecules (sRNAs are key mediators of virulence and stress inducible gene expressions in some pathogens. In this work we identify sRNAs in the gram positive opportunistic pathogen Enterococcus faecalis. We characterized 11 sRNAs by tiling microarray analysis, 5' and 3' RACE-PCR, and Northern blot analysis. Six sRNAs were specifically expressed at exponential phase, two sRNAs were observed at stationary phase, and three were detected during both phases. Searches of putative functions revealed that three of them (EFA0080_EFA0081 and EFB0062_EFB0063 on pTF1 and pTF2 plasmids, respectively, and EF0408_EF04092 located on the chromosome are similar to antisense RNA involved in plasmid addiction modules. Moreover, EF1097_EF1098 shares strong homologies with tmRNA (bi-functional RNA acting as both a tRNA and an mRNA and EF2205_EF2206 appears homologous to 4.5S RNA member of the Signal Recognition Particle (SRP ribonucleoprotein complex. In addition, proteomic analysis of the ΔEF3314_EF3315 sRNA mutant suggests that it may be involved in the turnover of some abundant proteins. The expression patterns of these transcripts were evaluated by tiling array hybridizations performed with samples from cells grown under eleven different conditions some of which may be encountered during infection. Finally, distribution of these sRNAs among genome sequences of 54 E. faecalis strains was assessed. This is the first experimental genome-wide identification of sRNAs in E. faecalis and provides impetus to the understanding of gene regulation in this important human pathogen.

  12. Characterization of Serratia fonticola, an opportunistic pathogen isolated from drinking water

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    Tasić S.

    2013-01-01

    Full Text Available We characterized the ST2 strain of Serratia fonticola isolated from drinking water of a capping spring on Mt. Vlasina. The ST2 strain isolated from bottled water showed the characteristics of Enterobacteriaceae family but not of the Serratia genus. S. fonticola belongs to a group of opportunistic pathogens and can cause illness in people with weak or damaged immune systems. A biochemical characterization of the strain was made by using the identification system API (bioMèrieux®. Molecular characterization was done by PCR amplification of 16S rDNA gene using the thermal cycling sequencing method and by sequencing. By comparing the obtained 1016 nucleotide sequence with the NCBI collection of all deposited sequences for 16S rDNK, and by using the BLAST search service, the highest identity (98% uniformity was obtained with the S. fonticola strain, designated as LMG 7882 (gi|15054669|gb|AF286869.1. The identity of 16S rDNA between the referent strain and ST2 is not absolute, indicating an autochthonous origin of strain ST2.

  13. Pathogenic and opportunistic free-living amoebae: Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri, and Sappinia diploidea.

    Science.gov (United States)

    Visvesvara, Govinda S; Moura, Hercules; Schuster, Frederick L

    2007-06-01

    Among the many genera of free-living amoebae that exist in nature, members of only four genera have an association with human disease: Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri and Sappinia diploidea. Acanthamoeba spp. and B. mandrillaris are opportunistic pathogens causing infections of the central nervous system, lungs, sinuses and skin, mostly in immunocompromised humans. Balamuthia is also associated with disease in immunocompetent children, and Acanthamoeba spp. cause a sight-threatening infection, Acanthamoeba keratitis, mostly in contact-lens wearers. Of more than 30 species of Naegleria, only one species, N. fowleri, causes an acute and fulminating meningoencephalitis in immunocompetent children and young adults. In addition to human infections, Acanthamoeba, Balamuthia and Naegleria can cause central nervous system infections in animals. Because only one human case of encephalitis caused by Sappinia diploidea is known, generalizations about the organism as an agent of disease are premature. In this review we summarize what is known of these free-living amoebae, focusing on their biology, ecology, types of disease and diagnostic methods. We also discuss the clinical profiles, mechanisms of pathogenesis, pathophysiology, immunology, antimicrobial sensitivity and molecular characteristics of these amoebae.

  14. Agent-based modeling approach of immune defense against spores of opportunistic human pathogenic fungi

    Directory of Open Access Journals (Sweden)

    Christian eTokarski

    2012-04-01

    Full Text Available Opportunistic human pathogenic fungi like the ubiquitous fungus Aspergillus fumigatus are a majorthreat to immunocompromised patients. An impaired immune system renders the body vulnerable to inva-sive mycoses that often lead to the death of the patient. While the number of immunocompromised patientsis rising with medical progress, the process and dynamics of defence against invaded and ready to germinatefungal conidia are still insufficiently understood.Besides macrophages, neutrophil granulocytes form an important line of defence in that they clear conidia.Live imaging shows the interaction of those phagocytes and conidia as a dynamic process of touching, drag-ging and phagocytosis. To unravel strategies of phagocytes on the hunt for conidia an agent-based modelingapproach is used, implemented in NetLogo. Different modes of movement of phagocytes are tested regard-ing their clearing efficiency: random walk, short term persistence in their recent direction, chemotaxis ofchemokines excreted by conidia and communication between phagocytes.

  15. Ergothioneine Biosynthesis and Functionality in the Opportunistic Fungal Pathogen, Aspergillus fumigatus

    Science.gov (United States)

    Sheridan, Kevin J.; Lechner, Beatrix Elisabeth; Keeffe, Grainne O’; Keller, Markus A.; Werner, Ernst R.; Lindner, Herbert; Jones, Gary W.; Haas, Hubertus; Doyle, Sean

    2016-01-01

    Ergothioneine (EGT; 2-mercaptohistidine trimethylbetaine) is a trimethylated and sulphurised histidine derivative which exhibits antioxidant properties. Here we report that deletion of Aspergillus fumigatus egtA (AFUA_2G15650), which encodes a trimodular enzyme, abrogated EGT biosynthesis in this opportunistic pathogen. EGT biosynthetic deficiency in A. fumigatus significantly reduced resistance to elevated H2O2 and menadione, respectively, impaired gliotoxin production and resulted in attenuated conidiation. Quantitative proteomic analysis revealed substantial proteomic remodelling in ΔegtA compared to wild-type under both basal and ROS conditions, whereby the abundance of 290 proteins was altered. Specifically, the reciprocal differential abundance of cystathionine γ-synthase and β-lyase, respectively, influenced cystathionine availability to effect EGT biosynthesis. A combined deficiency in EGT biosynthesis and the oxidative stress response regulator Yap1, which led to extreme oxidative stress susceptibility, decreased resistance to heavy metals and production of the extracellular siderophore triacetylfusarinine C and increased accumulation of the intracellular siderophore ferricrocin. EGT dissipated H2O2 in vitro, and elevated intracellular GSH levels accompanied abrogation of EGT biosynthesis. EGT deficiency only decreased resistance to high H2O2 levels which suggests functionality as an auxiliary antioxidant, required for growth at elevated oxidative stress conditions. Combined, these data reveal new interactions between cellular redox homeostasis, secondary metabolism and metal ion homeostasis. PMID:27748436

  16. Pneumocystis carinii: A Review of an Important Opportunistic Pathogen in AIDS

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    M John Gill

    1991-01-01

    Full Text Available Since the first report of human infection with Pneumocystis carinii in 1942, cases of pneumonia due to this opportunistic pathogen have become increasingly common. Animal studies and clinical observations show that a significant depletion or dysfunction of T helper lymphocytes predisposes to clinical disease. Individuals with damaged T helper cells secondary to malignancies (eg, Hodgkin’s lymphoma, drugs (eg, cyclosporine, steroids, or certain infections (eg, human immunodeficiency virus are at particular risk. Serological studies suggest that disease is most often secondary to the reactivation of an asymptomatic infection, usually acquired during childhood. Increasing shortness of breath, a nonproductive cough and hypoxia often preceded by several weeks of lethargy, fever and weight loss are the classical features of P carinii pneumonia in acquired immune deficiency syndrome. Bronchoalveolar lavage is usually the optimal diagnostic test. Immunofluorescent staining on liquified sputum induced by nebulized saline appears to be a promising and noninvasive test. Early empiric therapy with trimethoprim-sulphamethoxazole (trimethoprim 5 mg-sulphamethoxazole 25 mg/kg/day every 6 h or intravenous pentamidine (4 mg/kg/day for 21 days is usually effective, but infection is not eradicated, and clinical disease is likely to recur. Prophylaxis using aerosolized pentamidine reduces the risk of pulmonary disease but can predispose to extrapulmonary infection. Improved in vitro and in vivo models of human pneumocystis infection would significantly increase understanding of the molecular biology of the organism, the pathogenesis of disease, and the optimal therapeutic regimens.

  17. Evaluation of two novel barcodes for species recognition of opportunistic pathogens in Fusarium.

    Science.gov (United States)

    Al-Hatmi, Abdullah M S; Van Den Ende, A H G Gerrits; Stielow, J Benjamin; Van Diepeningen, Anne D; Seifert, Keith A; McCormick, Wayne; Assabgui, Rafik; Gräfenhan, Tom; De Hoog, G Sybren; Levesque, C André

    2016-02-01

    The genus Fusarium includes more than 200 species of which 73 have been isolated from human infections. Fusarium species are opportunistic human pathogens with variable aetiology. Species determination is best made with the combined phylogeny of protein-coding genes such as elongation factor (TEF1), RNA polymerase (RPB2) and the partial β-tubulin (BT2) gene. The internal transcribed spacers 1, 2 and 5.8S rRNA gene (ITS) have also been used, however, ITS cannot discriminate several closely related species and has nonorthologous copies in Fusarium. Currently, morphological approaches and tree-building methods are in use to define species and to discover hitherto undescribed species. Aftter a species is defined, DNA barcoding approaches can be used to identify species by the presence or absence of discrete nucleotide characters. We demonstrate the potential of two recently discovered DNA barcode loci, topoisomerase I (TOP1) and phosphoglycerate kinase (PGK), in combination with other routinely used markers such as TEF1, in an analysis of 144 Fusarium strains belonging to 52 species. Our barcoding study using TOP1 and PKG provided concordance of molecular data with TEF1. The currently accepted Fusarium species sampled were well supported in phylogenetic trees of both new markers. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  18. Label-free molecular imaging of bacterial communities of the opportunistic pathogen Pseudomonas aeruginosa

    Science.gov (United States)

    Baig, Nameera; Polisetti, Sneha; Morales-Soto, Nydia; Dunham, Sage J. B.; Sweedler, Jonathan V.; Shrout, Joshua D.; Bohn, Paul W.

    2016-09-01

    Biofilms, such as those formed by the opportunistic human pathogen Pseudomonas aeruginosa are complex, matrix enclosed, and surface-associated communities of cells. Bacteria that are part of a biofilm community are much more resistant to antibiotics and the host immune response than their free-floating counterparts. P. aeruginosa biofilms are associated with persistent and chronic infections in diseases such as cystic fibrosis and HIV-AIDS. P. aeruginosa synthesizes and secretes signaling molecules such as the Pseudomonas quinolone signal (PQS) which are implicated in quorum sensing (QS), where bacteria regulate gene expression based on population density. Processes such as biofilms formation and virulence are regulated by QS. This manuscript describes the powerful molecular imaging capabilities of confocal Raman microscopy (CRM) and surface enhanced Raman spectroscopy (SERS) in conjunction with multivariate statistical tools such as principal component analysis (PCA) for studying the spatiotemporal distribution of signaling molecules, secondary metabolites and virulence factors in biofilm communities of P. aeruginosa. Our observations reveal that the laboratory strain PAO1C synthesizes and secretes 2-alkyl-4-hydroxyquinoline N-oxides and 2-alkyl-4-hydroxyquinolones in high abundance, while the isogenic acyl homoserine lactone QS-deficient mutant (ΔlasIΔrhlI) strain produces predominantly 2-alkyl-quinolones during biofilm formation. This study underscores the use of CRM, along with traditional biological tools such as genetics, for studying the behavior of microbial communities at the molecular level.

  19. What It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated.

    Directory of Open Access Journals (Sweden)

    Benoît Valot

    Full Text Available Pseudomonas aeruginosa is an opportunistic bacterial pathogen able to thrive in highly diverse ecological niches and to infect compromised patients. Its genome exhibits a mosaic structure composed of a core genome into which accessory genes are inserted en bloc at specific sites. The size and the content of the core genome are open for debate as their estimation depends on the set of genomes considered and the pipeline of gene detection and clustering. Here, we redefined the size and the content of the core genome of P. aeruginosa from fully re-analyzed genomes of 17 reference strains. After the optimization of gene detection and clustering parameters, the core genome was defined at 5,233 orthologs, which represented ~ 88% of the average genome. Extrapolation indicated that our panel was suitable to estimate the core genome that will remain constant even if new genomes are added. The core genome contained resistance determinants to the major antibiotic families as well as most metabolic, respiratory, and virulence genes. Although some virulence genes were accessory, they often related to conserved biological functions. Long-standing prophage elements were subjected to a genetic drift to eventually display a G+C content as higher as that of the core genome. This contrasts with the low G+C content of highly conserved ribosomal genes. The conservation of metabolic and respiratory genes could guarantee the ability of the species to thrive on a variety of carbon sources for energy in aerobiosis and anaerobiosis. Virtually all the strains, of environmental or clinical origin, have the complete toolkit to become resistant to the major antipseudomonal compounds and possess basic pathogenic mechanisms to infect humans. The knowledge of the genes shared by the majority of the P. aeruginosa isolates is a prerequisite for designing effective therapeutics to combat the wide variety of human infections.

  20. What It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated.

    Science.gov (United States)

    Valot, Benoît; Guyeux, Christophe; Rolland, Julien Yves; Mazouzi, Kamel; Bertrand, Xavier; Hocquet, Didier

    2015-01-01

    Pseudomonas aeruginosa is an opportunistic bacterial pathogen able to thrive in highly diverse ecological niches and to infect compromised patients. Its genome exhibits a mosaic structure composed of a core genome into which accessory genes are inserted en bloc at specific sites. The size and the content of the core genome are open for debate as their estimation depends on the set of genomes considered and the pipeline of gene detection and clustering. Here, we redefined the size and the content of the core genome of P. aeruginosa from fully re-analyzed genomes of 17 reference strains. After the optimization of gene detection and clustering parameters, the core genome was defined at 5,233 orthologs, which represented ~ 88% of the average genome. Extrapolation indicated that our panel was suitable to estimate the core genome that will remain constant even if new genomes are added. The core genome contained resistance determinants to the major antibiotic families as well as most metabolic, respiratory, and virulence genes. Although some virulence genes were accessory, they often related to conserved biological functions. Long-standing prophage elements were subjected to a genetic drift to eventually display a G+C content as higher as that of the core genome. This contrasts with the low G+C content of highly conserved ribosomal genes. The conservation of metabolic and respiratory genes could guarantee the ability of the species to thrive on a variety of carbon sources for energy in aerobiosis and anaerobiosis. Virtually all the strains, of environmental or clinical origin, have the complete toolkit to become resistant to the major antipseudomonal compounds and possess basic pathogenic mechanisms to infect humans. The knowledge of the genes shared by the majority of the P. aeruginosa isolates is a prerequisite for designing effective therapeutics to combat the wide variety of human infections.

  1. Proteogenomics of Candida tropicalis--An Opportunistic Pathogen with Importance for Global Health.

    Science.gov (United States)

    Datta, Keshava K; Patil, Arun H; Patel, Krishna; Dey, Gourav; Madugundu, Anil K; Renuse, Santosh; Kaviyil, Jyothi E; Sekhar, Raja; Arunima, Aryashree; Daswani, Bhavna; Kaur, Inderjeet; Mohanty, Jyotirmaya; Sinha, Ranjana; Jaiswal, Sangeeta; Sivapriya, S; Sonnathi, Yeshwanth; Chattoo, Bharat B; Gowda, Harsha; Ravikumar, Raju; Prasad, T S Keshava

    2016-04-01

    The frequency of Candida infections is currently rising, and thus adversely impacting global health. The situation is exacerbated by azole resistance developed by fungal pathogens. Candida tropicalis is an opportunistic pathogen that causes candidiasis, for example, in immune-compromised individuals, cancer patients, and those who undergo organ transplantation. It is a member of the non-albicans group of Candida that are known to be azole-resistant, and is frequently seen in individuals being treated for cancers, HIV-infection, and those who underwent bone marrow transplantation. Although the genome of C. tropicalis was sequenced in 2009, the genome annotation has not been supported by experimental validation. In the present study, we have carried out proteomics profiling of C. tropicalis using high-resolution Fourier transform mass spectrometry. We identified 2743 proteins, thus mapping nearly 44% of the computationally predicted protein-coding genes with peptide level evidence. In addition to identifying 2591 proteins in the cell lysate of this yeast, we also analyzed the proteome of the conditioned media of C. tropicalis culture and identified several unique secreted proteins among a total of 780 proteins. By subjecting the mass spectrometry data derived from cell lysate and conditioned media to proteogenomic analysis, we identified 86 novel genes, 12 novel exons, and corrected 49 computationally-predicted gene models. To our knowledge, this is the first high-throughput proteomics study of C. tropicalis validating predicted protein coding genes and refining the current genome annotation. The findings may prove useful in future global health efforts to fight against Candida infections.

  2. Scabies mites alter the skin microbiome and promote growth of opportunistic pathogens in a porcine model.

    Directory of Open Access Journals (Sweden)

    Pearl M Swe

    Full Text Available BACKGROUND: The resident skin microbiota plays an important role in restricting pathogenic bacteria, thereby protecting the host. Scabies mites (Sarcoptes scabiei are thought to promote bacterial infections by breaching the skin barrier and excreting molecules that inhibit host innate immune responses. Epidemiological studies in humans confirm increased incidence of impetigo, generally caused by Staphylococcus aureus and Streptococcus pyogenes, secondary to the epidermal infestation with the parasitic mite. It is therefore possible that mite infestation could alter the healthy skin microbiota making way for the opportunistic pathogens. A longitudinal study to test this hypothesis in humans is near impossible due to ethical reasons. In a porcine model we generated scabies infestations closely resembling the disease manifestation in humans and investigated the scabies associated changes in the skin microbiota over the course of a mite infestation. METHODOLOGY/PRINCIPAL FINDINGS: In a 21 week trial, skin scrapings were collected from pigs infected with S. scabies var. suis and scabies-free control animals. A total of 96 skin scrapings were collected before, during infection and after acaricide treatment, and analyzed by bacterial 16S rDNA tag-encoded FLX-titanium amplicon pyrosequencing. We found significant changes in the epidermal microbiota, in particular a dramatic increase in Staphylococcus correlating with the onset of mite infestation in animals challenged with scabies mites. This increase persisted beyond treatment from mite infection and healing of skin. Furthermore, the staphylococci population shifted from the commensal S. hominis on the healthy skin prior to scabies mite challenge to S. chromogenes, which is increasingly recognized as being pathogenic, coinciding with scabies infection in pigs. In contrast, all animals in the scabies-free cohort remained relatively free of Staphylococcus throughout the trial. CONCLUSIONS

  3. Monitoring of opportunistic and pathogenic microorganisms in surgical departments of Dniprodzerzhynsk

    Directory of Open Access Journals (Sweden)

    N. N. Donets

    2013-03-01

    Full Text Available The paper presents monitoring results of the spread of opportunistic and pathogenic microorganisms in patients of surgical departments of the Dniprodzerzhynsk city hospital No 7. 1464 strains of bacteria isolated from biological material of the patients from January to December 2012 were studied. Relevant standard methods of research and data interpretation in accordance with the regulatory guidelines were used. The microorganisms’ sensitivity to antibiotics was determined by the disk diffusion method. Assessment of the resistance of isolated microorganisms to antibiotics was made with the software Whonet 5.1. At the first stage of investigation sampling biological material and inoculation in the culture medium were made. The discharges of wounds, throat, nose, ears, vagina and urethra, and also urine from patients of surgical departments were sampled for bacteriological analysis. The main substratum was 5% blood agar. There may additionally be used the selective growth media (yolk-salt agar, Endo, and Saburo. At the second stage we identify microorganisms with bacterioscopic, bacteriological and biochemical methods. Identifying microorganisms of the genus Staphylococcus was made by the reaction of lecithinase presence, plasma-coagulation reaction and the mannitol oxidation reaction. For the identification of bacteria of the family Streptococcaceae the growth pattern in 0.5% sugar medium was used. It was differentiated from bacteria of the genus Enterococcus by plating onto egg yolk agar base and milk with 0.1% methylene blue. Identification of bacteria of the Enterobacteriaceae family was made by studying their colonies on dense differential diagnostic media. Suspicious colonies were transferred on a combined medium for primary identification (Olkenitsky's medium. Then the biochemical signs of enterobacteria were studied in the minimum number of tests. The third phase of the study included the determination of the sensitivity of

  4. Opportunistic pathogens and elements of the resistome that are common in bottled mineral water support the need for continuous surveillance.

    Directory of Open Access Journals (Sweden)

    Maria Fernanda Falcone-Dias

    Full Text Available Several differences concerning bacterial species, opportunistic pathogens, elements of the resistome as well as variations concerning the CFU/mL counts were identified in some of the five most marketed bottled mineral water from Araraquara city, São Paulo, Brazil. Two out of five brands tested were confirmed as potential source of opportunistic pathogens, including Mycobacterium gordonae, Ralstonia picketti and Burkholderia cepacia complex (Bcc. A total of one hundred and six isolates were recovered from four of these bottled mineral water brands. Betaproteobacteria was predominant followed by Alphaproteobacteria, Gammaproteobacteria and Firmicutes. Ninety percent of the bacteria isolated demonstrated resistance to seventeen of the nineteen antimicrobials tested. These antimicrobials included eight different classes, including 3rd and 4th generation cephalosporins, carbapenems and fluoroquinolones. Multidrug resistant bacteria were detected for fifty-nine percent of isolates in three water brands at counts up to 103 CFU/ml. Of major concern, the two bottled mineral water harboring opportunistic pathogens were also source of elements of the resistome that could be directly transferred to humans. All these differences found among brands highlight the need for continuous bacteriological surveillance of bottled mineral water.

  5. Opportunistic pathogens and elements of the resistome that are common in bottled mineral water support the need for continuous surveillance.

    Science.gov (United States)

    Falcone-Dias, Maria Fernanda; Centrón, Daniela; Pavan, Fernando; Moura, Adriana Candido da Silva; Naveca, Felipe Gomes; de Souza, Victor Costa; Farache Filho, Adalberto; Leite, Clarice Queico Fujimura

    2015-01-01

    Several differences concerning bacterial species, opportunistic pathogens, elements of the resistome as well as variations concerning the CFU/mL counts were identified in some of the five most marketed bottled mineral water from Araraquara city, São Paulo, Brazil. Two out of five brands tested were confirmed as potential source of opportunistic pathogens, including Mycobacterium gordonae, Ralstonia picketti and Burkholderia cepacia complex (Bcc). A total of one hundred and six isolates were recovered from four of these bottled mineral water brands. Betaproteobacteria was predominant followed by Alphaproteobacteria, Gammaproteobacteria and Firmicutes. Ninety percent of the bacteria isolated demonstrated resistance to seventeen of the nineteen antimicrobials tested. These antimicrobials included eight different classes, including 3rd and 4th generation cephalosporins, carbapenems and fluoroquinolones. Multidrug resistant bacteria were detected for fifty-nine percent of isolates in three water brands at counts up to 103 CFU/ml. Of major concern, the two bottled mineral water harboring opportunistic pathogens were also source of elements of the resistome that could be directly transferred to humans. All these differences found among brands highlight the need for continuous bacteriological surveillance of bottled mineral water.

  6. Relationship between Organic Carbon and Opportunistic Pathogens in Simulated Glass Water Heaters

    Directory of Open Access Journals (Sweden)

    Krista Williams

    2015-06-01

    Full Text Available Controlling organic carbon levels in municipal water has been hypothesized to limit downstream growth of bacteria and opportunistic pathogens in premise plumbing (OPPPs. Here, the relationships between influent organic carbon (0–15,000 µg ozonated fulvic acid /L and the number of total bacteria [16S rRNA genes and heterotrophic plate counts (HPCs] and a wide range of OPPPs (gene copy numbers of Acanthamoeba polyphaga, Vermamoeba vermiformis, Legionella pneumophila, and Mycobacterium avium were examined in the bulk water of 120-mL simulated glass water heaters (SGWHs. The SGWHs were operated at 32–37 °C, which is representative of conditions encountered at the bottom of electric water heaters, with water changes of 80% three times per week to simulate low use. This design presented advantages of controlled and replicated (triplicate conditions and avoided other potential limitations to OPPP growth in order to isolate the variable of organic carbon. Over seventeen months, strong correlations were observed between total organic carbon (TOC and both 16S rRNA gene copy numbers and HPC counts (avg. R2 > 0.89. Although M. avium gene copies were occasionally correlated with TOC (avg. R2 = 0.82 to 0.97, for 2 out of 4 time points and over a limited TOC range (0–1000 µg/L, no other correlations were identified between other OPPPs and added TOC. These results suggest that reducing organic carbon in distributed water is not adequate as a sole strategy for controlling OPPPs, although it may have promise in conjunction with other approaches.

  7. Doxycycline-regulated gene expression in the opportunistic fungal pathogen Aspergillus fumigatus

    Directory of Open Access Journals (Sweden)

    Askew David S

    2005-01-01

    Full Text Available Abstract Background Although Aspergillus fumigatus is an important human fungal pathogen there are few expression systems available to study the contribution of specific genes to the growth and virulence of this opportunistic mould. Regulatable promoter systems based upon prokaryotic regulatory elements in the E. coli tetracycline-resistance operon have been successfully used to manipulate gene expression in several organisms, including mice, flies, plants, and yeast. However, the system has not yet been adapted for Aspergillus spp. Results Here we describe the construction of plasmid vectors that can be used to regulate gene expression in A. fumigatus using a simple co-transfection approach. Vectors were generated in which the tetracycline transactivator (tTA or the reverse tetracycline transactivator (rtTA2s-M2 are controlled by the A. nidulans gpdA promoter. Dominant selectable cassettes were introduced into each plasmid, allowing for selection following gene transfer into A. fumigatus by incorporating phleomycin or hygromycin into the medium. To model an essential gene under tetracycline regulation, the E. coli hygromycin resistance gene, hph, was placed under the control of seven copies of the TetR binding site (tetO7 in a plasmid vector and co-transfected into A. fumigatus protoplasts together with one of the two transactivator plasmids. Since the hph gene is essential to A. fumigatus in the presence of hygromycin, resistance to hygromycin was used as a marker of hph reporter gene expression. Transformants were identified in which the expression of tTA conferred hygromycin resistance by activating expression of the tetO7-hph reporter gene, and the addition of doxycycline to the medium suppressed hygromycin resistance in a dose-dependent manner. Similarly, transformants were identified in which expression of rtTA2s-M2 conferred hygromycin resistance only in the presence of doxycycline. The levels of doxycycline required to regulate

  8. Complete Genome Sequence of Staphylococcus xylosus HKUOPL8, a Potential Opportunistic Pathogen of Mammals.

    Science.gov (United States)

    Ma, Angel Po Yee; Jiang, Jingwei; Tun, Hein Min; Mauroo, Nathalie France; Yuen, Chan San; Leung, Frederick Chi-Ching

    2014-07-24

    We report here the first complete genome sequence of Staphylococcus xylosus strain HKUOPL8, isolated from giant panda feces. The whole genome sequence of this strain will provide an important framework for investigating the genes responsible for potential opportunistic infections with this species, as well as its survival in various environments. Copyright © 2014 Ma et al.

  9. Assessing the Groundwater Quality at a Saudi Arabian Agricultural Site and the Occurrence of Opportunistic Pathogens on Irrigated Food Produce.

    Science.gov (United States)

    Alsalah, Dhafer; Al-Jassim, Nada; Timraz, Kenda; Hong, Pei-Ying

    2015-10-05

    This study examines the groundwater quality in wells situated near agricultural fields in Saudi Arabia. Fruits (e.g., tomato and green pepper) irrigated with groundwater were also assessed for the occurrence of opportunistic pathogens to determine if food safety was compromised by the groundwater. The amount of total nitrogen in most of the groundwater samples exceeded the 15 mg/L permissible limit for agricultural irrigation. Fecal coliforms in densities > 12 MPN/100 mL were detected in three of the groundwater wells that were in close proximity to a chicken farm. These findings, coupled with qPCR-based fecal source tracking, show that groundwater in wells D and E, which were nearest to the chicken farm, had compromised quality. Anthropogenic contamination resulted in a shift in the predominant bacterial phyla within the groundwater microbial communities. For example, there was an elevated presence of Proteobacteria and Cyanobacteria in wells D and E but a lower overall microbial richness in the groundwater perturbed by anthropogenic contamination. In the remaining wells, the genus Acinetobacter was detected at high relative abundance ranging from 1.5% to 48% of the total groundwater microbial community. However, culture-based analysis did not recover any antibiotic-resistant bacteria or opportunistic pathogens from these groundwater samples. In contrast, opportunistic pathogenic Enterococcus faecalis and Pseudomonas aeruginosa were isolated from the fruits irrigated with the groundwater from wells B and F. Although the groundwater was compromised, quantitative microbial risk assessment suggests that the annual risk incurred from accidental consumption of E. faecalis on these fruits was within the acceptable limit of 10(-4). However, the annual risk arising from P. aeruginosa was 9.55 × 10(-4), slightly above the acceptable limit. Our findings highlight that the groundwater quality at this agricultural site in western Saudi Arabia is not pristine and that better

  10. Assessing the Groundwater Quality at a Saudi Arabian Agricultural Site and the Occurrence of Opportunistic Pathogens on Irrigated Food Produce

    Science.gov (United States)

    Alsalah, Dhafer; Al-Jassim, Nada; Timraz, Kenda; Hong, Pei-Ying

    2015-01-01

    This study examines the groundwater quality in wells situated near agricultural fields in Saudi Arabia. Fruits (e.g., tomato and green pepper) irrigated with groundwater were also assessed for the occurrence of opportunistic pathogens to determine if food safety was compromised by the groundwater. The amount of total nitrogen in most of the groundwater samples exceeded the 15 mg/L permissible limit for agricultural irrigation. Fecal coliforms in densities > 12 MPN/100 mL were detected in three of the groundwater wells that were in close proximity to a chicken farm. These findings, coupled with qPCR-based fecal source tracking, show that groundwater in wells D and E, which were nearest to the chicken farm, had compromised quality. Anthropogenic contamination resulted in a shift in the predominant bacterial phyla within the groundwater microbial communities. For example, there was an elevated presence of Proteobacteria and Cyanobacteria in wells D and E but a lower overall microbial richness in the groundwater perturbed by anthropogenic contamination. In the remaining wells, the genus Acinetobacter was detected at high relative abundance ranging from 1.5% to 48% of the total groundwater microbial community. However, culture-based analysis did not recover any antibiotic-resistant bacteria or opportunistic pathogens from these groundwater samples. In contrast, opportunistic pathogenic Enterococcus faecalis and Pseudomonas aeruginosa were isolated from the fruits irrigated with the groundwater from wells B and F. Although the groundwater was compromised, quantitative microbial risk assessment suggests that the annual risk incurred from accidental consumption of E. faecalis on these fruits was within the acceptable limit of 10−4. However, the annual risk arising from P. aeruginosa was 9.55 × 10−4, slightly above the acceptable limit. Our findings highlight that the groundwater quality at this agricultural site in western Saudi Arabia is not pristine and that better

  11. Assessing the Groundwater Quality at a Saudi Arabian Agricultural Site and the Occurrence of Opportunistic Pathogens on Irrigated Food Produce

    KAUST Repository

    Alsalah, Dhafer

    2015-10-05

    This study examines the groundwater quality in wells situated near agricultural fields in Saudi Arabia. Fruits (e.g., tomato and green pepper) irrigated with groundwater were also assessed for the occurrence of opportunistic pathogens to determine if food safety was compromised by the groundwater. The amount of total nitrogen in most of the groundwater samples exceeded the 15 mg/L permissible limit for agricultural irrigation. Fecal coliforms in densities > 12 MPN/100 mL were detected in three of the groundwater wells that were in close proximity to a chicken farm. These findings, coupled with qPCR-based fecal source tracking, show that groundwater in wells D and E, which were nearest to the chicken farm, had compromised quality. Anthropogenic contamination resulted in a shift in the predominant bacterial phyla within the groundwater microbial communities. For example, there was an elevated presence of Proteobacteria and Cyanobacteria in wells D and E but a lower overall microbial richness in the groundwater perturbed by anthropogenic contamination. In the remaining wells, the genus Acinetobacter was detected at high relative abundance ranging from 1.5% to 48% of the total groundwater microbial community. However, culture-based analysis did not recover any antibiotic-resistant bacteria or opportunistic pathogens from these groundwater samples. In contrast, opportunistic pathogenic Enterococcus faecalis and Pseudomonas aeruginosa were isolated from the fruits irrigated with the groundwater from wells B and F. Although the groundwater was compromised, quantitative microbial risk assessment suggests that the annual risk incurred from accidental consumption of E. faecalis on these fruits was within the acceptable limit of 10−4. However, the annual risk arising from P. aeruginosa was 9.55 × 10−4, slightly above the acceptable limit. Our findings highlight that the groundwater quality at this agricultural site in western Saudi Arabia is not pristine and that better

  12. Skin microbiota is the main reservoir of Roseomonas mucosa, an emerging opportunistic pathogen so far assumed to be environmental.

    Science.gov (United States)

    Romano-Bertrand, S; Bourdier, A; Aujoulat, F; Michon, A-L; Masnou, A; Parer, S; Marchandin, H; Jumas-Bilak, E

    2016-08-01

    Roseomonas spp. are increasingly involved in human infectious diseases. The environmental source for infection is generally admitted in published cases owing to the origin of most Roseomonas species and to their affiliation to the family Acetobacteraceae in Rhodospirillales, which mainly groups environmental bacteria. For a better delineation of Roseomonas habitat and infectious reservoir, we related phenotype, phylotype (16S rRNA gene), genomotype (pulsed-field gel electrophoresis) and origin of 33 strains isolated from humans, hospital environment and natural environment. Genetic and metagenomic databases were also surveyed. The population structure of the genus showed clades associated with humans, whereas others grouped environmental strains only. Roseomonas mucosa is the main human-associated species and the study supported the idea that opportunistic infections due to this species are related to the patient skin microbiota rather than to the environment. In contrast, some strains belonging to other species isolated from patients with cystic fibrosis were related to environmental clades, suggesting an exogenous source for patient colonization. Accurate knowledge about the reservoirs of opportunistic pathogens that have long been considered of environmental origin is still needed and would be helpful to improve infection control and epidemiological survey of emerging human pathogens.

  13. Annual variations and effects of temperature on Legionella spp. and other potential opportunistic pathogens in a bathroom.

    Science.gov (United States)

    Lu, Jingrang; Buse, Helen; Struewing, Ian; Zhao, Amy; Lytle, Darren; Ashbolt, Nicholas

    2017-01-01

    Opportunistic pathogens (OPs) in drinking water, like Legionella spp., mycobacteria, Pseudomonas aeruginosa, and free-living amobae (FLA) are a risk to human health, due to their post-treatment growth in water systems. To assess and manage these risks, it is necessary to understand their variations and environmental conditions for the water routinely used. We sampled premise tap (N cold = 26, N hot = 26) and shower (N shower = 26) waters in a bathroom and compared water temperatures to levels of OPs via qPCR and identified Legionella spp. by 16S ribosomal RNA (rRNA) gene sequencing. The overall occurrence and cell equivalent quantities (CE L(-1)) of Mycobacterium spp. were highest (100 %, 1.4 × 10(5)), followed by Vermamoeba vermiformis (91 %, 493), Legionella spp. (59 %, 146), P. aeruginosa (14 %, 10), and Acanthamoeba spp. (5 %, 6). There were significant variations of OP's occurrence and quantities, and water temperatures were associated with their variations, especially for Mycobacterium spp., Legionella spp., and V. vermiformis. The peaks observed for Legionella, mainly consisted of Legionella pneumophila sg1 or Legionella anisa, occurred in the temperature ranged from 19 to 49 °C, while Mycobacterium spp. and V. vermiformis not only co-occurred with Legionella spp. but also trended to increase with increasing temperatures. There were higher densities of Mycobacterium in first than second draw water samples, indicating their release from faucet/showerhead biofilm. Legionella spp. were mostly at detectable levels and mainly consisted of L. pneumophila, L. anisa, Legionella donaldsonii, Legionella tunisiensis, and an unknown drinking water isolate based on sequence analysis. Results from this study suggested potential health risks caused by opportunistic pathogens when exposed to warm shower water with low chlorine residue and the use of Mycobacterium spp. as an indicator of premise pipe biofilm and the control management of those potential

  14. Genome Sequence of Pantoea sp. Strain Sc 1, an Opportunistic Cotton Pathogen

    OpenAIRE

    Medrano, Enrique G.; Bell, Alois A.

    2012-01-01

    Pantoea is comprised of a broad spectrum of species, including plant pathogens. Here, we provide an annotated genome sequence of Pantoea sp. strain Sc 1, which was isolated from a diseased cotton boll. This research provides the first genome sequence of a bona fide Pantoea sp. insect-vectored cotton pathogen.

  15. Genome sequence of Pantoea sp. strain Sc 1, an opportunistic cotton pathogen.

    Science.gov (United States)

    Medrano, Enrique G; Bell, Alois A

    2012-06-01

    Pantoea is comprised of a broad spectrum of species, including plant pathogens. Here, we provide an annotated genome sequence of Pantoea sp. strain Sc 1, which was isolated from a diseased cotton boll. This research provides the first genome sequence of a bona fide Pantoea sp. insect-vectored cotton pathogen.

  16. Memory CD4+ T cells are required for optimal NK cell effector functions against the opportunistic fungal pathogen Pneumocystis murina.

    Science.gov (United States)

    Kelly, Michelle N; Zheng, Mingquan; Ruan, Sanbao; Kolls, Jay; D'Souza, Alain; Shellito, Judd E

    2013-01-01

    Little is known about the role of NK cells or their interplay with other immune cells during opportunistic infections. Using our murine model of Pneumocystis pneumonia, we found that loss of NK cells during immunosuppression results in substantial Pneumocystis lung burden. During early infection of C57B/6 CD4(+) T cell-depleted mice, there were significantly fewer NK cells in the lung tissue compared with CD4(+) T cell-intact animals, and the NK cells present demonstrated decreased upregulation of the activation marker NKp46 and production of the effector cytokine, IFN-γ. Furthermore, coincubation studies revealed a significant increase in fungal killing when NK cells were combined with CD4(+) T cells compared with either cell alone, which was coincident with a significant increase in perforin production by NK cells. Finally, however, we found through adoptive transfer that memory CD4(+) T cells are required for significant NK cell upregulation of the activation marker NK group 2D and production of IFN-γ, granzyme B, and perforin during Pneumocystis infection. To the best of our knowledge, this study is the first to demonstrate a role for NK cells in immunity to Pneumocystis pneumonia, as well as to establish a functional relationship between CD4(+) T cells and NK cells in the host response to an opportunistic fungal pathogen.

  17. Human lysozyme peptidase resistance is perturbed by the anionic glycolipid biosurfactant rhamnolipid produced by the opportunistic pathogen Pseudomonas aeruginosa

    DEFF Research Database (Denmark)

    Andersen, Kell K; Vad, Brian Stougaard; Scavenius, Carsten;

    2016-01-01

    Infection by the opportunistic pathogen Pseudomonas aeruginosa (PA) is accompanied by the secretion of virulence factors such as the secondary metabolite rhamnolipid (RL) as well as an array of bacterial enzymes, including the protease elastase. The human immune system tries to counter this via...... defensive proteins such as human lysozyme (HLZ). HLZ targets the bacterial cell wall but may also have other antimicrobial activities. The enzyme contains four disulfide bonds and shows high thermodynamic stability and resistance to proteolytic attack. Here we show that RL promotes HLZ degradation...... by several unrelated proteases, including the PA elastase and human proteases. This occurs although RL does not by itself denature HLZ. Nevertheless, RL binds in a sufficiently high stoichiometry (8 RL:1 HLZ) to neutralize the highly cationic surface of HLZ. The initial cleavage sites agree well...

  18. [Advances in humans and animals opportunistic pathogens from environment infecting plants by crossing kingdoms].

    Science.gov (United States)

    Huang, Min; Wu, Yixin; He, Pengfei

    2016-02-04

    Some pathogenic microorganisms ubiquitous in the environment could cross kingdoms to infect diverse hosts. Several cross-kingdom human pathogens were summarized in this paper, including Serratia marcescens, Enterobacter cloacae and Pseudomonas aeuriginosa. They are ubiquitous in the nature and could cause plant diseases using the same or different infection strategies with which they infect humans and broaden host range. Among these bacteria, Klebsiella pneumoniae causes top rot disease of maize in the nature, revealing some plants in the environment could serve as a reservoir of various pathogens which might infect animals and probably humans when conditions are favorable, and even potentially harm food. Research on these cross-kingdom pathogens may play a very important role in the epidemiology of human, animal and plant diseases and be a hot topic in environment science.

  19. From Environment to Man: Genome Evolution and Adaptation of Human Opportunistic Bacterial Pathogens

    OpenAIRE

    Estelle Jumas-Bilak; Hélène Marchandin; Brigitte Lamy; Anne Lotthé; Fabien Aujoulat; Frédéric Roger; Alice Bourdier

    2012-01-01

    Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. The versatility of bacterial life-style involves adaptation to various niches. Adaptation to both open environment and human specific niches is a major challe...

  20. The Intraperitoneal Transcriptome of the Opportunistic Pathogen Enterococcus faecalis in Mice.

    Directory of Open Access Journals (Sweden)

    Cécile Muller

    Full Text Available Enterococcus faecalis is a Gram-positive lactic acid intestinal opportunistic bacterium with virulence potential. For a better understanding of the adapation of this bacterium to the host conditions, we performed a transcriptome analysis of bacteria isolated from an infection site (mouse peritonitis by RNA-sequencing. We identified a total of 211 genes with significantly higher transcript levels and 157 repressed genes. Our in vivo gene expression database reflects well the infection process since genes encoding important virulence factors like cytolysin, gelatinase or aggregation substance as well as stress response proteins, are significantly induced. Genes encoding metabolic activities are the second most abundant in vivo induced genes demonstrating that the bacteria are metabolically active and adapt to the special nutrient conditions of the host. α- and β- glucosides seem to be important substrates for E. faecalis inside the host. Compared to laboratory conditions, the flux through the upper part of glycolysis seems to be reduced and more carbon may enter the pentose phosphate pathway. This may reflect the need of the bacteria under infection conditions to produce more reducing power for biosynthesis. Another important substrate is certainly glycerol since both pathways of glycerol catabolism are strongly induced. Strongly in vivo induced genes should be important for the infection process. This assumption has been verified in a virulence test using well characterized mutants affected in glycerol metabolism. This showed indeed that mutants unable to metabolize this sugar alcohol are affected in organ colonisation in a mouse model.

  1. Biochemical characterization of recombinant dihydroorotate dehydrogenase from the opportunistic pathogenic yeast Candida albicans

    DEFF Research Database (Denmark)

    Zameitat, E.; Gojkovic, Zoran; Knecht, Wolfgang

    2006-01-01

    Candida albicans is the most prevalent yeast pathogen in humans, and recently it has become increasingly resistant to the current antifungal agents. In this study we investigated C. albicans dihydroorotate dehydrogenase (DHODH, EC 1.3.99.11), which catalyzes the fourth step of de novo pyrimidine...

  2. Biochemical characterization of recombinant dihydroorotate dehydrogenase from the opportunistic pathogenic yeast Candida albicans

    DEFF Research Database (Denmark)

    Zameitat, E.; Gojkovic, Zoran; Knecht, Wolfgang

    2006-01-01

    Candida albicans is the most prevalent yeast pathogen in humans, and recently it has become increasingly resistant to the current antifungal agents. In this study we investigated C. albicans dihydroorotate dehydrogenase (DHODH, EC 1.3.99.11), which catalyzes the fourth step of de novo pyrimidine...

  3. Manipulation of host diet to reduce gastrointestinal colonization by the opportunistic pathogen Candida albicans

    Science.gov (United States)

    Candida albicans, the most common human fungal pathogen, can cause systemic infections with a mortality rate of ~40%. Infections arise from colonization of the gastrointestinal (GI) tract, where C. albicans is part of the normal microflora. Reducing colonization in at-risk patients using antifungal ...

  4. Characterization and genome analysis of novel bacteriophages infecting the opportunistic human pathogens Klebsiella oxytoca and K. pneumoniae.

    Science.gov (United States)

    Park, Eun-Ah; Kim, You-Tae; Cho, Jae-Hyun; Ryu, Sangryeol; Lee, Ju-Hoon

    2017-04-01

    Klebsiella is a genus of well-known opportunistic human pathogens that are associated with diabetes mellitus and chronic pulmonary obstruction; however, this pathogen is often resistant to multiple drugs. To control this pathogen, two Klebsiella-infecting phages, K. oxytoca phage PKO111 and K. pneumoniae phage PKP126, were isolated from a sewage sample. Analysis of their host range revealed that they infect K. pneumoniae and K. oxytoca, suggesting host specificity for members of the genus Klebsiella. Stability tests confirmed that the phages are stable under various temperature (4 to 60 °C) and pH (3 to 11) conditions. A challenge assay showed that PKO111 and PKP126 inhibit growth of their host strains by 2 log and 4 log, respectively. Complete genome sequencing of the phages revealed that their genome sizes are quite different (168,758 bp for PKO111 and 50,934 bp for PKP126). Their genome annotation results showed that they have no human virulence-related genes, an important safety consideration. In addition, no lysogen-formation gene cluster was detected in either phage genome, suggesting that they are both virulent phages in their bacterial hosts. Based on these results, PKO111 and PKP126 may be good candidates for development of biocontrol agents against members of the genus Klebsiella for therapeutic purposes. A comparative analysis of tail-associated gene clusters of PKO111 and PKP126 revealed relatively low homology, suggesting that they might differ in the way they recognize and infect their specific hosts.

  5. Multicenter Outbreak of Infections by Saprochaete clavata, an Unrecognized Opportunistic Fungal Pathogen

    Science.gov (United States)

    Vaux, Sophie; Criscuolo, Alexis; Desnos-Ollivier, Marie; Diancourt, Laure; Tarnaud, Chloé; Vandenbogaert, Matthias; Brisse, Sylvain; Coignard, Bruno; Garcia-Hermoso, Dea; Blanc, Catherine; Hoinard, Damien; Lortholary, Olivier; Bretagne, Stéphane; Thiolet, Jean-Michel; de Valk, Henriette; Courbil, Rémi; Chabanel, Anne; Simonet, Marion; Maire, Francoise; Jbilou, Saadia; Tiberghien, Pierre; Blanchard, Hervé; Venier, Anne-Gaëlle; Bernet, Claude; Simon, Loïc; Sénéchal, Hélène; Pouchol, Elodie; Angot, Christiane; Ribaud, Patricia; Socié, G.; Flèche, M.; Brieu, Nathalie; Lagier, Evelyne; Chartier, Vanessa; Allegre, Thierry; Maulin, Laurence; Lanic, Hélène; Tilly, Hervé; Bouchara, Jean-Philippe; Pihet, Marc; Schmidt, Aline; Kouatchet, Achille; Vandamme, Yves-Marie; Ifrah, Norbert; Mercat, Alain; Accoceberry, Isabelle; Albert, Olivier; Leguay, Thibaut; Rogues, Anne-Marie; Bonhomme, Julie; Reman, Oumédaly; Lesteven, Claire; Poirier, Philippe; Chabrot, Cécile Molucon; Calvet, Laure; Baud, Olivier; Cambon, Monique; Farkas, Jean Chistophe; Lafon, Bruno; Dalle, Frédéric; Caillot, Denis; Lazzarotti, Aline; Aho, Serge; Combret, Sandrine; Facon, Thierry; Sendid, Boualem; Loridant, Séverine; Louis, Terriou; Cazin, Bruno; Grandbastien, Bruno; Bourgeois, Nathalie; Lotthé, Anne; Cartron, Guillaume; Ravel, Christophe; Colson, Pascal; Gaudard, Philippe; Bonmati, Caroline; Simon, Loic; Rabaud, Christian; Machouart, Marie; Poisson, Didier; Carp, Diana; Meunier, Jérôme; Gaschet, Anne; Miquel, Chantal; Sanhes, Laurence; Ferreyra, Milagros; Leibinger, Franck; Geudet, Philippe; Toubas, Dominique; Himberlin, Chantal; Bureau-Chalot, Florence; Delmer, Alain; Favennec, Loïc; Gargala, Gilles; Michot, Jean-Baptiste; Girault, Christophe; David, Marion; Leprêtre, Stéphane; Jardin, Fabrice; Honderlick, Pierre; Caille, Vincent; Cerf, Charles; Cassaing, Sophie; Recher, Christian; Picard, Muriel; Protin, Caroline; Huguet, Françoise; Huynh, Anne; Ruiz, Jean; Riu-Poulenc, Béatrice; Letocart, Philippe; Marchou, Bruno; Verdeil, Xavier; Cavalié, Laurent; Chauvin, Pamela; Iriart, Xavier; Valentin, Alexis; Bouvet, Emmanuelle; Delmas-Marsalet, Béatrice; Jeblaoui, Asma; Kassis-Chikhani, Najiby; Mühlethaler, Konrad; Zimmerli, Stefan; Zalar, Polona; Sánchez-Reus, Ferran; Gurgui, Merce

    2014-01-01

    ABSTRACT Rapidly fatal cases of invasive fungal infections due to a fungus later identified as Saprochaete clavata were reported in France in May 2012. The objectives of this study were to determine the clonal relatedness of the isolates and to investigate possible sources of contamination. A nationwide alert was launched to collect cases. Molecular identification methods, whole-genome sequencing (WGS), and clone-specific genotyping were used to analyze recent and historical isolates, and a case-case study was performed. Isolates from thirty cases (26 fungemias, 22 associated deaths at day 30) were collected between September 2011 and October 2012. Eighteen cases occurred within 8 weeks (outbreak) in 10 health care facilities, suggesting a common source of contamination, with potential secondary cases. Phylogenetic analysis identified one clade (clade A), which accounted for 16/18 outbreak cases. Results of microbiological investigations of environmental, drug, or food sources were negative. Analysis of exposures pointed to a medical device used for storage and infusion of blood products, but no fungal contamination was detected in the unused devices. Molecular identification of isolates from previous studies demonstrated that S. clavata can be found in dairy products and has already been involved in monocentric outbreaks in hematology wards. The possibility that S. clavata may transmit through contaminated medical devices or can be associated with dairy products as seen in previous European outbreaks is highly relevant for the management of future outbreaks due to this newly recognized pathogen. This report also underlines further the potential of WGS for investigation of outbreaks due to uncommon fungal pathogens. PMID:25516620

  6. Opportunistic invasive fungal pathogen Macrophomina phaseolina prognosis from immunocompromised humans to potential mitogenic RBL with an exceptional and novel antitumor and cytotoxic effect.

    Science.gov (United States)

    Arora, P; Dilbaghi, N; Chaudhury, A

    2012-02-01

    With the ever-increasing risk for fungal infections, one can no longer ignore fungi. It is imperative that clinical manifestations "presume fungus" with their epidemiologic and pathogenic features when evaluating a potentially infected patient. In the high-risk patient groups, fungi with intrinsic resistance to antifungal agents already exist, with a tendency to emerge as opportunistic pathogens. One of the smart pathogens is Macrophomina phaseolina, with the potential to disarm plant, animal, and human immunity. The response prophylaxis may vary from antifungal therapy and surgical measures to biochemical (Rhizoctonia bataticola lectin [RBL] with antitumor and cytotoxic nature) and gene therapeutics.

  7. Aerosol dissemination veterinary pathogenic and human opportunistic thermophilic and thermotolerant fungi from thermal effluents of nuclear production reactors

    Energy Technology Data Exchange (ETDEWEB)

    Tansey, M.R.; Fliermans, C.B.; Kern, C.D.

    1979-01-01

    The extent to which veterinary pathogenic and human opportunistic species of thermophilic and thermotolerant fungi disseminate in aerosols from heated effluents of nuclear production reactors of the Savannah River Plant (SRP), South Carolina, has been measured. Aerosol samples were taken at 140 sites, from directly over thermal effluents to more than 100 kilometers from the SRP boundary. Sampling methods included settle plates, liquid impingement, filtration, and a particle sizing cascade impactor (Andersen Sampler). Soils, foams, and microbial mats from thermal effluents, and vegetation were sampled to study distribution of particular species. Sampling was done under a variety of conditions; hot weather and cold, wet and dry, day and night, windy and calm, reactor(s) operating and not, disturbed vegetation and undisturbed. At 102 of the aerosol sampling sites, sophisticated meterological analysis were used to allow sampling of air in the plume which originated from thermal effluents. Soil, foam, microbial mat, vegetation, and aerosol samples were quantitatively plated for detection of viable units; filters were halved and then both plated and observed microscopically. Significant dissemination of thermophilic and thermotolerant fungi from thermal effluents was not detected. Thermophilic and thermotolerant fungi were widely distributed in soil, air, and on vegetation. Dactylaria gallopava, the indicator species and dominant fungus in microbial mats lining SRP thermal effluents and the cause of epidemic fatal phaeohyphomycosis in flocks of turkeys and chickens in South Carolina, Georgia, and elsewhere, was isolated from air at a maximum of 50 meters from effluents.

  8. β-1,3-Glucan recognition protein (βGRP) is essential for resistance against fungal pathogen and opportunistic pathogenic gut bacteria in Locusta migratoria manilensis.

    Science.gov (United States)

    Zheng, Xiaoli; Xia, Yuxian

    2012-03-01

    Pattern recognition proteins, which form part of the innate immune system, initiate host defense reactions in response to pathogen surface molecules. The pattern recognition protein β-1,3-glucan recognition protein (βGRP) binds to β-1,3-glucan on fungal surfaces to mediate melanization via the prophenoloxidase (PPO)-activating cascade. In this study, cDNA encoding a 53-kDa βGRP (LmβGRP) was cloned from Locusta migratoria manilensis. LmβGRP mRNA shown to be constitutively expressed specifically in hemocytes and was highly upregulated following fungal infection. LmβGRP-silenced (LmβGRP-RNAi) mutant locusts exhibited significantly reduced survival rate following fungal infection (Metarhizium acridum) compared with the wild-type. Furthermore, LmβGRP-RNAi mutants exhibited abnormally loose stools indicative of a gut defect. 16S rRNA gene analysis detected the opportunistic pathogenic bacterium, Vibrio vulnificus in LmβGRP mutant but not wild-type locusts, suggesting changes in the composition of gut bacterial communities. These results indicate that LmβGRP is essential to gut immunity in L. migratoria manilensis.

  9. AsrR is an oxidative stress sensing regulator modulating Enterococcus faecium opportunistic traits, antimicrobial resistance, and pathogenicity.

    Directory of Open Access Journals (Sweden)

    François Lebreton

    Full Text Available Oxidative stress serves as an important host/environmental signal that triggers a wide range of responses in microorganisms. Here, we identified an oxidative stress sensor and response regulator in the important multidrug-resistant nosocomial pathogen Enterococcus faecium belonging to the MarR family and called AsrR (antibiotic and stress response regulator. The AsrR regulator used cysteine oxidation to sense the hydrogen peroxide which results in its dissociation to promoter DNA. Transcriptome analysis showed that the AsrR regulon was composed of 181 genes, including representing functionally diverse groups involved in pathogenesis, antibiotic and antimicrobial peptide resistance, oxidative stress, and adaptive responses. Consistent with the upregulated expression of the pbp5 gene, encoding a low-affinity penicillin-binding protein, the asrR null mutant was found to be more resistant to β-lactam antibiotics. Deletion of asrR markedly decreased the bactericidal activity of ampicillin and vancomycin, which are both commonly used to treat infections due to enterococci, and also led to over-expression of two major adhesins, acm and ecbA, which resulted in enhanced in vitro adhesion to human intestinal cells. Additional pathogenic traits were also reinforced in the asrR null mutant including greater capacity than the parental strain to form biofilm in vitro and greater persistance in Galleria mellonella colonization and mouse systemic infection models. Despite overexpression of oxidative stress-response genes, deletion of asrR was associated with a decreased oxidative stress resistance in vitro, which correlated with a reduced resistance to phagocytic killing by murine macrophages. Interestingly, both strains showed similar amounts of intracellular reactive oxygen species. Finally, we observed a mutator phenotype and enhanced DNA transfer frequencies in the asrR deleted strain. These data indicate that AsrR plays a major role in antimicrobial

  10. Pathogenic and opportunistic gram-negative bacteria in soil, leachate and air in San Nicolás landfill at Aguascalientes, Mexico.

    Science.gov (United States)

    Flores-Tena, Francisco J; Guerrero-Barrera, Alma L; Avelar-González, Francisco J; Ramírez-López, E Marcela; Martínez-Saldaña, M Consolación

    2007-01-01

    The occurrence of Gram-negative pathogenic and opportunistic species, was studied for two years on air. soil and leachate from the San Nicolás Landfill. Aguascalientes, Mexico. For soil and leachate four samplings were done, two during the dry season and two during the rainy season. For soil there were 15 sampling points, the leachate samples were taken on the leachate tank. For air, twelve sampling were done in three points of the landfill. Twenty pathogenic and/or opportunistic bacteria were identified from air, twenty from soil and eleven from leachate. Most of them were enteric; however respiratory tract pathogenic bacteria were also identified. Pasteurella haemolytica were isolated in all air samples. Nine species were found in the a half of the soil samples. The most frequent species in leachate were Acinetobacter baumanii, Bordetella sp, Brucella sp. and Escherichia coli var II. The occurrence of pathogenic and opportunistic species points out to the nosocomial and domestic clinical wastes discharged in the landfill as a potential risk for public and occupational health.

  11. [A sepsis case caused by a rare opportunistic pathogen: Bacillus pumilus].

    Science.gov (United States)

    Borsa, Barış Ata; Aldağ, Mehmet Ersoy; Tunalı, Birsen; Dinç, Uğur; Güngördü Dalar, Zeynep; Özalp, Veli Cengiz

    2016-07-01

    The high prevalence of Bacillus species in nature and the detection of these bacteria as contaminant in cultures may lead diagnostic dilemma, however they should still be considered as a pathogen particularly in case of repeated positive cultures from patients with risk factors. Bacillus pumilus is a bacteria, though rarely, been reported as the causative agent of various infections such as sepsis, endocarditis, skin infections and food poisoning in human. In this report, a sepsis case in an immunocompetent patient caused by B.pumilus was presented. A 38-year-old female patient was admitted to emergency service of our hospital with the complaints of headache, dizziness and diarrhea. She had not any risk factors except a history of heart valve replacement operation two years ago. In physical examination, she had abdominal retention, high fever and hypotension, together with the high levels of sedimentation rate (ESR) and C-reactive protein (CRP). The patient was hospitalized with the preliminary diagnosis of sepsis. Three sets of blood samples at two different periods were taken for the culture. All blood culture vials had a positive signal at the second day of incubation in BD BACTEC™ 9050 system, therefore subcultures were performed in sheep blood agar, chocolate agar and MacConkey agar, and incubated in aerobic and anaerobic conditions. Beta-haemolytic, gray-colored large colonies were isolated from anaerobic culture at the end of 18-24 hours incubation, and Gram staining from colonies showed gram-positive rods. The isolate was identified as B.pumilus with 99% accuracy rate by using BD Phoenix™ 100 identification system. This result was also confirmed by MALDI-TOF based VITEK® MS system and 16S rRNA sequencing by Illumina MiSeq® platform. Antibiotic susceptibility test performed by BD Phoenix™ 100 system and the isolate was found to be resistant against penicillin, while it was susceptible to vancomycin, erythromycin, clindamycin, levofloxacin, and

  12. Safe interruption of maintenance therapy against previous infection with four common HIV-associated opportunistic pathogens during potent antiretroviral therapy

    DEFF Research Database (Denmark)

    Kirk, Ole; Reiss, Peter; Uberti-Foppa, Caterina;

    2002-01-01

    BACKGROUND: The safety of interrupting maintenance therapy for previous opportunistic infections other than Pneumocystis carinii pneumonia among patients with HIV infection who respond to potent antiretroviral therapy has not been well documented. OBJECTIVE: To assess the safety of interrupting m...

  13. Safe interruption of maintenance therapy against previous infection with four common HIV-associated opportunistic pathogens during potent antiretroviral therapy

    DEFF Research Database (Denmark)

    Kirk, Ole; Reiss, Peter; Uberti-Foppa, Caterina

    2002-01-01

    BACKGROUND: The safety of interrupting maintenance therapy for previous opportunistic infections other than Pneumocystis carinii pneumonia among patients with HIV infection who respond to potent antiretroviral therapy has not been well documented. OBJECTIVE: To assess the safety of interrupting m...

  14. Dectin-2 Recognizes Mannosylated O-antigens of Human Opportunistic Pathogens and Augments Lipopolysaccharide Activation of Myeloid Cells*

    Science.gov (United States)

    Wittmann, Alexandra; Lamprinaki, Dimitra; Bowles, Kristian M.; Katzenellenbogen, Ewa; Knirel, Yuriy A.; Whitfield, Chris; Nishimura, Takashi; Matsumoto, Naoki; Yamamoto, Kazuo; Iwakura, Yoichiro; Saijo, Shinobu; Kawasaki, Norihito

    2016-01-01

    LPS consists of a relatively conserved region of lipid A and core oligosaccharide and a highly variable region of O-antigen polysaccharide. Whereas lipid A is known to bind to the Toll-like receptor 4 (TLR4)-myeloid differentiation factor 2 (MD2) complex, the role of the O-antigen remains unclear. Here we report a novel molecular interaction between dendritic cell-associated C-type lectin-2 (Dectin-2) and mannosylated O-antigen found in a human opportunistic pathogen, Hafnia alvei PCM 1223, which has a repeating unit of [-Man-α1,3-Man-α1,2-Man-α1,2-Man-α1,2-Man-α1,3-]. H. alvei LPS induced higher levels of TNFα and IL-10 from mouse bone marrow-derived dendritic cells (BM-DCs), when compared with Salmonella enterica O66 LPS, which has a repeat of [-Gal-α1,6-Gal-α1,4-[Glc-β1,3]GalNAc-α1,3-GalNAc-β1,3-]. In a cell-based reporter assay, Dectin-2 was shown to recognize H. alvei LPS. This binding was inhibited by mannosidase treatment of H. alvei LPS and by mutations in the carbohydrate-binding domain of Dectin-2, demonstrating that H. alvei LPS is a novel glycan ligand of Dectin-2. The enhanced cytokine production by H. alvei LPS was Dectin-2-dependent, because Dectin-2 knock-out BM-DCs failed to do so. This receptor cross-talk between Dectin-2 and TLR4 involved events including spleen tyrosine kinase (Syk) activation and receptor juxtaposition. Furthermore, another mannosylated LPS from Escherichia coli O9a also bound to Dectin-2 and augmented TLR4 activation of BM-DCs. Taken together, these data indicate that mannosylated O-antigens from several Gram-negative bacteria augment TLR4 responses through interaction with Dectin-2. PMID:27358401

  15. Annual variations and effects of temperature on Legionella spp. and other potential opportunistic pathogens in tap and shower water

    Data.gov (United States)

    U.S. Environmental Protection Agency — The data contained in this worksheet provides the quantitative detection of potential pathogens for the bathroom water samples used in this study. This dataset is...

  16. Banana infecting fungus, Fusarium musae, is also an opportunistic human pathogen: are bananas potential carriers and source of fusariosis?

    Science.gov (United States)

    Triest, David; Stubbe, Dirk; De Cremer, Koen; Piérard, Denis; Detandt, Monique; Hendrickx, Marijke

    2015-01-01

    During re-identification of Fusarium strains in the BCCM™/IHEM fungal collection by multilocus sequence-analysis we observed that five strains, previously identified as Fusarium verticillioides, were Fusarium musae, a species described in 2011 from banana fruits. Four strains were isolated from blood samples or biopsies of immune-suppressed patients and one was isolated from the clinical environment, all originating from different hospitals in Belgium or France, 2001-2008. The F. musae identity of our isolates was confirmed by phylogenetic analysis using reference sequences of type material. Absence of the gene cluster necessary for fumonisin biosynthesis, characteristic to F. musae, was also the case for our isolates. In vitro antifungal susceptibility testing revealed no important differences in their susceptibility compared to clinical F. verticillioides strains and terbinafine was the most effective drug. Additional clinical F. musae strains were searched by performing BLAST queries in GenBank. Eight strains were found, of which six were keratitis cases from the U.S. multistate contact lens-associated outbreak in 2005 and 2006. The two other strains were also from the U.S., causing either a skin infection or sinusitis. This report is the first to describe F. musae as causative agent of superficial and opportunistic, disseminated infections in humans. Imported bananas might act as carriers of F. musae spores and be a potential source of infection with F. musae in humans. An alternative hypothesis is that the natural distribution of F. musae is geographically a lot broader than originally suspected and F. musae is present on different plant hosts. © 2015 by The Mycological Society of America.

  17. Opportunistic Music

    OpenAIRE

    Hachet, Martin; Kian, Arash; Berthaut, Florent; Franco, Jean-Sébastien; Desainte-Catherine, Myriam

    2009-01-01

    International audience; While mixed reality has inspired the development of many new musical instruments, few approaches explore the potential of mobile setups. We present a new musical interaction concept, called "opportunistic music". It allows musicians to recreate a hardware musical controller using any objects of their immediate environment. This approach benefits from the physical properties of real objects for controlling music. Our prototype is based on a stereo-vision tracking system...

  18. Onychomycosis due to opportunistic molds*

    OpenAIRE

    Martínez-Herrera, Erick Obed; Arroyo-Camarena,Stefanie; Tejada-García, Diana Luz; Porras-López, Carlos Francisco; Arenas, Roberto

    2015-01-01

    Abstract BACKGROUND: Onychomycosis are caused by dermatophytes and Candida, but rarely by non- dermatophyte molds. These opportunistic agents are filamentous fungi found as soil and plant pathogens. OBJECTIVES: To determine the frequency of opportunistic molds in onychomycosis. METHODS: A retrospective analysis of 4,220 cases with onychomycosis, diagnosed in a 39-month period at the Institute of Dermatology and Skin surgery "Prof. Dr. Fernando A. Cordero C." in Guatemala City, and confirmed w...

  19. Legionella pneumophila: the paradox of a highly sensitive opportunistic waterborne pathogen able to persist in the environment

    Directory of Open Access Journals (Sweden)

    Jean-Marc eBerjeaud

    2016-04-01

    Full Text Available Legionella pneumophila, the major causative agent of Legionnaires’ disease, is found in freshwater environments in close association with free-living amoebae and multispecies biofilms, leading to persistence, spread, biocide resistance, and elevated virulence of the bacterium. Indeed, legionellosis outbreaks are mainly due to the ability of this bacterium to colonize and persist in water facilities, despite harsh physical and chemical treatments. However, these treatments are not totally efficient and, after a lag period, L. pneumophila may be able to quickly re-colonize these systems. Several natural compounds (biosurfactants, antimicrobial peptides… with anti-Legionella properties have recently been described in the literature, highlighting their specific activities against this pathogen. In this review, we first consider this hallmark of Legionella to resist killing, in regard to its biofilm or host-associated life style. Then, we focus more accurately on natural anti-Legionella molecules described so far, which could provide new eco-friendly and alternative ways to struggle against this important pathogen in plumbing.

  20. Candida and candidiasis in HIV-infected patients: where commensalism, opportunistic behavior and frank pathogenicity lose their borders.

    Science.gov (United States)

    Cassone, Antonio; Cauda, Roberto

    2012-07-31

    In this era of efficacious antiretroviral therapy and consequent immune reconstitution, oropharyngeal and esophageal candidiasis (OPC and OEC) still remain two clinically relevant presentations in the global HIV setting. Both diseases are predominantly caused by Candida albicans, a polymorphic fungus which is a commensal microbe in the healthy individual but can become an aggressive pathogen in a debilitated host. Actually, C. albicans commensalism is not the result of a benign behavior of one of the many components of human microbiota, but rather the result of host's potent innate and adaptive immune responses that restrict the growth of a potentially dangerous microrganism on the epithelia. An important asset guarding against the fungus is the Th17 functional subset of T helper cells. The selective loss of these cells with the progression of HIV infection causes the decay of fungal containment on the oral epithelium and allows C. albicans to express its pathogenic potential. An important part of this potential is represented by mechanisms to evade host immunity and enhance inflammation and immunoactivation. In C. albicans, these mechanisms are mostly incorporated into and expressed by characteristic morphogenic transitions such as the yeast-to-hyphal growth and the white-to-opaque switch. In addition, HIV infection generates an 'environment' selecting for overexpression of the virulence potential by the fungus, particularly concerning the secreted aspartyl proteinases (Saps). These enzymes can degrade critical host defense components such as complement and epithelial defensive proteins such as histatin-5 and E-cadherin. It appears that part of this enhanced Candida virulence could be induced by the binding of the fungus to HIV and/or induced by HIV proteins such as GP160 and tat. Both OPC and OEC can be controlled by old and new antimycotics, but in the absence of host collaboration, anticandidal therapy may become ineffective in the long run. For these reasons

  1. Identification of Opportunistic Pathogenic Bacteria in Drinking Water Samples of Different Rural Health Centers and Their Clinical Impacts on Humans

    Directory of Open Access Journals (Sweden)

    Pavan Kumar Pindi

    2013-01-01

    Full Text Available International drinking water quality monitoring programs have been established in order to prevent or to reduce the risk of contracting water-related infections. A survey was performed on groundwater-derived drinking water from 13 different hospitals in the Mahabubnagar District. A total of 55 bacterial strains were isolated which belonged to both gram-positive and gram-negative bacteria. All the taxa were identified based on the 16S rRNA gene sequence analysis based on which they are phylogenetically close to 27 different taxa. Many of the strains are closely related to their phylogenetic neighbors and exhibit from 98.4 to 100% sequence similarity at the 16S rRNA gene sequence level. The most common group was similar to Acinetobacter junii (21.8% and Acinetobacter calcoaceticus (10.9% which were shared by 7 and 5 water samples, respectively. Out of 55 isolates, only 3 isolates belonged to coliform group which are Citrobacter freundii and Pantoea anthophila. More than half (52.7%, 29 strains of the phylogenetic neighbors which belonged to 12 groups were reported to be pathogenic and isolated from clinical specimens. Out of 27 representative taxa are affiliated have eight representative genera in drinking water except for those affiliated with the genera Exiguobacterium, Delftia, Kocuria, and Lysinibacillus.

  2. [Evaluation of epidemic risk from pathogenic and opportunistic bacteria isolated from water of its various use types].

    Science.gov (United States)

    Zagaĭnova, A V; Talaeva, Iu G; Dmitrieva, R A; Ingel', F I; Iurchenko, V V; Artemova, T Z; Nedachin, A E; Gipp, E K; Butorina, N N; Snegirev, D V

    2010-01-01

    The investigation was concerned with wild gram-positive and gram-negative microorganisms (E. coli spp., Klebsiella spp., Salmonella spp., and the nonfermentative bacteria Pseudomonas spp.) isolated from the waters of different types, as well as museum cultures (E. coli strain 1257, E. coli strain 675, Salmonella enteritidis ATCC 5765, Staphylococcus aureus 906, and Pseudomonas aeruginosa ATCC 10145). The wild strains were isolated from water when conducting experimental and field studies; these are able to survive in the waters disinfected by various procedures (a guanidine-containing disinfectant in non-toxic concentrations; photo-activated decontamination with sensitizers; exposure to magnetic and ultrasound waves). The cytotoxic, adhesive, and invasive activities of the bacteria isolated from environmental water objects increased on their cultivation on nutrient growth media, by simulating their possible effects in man. The developed experimental approach makes it possible to estimate the hazard of potentially pathogenic bacteria in one test trial, by applying the BGM cells and may be used to assess the microbial risk.

  3. Characterization of the gacA-dependent surface and coral mucus colonization by an opportunistic coral pathogen Serratia marcescens PDL100.

    Science.gov (United States)

    Krediet, Cory J; Carpinone, Emily M; Ritchie, Kim B; Teplitski, Max

    2013-05-01

    Opportunistic pathogens rely on global regulatory systems to assess the environment and to control virulence and metabolism to overcome host defenses and outcompete host-associated microbiota. In Gammaproteobacteria, GacS/GacA is one such regulatory system. GacA orthologs direct the expression of the csr (rsm) small regulatory RNAs, which through their interaction with the RNA-binding protein CsrA (RsmA), control genes with functions in carbon metabolism, motility, biofilm formation, and virulence. The csrB gene was controlled by gacA in Serratia marcescens PDL100. A disruption of the S. marcescens gacA gene resulted in an increased fitness of the mutant on mucus of the host coral Acropora palmata and its high molecular weight fraction, whereas the mutant was as competitive as the wild type on the low molecular weight fraction of the mucus. Swarming motility and biofilm formation were reduced in the gacA mutant. This indicates a critical role for gacA in the efficient utilization of specific components of coral mucus and establishment within the surface mucopolysaccharide layer. While significantly affecting early colonization behaviors (coral mucus utilization, swarming motility, and biofilm formation), gacA was not required for virulence of S. marcescens PDL100 in either a model polyp Aiptasia pallida or in brine shrimp Artemia nauplii.

  4. Rabbit hepatitis E virus is an opportunistic pathogen in specific-pathogen-free rabbits with the capability of cross-species transmission.

    Science.gov (United States)

    Liu, Baoyuan; Sun, Yani; Du, Taofeng; Chen, Yiyang; Wang, Xinjie; Huang, Baicheng; Li, Huixia; Nan, Yuchen; Xiao, Shuqi; Zhang, Gaiping; Hiscox, Julian A; Zhou, En-Min; Zhao, Qin

    2017-03-01

    Hepatitis E virus (HEV) has been detected in rabbits, a recently identified natural reservoir. In this study, anti-HEV antibodies and viral RNA were detected in rabbits sourced from a specific-pathogen-free (SPF) rabbit vendor in Shaanxi Province, China. BLAST results of partial HEV ORF2 genes cloned here indicated that two viral strains circulated in the rabbits. Sequence determination of the complete genome (7302bp) of one strain and a partial ORF1 gene (1537bp) of the other strain showed that they shared 90% identity with one another and 78%-94% identity with other known rabbit HEVs. In addition, inoculation with rabbit HEV from SPF rabbits studied here resulted in infection of SPF pigs; this cross-species transmission was evidenced by seroconversion, viremia and faecal virus shedding. These results suggest that to prevent spread of this zoonotic pathogen, rabbits should be tested routinely for HEV RNA in SPF vendor facilities.

  5. Fucose-binding lectin from opportunistic pathogen Burkholderia ambifaria binds to both plant and human oligosaccharidic epitopes.

    Science.gov (United States)

    Audfray, Aymeric; Claudinon, Julie; Abounit, Saïda; Ruvoën-Clouet, Nathalie; Larson, Göran; Smith, David F; Wimmerová, Michaela; Le Pendu, Jacques; Römer, Winfried; Varrot, Annabelle; Imberty, Anne

    2012-02-03

    Burkholderia ambifaria is generally associated with the rhizosphere of plants where it has biocontrol effects on other microorganisms. It is also a member of the Burkholderia cepacia complex, a group of closely related bacteria that cause lung infections in immunocompromised patients as well as in patients with granulomatous disease or cystic fibrosis. Our previous work indicated that fucose on human epithelia is a frequent target for lectins and adhesins of lung pathogens (Sulák, O., Cioci, G., Lameignère, E., Balloy, V., Round, A., Gutsche, I., Malinovská, L., Chignard, M., Kosma, P., Aubert, D. F., Marolda, C. L., Valvano, M. A., Wimmerová, M., and Imberty, A. (2011) PLoS Pathog. 7, e1002238). Analysis of the B. ambifaria genome identified BambL as a putative fucose-binding lectin. The 87-amino acid protein was produced recombinantly and demonstrated to bind to fucosylated oligosaccharides with a preference for αFuc1-2Gal epitopes. Crystal structures revealed that it associates as a trimer with two fucose-binding sites per monomer. The overall fold is a six-bladed β-propeller formed by oligomerization as in the Ralstonia solanacearum lectin and not by sequential domains like the fungal fucose lectin from Aleuria aurantia. The affinity of BambL for small fucosylated glycans is very high as demonstrated by microcalorimetry (K(D) < 1 μM). Plant cell wall oligosaccharides and human histo-blood group oligosaccharides H-type 2 and Lewis Y are bound with equivalent efficiency. Binding to artificial glycosphingolipid-containing vesicles, human saliva, and lung tissues confirmed that BambL could recognize a wide spectrum of fucosylated epitopes, albeit with a lower affinity for biological material from nonsecretor individuals.

  6. Effect of ethanol on differential protein production and expression of potential virulence functions in the opportunistic pathogen Acinetobacter baumannii.

    Science.gov (United States)

    Nwugo, Chika C; Arivett, Brock A; Zimbler, Daniel L; Gaddy, Jennifer A; Richards, Ashley M; Actis, Luis A

    2012-01-01

    Acinetobacter baumannii persists in the medical environment and causes severe human nosocomial infections. Previous studies showed that low-level ethanol exposure increases the virulence of A. baumannii ATCC 17978. To better understand the mechanisms involved in this response, 2-D gel electrophoresis combined with mass spectrometry was used to investigate differential protein production in bacteria cultured in the presence or absence of ethanol. This approach showed that the presence of ethanol significantly induces and represses the production of 22 and 12 proteins, respectively. Although over 25% of the ethanol-induced proteins were stress-response related, the overall bacterial viability was uncompromised when cultured under these conditions. Production of proteins involved in lipid and carbohydrate anabolism was increased in the presence of ethanol, a response that correlates with increased carbohydrate biofilm content, enhanced biofilm formation on abiotic surfaces and decrease bacterial motility on semi-solid surfaces. The presence of ethanol also induced the acidification of bacterial cultures and the production of indole-3-acetic acid (IAA), a ubiquitous plant hormone that signals bacterial stress-tolerance and promotes plant-bacteria interactions. These responses could be responsible for the significantly enhanced virulence of A. baumannii ATCC 17978 cells cultured in the presence of ethanol when tested with the Galleria mellonella experimental infection model. Taken together, these observations provide new insights into the effect of ethanol in bacterial virulence. This alcohol predisposes the human host to infections by A. baumannii and could favor the survival and adaptation of this pathogen to medical settings and adverse host environments.

  7. Effect of ethanol on differential protein production and expression of potential virulence functions in the opportunistic pathogen Acinetobacter baumannii.

    Directory of Open Access Journals (Sweden)

    Chika C Nwugo

    Full Text Available Acinetobacter baumannii persists in the medical environment and causes severe human nosocomial infections. Previous studies showed that low-level ethanol exposure increases the virulence of A. baumannii ATCC 17978. To better understand the mechanisms involved in this response, 2-D gel electrophoresis combined with mass spectrometry was used to investigate differential protein production in bacteria cultured in the presence or absence of ethanol. This approach showed that the presence of ethanol significantly induces and represses the production of 22 and 12 proteins, respectively. Although over 25% of the ethanol-induced proteins were stress-response related, the overall bacterial viability was uncompromised when cultured under these conditions. Production of proteins involved in lipid and carbohydrate anabolism was increased in the presence of ethanol, a response that correlates with increased carbohydrate biofilm content, enhanced biofilm formation on abiotic surfaces and decrease bacterial motility on semi-solid surfaces. The presence of ethanol also induced the acidification of bacterial cultures and the production of indole-3-acetic acid (IAA, a ubiquitous plant hormone that signals bacterial stress-tolerance and promotes plant-bacteria interactions. These responses could be responsible for the significantly enhanced virulence of A. baumannii ATCC 17978 cells cultured in the presence of ethanol when tested with the Galleria mellonella experimental infection model. Taken together, these observations provide new insights into the effect of ethanol in bacterial virulence. This alcohol predisposes the human host to infections by A. baumannii and could favor the survival and adaptation of this pathogen to medical settings and adverse host environments.

  8. Opportunists and opportunities: the 2010 SHEA Lecture.

    Science.gov (United States)

    Henderson, David K

    2010-11-01

    My experience as a hospital epidemiologist at the National Institutes of Health Clinical Center has underscored the importance of aggressively managing infection with opportunistic pathogens and of taking advantage of opportunities as they arise (most often as crises). I review selected aspects of my career and use these as examples of the opportunists and opportunities now facing healthcare epidemiology.

  9. Characterization of the mrgRS locus of the opportunistic pathogen Burkholderia pseudomallei: temperature regulates the expression of a two-component signal transduction system

    Directory of Open Access Journals (Sweden)

    Dance David AB

    2006-08-01

    Full Text Available Abstract Background Burkholderia pseudomallei is a saprophyte in tropical environments and an opportunistic human pathogen. This versatility requires a sensing mechanism that allows the bacterium to respond rapidly to altered environmental conditions. We characterized a two-component signal transduction locus from B. pseudomallei 204, mrgR and mrgS, encoding products with extensive homology with response regulators and histidine protein kinases of Escherichia coli, Bordetella pertussis, and Vibrio cholerae. Results The locus was present and expressed in a variety of B. pseudomallei human and environmental isolates but was absent from other Burkholderia species, B. cepacia, B. cocovenenans, B. plantarii, B. thailandensis, B. vandii, and B. vietnamiensis. A 2128 bp sequence, including the full response regulator mrgR, but not the sensor kinase mrgS, was present in the B. mallei genome. Restriction fragment length polymorphism downstream from mrgRS showed two distinct groups were present among B. pseudomallei isolates. Our analysis of the open reading frames in this region of the genome revealed that transposase and bacteriophage activity may help explain this variation. MrgR and MrgS proteins were expressed in B. pseudomallei 204 cultured at different pH, salinity and temperatures and the expression was substantially reduced at 25°C compared with 37°C or 42°C but was mostly unaffected by pH or salinity, although at 25°C and 0.15% NaCl a small increase in MrgR expression was observed at pH 5. MrgR was recognized by antibodies in convalescent sera pooled from melioidosis patients. Conclusion The results suggest that mrgRS regulates an adaptive response to temperature that may be essential for pathogenesis, particularly during the initial phases of infection. B. pseudomallei and B. mallei are very closely related species that differ in their capacity to adapt to changing environmental conditions. Modifications in this region of the genome may

  10. Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus

    Science.gov (United States)

    Lechner, Judith; Porter, Louise F.; Rice, Aine; Vitart, Veronique; Armstrong, David J.; Schorderet, Daniel F.; Munier, Francis L.; Wright, Alan F.; Inglehearn, Chris F.; Black, Graeme C.; Simpson, David A.; Manson, Forbes; Willoughby, Colin E.

    2014-01-01

    Keratoconus, a common inherited ocular disorder resulting in progressive corneal thinning, is the leading indication for corneal transplantation in the developed world. Genome-wide association studies have identified common SNPs 100 kb upstream of ZNF469 strongly associated with corneal thickness. Homozygous mutations in ZNF469 and PR domain-containing protein 5 (PRDM5) genes result in brittle cornea syndrome (BCS) Types 1 and 2, respectively. BCS is an autosomal recessive generalized connective tissue disorder associated with extreme corneal thinning and a high risk of corneal rupture. Some individuals with heterozygous PRDM5 mutations demonstrate a carrier ocular phenotype, which includes a mildly reduced corneal thickness, keratoconus and blue sclera. We hypothesized that heterozygous variants in PRDM5 and ZNF469 predispose to the development of isolated keratoconus. We found a significant enrichment of potentially pathologic heterozygous alleles in ZNF469 associated with the development of keratoconus (P = 0.00102) resulting in a relative risk of 12.0. This enrichment of rare potentially pathogenic alleles in ZNF469 in 12.5% of keratoconus patients represents a significant mutational load and highlights ZNF469 as the most significant genetic factor responsible for keratoconus identified to date. PMID:24895405

  11. Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus.

    Science.gov (United States)

    Lechner, Judith; Porter, Louise F; Rice, Aine; Vitart, Veronique; Armstrong, David J; Schorderet, Daniel F; Munier, Francis L; Wright, Alan F; Inglehearn, Chris F; Black, Graeme C; Simpson, David A; Manson, Forbes; Willoughby, Colin E

    2014-10-15

    Keratoconus, a common inherited ocular disorder resulting in progressive corneal thinning, is the leading indication for corneal transplantation in the developed world. Genome-wide association studies have identified common SNPs 100 kb upstream of ZNF469 strongly associated with corneal thickness. Homozygous mutations in ZNF469 and PR domain-containing protein 5 (PRDM5) genes result in brittle cornea syndrome (BCS) Types 1 and 2, respectively. BCS is an autosomal recessive generalized connective tissue disorder associated with extreme corneal thinning and a high risk of corneal rupture. Some individuals with heterozygous PRDM5 mutations demonstrate a carrier ocular phenotype, which includes a mildly reduced corneal thickness, keratoconus and blue sclera. We hypothesized that heterozygous variants in PRDM5 and ZNF469 predispose to the development of isolated keratoconus. We found a significant enrichment of potentially pathologic heterozygous alleles in ZNF469 associated with the development of keratoconus (P = 0.00102) resulting in a relative risk of 12.0. This enrichment of rare potentially pathogenic alleles in ZNF469 in 12.5% of keratoconus patients represents a significant mutational load and highlights ZNF469 as the most significant genetic factor responsible for keratoconus identified to date.

  12. Enrichment, Amplification, and Sequence-Based Typing of Salmonella enterica and Other Foodborne Pathogens.

    Science.gov (United States)

    Edlind, Tom; Brewster, Jeffrey D; Paoli, George C

    2017-01-01

    Detection of Salmonella enterica in foods typically involves microbiological enrichment, molecular-based assay, and subsequent isolation and identification of a pure culture. This is ideally followed by strain typing, which provides information critical to the investigation of outbreaks and the attribution of their sources. Pulsed-field gel electrophoresis is the "gold standard" for S. enterica strain typing, but its limitations have encouraged the search for alternative methods, including whole genome sequencing. Both methods typically require a pure culture, which adds to the cost and turnaround time. A more rapid and cost-effective method with sufficient discriminatory power would benefit food industries, regulatory agencies, and public health laboratories. To address this need, a novel enrichment, amplification, and sequence-based typing (EAST) approach was developed involving (i) overnight enrichment and total DNA preparation, (ii) amplification of polymorphic tandem repeat-containing loci with electrophoretic detection, and (iii) DNA sequencing and bioinformatic analysis to identify related strains. EAST requires 3 days or less and provides a strain resolution that exceeds serotyping and is comparable to pulsed-field gel electrophoresis. Evaluation with spiked ground turkey demonstrated its sensitivity (with a starting inoculum of ≤1 CFU/g) and specificity (with unique or nearly unique alleles relative to databases of >1,000 strains). In tests with unspiked retail chicken parts, 3 of 11 samples yielded S. enterica -specific PCR products. Sequence analysis of three distinct typing targets (SeMT1, SeCRISPR1, and SeCRISPR2) revealed consistent similarities to specific serotype Schwarzengrund, Montevideo, and Typhimurium strains. EAST provides a time-saving and cost-effective approach for detecting and typing foodborne S. enterica , and postenrichment steps can be commercially outsourced to facilitate its implementation. Initial studies with Listeria

  13. Diversity and antifungal resistance patterns of prevalent opportunistic pathogenic yeasts colonizing the oral cavities of asymptomatic human immunodeficiency virus-infected individuals, and their relation to CD4 + counts

    Directory of Open Access Journals (Sweden)

    Deepa Anil Kumar

    2015-01-01

    Full Text Available Background: Yeasts are important opportunistic pathogens, in individuals infected with human immunodeficiency virus (HIV. Yeast species inhabiting the oral mucosa of HIV-infected persons can act as source of oral lesions, especially as the individual progresses towards immunocompromised state. Present study was conducted to evaluate the diversity of yeasts in oral cavities of asymptomatic HIV-infected persons and their association with CD4 + cell counts. Materials and Methods: 100 HIV seropositive subjects and 100 healthy controls were screened for oral yeast carriage using standard procedures. Results: Of the 100 HIV-seropositive persons screened, 48 were colonized by different yeasts, either alone or in association with another species. Candida albicans was the most common species (56.90% while non C. albicans Candida (NCAC accounted for 39.65%. Among NCAC, Candida tropicalis and Candida krusei were most common. One isolate each of rare opportunistic pathogenic yeasts, Geotrichum candidum and Saccharomyces cereviseae, was recovered. The control group had an oral candidal carriage rate of 23%; C. albicans was the predominant species, followed by Candida glabrata, C. tropicalis and Candida parapsilosis. Antifungal susceptibility testing revealed no resistance in C. albicans, to the commonly used antifungal agents, whereas resistance or dose dependent susceptibility to fluconazole was observed in some of the NCAC species. Conclusion: Oral carriage of opportunistic pathogenic yeasts was greater in HIV-seropositive persons heading towards immunocompromised state, as evidenced by their CD4 + cell count. The predominant yeast isolated in this study (C. albicans, was found to be susceptible to commonly used antifungals.

  14. Corynebacterium striatum infecting a malignant cutaneous lesion: the emergence of an opportunistic pathogen Corynebacterium striatum infectando lesão cutânea maligna: a emergência de um patógeno oportunista

    Directory of Open Access Journals (Sweden)

    Silvana Vargas Superti

    2009-04-01

    Full Text Available We described a case of a 27-year old male patient with skin and soft tissue infection of a neoplastic lesion caused by Corynebacterium striatum, an organism which has been rarely described as a human pathogen. Identification was confirmed by DNA sequencing. Successful treatment with penicillin was achieved. The role of the C. striatum as an emerging opportunistic pathogen is discussed.Descrevemos infecção de lesão neoplásica em paciente masculino de 27 anos, envolvendo pele e partes moles, causada por Corynebacterium striatum, um microrganismo raramente descrito como patógeno humano. A identificação foi confirmada por seqüenciamento de DNA. O paciente foi tratado com penicilina, com sucesso. O papel do C. striatum como patógeno oportunista é discutido.

  15. [Genetic virulence markers of opportunistic bacteria].

    Science.gov (United States)

    Bondarenko, V M

    2011-01-01

    The analysis of opportunistic bacteria phenotypic and genetic virulence markers indicates that pathogenicity formation is based on a structural modification of bacterial DNA which is linked with migration of interbacterial pathogenicity "islands" genetic determinants. Structural organization features of these mobile genetic elements determine high expression probability, and PCR detection of pathogenicity "islands" determinants that control adhesins, invasins, cytotoxic and cytolitic toxines synthesis may indicate etiopathogenetic significance of clinical isolates.

  16. The effects of indoor and outdoor dust exposure on the growth, sensitivity to oxidative-stress, and biofilm production of three opportunistic bacterial pathogens.

    Science.gov (United States)

    Suraju, Mohammed O; Lalinde-Barnes, Sloan; Sanamvenkata, Sachindra; Esmaeili, Mahsa; Shishodia, Shishir; Rosenzweig, Jason A

    2015-12-15

    Within the last decade, many studies have highlighted the radical changes in the components of indoor and outdoor dust. For example, agents like automobile emitted platinum group elements and different kinds of organic phthalates and esters have been reported to be accumulating in the biosphere. Humans consistently face dermal, respiratory, and dietary exposures to these particles while indoors and outdoors. In fact, dust particulate matter has been associated with close to 500,000 deaths per year in Europe and about 200,000 deaths per year in the United States. To date, there has been limited examination of the physiological impact of indoor and outdoor dust exposure on normal flora microbes. In this study, the effect of indoor- and outdoor-dust exposure on three opportunistic bacterial species (Escherichia coli, Enterococcus faecalis, and Pseudomonas aeruginosa) was assessed. Specifically, bacterial growth, oxidative stress resistance, and biofilm production were measured following indoor- and outdoor-dust exposures. Studies were conducted in nutritionally-rich and -poor environments typically encountered by bacteria. Surprisingly, indoor-dust (200μg/mL), enhanced the growth of all three bacterial species in nutrient-poor conditions, but slowed growth in nutrient-rich conditions. In nutrient-rich medium, 100μg/mL exposure of either indoor- or outdoor-dust resulted in significantly reduced oxidative stress resistance in E. coli. Most interestingly, dust (indoor and outdoor), either in nutrient-rich or -poor conditions, significantly increased biofilm production in all three bacterial species. These data suggest that indoor and outdoor dust, can modify opportunistic bacteria through altering growth, sensitivity to oxidative stress, and their virulence potential through enhanced biofilm formation.

  17. Onychomycosis due to opportunistic molds*

    Science.gov (United States)

    Martínez-Herrera, Erick Obed; Arroyo-Camarena, Stefanie; Tejada-García, Diana Luz; Porras-López, Carlos Francisco; Arenas, Roberto

    2015-01-01

    BACKGROUND: Onychomycosis are caused by dermatophytes and Candida, but rarely by non- dermatophyte molds. These opportunistic agents are filamentous fungi found as soil and plant pathogens. OBJECTIVES: To determine the frequency of opportunistic molds in onychomycosis. METHODS: A retrospective analysis of 4,220 cases with onychomycosis, diagnosed in a 39-month period at the Institute of Dermatology and Skin surgery "Prof. Dr. Fernando A. Cordero C." in Guatemala City, and confirmed with a positive KOH test and culture. RESULTS: 32 cases (0.76%) of onychomycosis caused by opportunistic molds were confirmed. The most affected age group ranged from 41 to 65 years (15 patients, 46.9%) and females were more commonly affected (21 cases, 65.6%) than males. Lateral and distal subungual onychomycosis (OSD-L) was detected in 20 cases (62.5%). The microscopic examination with KOH showed filaments in 19 cases (59.4%), dermatophytoma in 9 cases (28.1%), spores in 2 cases (6.25%), and filaments and spores in 2 cases (6.25%). Etiologic agents: Aspergillus sp., 11 cases (34.4%); Scopulariopsis brevicaulis, 8 cases (25.0%); Cladosporium sp., 3 cases (9.4%); Acremonium sp., 2 cases (6.25%); Paecilomyces sp., 2 cases (6.25%); Tritirachium oryzae, 2 cases (6.25%); Fusarium sp., Phialophora sp., Rhizopus sp. and Alternaria alternate, 1 case (3.1%) each. CONCLUSIONS: We found onychomycosis by opportunistic molds in 0.76% of the cases and DLSO was present in 62.5%. The most frequent isolated etiological agents were: Aspergillus sp. and Scopulariopsis brevicaulis. PMID:26131862

  18. Keratitis by Fusarium temperatum , a novel opportunist

    NARCIS (Netherlands)

    Al-Hatmi, Abdullah; Bonifaz, Alexandro; de Hoog, G; Vazquez-Maya, Leticia; Garcia-Carmona, Karla; Meis, Jacques F; van Diepeningen, Anne D

    2014-01-01

    Background Fusarium species are among the most common fungi present in the environment and some species have emerged as major opportunistic fungal infection in human. However, in immunocompromised hosts they can be virulent pathogens and can cause death. The pathogenesis of this infection relies on

  19. Non-nucleoside Inhibitors of BasE, An Adenylating Enzyme in the Siderophore Biosynthetic Pathway of the Opportunistic Pathogen Acinetobacter baumannii

    OpenAIRE

    Neres, João; Engelhart, Curtis A.; Drake, Eric J.; Daniel J Wilson; Fu, Peng; Boshoff, Helena I.; Barry, Clifton E.; Gulick, Andrew M.; Aldrich, Courtney C.

    2013-01-01

    Siderophores are small-molecule iron chelators produced by bacteria and other microorganisms for survival under iron limiting conditions, such as found in a mammalian host. Siderophore biosynthesis is essential for the virulence of many important Gram-negative pathogens including Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli. We performed high-throughput screening of against BasE, which is involved in siderophore biosynthesis in A. baumannii and ...

  20. Toxoplasmosis and Polygenic Disease Susceptibility Genes: Extensive Toxoplasma gondii Host/Pathogen Interactome Enrichment in Nine Psychiatric or Neurological Disorders

    Directory of Open Access Journals (Sweden)

    C. J. Carter

    2013-01-01

    Full Text Available Toxoplasma gondii is not only implicated in schizophrenia and related disorders, but also in Alzheimer's or Parkinson's disease, cancer, cardiac myopathies, and autoimmune disorders. During its life cycle, the pathogen interacts with ~3000 host genes or proteins. Susceptibility genes for multiple sclerosis, Alzheimer's disease, schizophrenia, bipolar disorder, depression, childhood obesity, Parkinson's disease, attention deficit hyperactivity disorder (multiple sclerosis, and autism (, but not anorexia or chronic fatigue are highly enriched in the human arm of this interactome and 18 (ADHD to 33% (MS of the susceptibility genes relate to it. The signalling pathways involved in the susceptibility gene/interactome overlaps are relatively specific and relevant to each disease suggesting a means whereby susceptibility genes could orient the attentions of a single pathogen towards disruption of the specific pathways that together contribute (positively or negatively to the endophenotypes of different diseases. Conditional protein knockdown, orchestrated by T. gondii proteins or antibodies binding to those of the host (pathogen derived autoimmunity and metabolite exchange, may contribute to this disruption. Susceptibility genes may thus be related to the causes and influencers of disease, rather than (and as well as to the disease itself.

  1. Multihop Wireless Networks Opportunistic Routing

    CERN Document Server

    Zeng, Kai; Li, Ming

    2011-01-01

    This book provides an introduction to opportunistic routing an emerging technology designed to improve the packet forwarding reliability, network capacity and energy efficiency of multihop wireless networks This book presents a comprehensive background to the technological challenges lying behind opportunistic routing. The authors cover many fundamental research issues for this new concept, including the basic principles, performance limit and performance improvement of opportunistic routing compared to traditional routing, energy efficiency and distributed opportunistic routing protocol desig

  2. [Acanthamoeba spp. as opportunistic pathogens parasites].

    Science.gov (United States)

    Castrillón, Juan C; Orozco, Lina P

    2013-04-01

    Among free-living amoeba in nature, species of the genus Acanthamoeba have been associated with human disease. These amoeba are among the most abundant protozoa in nature due to its cosmopolitan distribution and are able to survive in a wide variety of habitats because its low demand for food and in harsh environments by forming structures known as cysts. However, ecological changes and incursion of its different habitats have made this organism can invade a host and live as parasites within him. That's why this type of protozoa are known as amphizoic organism, because human can be constituted as its host, causing infections in the central nervous system, disseminated infections in skin and lungs, and keratitis. Thus, since an increase in the number of cases of Acanthamoeba infections has occurred worldwide, these protozoa have become increasingly important as agents of human disease. This review summarizes what is known of this kind of free-living amoeba, focusing on the biology, ecology, pathogenesis, diagnosis, treatment and human defense mechanism against infection by the amoeba.

  3. Arcobacter: An Opportunistic Human Foodborne Pathogen?

    Science.gov (United States)

    Arcobacter are gram negative, motile, aerotolerant campylobacter-like microbes which grow at 30C. The 10 described Arcobacter species are but a fraction of the total taxa, which encompass bacteria exploiting diverse ecological niches, such as seawater, oil fields, and estuaries. This physiological r...

  4. Smooth Tubercle Bacilli: Neglected Opportunistic Tropical Pathogens

    Directory of Open Access Journals (Sweden)

    Djaltou eAboubaker

    2016-01-01

    Full Text Available Smooth tubercle bacilli (STB including ‘‘Mycobacterium canettii’’ are members of the Mycobacterium tuberculosis complex (MTBC which cause non-contagious tuberculosis in human. This group comprises less than one hundred isolates characterized by smooth colonies and cordless organisms. Most STB isolates have been obtained from patients exposed to the Republic of Djibouti but seven isolates, including the three seminal ones obtained by Georges Canetti between 1968 and 1970, were recovered from patients in France, Madagascar, Sub-Sahara East Africa and French Polynesia. STB form a genetically heterogeneous group of MTBC organisms with large 4.48 ± 0.05 Mb genomes which may link Mycobacterium kansasii to MTBC organisms. Lack of inter-human transmission suggested a yet unknown environmental reservoir. Clinical data indicate a respiratory tract route of contamination and the digestive tract as an alternative route of contamination. Further epidemiological and clinical studies are warranted to elucidate areas of uncertainty regarding these unusual mycobacteria and the tuberculosis they cause.

  5. Multiplex detection of nine food-borne pathogens by mPCR and capillary electrophoresis after using a universal pre-enrichment medium

    Science.gov (United States)

    Villamizar-Rodríguez, Germán; Fernández, Javier; Marín, Laura; Muñiz, Juan; González, Isabel; Lombó, Felipe

    2015-01-01

    Routine microbiological quality analyses in food samples require, in some cases, an initial incubation in pre-enrichment medium. This is necessary in order to ensure that small amounts of pathogenic strains are going to be detected. In this work, a universal pre-enrichment medium has been developed for the simultaneous growth of Bacillus cereus, Campylobacter jejuni, Clostridium perfringens, Cronobacter sakazakii, Escherichia coli, Enterobacteriaceae family (38 species, 27 genera), Listeria monocytogenes, Staphylococcus aureus, Salmonella spp. (two species, 13 strains). Growth confirmation for all these species was achieved in all cases, with excellent enrichments. This was confirmed by plating on the corresponding selective agar media for each bacterium. This GVUM universal pre-enrichment medium could be useful in food microbiological analyses, where different pathogenic bacteria must be detected after a pre-enrichment step. Following, a mPCR reaction for detection of all these pathogens was developed, after designing a set of nine oligonucleotide pairs from specific genetic targets on gDNA from each of these bacteria, covering all available strains already sequenced in GenBank for each pathogen type. The detection limits have been 1 Genome Equivalent (GE), with the exception of the Fam. Enterobacteriaceae (5 GEs). We obtained amplification for all targets (from 70 to 251 bp, depending on the bacteria type), showing the capability of this method to detect the most important industrial and sanitary food-borne pathogens from a universal pre-enrichment medium. This method includes an initial pre-enrichment step (18 h), followed by a mPCR (2 h) and a capillary electrophoresis (30 min); avoiding the tedious and long lasting growing on solid media required in traditional analysis (1–4 days, depending on the specific pathogen and verification procedure). An external testing of this method was conducted in order to compare classical and mPCR methods. This evaluation was

  6. Multiplex detection of nine food-borne pathogens by mPCR and capillary electrophoresis after using a universal pre-enrichment medium

    Directory of Open Access Journals (Sweden)

    Germán eVillamizar-Rodríguez

    2015-11-01

    Full Text Available Routine microbiological quality analyses in food samples require, in some cases, an initial incubation in pre-enrichment medium. This is necessary in order to assure that small amounts of pathogenic strains are going to be detected. In this work, a universal pre-enrichment medium has been developed for simultaneous growth of Bacillus cereus, Campylobacter jejuni, Clostridium perfringens, Cronobacter sakazakii, Escherichia coli, Enterobacteriaceae family (thirty eight species, twenty seven genera, Listeria monocytogenes, Staphylococcus aureus, Salmonella spp. (two species, thirteen strains. Growth confirmation for all these species was achieved in all cases, with excellent enrichments. This was confirmed by plating on the corresponding selective agar media for each bacterium. This GVUM universal pre-enrichment medium could be useful in food microbiological analyses, where different pathogenic bacteria must be detected after a pre-enrichment step. Following, a mPCR reaction for detection of all these pathogens was developed, after designing a set of nine oligonucleotide pairs from specific genetic targets on gDNA from each of these bacteria, covering all available strains already sequenced in GenBank for them. The detection limits have been 1 Genome Equivalent, with the exception of Fam. Enterobacteriaceae (5 GEs. We obtained amplification for all targets (from 70 to 251 bp, depending on the bacteria type, showing the capability of this method to detect the most important industrial and sanitary food-borne pathogens from a universal pre-enrichment medium. This method includes an initial pre-enrichment step (18 h, followed by a mPCR (2 h and a capillary electrophoresis (30 min; avoiding the tedious and long lasting growing on solid media required in traditional analysis (1 to 4 days, depending on the specific pathogen and verification procedure. An external testing of this method was conducted in order to compare classical and mPCR methods. This

  7. Opportunistic infections after blood and marrow transplantation.

    Science.gov (United States)

    Wingard, J R

    1999-03-01

    Opportunistic infections are major causes of morbidity and mortality following bone marrow transplantation. Technological advances in stem cell procurement, the introduction of hematologic growth factors to speed engraftment, the development of new immunosuppressive regimens to control graft-versus-host disease (GVHD), the development of technology to perform graft engineering with removal of T lymphocytes in toto or subpopulations of T lymphocytes, the use of molecular techniques to optimize donor and recipient matching, advances in blood banking, and development of international donor registries, are among the various factors that have led to tremendous changes in transplant practices. Because of such changes in transplant practices, along with the advent of new antimicrobial agents, and development of infection control measures affecting pathogen exposure, alterations in the interplay between host and potential pathogens have occurred. Shifts in the incidence and types of opportunistic pathogens are taking place. Several historically important infectious syndromes are today well controlled; others have diminished in importance early after transplant but are more problematic at a later time; new emerging pathogens are being recognized due to selection pressures from antimicrobial usage and new hosts, such as recipients of alternate donor allogeneic transplant procedures, with even more profound and prolonged immune suppression. Such shifts and new syndromes pose continuing new challenges to the transplant clinician.

  8. Opportunistic infections following renal transplantation

    Directory of Open Access Journals (Sweden)

    Rao K

    2002-01-01

    Full Text Available Opportunistic infection is common following renal transplantation. Prompt diagnosis and management can be life saving. Four different types of opportunistic respiratory infections diagnosed at our center during the period of January 1998 to December 2000 are discussed. Of the four cases one had Aspergillus, second had Sporothrix, third had Nocardia and fourth case Actinomyces species. Microbiologist has an important role to play by being aware of such opportunistic infections and helping the clinician to make early aetiological diagnosis.

  9. Opportunistic Infections—Coming to the Limits of Immunosuppression?

    OpenAIRE

    Fishman, Jay A.

    2013-01-01

    Possible etiologies of infection in the solid organ recipient are diverse, ranging from common bacterial and viral pathogens to opportunistic pathogens that cause invasive disease only in immunocompromised hosts. The recognition of infectious syndromes in this population is limited by alterations in the clinical manifestations by immunosuppression. The risk of serious infections in the organ transplant patient is determined by the interaction between the patients’ recent and distant epidemiol...

  10. Towards New Antifolates Targeting Eukaryotic Opportunistic Infections

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.; Bolstad, D; Bolstad, E; Wright, D; Anderson, A

    2009-01-01

    Trimethoprim, an antifolate commonly prescribed in combination with sulfamethoxazole, potently inhibits several prokaryotic species of dihydrofolate reductase (DHFR). However, several eukaryotic pathogenic organisms are resistant to trimethoprim, preventing its effective use as a therapeutic for those infections. We have been building a program to reengineer trimethoprim to more potently and selectively inhibit eukaryotic species of DHFR as a viable strategy for new drug discovery targeting several opportunistic pathogens. We have developed a series of compounds that exhibit potent and selective inhibition of DHFR from the parasitic protozoa Cryptosporidium and Toxoplasma as well as the fungus Candida glabrata. A comparison of the structures of DHFR from the fungal species Candida glabrata and Pneumocystis suggests that the compounds may also potently inhibit Pneumocystis DHFR.

  11. Data Dissemination in Opportunistic Networks

    CERN Document Server

    Ciobanu, Radu

    2012-01-01

    Mobile devices integrating wireless short-range communication technologies make possible new applications for spontaneous communication, interaction and collaboration. An interesting approach is to use collaboration to facilitate communication when mobile devices are not able to establish direct communication paths. Opportunistic networks, formed when mobile devices communicate with each other while users are in close proximity, can help applications still exchange data in such cases. In opportunistic networks routes are built dynamically, as each mobile device acts according to the store-carry-and-forward paradigm. Thus, contacts between mobile devices are seen as opportunities to move data towards destination. In such networks data dissemination is done using forwarding and is usually based on a publish/subscribe model. Opportunistic data dissemination also raises questions concerning user privacy and incentives. Such problems are addressed di?erently by various opportunistic data dissemination techniques. ...

  12. Special issue Oceans and Humans Health: the ecology of marine opportunists.

    Science.gov (United States)

    Burge, Colleen A; Kim, Catherine J S; Lyles, Jillian M; Harvell, C Drew

    2013-05-01

    Opportunistic marine pathogens, like opportunistic terrestrial pathogens, are ubiquitous in the environment (waters, sediments, and organisms) and only cause disease in immune-compromised or stressed hosts. In this review, we discuss four host-pathogen interactions within the marine environment that are typically considered opportunistic: sea fan coral-fungus, eelgrass-Labyrinthula zosterae, sea fan-Labyrinthulomycetes, and hard clam-Quahog Parasite Unknown with particular focus on disease ecology, parasite pathology, host response, and known associated environmental conditions. Disease is a natural part of all ecosystems; however, in some cases, a shift in the balance between the host, pathogen, and the environment may lead to epizootics in natural or cultured populations. In marine systems, host-microbe interactions are less understood than their terrestrial counterparts. The biological and physical changes to the world's oceans, coupled with other anthropogenic influences, will likely lead to more opportunistic diseases in the marine environment.

  13. Uncommon opportunistic fungal infections of oral cavity: A review

    Directory of Open Access Journals (Sweden)

    A G Deepa

    2014-01-01

    Full Text Available The majority of opportunistic oral mucosal fungal infections are due to Candida albicans and Aspergillus fumigatus species. Mucor and Cryptococcus also have a major role in causing oral infections, whereas Geotrichum, Fusarium, Rhodotorula, Saccharomyces and Penicillium marneffei are uncommon pathogens in the oral cavity. The broad spectrum of clinical presentation includes pseudo-membranes, abscesses, ulcers, pustules and extensive tissue necrosis involving bone. This review discusses various uncommon opportunistic fungal infections affecting the oral cavity including their morphology, clinical features and diagnostic methods.

  14. Keratitis by Fusarium temperatum, a novel opportunist.

    Science.gov (United States)

    Al-Hatmi, Abdullah M S; Bonifaz, Alexandro; de Hoog, G Sybren; Vazquez-Maya, Leticia; Garcia-Carmona, Karla; Meis, Jacques F; van Diepeningen, Anne D

    2014-11-12

    Fusarium species are among the most common fungi present in the environment and some species have emerged as major opportunistic fungal infection in human. However, in immunocompromised hosts they can be virulent pathogens and can cause death. The pathogenesis of this infection relies on three factors: colonization, tissue damage, and immunosuppression. A novel Fusarium species is reported for the first time from keratitis in an agriculture worker who acquired the infection from plant material of maize. Maize plants are the natural host of this fungus where it causes stalk rot and seeding malformation under temperate and humid climatic conditions. The clinical manifestation, microbiological morphology, physiological features and molecular data are described. Diagnosis was established by using polymerase chain reaction of fungal DNA followed by sequencing portions of translation elongation factor 1 alpha (TEF1 α) and beta-tubulin (BT2) genes. Susceptibility profiles of this fungus were evaluated using CLSI broth microdilution method. The analyses of these two genes sequences support a novel opportunist with the designation Fusarium temperatum. Phylogenetic analyses showed that the reported clinical isolate was nested within the Fusarium fujikuroi species complex. Antifungal susceptibility testing demonstrated that the fungus had low MICs of micafungin (0.031 μg/ml), posaconazole (0.25 μg/ml) and amphotericin B (0.5 μg/ml). The present case extends the significance of the genus Fusarium as agents of keratitis and underscores the utility of molecular verification of these emerging fungi in the human host.

  15. Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.

    Science.gov (United States)

    Bent, Zachary W; Brazel, David M; Tran-Gyamfi, Mary B; Hamblin, Rachelle Y; VanderNoot, Victoria A; Branda, Steven S

    2013-01-01

    Francisella tularensis is a zoonotic intracellular pathogen that is capable of causing potentially fatal human infections. Like all successful bacterial pathogens, F. tularensis rapidly responds to changes in its environment during infection of host cells, and upon encountering different microenvironments within those cells. This ability to appropriately respond to the challenges of infection requires rapid and global shifts in gene expression patterns. In this study, we use a novel pathogen transcript enrichment strategy and whole transcriptome sequencing (RNA-Seq) to perform a detailed characterization of the rapid and global shifts in F. tularensis LVS gene expression during infection of murine macrophages. We performed differential gene expression analysis on all bacterial genes at two key stages of infection: phagosomal escape, and cytosolic replication. By comparing the F. tularensis transcriptome at these two stages of infection to that of the bacteria grown in culture, we were able to identify sets of genes that are differentially expressed over the course of infection. This analysis revealed the temporally dynamic expression of a number of known and putative transcriptional regulators and virulence factors, providing insight into their role during infection. In addition, we identified several F. tularensis genes that are significantly up-regulated during infection but had not been previously identified as virulence factors. These unknown genes may make attractive therapeutic or vaccine targets.

  16. Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.

    Directory of Open Access Journals (Sweden)

    Zachary W Bent

    Full Text Available Francisella tularensis is a zoonotic intracellular pathogen that is capable of causing potentially fatal human infections. Like all successful bacterial pathogens, F. tularensis rapidly responds to changes in its environment during infection of host cells, and upon encountering different microenvironments within those cells. This ability to appropriately respond to the challenges of infection requires rapid and global shifts in gene expression patterns. In this study, we use a novel pathogen transcript enrichment strategy and whole transcriptome sequencing (RNA-Seq to perform a detailed characterization of the rapid and global shifts in F. tularensis LVS gene expression during infection of murine macrophages. We performed differential gene expression analysis on all bacterial genes at two key stages of infection: phagosomal escape, and cytosolic replication. By comparing the F. tularensis transcriptome at these two stages of infection to that of the bacteria grown in culture, we were able to identify sets of genes that are differentially expressed over the course of infection. This analysis revealed the temporally dynamic expression of a number of known and putative transcriptional regulators and virulence factors, providing insight into their role during infection. In addition, we identified several F. tularensis genes that are significantly up-regulated during infection but had not been previously identified as virulence factors. These unknown genes may make attractive therapeutic or vaccine targets.

  17. Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death.

    Science.gov (United States)

    Schuenemann, Verena J; Bos, Kirsten; DeWitte, Sharon; Schmedes, Sarah; Jamieson, Joslyn; Mittnik, Alissa; Forrest, Stephen; Coombes, Brian K; Wood, James W; Earn, David J D; White, William; Krause, Johannes; Poinar, Hendrik N

    2011-09-20

    Although investigations of medieval plague victims have identified Yersinia pestis as the putative etiologic agent of the pandemic, methodological limitations have prevented large-scale genomic investigations to evaluate changes in the pathogen's virulence over time. We screened over 100 skeletal remains from Black Death victims of the East Smithfield mass burial site (1348-1350, London, England). Recent methods of DNA enrichment coupled with high-throughput DNA sequencing subsequently permitted reconstruction of ten full human mitochondrial genomes (16 kb each) and the full pPCP1 (9.6 kb) virulence-associated plasmid at high coverage. Comparisons of molecular damage profiles between endogenous human and Y. pestis DNA confirmed its authenticity as an ancient pathogen, thus representing the longest contiguous genomic sequence for an ancient pathogen to date. Comparison of our reconstructed plasmid against modern Y. pestis shows identity with several isolates matching the Medievalis biovar; however, our chromosomal sequences indicate the victims were infected with a Y. pestis variant that has not been previously reported. Our data reveal that the Black Death in medieval Europe was caused by a variant of Y. pestis that may no longer exist, and genetic data carried on its pPCP1 plasmid were not responsible for the purported epidemiological differences between ancient and modern forms of Y. pestis infections.

  18. Opportunistic Resource Usage in CMS

    Energy Technology Data Exchange (ETDEWEB)

    Kreuzer, Peter [RWTH Aachen U.; Hufnagel, Dirk [Fermilab; Dykstra, D. [Fermilab; Gutsche, O. [Fermilab; Tadel, M. [UC, San Diego; Sfiligoi, I. [UC, San Diego; Letts, J. [UC, San Diego; Wuerthwein, F. [UC, San Diego; McCrea, A. [UC, San Diego; Bockelman, B. [Nebraska U.; Fajardo, E. [Andes U., Merida; Linares, L. [Andes U., Merida; Wagner, R. [TI, San Diego; Konstantinov, P. [Sofiya, Inst. Nucl. Res.; Blumenfeld, B. [Johns Hopkins U.; Bradley, D. [Wisconsin U., Madison

    2014-01-01

    CMS is using a tiered setup of dedicated computing resources provided by sites distributed over the world and organized in WLCG. These sites pledge resources to CMS and are preparing them especially for CMS to run the experiment's applications. But there are more resources available opportunistically both on the GRID and in local university and research clusters which can be used for CMS applications. We will present CMS' strategy to use opportunistic resources and prepare them dynamically to run CMS applications. CMS is able to run its applications on resources that can be reached through the GRID, through EC2 compliant cloud interfaces. Even resources that can be used through ssh login nodes can be harnessed. All of these usage modes are integrated transparently into the GlideIn WMS submission infrastructure, which is the basis of CMS' opportunistic resource usage strategy. Technologies like Parrot to mount the software distribution via CVMFS and xrootd for access to data and simulation samples via the WAN are used and will be described. We will summarize the experience with opportunistic resource usage and give an outlook for the restart of LHC data taking in 2015.

  19. Stimulating Creativity Through Opportunistic Software Development

    NARCIS (Netherlands)

    Obrenovic, Z.; Gasevic, D.; Eliëns, A.

    2008-01-01

    Using opportunistic software development principles in computer engineering education encourages students to be creative and to develop solutions that cross the boundaries of diverse technologies. A framework for opportunistic software development education helps to create a space in which students

  20. Immunotherapy for opportunistic infections: Current status and future perspectives.

    Science.gov (United States)

    Fuji, Shigeo; Löffler, Jürgen; Einsele, Hermann; Kapp, Markus

    2016-11-16

    The outcome after allogeneic haematopoietic stem cell transplantation (allo-HSCT) has significantly improved during the last decades. However, opportunistic infections such as viral and mold infections are still a major obstacle for cure. Within this field, adoptive T cell therapy against pathogens is a promising treatment approach. Recently, the techniques to develop T cell products including pathogen-specific T cells have been sophisticated and are now available in accordance to good manufacturing practice (GMP). Here, we aim to summarize current knowledge about adoptive T cell therapy against viral and mold infections.

  1. Opportunistic amoebae: challenges in prophylaxis and treatment.

    Science.gov (United States)

    Schuster, Frederick L; Visvesvara, Govinda S

    2004-02-01

    This review focuses on free-living amoebae, widely distributed in soil and water, causing opportunistic and non-opportunistic infections in humans: Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri, and Sappinia diploidea. Diseases include primary amoebic meningoencephalitis (N. fowleri), granulomatous amoebic encephalitis, cutaneous and nasopharyngeal infections (Acanthamoeba spp., Balamuthia mandrillaris, S. diploidea), and amoebic keratitis (Acanthamoeba spp). Acanthamoeba, Balamuthia, and Naegleria have been repeatedly isolated; S. diploidea has been reported only once, from a brain infection. Antimicrobial therapy for these infections is generally empirical and patient recovery often problematic. N. fowleri is highly sensitive to the antifungal agent amphotericin B, but delay in diagnosis and the fulminant nature of the disease result in few survivors. Encephalitis and other infections caused by Acanthamoeba and Balamuthia have been treated, more or less successfully, with antimicrobial combinations including sterol-targeting azoles (clotrimazole, miconazole, ketoconazole, fluconazole, itraconazole), pentamidine isethionate, 5-fluorocytosine, and sulfadiazine. The use of drug combinations addresses resistance patterns that may exist or develop during treatment, ensuring that at least one of the drugs may be effective against the amoebae. Favorable drug interactions (additive or synergistic) are another potential benefit. In vitro drug testing of clinical isolates points up strain and species differences in sensitivity, so that no single drug can be assumed effective against all amoebae. Another complication is risk of activation of dormant cysts that form in situ in Acanthamoeba and Balamuthia infections, and which can lead to patient relapse following apparently effective treatment. This is particularly true in Acanthamoeba keratitis, a non-opportunistic infection of the cornea, which responds well to treatment with chlorhexidine gluconate and

  2. Spectrum Of Opportunistic Infections In Aids Cases In A Tertiary Care Hospital In Nepal

    OpenAIRE

    Hari Shanker Joshi; Rabindranath Das; Arun Kumar Agnihotri; Subba, Sonu H; Ramnesh Murthy; S B Dabral

    2006-01-01

    A retrospective study was carried out, 404 clinically suspected cases attending AIDS clinic at Manipal Teaching Hospital, Pokhara, Nepal to assess an occurance of opportunistic infections in AIDS cases. Study reveals that Tuberculosis (60%), Cryptospridiosis (13.33%) and candidasis (11.11%) are the predominant opportunistic infection in HIV/AIDS patients in the Pokharo village. Next common pathogen was found an ubiquitous yeast. Candida obtained from skin, oral cavity, oesophagus, sputum and ...

  3. Biofilm spatial organization by the emerging pathogen Campylobacter jejuni: comparison between NCTC 11168 and 81-176 strains under microaerobic and oxygen-enriched conditions

    Directory of Open Access Journals (Sweden)

    Hana eTuronova

    2015-07-01

    Full Text Available During the last years, Campylobacter has emerged as the leading cause of bacterial foodborne infections in developed countries. Described as an obligate microaerophile, Campylobacter has puzzled scientists by surviving a wide range of environmental oxidative stresses on foods farm to retail, and thereafter intestinal transit and oxidative damage from macrophages to cause human infection. In this study, confocal laser scanning microscopy was used to explore the biofilm development of two well-described Campylobacter jejuni strains (NCTC 11168 and 81-176 prior to or during cultivation under oxygen-enriched conditions. Quantitative and qualitative appraisal indicated that C. jejuni formed finger-like biofilm structures with an open ultrastructure for 81-176 and a multilayer-like structure for NCTC 11168 under microaerobic conditions. The presence of motile cells within the biofilm confirmed the maturation of the C. jejuni 81-176 biofilm. Acclimation of cells to oxygen-enriched conditions led to significant enhancement of biofilm formation during the early stages of the process. Exposure to these conditions during biofilm cultivation induced an even greater biofilm development for both strains, indicating that oxygen demand for biofilm formation is higher than for planktonic growth counterparts. Overexpression of cosR in the poorer biofilm-forming strain, NCTC 11168, enhanced biofilm development dramatically by promoting an open ultrastructure similar to that observed for 81-176. Consequently, the regulator CosR is likely to be a key protein in the maturation of C. jejuni biofilm, although it is not linked to oxygen stimulation. These unexpected data advocate challenging studies by reconsidering the paradigm of fastidious requirements for C. jejuni growth when various subpopulations (from quiescent to motile cells coexist in biofilms. These findings constitute a clear example of a survival strategy used by this emerging human pathogen.

  4. Biofilm spatial organization by the emerging pathogen Campylobacter jejuni: comparison between NCTC 11168 and 81-176 strains under microaerobic and oxygen-enriched conditions

    Science.gov (United States)

    Turonova, Hana; Briandet, Romain; Rodrigues, Ramila; Hernould, Mathieu; Hayek, Nabil; Stintzi, Alain; Pazlarova, Jarmila; Tresse, Odile

    2015-01-01

    During the last years, Campylobacter has emerged as the leading cause of bacterial foodborne infections in developed countries. Described as an obligate microaerophile, Campylobacter has puzzled scientists by surviving a wide range of environmental oxidative stresses on foods farm to retail, and thereafter intestinal transit and oxidative damage from macrophages to cause human infection. In this study, confocal laser scanning microscopy (CLSM) was used to explore the biofilm development of two well-described Campylobacter jejuni strains (NCTC 11168 and 81-176) prior to or during cultivation under oxygen-enriched conditions. Quantitative and qualitative appraisal indicated that C. jejuni formed finger-like biofilm structures with an open ultrastructure for 81-176 and a multilayer-like structure for NCTC 11168 under microaerobic conditions (MAC). The presence of motile cells within the biofilm confirmed the maturation of the C. jejuni 81-176 biofilm. Acclimation of cells to oxygen-enriched conditions led to significant enhancement of biofilm formation during the early stages of the process. Exposure to these conditions during biofilm cultivation induced an even greater biofilm development for both strains, indicating that oxygen demand for biofilm formation is higher than for planktonic growth counterparts. Overexpression of cosR in the poorer biofilm-forming strain, NCTC 11168, enhanced biofilm development dramatically by promoting an open ultrastructure similar to that observed for 81-176. Consequently, the regulator CosR is likely to be a key protein in the maturation of C. jejuni biofilm, although it is not linked to oxygen stimulation. These unexpected data advocate challenging studies by reconsidering the paradigm of fastidious requirements for C. jejuni growth when various subpopulations (from quiescent to motile cells) coexist in biofilms. These findings constitute a clear example of a survival strategy used by this emerging human pathogen. PMID:26217332

  5. Biofilm spatial organization by the emerging pathogen Campylobacter jejuni: comparison between NCTC 11168 and 81-176 strains under microaerobic and oxygen-enriched conditions.

    Science.gov (United States)

    Turonova, Hana; Briandet, Romain; Rodrigues, Ramila; Hernould, Mathieu; Hayek, Nabil; Stintzi, Alain; Pazlarova, Jarmila; Tresse, Odile

    2015-01-01

    During the last years, Campylobacter has emerged as the leading cause of bacterial foodborne infections in developed countries. Described as an obligate microaerophile, Campylobacter has puzzled scientists by surviving a wide range of environmental oxidative stresses on foods farm to retail, and thereafter intestinal transit and oxidative damage from macrophages to cause human infection. In this study, confocal laser scanning microscopy (CLSM) was used to explore the biofilm development of two well-described Campylobacter jejuni strains (NCTC 11168 and 81-176) prior to or during cultivation under oxygen-enriched conditions. Quantitative and qualitative appraisal indicated that C. jejuni formed finger-like biofilm structures with an open ultrastructure for 81-176 and a multilayer-like structure for NCTC 11168 under microaerobic conditions (MAC). The presence of motile cells within the biofilm confirmed the maturation of the C. jejuni 81-176 biofilm. Acclimation of cells to oxygen-enriched conditions led to significant enhancement of biofilm formation during the early stages of the process. Exposure to these conditions during biofilm cultivation induced an even greater biofilm development for both strains, indicating that oxygen demand for biofilm formation is higher than for planktonic growth counterparts. Overexpression of cosR in the poorer biofilm-forming strain, NCTC 11168, enhanced biofilm development dramatically by promoting an open ultrastructure similar to that observed for 81-176. Consequently, the regulator CosR is likely to be a key protein in the maturation of C. jejuni biofilm, although it is not linked to oxygen stimulation. These unexpected data advocate challenging studies by reconsidering the paradigm of fastidious requirements for C. jejuni growth when various subpopulations (from quiescent to motile cells) coexist in biofilms. These findings constitute a clear example of a survival strategy used by this emerging human pathogen.

  6. The ppuI-rsaL-ppuR quorum-sensing system regulates cellular motility, pectate lyase activity, and virulence in potato opportunistic pathogen Pseudomonas sp. StFLB209.

    Science.gov (United States)

    Kato, Taro; Morohoshi, Tomohiro; Someya, Nobutaka; Ikeda, Tsukasa

    2015-01-01

    Pseudomonas sp. StFLB209 was isolated from potato leaf as an N-acylhomoserine lactone (AHL)-producing bacterium and showed a close phylogenetic relationship with P. cichorii, a known plant pathogen. Although there are no reports of potato disease caused by pseudomonads in Japan, StFLB209 was pathogenic to potato leaf. In this study, we reveal the complete genome sequence of StFLB209, and show that the strain possesses a ppuI-rsaL-ppuR quorum-sensing system, the sequence of which shares a high similarity with that of Pseudomonas putida. Disruption of ppuI results in a loss of AHL production as well as remarkable reduction in motility. StFLB209 possesses strong pectate lyase activity and causes maceration on potato tuber and leaf, which was slightly reduced in the ppuI mutant. These results suggest that the quorum-sensing system is well conserved between StFLB209 and P. putida and that the system is essential for motility, full pectate lyase activity, and virulence in StFLB209.

  7. 橙汁中的条件致病酵母菌及其控制策略%The opportunistic pathogenic yeast in orange juice and its control strategy

    Institute of Scientific and Technical Information of China (English)

    曹敏; 段倩倩; 刘家艳; 黄茜; 杨晓红

    2014-01-01

    Yeasts are ubiquitous in orange juice some of them are harmless to the human body. However, recent studies show that the existence of some yeast not only can result in spoilage of orange juice, but also can cause disease to human. Yeast is one of the most common pathogens in orange juice. Considering the drink se-curity of orange juice and its potential threat to human body health, more attention is paid to the pathogenic yeast by the people. Therefore, research on pathogenic yeasts has become a hot topic in life science fields. Now 14 species of pathogen yeast in orange juice were reported those are Candida parapsilosis, C. stellata, C. trop-icalis, C. famata, C. colliculosa, C. zeylanoides, Clavispora lusitaniae, Cryptococcus neoformans, Debaryo-myces hansenii, Hanseniaspora uvarum, Issatchenkia orientalis, Pichia anomala, Rhodotorula mucilaginosa and Trichosporon asahii. The present paper reviewed the species, identification methods and control strategy of pathogenic yeasts which would provide useful reference for the production, storage, sale and consumption of orange juice.%橙汁中普遍存在酵母菌,其中部分对人体是无害的。但是近年来的研究发现,一些酵母菌的存在不但会引起橙汁腐败,还会导致人体感染患病。酵母菌是橙汁中最常见的条件致病菌之一,随着人们对橙汁饮用安全和人体健康潜在威胁的深入认识,条件致病酵母菌日趋受到重视。对致病酵母菌的研究也成为生命科学研究的热点。目前已知的橙汁酵母致病菌有14种:近平滑假丝酵母(Candida parapsilosis)、星形假丝酵母(C.stellata)、热带假丝酵母(C. tropicalis)、无名假丝酵母(C. famata)、小丘假丝酵母(C. colliculosa)、涎沫假丝酵母(C. zey-lanoides)、葡萄牙棒孢酵母(Clavispora lusitaniae)、新型隐球酵母(Cryptococcus neoformans)、汉逊德巴利酵母(Debaryomyces hansenii)、葡萄汁有孢汉逊酵母(Hanseniaspora uvarum

  8. Opportunistic Infections—Coming to the Limits of Immunosuppression?

    Science.gov (United States)

    Fishman, Jay A.

    2013-01-01

    Possible etiologies of infection in the solid organ recipient are diverse, ranging from common bacterial and viral pathogens to opportunistic pathogens that cause invasive disease only in immunocompromised hosts. The recognition of infectious syndromes in this population is limited by alterations in the clinical manifestations by immunosuppression. The risk of serious infections in the organ transplant patient is determined by the interaction between the patients’ recent and distant epidemiological exposures and all factors that contribute to the patient’s net state of immune suppression. This risk is altered by antimicrobial prophylaxis and changes in immunosuppressive therapies. In addition to the direct effects of infection, opportunistic infections, and the microbiome may adversely shape the host immune responses with diminished graft and patient survivals. Antimicrobial therapies are more complex than in the normal host with a significant incidence of drug toxicity and a propensity for drug interactions with the immunosuppressive agents used to maintain graft function. Rapid and specific microbiologic diagnosis is essential. Newer microbiologic assays have improved the diagnosis and management of opportunistic infections. These tools coupled with assays that assess immune responses to infection and to graft antigens may allow optimization of management for graft recipients in the future. PMID:24086067

  9. Opportunistic infections--coming to the limits of immunosuppression?

    Science.gov (United States)

    Fishman, Jay A

    2013-10-01

    Possible etiologies of infection in the solid organ recipient are diverse, ranging from common bacterial and viral pathogens to opportunistic pathogens that cause invasive disease only in immunocompromised hosts. The recognition of infectious syndromes in this population is limited by alterations in the clinical manifestations by immunosuppression. The risk of serious infections in the organ transplant patient is determined by the interaction between the patients' recent and distant epidemiological exposures and all factors that contribute to the patient's net state of immune suppression. This risk is altered by antimicrobial prophylaxis and changes in immunosuppressive therapies. In addition to the direct effects of infection, opportunistic infections, and the microbiome may adversely shape the host immune responses with diminished graft and patient survivals. Antimicrobial therapies are more complex than in the normal host with a significant incidence of drug toxicity and a propensity for drug interactions with the immunosuppressive agents used to maintain graft function. Rapid and specific microbiologic diagnosis is essential. Newer microbiologic assays have improved the diagnosis and management of opportunistic infections. These tools coupled with assays that assess immune responses to infection and to graft antigens may allow optimization of management for graft recipients in the future.

  10. Inhibition of quorum sensing in the opportunistic pathogenic bacterium Chromobacterium violaceum by an extract from fruiting bodies of Lingzhi or Reishi medicinal mushroom, Ganoderma lucidum (W.Curt.:Fr.) P. Karst. (higher Basidiomycetes).

    Science.gov (United States)

    Zhu, Hu; Liu, Wei; Tian, Baozhen; Liu, Huijun; Ning, Shoujiao

    2011-01-01

    Extracts of Lingzhi or Reishi medicinal mushroom, Ganoderma lucidum, inhibited quorum sensing in Chromobacterium violaceum CV026. G. lucidum fruiting bodies were milled and extracted with ethyl acetate. The crude extract was dissolved in an appropriate concentration of methanol, sterilized by filtration through a 0.22-μm membrane filter, and added to Ch. Violaceum CV026 cultures, which were used as an indicator to monitor quorum sensing inhibition. Inhibitory activity was measured by quantifying violacein production using a microplate reader. Methanol-soluble compounds extracted from G. lucidum significantly inhibited quorum sensing-controlled behavior in Ch. Violaceum in a concentration-dependent manner. The results suggest that compounds in G. lucidum might be useful to control and handle detrimental infections caused by human, animal, and plant pathogens. Further studies are in progress in our lab to isolate the specific compounds from G. lucidum extract, evaluate them as quorum sensing inhibitors, and analyze their mechanism of action.

  11. OPPORTUNISTIC MICROORGANISMS IN RHEUMATIC DISEASES

    Directory of Open Access Journals (Sweden)

    M. Yu. Gulneva

    2016-01-01

    Full Text Available The paper gives the data available in the literature on the role of opportunistic microorganisms (OMs in rheumatic diseases (RDs. OMs are anticipated to be involved as triggers initiating the development of chronic inflammation. Along with this, OMs in autoimmune diseases may play a defensive role through the interaction with Toll-like receptors and the activation of T cells that have suppressor activity. The possible involvement of OMs in the pathogenesis of RDs provides support not only the isolation of microorganisms, but also the detection of antibacterial antibodies of different classes. Of great importance are OMs in the etiology of comorbid infections, the risk of which is due to both the presence of autoimmune RDs and the necessity of using the drugs having immunosuppressive activity. The active clinical introduction of biological agents is followed by a rise in the rate and severity of different infections, including those caused by OMs. Having a marked biological and environmental plasticity, OMs are able to persist long when there are changes in the immune defense of patients with RDs. There is evidence for the higher adhesive properties and persistent potential of the microorganisms that colonize the body of patients with RDs. In the latter, OMs that are distinguished by pronounced antibiotic polyresistance are isolated, making the treatment and prevention of opportunistic infections more difficult in rheumatology. The results of the papers analyzed in the review suggest that the study of OMs in RDs is of practical importance.

  12. Opportunistic Identification of Vertebral Fractures.

    Science.gov (United States)

    Adams, Judith E

    2016-01-01

    Vertebral fractures are powerful predictors of future fracture, so, their identification is important to ensure that patients are commenced on appropriate bone protective or bone-enhancing therapy. Risk factors (e.g., low bone mineral density and increasing age) and symptoms (back pain, loss of height) may herald the presence of vertebral fractures, which are usually confirmed by performing spinal radiographs or, increasingly, using vertebral fracture assessment with dual-energy X-ray absorptiometry scanners. However, a large number (30% or more) of vertebral fractures are asymptomatic and do not come to clinical attention. There is, therefore, scope for opportunistic (fortuitous) identification of vertebral fractures from various imaging modalities (radiographs, computed tomography, magnetic resonance imaging, and radionuclide scans) performed for other clinical indications and which include the spine in the field of view, with midline sagittal reformatted images from computed tomography having the greatest potential for such opportunistic detection. Numerous studies confirm this potential for identification but consistently find underreporting of vertebral fractures. So, a valuable opportunity to improve the management of patients at increased risk of future fracture is being squandered. Educational training programs for all clinicians and constant reiteration, stressing the importance of the accurate and clear reporting of vertebral fractures ("you only see what you look for"), can improve the situation, and automated computer-aided diagnostic tools also show promise to solve the problem of this underreporting of vertebral fractures. Copyright © 2016. Published by Elsevier Inc.

  13. Opportunistic ocular infections in AIDS

    Institute of Scientific and Technical Information of China (English)

    Shikha Baisakhiya DOMS; FGO

    2008-01-01

    As the number of HIV infected patients is multiplying exponentially day by day so are the associated ocular complications.The increasing longevity of individuals with HIV disease has resulted in greater numbers of pa-tients with ocular opportunistic infection.By the means of this article we describe various opportunistic ocular infections in AIDS and their clinical manifestations,discussed under four headings;1 )adnexal manifestation;2)anterior segment manifestation;3)posterior segment manifestation;4)neuro ophthalmic manifestation . Herpes zoster ophthalmicus,molluscum contagiosum and Kaposi sarcoma are common adnexal manifestations. Molluscum contagiosum being the commonest.Varicella Zoster Virus (VZV)and herpes simplex virus (HSV) most commonly cause infectious keratitis in HIV-positive patients .As compared to the immunocompetent indi-viduals the frequency of bacterial and fungal keratitis is not more in HIV patients,but it tends to be more se-vere.Posterior segment structures involved in HIV-positive patients include the retina,choroid,and optic nerve head.The herpesvirus family is implicated most commonly in infections of the retina and choroid in HIV positive patients.CMV is the most common cause of retinitis and the commonest intraocular infection in AIDS. Atypical presentations resistance to conventional treatment and higher rate of recurrence make the diagnosis and therapeutic intervention more difficult and challenging.In addition,in one eye,several infections may occur at the same time,rendering the situation more difficult.

  14. Staphylococcus aureus α toxin potentiates opportunistic bacterial lung infections.

    Science.gov (United States)

    Cohen, Taylor S; Hilliard, Jamese J; Jones-Nelson, Omari; Keller, Ashley E; O'Day, Terrence; Tkaczyk, Christine; DiGiandomenico, Antonio; Hamilton, Melissa; Pelletier, Mark; Wang, Qun; Diep, Binh An; Le, Vien T M; Cheng, Lily; Suzich, JoAnn; Stover, C Kendall; Sellman, Bret R

    2016-03-01

    Broad-spectrum antibiotic use may adversely affect a patient's beneficial microbiome and fuel cross-species spread of drug resistance. Although alternative pathogen-specific approaches are rationally justified, a major concern for this precision medicine strategy is that co-colonizing or co-infecting opportunistic bacteria may still cause serious disease. In a mixed-pathogen lung infection model, we find that the Staphylococcus aureus virulence factor α toxin potentiates Gram-negative bacterial proliferation, systemic spread, and lethality by preventing acidification of bacteria-containing macrophage phagosomes, thereby reducing effective killing of both S. aureus and Gram-negative bacteria. Prophylaxis or early treatment with a single α toxin neutralizing monoclonal antibody prevented proliferation of co-infecting Gram-negative pathogens and lethality while also promoting S. aureus clearance. These studies suggest that some pathogen-specific, antibody-based approaches may also work to reduce infection risk in patients colonized or co-infected with S. aureus and disparate drug-resistant Gram-negative bacterial opportunists.

  15. Routing Issues in Opportunistic Networks

    Science.gov (United States)

    Conti, Marco; Crowcroft, Jon; Giordano, Silvia; Hui, Pan; Nguyen, Hoang Anh; Passarella, Andrea

    The opportunistic networking idea stems from the critical review of the research field on Mobile Ad hoc Networks (MANET). After more than ten years of research in the MANET field, this promising technology still has not massively entered the mass market. One of the main reasons of this is nowadays seen in the lack of a practical approach to the design of infrastructure-less multi-hop ad hoc networks [186, 185]. One of the main approaches of conventional MANET research is to design protocols that mask the features of mobile networks via the routing (and transport) layer, so as to expose to higher layers an Internet-like network abstraction. Wireless networks’ peculiarities, such as mobility of users, disconnection of nodes, network partitions, links’ instability, are seen—as in the legacy Internet—as exceptions. This often results in the design of MANET network stacks that are significantly complex and unstable [107].

  16. Shared Physiological Traits of Exophiala Species in Cold-Blooded Vertebrates, as Opportunistic Black Yeasts

    NARCIS (Netherlands)

    do Nascimento, Mariana Machado Fidelis; de Hoog, G Sybren; Gomes, Renata Rodrigues; Furuie, Jason Lee; Gelinski, Jane Mary Lafayette; Najafzadeh, Mohammad Javad; Boeger, Walter Antonio Pereira; Vicente, Vania Aparecida

    2016-01-01

    Several species of the genus Exophiala are found as opportunistic pathogens on humans, while others cause infections in cold-blooded waterborne vertebrates. Opportunism of these fungi thus is likely to be multifactorial. Ecological traits [thermotolerance and pH tolerance, laccase activity, assimila

  17. Opportunistic Interference Alignment for Random Access Networks

    OpenAIRE

    Jin, Hu; Jeon, Sang-Woon; Jung, Bang Chul

    2015-01-01

    An interference management problem among multiple overlapped random access networks (RANs) is investigated, each of which operates with slotted ALOHA protocol. Assuming that access points and users have multiple antennas, a novel opportunistic interference alignment~(OIA) is proposed to mitigate interference among overlapped RANs. The proposed technique intelligently combines the transmit beamforming technique at the physical layer and the opportunistic packet transmission at the medium acces...

  18. Evaluation and Innovation in Opportunistic Networks

    OpenAIRE

    Islam, Muhammad

    2011-01-01

    The presence of an increasing number of mobile devices has prompted the demand to use them for information dispersion through opportunistic networks, which they form coincidently due to their geographic location. Opportunistic networks pose several new challenges to the current transmission protocols as they are not only capable of store and forward routing, but also lack the offline routing capability, i.e. source and destination must be connected to the network simultaneously. We can find s...

  19. Spectrum Of Opportunistic Infections In Aids Cases In A Tertiary Care Hospital In Nepal

    Directory of Open Access Journals (Sweden)

    Hari Shanker Joshi

    2006-12-01

    Full Text Available A retrospective study was carried out, 404 clinically suspected cases attending AIDS clinic at Manipal Teaching Hospital, Pokhara, Nepal to assess an occurance of opportunistic infections in AIDS cases. Study reveals that Tuberculosis (60%, Cryptospridiosis (13.33% and candidasis (11.11% are the predominant opportunistic infection in HIV/AIDS patients in the Pokharo village. Next common pathogen was found an ubiquitous yeast. Candida obtained from skin, oral cavity, oesophagus, sputum and stool. The least common documented documented infection was pneumocystis carini pneumonia (2.22%.

  20. Evaluation of Opportunistic Routing Algorithms on Opportunistic Mobile Sensor Networks with Infrastructure Assistance

    NARCIS (Netherlands)

    Le, Viet-Duc; Scholten, Hans; Havinga, Paul

    2012-01-01

    Recently the increasing number of sensors integrated in smartphones, especially the iPhone and Android phones, has motivated the development of routing algorithms for Opportunistic Mobile Sensor Networks (OppMSNs). Although there are many existing opportunistic routing algorithms, researchers still

  1. Performance analysis of opportunistic nonregenerative relaying

    KAUST Repository

    Tourki, Kamel

    2013-01-01

    Opportunistic relaying in cooperative communication depends on careful relay selection. However, the traditional centralized method used for opportunistic amplify-and-forward protocols requires precise measurements of channel state information at the destination. In this paper, we adopt the max-min criterion as a relay selection framework for opportunistic amplify-and-forward cooperative communications, which was exhaustively used for the decode-and-forward protocol, and offer an accurate performance analysis based on exact statistics of the local signal-to-noise ratios of the best relay. Furthermore, we evaluate the asymptotical performance and deduce the diversity order of our proposed scheme. Finally, we validate our analysis by showing that performance simulation results coincide with our analytical results over Rayleigh fading channels, and we compare the max-min relay selection with their centralized channel state information-based and partial relay selection counterparts.

  2. Opportunistic spectrum utilization in vehicular communication networks

    CERN Document Server

    Cheng, Nan

    2016-01-01

    This brief examines current research on improving Vehicular Networks (VANETs), examining spectrum scarcity due to the dramatic growth of mobile data traffic and the limited bandwidth of dedicated vehicular communication bands and the use of opportunistic spectrum bands to mitigate congestion. It reviews existing literature on the use of opportunistic spectrum bands for VANETs, including licensed and unlicensed spectrum bands and a variety of related technologies, such as cognitive radio, WiFi and device-to-device communications. Focused on analyzing spectrum characteristics, designing efficient spectrum exploitation schemes, and evaluating the date delivery performance when utilizing different opportunistic spectrum bands, the results presented in this brief provide valuable insights on improving the design and deployment of future VANETs.

  3. Economic transactions, opportunistic behavior and protective mechanisms

    DEFF Research Database (Denmark)

    Koch, Carsten Allan

    Whenever actors participate in transactions they expose themselves to risks of various kinds. Some of these risks are attributable to events outside the control of the participants and are unavoidable. Others originate in, or are aggrevated by, opportunistic actions undertaken by contract partners...... and other co-operators. This paper is concerned with the latter type of risk and the protection against it. Six protective mechanisms, which may serve as safeguards against opportunistic behavior, are presented and discussed. Special attention is paid to reputation effects. It is noted that such effects may...... account for the lack of opportunistic behavior with which networks are often credited. No protective mechanism is, however, effective under all circumstances....

  4. Distance-Based Opportunistic Mobile Data Offloading

    Science.gov (United States)

    Lu, Xiaofeng; Lio, Pietro; Hui, Pan

    2016-01-01

    Cellular network data traffic can be offload onto opportunistic networks. This paper proposes a Distance-based Opportunistic Publish/Subscribe (DOPS) content dissemination model, which is composed of three layers: application layer, decision-making layer and network layer. When a user wants new content, he/she subscribes on a subscribing server. Users having the contents decide whether to deliver the contents to the subscriber based on the distance information. If in the meantime a content owner has traveled further in the immediate past time than the distance between the owner and the subscriber, the content owner will send the content to the subscriber through opportunistic routing. Simulations provide an evaluation of the data traffic offloading efficiency of DOPS. PMID:27314361

  5. Incentive mechanisms for Opportunistic Cloud Computing Services

    DEFF Research Database (Denmark)

    Kuada, Eric; Olesen, Henning

    2012-01-01

    Opportunistic Cloud Computing Service (OCCS) is a social network approach to the provisioning and management of cloud computing services for enterprises. The OCCS network may suffer from the free riding problem where members are selfish and will only want to use services on the platform without e......, incentive compatibility, allocative efficiency, robustness, and flexible to accommodate changing user behavior on the platform.......Opportunistic Cloud Computing Service (OCCS) is a social network approach to the provisioning and management of cloud computing services for enterprises. The OCCS network may suffer from the free riding problem where members are selfish and will only want to use services on the platform without...

  6. Opportunistic microorganisms in patients undergoing antibiotic therapy for pulmonary tuberculosis

    Directory of Open Access Journals (Sweden)

    Silvia Maria Rodrigues Querido

    2011-12-01

    Full Text Available Antimicrobial therapy may cause changes in the resident oral microbiota, with the increase of opportunistic pathogens. The aim of this study was to compare the prevalence of Candida, Staphylococcus, Pseudomonas and Enterobacteriaceae in the oral cavity of fifty patients undergoing antibiotic therapy for pulmonary tuberculosis and systemically healthy controls. Oral rinsing and subgingival samples were obtained, plated in Sabouraud dextrose agar with chloramphenicol, mannitol agar and MacConkey agar, and incubated for 48 h at 37ºC. Candida spp. and coagulase-positive staphylococci were identified by phenotypic tests, C. dubliniensis, by multiplex PCR, and coagulase-negative staphylococci, Enterobacteriaceae and Pseudomonas spp., by the API systems. The number of Candida spp. was significantly higher in tuberculosis patients, and C. albicans was the most prevalent specie. No significant differences in the prevalence of other microorganisms were observed. In conclusion, the antimicrobial therapy for pulmonary tuberculosis induced significant increase only in the amounts of Candida spp.

  7. Incentive mechanisms for Opportunistic Cloud Computing Services

    DEFF Research Database (Denmark)

    Kuada, Eric; Olesen, Henning

    2012-01-01

    Opportunistic Cloud Computing Service (OCCS) is a social network approach to the provisioning and management of cloud computing services for enterprises. The OCCS network may suffer from the free riding problem where members are selfish and will only want to use services on the platform without...

  8. Government Spending Cycles: Ideological or Opportunistic?

    NARCIS (Netherlands)

    H.P. van Dalen (Hendrik); O.H. Swank (Otto)

    1996-01-01

    textabstractands. The time series analysis, covering the period 1953–1993, allows for different types of government spending. In general, spending is inspired by ideological and opportunistic motives: all government expenditure categories show an upward drift during election times and the partisan

  9. Species Diversity and Polymorphism in the Exophiala spinifera Clade Containing Opportunistic Black Yeast-Like Fungi

    OpenAIRE

    2003-01-01

    A monophyletic group of black yeast-like fungi containing opportunistic pathogens around Exophiala spinifera is analyzed using sequences of the small-subunit (SSU) and internal transcribed spacer (ITS) domains of ribosomal DNA. The group contains yeast-like and annellidic species (anamorph genus Exophiala) in addition to sympodial taxa (anamorph genera Ramichloridium and Rhinocladiella). The new species Exophiala oligosperma, Ramichloridium basitonum, and Rhinocladiella similis are introduced...

  10. Epidemiology of opportunistic invasive fungal infections in China: review of literature

    Institute of Scientific and Technical Information of China (English)

    LIAO Yong; CHEN Min; Thomas Hartmann; YANG Rong-ya; LIAO Wan-qing

    2013-01-01

    Objective To summarize the recent findings on the epidemiology of medically important,opportunistic invasive fungal infections (IFIs) in China and discuss the relevant social,economical reasons and medical factors.Data sources We performed a comprehensive search of both English and Chinese literatures of opportunistic IFIs from China up to April 2012.Study selection Relevant literatures involving researches and cases/case series were identified,retrieved and reviewed.Results The incidence of opportunistic IFIs in China was steadily increasing.The incidence and mortality of IFIs were different in patients with various underlying conditions/diseases,from 4.12% to 41.18% and 9.8% to 60.0%,respectively.Candida species,Aspergillus species and Cryptococcus neoformans species complex were the most frequent isolated pathogens.Other uncommon opportunistic IFIs were also been reported,including trichosporonosis,mucormycosis,hyalohyphomycosis (hyaline hyphomycetes) and phaeohyphomycosis (dematiaceous hyphomycetes).Reports of Chinese patients differed from those of many other countries as there were a higher number of patients without identifiable underlying diseases/conditions.Conclusions Because of the rapid economic development,changing population structure and a growing number of immunocompromised hosts with risk factors,today opportunistic IFIs in China have a significant impact on public health,associated with high morbidity/mortality and higher care costs.Now information related to the epidemiology of opportunistic IFIs in China is still sparse,so we need more organized groups of clinical scientists performing related researches to help the clinicians to obtain more accurate epidemiological characteristics.

  11. Opportunistic Interference Alignment in MIMO Interference Channels

    CERN Document Server

    Perlaza, Samir Medina; Lasaulce, Samson; Chaufray, Jean Marie

    2008-01-01

    We present two interference alignment techniques such that an opportunistic point-to-point multiple input multiple output (MIMO) link can reuse, without generating any additional interference, the same frequency band of a similar pre-existing primary link. In this scenario, we exploit the fact that under power constraints, although each radio maximizes independently its rate by water-filling on their channel transfer matrix singular values, frequently, not all of them are used. Therefore, by aligning the interference of the opportunistic radio it is possible to transmit at a significant rate while insuring zero-interference on the pre-existing link. We propose a linear pre-coder for a perfect interference alignment and a power allocation scheme which maximizes the individual data rate of the secondary link. Our numerical results show that significant data rates are achieved even for a reduced number of antennas.

  12. Opportunistic Migration in Spatial Evolutionary Games

    CERN Document Server

    Buesser, Pierre; Antonioni, Alberto

    2013-01-01

    We study evolutionary games in a spatial diluted grid environment in which agents strategically interact locally but can also opportunistically move to other positions within a given migration radius. Using the imitation of the best rule for strategy revision, it is shown that cooperation may evolve and be stable in the Prisoner's Dilemma game space for several migration distances but only for small game interaction radius while the Stag Hunt class of games become fully cooperative. We also show that only a few trials are needed for cooperation to evolve, i.e. searching costs are not an issue. When the stochastic Fermi strategy update protocol is used cooperation cannot evolve in the Prisoner's Dilemma if the selection intensity is high in spite of opportunistic migration. However, when imitation becomes more random, fully or partially cooperative states are reached in all games for all migration distances tested and for short to intermediate interaction radii.

  13. Integrated Routing Protocol for Opportunistic Networks

    CERN Document Server

    Verma, Anshul

    2012-01-01

    In opportunistic networks the existence of a simultaneous path is not assumed to transmit a message between a sender and a receiver. Information about the context in which the users communicate is a key piece of knowledge to design efficient routing protocols in opportunistic networks. But this kind of information is not always available. When users are very isolated, context information cannot be distributed, and cannot be used for taking efficient routing decisions. In such cases, context oblivious based schemes are only way to enable communication between users. As soon as users become more social, context data spreads in the network, and context based routing becomes an efficient solution. In this paper we design an integrated routing protocol that is able to use context data as soon as it becomes available and falls back to dissemination based routing when context information is not available. Then, we provide a comparison between Epidemic and PROPHET, these are representative of context oblivious and co...

  14. Opportunistic Cooperation in Cognitive Femtocell Networks

    OpenAIRE

    Urgaonkar, Rahul; Neely, Michael J.

    2011-01-01

    We investigate opportunistic cooperation between unlicensed secondary users and legacy primary users in a cognitive radio network. Specifically, we consider a model of a cognitive network where a secondary user can cooperatively transmit with the primary user in order to improve the latter's effective transmission rate. In return, the secondary user gets more opportunities for transmitting its own data when the primary user is idle. This kind of interaction between the primary and secondary u...

  15. Mobile opportunistic networks architectures, protocols and applications

    CERN Document Server

    Denko, Mieso K

    2011-01-01

    Widespread availability of pervasive and mobile devices coupled with recent advances in networking technologies make opportunistic networks one of the most promising communication technologies for a growing number of future mobile applications. Covering the basics as well as advanced concepts, this book introduces state-of-the-art research findings, technologies, tools, and innovations. Prominent researchers from academia and industry report on communication architectures, network algorithms and protocols, emerging applications, experimental studies, simulation tools, implementation test beds,

  16. Opportunistic infections in a renal transplant recipient

    Directory of Open Access Journals (Sweden)

    Vijaya V. Mysorekar

    2012-01-01

    Full Text Available With the present progress in transplantation procedures, there is an improvement in patient and allograft survival. However, the immunosuppression necessary to sustain the allograft predisposes these transplant recipients to infection, which is now a significant cause of morbidity and mortality. We describe a case of a 30-year-old renal transplant recipient with two opportunistic infections, namely, primary cutaneous aspergillosis and intestinal tuberculosis, with terminal enterococcal pleuritis and peritonitis. Control of the degree of immunosuppression, and prompt recognition and treatment of infection are vital for successful organ transplantation.

  17. Trust Management System for Opportunistic Cloud Services

    DEFF Research Database (Denmark)

    Kuada, Eric

    2013-01-01

    We have over the past three years been working on the feasibility of Opportunistic Cloud Services (OCS) for enterprises. OCS is about enterprises strategically contributing and utilizing spare IT resources as cloud services. One of the major challenges that such a platform faces is data security...... and trust management issues. This paper presents a trust management system for OCS platforms. It models the concept of trust and applies it to OCS platforms. The trust model and the trust management system are verified through the simulation of the computation of the trust values with Infrastructure...

  18. Reconfigurable cognitive transceiver for opportunistic networks

    Science.gov (United States)

    Maso, Marco; Baştuğ, Ejder; Cardoso, Leonardo S.; Debbah, Mérouane; Özdemir, Özgür

    2014-12-01

    In this work, we provide the implementation and analysis of a cognitive transceiver for opportunistic networks. We focus on a previously introduced dynamic spectrum access (DSA) - cognitive radio (CR) solution for primary-secondary coexistence in opportunistic orthogonal frequency division multiplexing (OFDM) networks, called cognitive interference alignment (CIA). The implementation is based on software-defined radio (SDR) and uses GNU Radio and the universal software radio peripheral (USRP) as the implementation toolkit. The proposed flexible transceiver architecture allows efficient on-the-fly reconfigurations of the physical layer into OFDM, CIA or a combination of both. Remarkably, its responsiveness is such that the uplink and downlink channel reciprocity from the medium perspective, inherent to time division duplex (TDD) communications, can be effectively verified and exploited. We show that CIA provides approximately 10 dB of interference isolation towards the OFDM receiver with respect to a fully random precoder. This result is obtained under suboptimal conditions, which indicates that further gains are possible with a better optimization of the system. Our findings point towards the usefulness of a practical CIA implementation, as it yields a non-negligible performance for the secondary system, while providing interference shielding to the primary receiver.

  19. Hybridizing Evolutionary Algorithms with Opportunistic Local Search

    DEFF Research Database (Denmark)

    Gießen, Christian

    2013-01-01

    There is empirical evidence that memetic algorithms (MAs) can outperform plain evolutionary algorithms (EAs). Recently the first runtime analyses have been presented proving the aforementioned conjecture rigorously by investigating Variable-Depth Search, VDS for short (Sudholt, 2008). Sudholt...... raised the question if there are problems where VDS performs badly. We answer this question in the affirmative in the following way. We analyze MAs with VDS, which is also known as Kernighan-Lin for the TSP, on an artificial problem and show that MAs with a simple first-improvement local search...... outperform VDS. Moreover, we show that the performance gap is exponential. We analyze the features leading to a failure of VDS and derive a new local search operator, coined Opportunistic Local Search, that can easily overcome regions of the search space where local optima are clustered. The power...

  20. Opportunistic Cooperation in Cognitive Femtocell Networks

    CERN Document Server

    Urgaonkar, Rahul

    2011-01-01

    We investigate opportunistic cooperation between unlicensed secondary users and legacy primary users in a cognitive radio network. Specifically, we consider a model of a cognitive network where a secondary user can cooperatively transmit with the primary user in order to improve the latter's effective transmission rate. In return, the secondary user gets more opportunities for transmitting its own data when the primary user is idle. This kind of interaction between the primary and secondary users is different from the traditional dynamic spectrum access model in which the secondary users try to avoid interfering with the primary users while seeking transmission opportunities on vacant primary channels. In our model, the secondary users need to balance the desire to cooperate more (to create more transmission opportunities) with the need for maintaining sufficient energy levels for their own transmissions. Such a model is applicable in the emerging area of cognitive femtocell networks. We formulate the problem...

  1. Optimal Selective Feedback Policies for Opportunistic Beamforming

    CERN Document Server

    Samarasinghe, Tharaka; Evans, Jamie S

    2011-01-01

    This paper studies the structure of downlink sum-rate maximizing selective decentralized feedback policies for opportunistic beamforming under finite feedback constraints on the average number of mobile users feeding back. Firstly, it is shown that any sum-rate maximizing selective decentralized feedback policy must be a threshold feedback policy. This result holds for all fading channel models with continuous distribution functions. Secondly, the resulting optimum threshold selection problem is analyzed in detail. This is a non-convex optimization problem over finite dimensional Euclidean spaces. By utilizing the theory of majorization, an underlying Schur-concave structure in the sum-rate function is identified, and the sufficient conditions for the optimality of homogenous threshold feedback policies are obtained. Applications of these results are illustrated for well known fading channel models such as Rayleigh, Nakagami and Rician fading channels, along with various engineering and design insights. Rathe...

  2. Directional Navigation Improves Opportunistic Communication for Emergencies

    Directory of Open Access Journals (Sweden)

    Andras Kokuti

    2014-08-01

    Full Text Available We present a novel direction based shortest path search algorithm to guide evacuees during an emergency. It uses opportunistic communications (oppcomms with low-cost wearable mobile nodes that can exchange packets at close range of a few to some tens of meters without help of an infrastructure. The algorithm seeks the shortest path to exits which are safest with regard to a hazard, and is integrated into an autonomous Emergency Support System (ESS to guide evacuees in a built environment. The algorithm proposed that ESSs are evaluated with the DBES (Distributed Building Evacuation Simulator by simulating a shopping centre where fire is spreading. The results show that the directional path finding algorithm can offer significant improvements for the evacuees.

  3. Enabling opportunistic resources for CMS Computing Operations

    Energy Technology Data Exchange (ETDEWEB)

    Hufnagel, Dick [Fermilab

    2015-11-19

    With the increased pressure on computing brought by the higher energy and luminosity from the LHC in Run 2, CMS Computing Operations expects to require the ability to utilize “opportunistic” resources — resources not owned by, or a priori configured for CMS — to meet peak demands. In addition to our dedicated resources we look to add computing resources from non CMS grids, cloud resources, and national supercomputing centers. CMS uses the HTCondor/glideinWMS job submission infrastructure for all its batch processing, so such resources will need to be transparently integrated into its glideinWMS pool. Bosco and parrot wrappers are used to enable access and bring the CMS environment into these non CMS resources. Here we describe our strategy to supplement our native capabilities with opportunistic resources and our experience so far using them.

  4. Alleviate Cellular Congestion Through Opportunistic Trough Filling

    Directory of Open Access Journals (Sweden)

    Yichuan Wang

    2014-04-01

    Full Text Available The demand for cellular data service has been skyrocketing since the debut of data-intensive smart phones and touchpads. However, not all data are created equal. Many popular applications on mobile devices, such as email synchronization and social network updates, are delay tolerant. In addition, cellular load varies significantly in both large and small time scales. To alleviate network congestion and improve network performance, we present a set of opportunistic trough filling schemes that leverage the time-variation of network congestion and delay-tolerance of certain traffic in this paper. We consider average delay, deadline, and clearance time as the performance metrics. Simulation results show promising performance improvement over the standard schemes. The work shed lights on addressing the pressing issue of cellular overload.

  5. Opportunistic hearing screening in elderly inpatients

    Directory of Open Access Journals (Sweden)

    Krishan Ramdoo

    2014-04-01

    Full Text Available Objective: To determine the prevalence of occult hearing loss in elderly inpatients, to evaluate feasibility of opportunistic hearing screening and to determine subsequent provision of hearing aids. Materials and methods: Subjects (>65 years were recruited from five elderly care wards. Hearing loss was detected by a ward-based hearing screen comprising patient-reported assessment of hearing disability and a whisper test. Subjects failing the whisper test or reporting hearing difficulties were offered formal audiological assessment. Results: Screening was performed on 51 patients aged between 70 and 95 years. Of the patients, 21 (41% reported hearing loss and 16 (31% failed the whisper test. A total of 37 patients (73% were referred for audiological assessment with 17 (33% found to have aidable hearing loss and 11 were fitted with hearing aids (22%. Discussion: This study highlights the high prevalence of occult hearing loss in elderly inpatients. Easy two-step screening can accurately identify patients with undiagnosed deafness resulting in significant proportions receiving hearing aids. Key sentences Approximately 14% of the elderly population use hearing aids despite a reported prevalence of deafness in up to 55%. The use of hearing aids is associated with an improvement in physical, emotional, mental and social well-being. An easy screening test for hearing loss consists of patient-reported hearing loss and a whisper test. Opportunistic screening of elderly inpatients resulted in referral of 73% of screened patients for formal audiology. Of the screened patients, 22% were provided with hearing aids.

  6. Raptor Codes for Use in Opportunistic Error Correction

    NARCIS (Netherlands)

    Zijnge, T.; Schiphorst, R.; Shao, X.; Slump, C.H.; Goseling, Jasper; Weber, Jos H.

    2010-01-01

    In this paper a Raptor code is developed and applied in an opportunistic error correction (OEC) layer for Coded OFDM systems. Opportunistic error correction [3] tries to recover information when it is available with the least effort. This is achieved by using Fountain codes in a COFDM system, which

  7. 冰鲜鸡肉中3种主要致病菌的共修复-增菌条件研究%Co-Recovery-Enrichment Conditions of Three Major Pathogenic Bacteria in Fresh Chicken Meat

    Institute of Scientific and Technical Information of China (English)

    王虎虎; 董洋; 闫振国; 徐幸莲; 周光宏

    2012-01-01

    In order to detect S.typhimurium,Listeria monocytogenes and E.coli O157:H7 in fresh chicken accurately and rapidly,traditional and multiple PCR methods were combined to explore co-recovery-enrichment conditions of heat-injured S.typhimurium,Listeria monocytogenes and E.coli O157:H7 in this study.The results showed that the scalding process could bring S.typhimurium,Listeria monocytogenes and E.coli O157: H7 into a sub-lethal state.TSB-YE was the best medium that could repair sub-lethal pathogenic bacteria.The recovery time of S.typhimurium and Listeria monocytogenes was 2 h,and that of E.coli O157:H7 was 4 h.After 16 h of enrichment,the best enrichment results were obtained for S.typhimurium,Listeria monocytogenes and E.coli O157: H7 in TSB-YE medium Under these co-recovery-enrichment conditions,the positive rates of S.typhimurium,Listeria monocytogenes and E.coli O157:H7 in 80 samples were 22.5%(18/80),11.3%(9/80) and 18.8%(15/80),respectively.%研究冰鲜鸡肉中鼠伤寒沙门氏菌(S.typhimurium)、单增李斯特菌(L.monocytogenes)和大肠杆菌(E.coli)O157:H7的共修复-增菌条件。通过传统技术和PCR技术相结合的方法,研究肉鸡屠宰浸烫脱毛工艺对3种目标菌的热激损伤及共修复-增菌条件,并利用共修复-增菌结果,对生产线和超市的冰鲜鸡肉样品中3种目标菌的污染状况进行调查。结果表明:肉鸡屠宰浸烫脱毛工艺条件能使部分S.typhimurium、L.monocytogenes和E.coli O157:H7处于亚致死状态;TSB-YE培养基对热损伤S.typhimurium、L.monocytogenes和E.coli O157:H7的修复效果最好,且对前两种菌的修复时间为2h,对后一种菌的修复时间为4h;TSB-YE培养基在16h对3种致病菌的共增菌效果最好;运用共修复-增菌条件,对80份实际样品中的3种致病菌检出率分别为:S.typhimurium 22.5%(18/80)、L.monocytogenes 11.3%(9/80)和E.coli O157:H7 18.8%(15/80)。

  8. Opportunistic fungi in lake water and fungal infections in associated human population in Dal Lake, Kashmir.

    Science.gov (United States)

    Bandh, Suhaib A; Kamili, Azra N; Ganai, Bashir A; Lone, Bashir A

    2016-04-01

    Natural habitats of opportunistic fungal pathogens are outside of the host; therefore, it is critically important to understand their ecology and routes of transmission. In this study, we investigated the presence of human pathogenic opportunistic fungi in lake water and incidence of fungal infections in associated population in Kashmir, India. Six hundred forty water samples were taken on seasonal basis from a wide network of sampling stations of the lake for an extended period of two years for screening their occurrence. The samples were inoculated onto rose bengal agar, malt extract agar, potato dextrose agar and other specified culture media supplemented with Chloramphenicol and Streptomycin followed by incubation at 37 °C. All the samples were positive for fungi, which were later identified by sequencing the rDNA internal transcribed spacer region aided by classical morphological culture techniques and physiological profiling. The whole process led to the isolation of sixteen species of opportunistic fungal pathogens belonging to genus Aspergillus, Candida, Penicillium, Cryptococcus, Fusarium, Rhizopus and Mucor in decreasing order of prevalence. Furthermore, 20% population (n = 384) of Dal inhabitants was examined for possible fungal infections and it was observed that only 8.07% individuals were positive for fungal infections with 4.68% skin infection cases, 2.34% onychomycosis cases and 1.04% candidiasis cases. Scrapings from onychomycosis and candidiasis patients showed the presence of Aversicolor and Calbicans respectively, resembling exactly the strains isolated from the lake water. However, the skin infection was because of a dermatophyte not isolated for the lake water. Higher prevalence of infection (6.77%) was seen in people using lake water followed by a positive prevalence of 1.30% using tap water. The results of present study suggest that the lake inhabitants are at a greater risk of getting life threatening fungal diseases which may lead to

  9. A graph model for opportunistic network coding

    KAUST Repository

    Sorour, Sameh

    2015-08-12

    © 2015 IEEE. Recent advancements in graph-based analysis and solutions of instantly decodable network coding (IDNC) trigger the interest to extend them to more complicated opportunistic network coding (ONC) scenarios, with limited increase in complexity. In this paper, we design a simple IDNC-like graph model for a specific subclass of ONC, by introducing a more generalized definition of its vertices and the notion of vertex aggregation in order to represent the storage of non-instantly-decodable packets in ONC. Based on this representation, we determine the set of pairwise vertex adjacency conditions that can populate this graph with edges so as to guarantee decodability or aggregation for the vertices of each clique in this graph. We then develop the algorithmic procedures that can be applied on the designed graph model to optimize any performance metric for this ONC subclass. A case study on reducing the completion time shows that the proposed framework improves on the performance of IDNC and gets very close to the optimal performance.

  10. Exploiting volatile opportunistic computing resources with Lobster

    Science.gov (United States)

    Woodard, Anna; Wolf, Matthias; Mueller, Charles; Tovar, Ben; Donnelly, Patrick; Hurtado Anampa, Kenyi; Brenner, Paul; Lannon, Kevin; Hildreth, Mike; Thain, Douglas

    2015-12-01

    Analysis of high energy physics experiments using the Compact Muon Solenoid (CMS) at the Large Hadron Collider (LHC) can be limited by availability of computing resources. As a joint effort involving computer scientists and CMS physicists at Notre Dame, we have developed an opportunistic workflow management tool, Lobster, to harvest available cycles from university campus computing pools. Lobster consists of a management server, file server, and worker processes which can be submitted to any available computing resource without requiring root access. Lobster makes use of the Work Queue system to perform task management, while the CMS specific software environment is provided via CVMFS and Parrot. Data is handled via Chirp and Hadoop for local data storage and XrootD for access to the CMS wide-area data federation. An extensive set of monitoring and diagnostic tools have been developed to facilitate system optimisation. We have tested Lobster using the 20 000-core cluster at Notre Dame, achieving approximately 8-10k tasks running simultaneously, sustaining approximately 9 Gbit/s of input data and 340 Mbit/s of output data.

  11. Impact of Strangers on Opportunistic Routing Performance

    Institute of Scientific and Technical Information of China (English)

    Pei-Yan Yuan; Hua-Dong Ma; Peng-Rui Duan

    2013-01-01

    Routing is one of the challenging tasks in Delay Tolerant Networks (DTNs),due to the lack of global knowledge and sporadic contacts between nodes.Most existing studies take a greedy scheme in data forwarding process,i.e.,only nodes with higher utility values than current carriers can be selected as relays.They lack an in-depth investigation on the main features of the optimal paths in Epidemic.These features are vital to any forwarding scheme that tends to make a trade-off between packet delivery delay and cost.This is mainly because Epidemic provides an upper bound on cost and a lower bound on delivery delay.Therefore,a deep understanding of these features is useful to make informed forwarding decisions.In this paper,we try to explore these features by observing the roles of different social relationships in the optimal paths through a set of real datasets.These datasets provide evidence that strangers have two sides in data forwarding process,and that the importance of strangers shows a decreasing trend along the forwarding paths.Using this heuristic knowledge,we propose STRON,a distributed and lightweight forwarding scheme.The distributed feature makes it very suitable for opportunistic scenarios and the low communication and computation features make it easy to be integrated with state-of-the-art work.The trace-driven simulations obviously confirm its effectiveness,especially in terms of packet delivery delay and cost.

  12. Efficient Online Learning for Opportunistic Spectrum Access

    CERN Document Server

    Dai, Wenhan; Krishnamachari, Bhaskar

    2011-01-01

    The problem of opportunistic spectrum access in cognitive radio networks has been recently formulated as a non-Bayesian restless multi-armed bandit problem. In this problem, there are N arms (corresponding to channels) and one player (corresponding to a secondary user). The state of each arm evolves as a finite-state Markov chain with unknown parameters. At each time slot, the player can select K < N arms to play and receives state-dependent rewards (corresponding to the throughput obtained given the activity of primary users). The objective is to maximize the expected total rewards (i.e., total throughput) obtained over multiple plays. The performance of an algorithm for such a multi-armed bandit problem is measured in terms of regret, defined as the difference in expected reward compared to a model-aware genie who always plays the best K arms. In this paper, we propose a new continuous exploration and exploitation (CEE) algorithm for this problem. When no information is available about the dynamics of th...

  13. Microgravity effects on pathogenicity of bacteria

    Directory of Open Access Journals (Sweden)

    Ya-juan WANG

    2013-01-01

    Full Text Available Microgravity is one of the important environmental conditions during spaceflight. A series of studies have shown that many kinds of bacteria could be detected in space station and space shuttle. Space environment or simulated microgravity may throw a certain influence on those opportunistic pathogens and lead to some changes on their virulence, biofilm formation and drug tolerance. The mechanism of bacteria response to space environment or simulated microgravity has not been defined. However, the conserved RNA-binding protein Hfq has been identified as a likely global regulator involved in the bacteria response to this environment. In addition, microgravity effects on bacterial pathogenicity may threaten astronauts' health. The present paper will focus on microgravity-induced alterations of pathogenicity and relative mechanism in various opportunistic pathogens.

  14. HIV-associated opportunistic CNS infections: pathophysiology, diagnosis and treatment.

    Science.gov (United States)

    Bowen, Lauren N; Smith, Bryan; Reich, Daniel; Quezado, Martha; Nath, Avindra

    2016-10-27

    Nearly 30 years after the advent of antiretroviral therapy (ART), CNS opportunistic infections remain a major cause of morbidity and mortality in HIV-positive individuals. Unknown HIV-positive disease status, antiretroviral drug resistance, poor drug compliance, and recreational drug abuse are factors that continue to influence the morbidity and mortality of infections. The clinical and radiographic pattern of CNS opportunistic infections is unique in the setting of HIV infection: opportunistic infections in HIV-positive patients often have characteristic clinical and radiological presentations that can differ from the presentation of opportunistic infections in immunocompetent patients and are often sufficient to establish the diagnosis. ART in the setting of these opportunistic infections can lead to a paradoxical worsening caused by an immune reconstitution inflammatory syndrome (IRIS). In this Review, we discuss several of the most common CNS opportunistic infections: cerebral toxoplasmosis, progressive multifocal leukoencephalopathy (PML), tuberculous meningitis, cryptococcal meningitis and cytomegalovirus infection, with an emphasis on clinical pearls, pathological findings, MRI findings and treatment. Moreover, we discuss the risk factors, pathophysiology and management of IRIS. We also summarize the challenges that remain in management of CNS opportunistic infections, which includes the lack of phase II and III clinical trials, absence of antimicrobials for infections such as PML, and controversy regarding the use of corticosteroids for treatment of IRIS.

  15. Opportunistic transmitter selection for selfless overlay cognitive radios

    KAUST Repository

    Shaqfeh, Mohammad

    2013-11-01

    We propose an opportunistic strategy to grant channel access to the primary and secondary transmitters in causal selfless overlay cognitive radios over block-fading channels. The secondary transmitter helps the primary transmitter by relaying the primary messages opportunistically, aided by a buffer to store the primary messages temporarily. The optimal channel-aware transmitter- selection strategy is the solution of the maximization of the average secondary rate under the average primary rate requirement and the buffer stability constraints. Numerical results demonstrate the gains of the proposed opportunistic selection strategy. © 2013 IEEE.

  16. Engineering human peripheral blood stem cell grafts that are depleted of naïve T cells and retain functional pathogen-specific memory T cells.

    Science.gov (United States)

    Bleakley, Marie; Heimfeld, Shelly; Jones, Lori A; Turtle, Cameron; Krause, Diane; Riddell, Stanley R; Shlomchik, Warren

    2014-05-01

    Graft-versus-host disease (GVHD) is a frequent major complication of allogeneic hematopoietic cell transplantation (HCT). Approaches that selectively deplete T cells that cause GVHD from allogeneic stem cell grafts and preserve T cells specific for pathogens may improve HCT outcomes. It has been hypothesized that the majority of T cells that can cause GVHD reside within the naïve T cell (TN) subset, and previous studies performed in mouse models and with human cells in vitro support this hypothesis. As a prelude to translating these findings to the clinic, we developed and evaluated a novel 2-step clinically compliant procedure for manipulating peripheral blood stem cells (PBSC) to remove TN, preserve CD34(+) hematopoietic stem cells, and provide for a fixed dose of memory T cells (TM) that includes T cells with specificity for common opportunistic pathogens encountered after HCT. Our studies demonstrate effective and reproducible performance of the immunomagnetic cell selection procedure for depleting TN. Moreover, after cell processing, the CD45RA-depleted PBSC products are enriched for CD4(+) and CD8(+) TM with a central memory phenotype and contain TM cells that are capable of proliferating and producing effector cytokines in response to opportunistic pathogens. Copyright © 2014 American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.

  17. Vegetable microbiomes: is there a connection among opportunistic infections, human health and our 'gut feeling'?

    Science.gov (United States)

    Berg, Gabriele; Erlacher, Armin; Smalla, Kornelia; Krause, Robert

    2014-11-01

    The highly diverse microbiomes of vegetables are reservoirs for opportunistic and emerging pathogens. In recent years, an increased consumption, larger scale production and more efficient distribution of vegetables together with an increased number of immunocompromised individuals resulted in an enhanced number of documented outbreaks of human infections associated with the consumption of vegetables. Here we discuss the occurrence of potential pathogens in vegetable microbiomes, the impact of farming and processing practices, and plant and human health issues. Based on these results, we discuss the question if vegetables can serve as a source of infection for immunocompromised individuals as well as possible solutions to avoid outbreaks. Moreover, the potentially positive aspects of the vegetables microbiome for the gut microbiota and human health are presented.

  18. Genome-Wide Screen for Haploinsufficient Cell Size Genes in the Opportunistic Yeast Candida albicans

    Directory of Open Access Journals (Sweden)

    Julien Chaillot

    2017-02-01

    Full Text Available One of the most critical but still poorly understood aspects of eukaryotic cell proliferation is the basis for commitment to cell division in late G1 phase, called Start in yeast and the Restriction Point in metazoans. In all species, a critical cell size threshold coordinates cell growth with cell division and thereby establishes a homeostatic cell size. While a comprehensive survey of cell size genetic determinism has been performed in the saprophytic yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, very little is known in pathogenic fungi. As a number of critical Start regulators are haploinsufficient for cell size, we applied a quantitative analysis of the size phenome, using elutriation-barcode sequencing methodology, to 5639 barcoded heterozygous deletion strains of the opportunistic yeast Candida albicans. Our screen identified conserved known regulators and biological processes required to maintain size homeostasis in the opportunistic yeast C. albicans. We also identified novel C. albicans-specific size genes and provided a conceptual framework for future mechanistic studies. Interestingly, some of the size genes identified were required for fungal pathogenicity suggesting that cell size homeostasis may be elemental to C. albicans fitness or virulence inside the host.

  19. Genome-Wide Screen for Haploinsufficient Cell Size Genes in the Opportunistic Yeast Candida albicans

    Science.gov (United States)

    Chaillot, Julien; Cook, Michael A.; Corbeil, Jacques; Sellam, Adnane

    2016-01-01

    One of the most critical but still poorly understood aspects of eukaryotic cell proliferation is the basis for commitment to cell division in late G1 phase, called Start in yeast and the Restriction Point in metazoans. In all species, a critical cell size threshold coordinates cell growth with cell division and thereby establishes a homeostatic cell size. While a comprehensive survey of cell size genetic determinism has been performed in the saprophytic yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, very little is known in pathogenic fungi. As a number of critical Start regulators are haploinsufficient for cell size, we applied a quantitative analysis of the size phenome, using elutriation-barcode sequencing methodology, to 5639 barcoded heterozygous deletion strains of the opportunistic yeast Candida albicans. Our screen identified conserved known regulators and biological processes required to maintain size homeostasis in the opportunistic yeast C. albicans. We also identified novel C. albicans-specific size genes and provided a conceptual framework for future mechanistic studies. Interestingly, some of the size genes identified were required for fungal pathogenicity suggesting that cell size homeostasis may be elemental to C. albicans fitness or virulence inside the host. PMID:28040776

  20. Opportunistic quantum network coding based on quantum teleportation

    Science.gov (United States)

    Shang, Tao; Du, Gang; Liu, Jian-wei

    2016-04-01

    It seems impossible to endow opportunistic characteristic to quantum network on the basis that quantum channel cannot be overheard without disturbance. In this paper, we propose an opportunistic quantum network coding scheme by taking full advantage of channel characteristic of quantum teleportation. Concretely, it utilizes quantum channel for secure transmission of quantum states and can detect eavesdroppers by means of quantum channel verification. What is more, it utilizes classical channel for both opportunistic listening to neighbor states and opportunistic coding by broadcasting measurement outcome. Analysis results show that our scheme can reduce the times of transmissions over classical channels for relay nodes and can effectively defend against classical passive attack and quantum active attack.

  1. Opportunistic intestinal parasites in hemodialysis patients - a systematic literature review

    Directory of Open Access Journals (Sweden)

    Solimar Almeida de Oliveira

    2013-12-01

    Full Text Available The objective of this systematic literature review was to identify the occurrence of opportunistic enteric parasites in chronic kidney patient undergoing hemodialysis. The review consisted on searching articles published on MEDLINE, LILACS, SciELO, and PubMed databases between 1991 and 2013. A total 178 articles were identified, ten of which were considered relevant for the present study. In the referred studies, the researchers demonstrated that immunosuppressed patients undergoing hemodialysis are potentially infected by opportunistic enteric agents. Further studies are needed on this topic, as there is a growing global concern with chronic kidney diseases and the potential for these patients contracting opportunistic diseases, which, inclusively, could contaminate hospital environments with opportunistic enteric protozoa. Descriptors: Renal Dialysis; Blastocystis hominis; Cryptosporidium; Cyclospora; Isospora.

  2. Achieving fairness by aggregate power allocation in opportunistic cooperation networks

    Institute of Scientific and Technical Information of China (English)

    Cao Jianfei; Zhong Zhangdui; Ai Bo

    2009-01-01

    Within a wireless opportunistic network, one of the lucky users gets an opportunity to utilize the whole radio resource. However some of the unlucky users keep silent during an unexpected period resulting from severe wireless environment and imperfect scheduling algorithms. An opportunistic cooperation protocol is proposed that can achieve equivalent performance measured in terms of outage probability, in which scheme the opportunistic user helps to relay what need retransmitting indicated by the destination and selects the appropriate power allocation to pursue fairness. The proposed scheme deploys superposition coding and successive interference cancellation at relay and destination, respectively. To improve the spectral efficiency, the modified cooperation architecture involves two opportunistic users which work in turn. The simulation results demonstrate that the protocol obtains better performance compared with the conventional methods.

  3. Capacity of Wireless Ad Hoc Networks with Opportunistic Collaborative Communications

    Directory of Open Access Journals (Sweden)

    Simeone O

    2007-01-01

    Full Text Available Optimal multihop routing in ad hoc networks requires the exchange of control messages at the MAC and network layer in order to set up the (centralized optimization problem. Distributed opportunistic space-time collaboration (OST is a valid alternative that avoids this drawback by enabling opportunistic cooperation with the source at the physical layer. In this paper, the performance of OST is investigated. It is shown analytically that opportunistic collaboration outperforms (centralized optimal multihop in case spatial reuse (i.e., the simultaneous transmission of more than one data stream is not allowed by the transmission protocol. Conversely, in case spatial reuse is possible, the relative performance between the two protocols has to be studied case by case in terms of the corresponding capacity regions, given the topology and the physical parameters of network at hand. Simulation results confirm that opportunistic collaborative communication is a promising paradigm for wireless ad hoc networks that deserves further investigation.

  4. Opportunistic yeast infections: candidiasis, cryptococcosis, trichosporonosis and geotrichosis.

    Science.gov (United States)

    Vázquez-González, Denisse; Perusquía-Ortiz, Ana María; Hundeiker, Max; Bonifaz, Alexandro

    2013-05-01

    Opportunistic yeast infections are diseases caused by fungi which normally are saprophytic and do not cause disease in humans or animals. The prevalence of these diseases has been increasing due to immunosuppressive, corticosteroid, and long-term antibiotic treatment following organ transplantation or after serious metabolic, hematological, or immunological diseases. We review epidemiological, clinical, diagnostic, and therapeutic aspects of the four "big" opportunistic yeast infections: candidiasis, cryptococcosis, trichosporonosis, and geotrichosis.

  5. An Analytical Approach to Opportunistic Transmission under Rayleigh Fading Channels

    OpenAIRE

    Yousaf Bin Zikria; Sung Won Kim; Heejung Yu; Seung Yeob Nam

    2015-01-01

    In cognitive radio sensor networks, the routing methods including multiple relays have been extensively studied to achieve higher throughput and lower end-to-end delay. As one of innovative approaches, the opportunistic routing scheme was proposed. In this paper, the effectiveness of the opportunistic transmission in terms of reliability and delay of transmission is verified with an analytical way. For the analysis, we establish the probabilistic model with respect to distance and the number ...

  6. SPECTRUM OF OPPORTUNISTIC INFECTIONS IN HIV-AIDS PATIENTS

    OpenAIRE

    S S Madkar; Ashok Jaykumar Vankudre; SL Nilekar

    2012-01-01

    Aim: AIDS is characterized by a number of opportunistic infections which are responsible for high morbidity and mortality. The spectrum and distribution of opportunistic infections (OIs) in AIDS patients is ever-expanding. This spectrum varies from continent to continent. The aim of the present study was to document the spectrum of OIs in HIV-infected patients in Ambajogai. Material and Method: 178 HIV positive symptomatic patients, either hospitalized or coming to ART (Antiretroviral Therapy...

  7. Opportunistic Wireless Relay Networks: Diversity-Multiplexing Tradeoff

    CERN Document Server

    Abouelseoud, Mohamed

    2011-01-01

    Opportunistic analysis has traditionally relied on independence assumptions that break down in many interesting and useful network topologies. This paper develops techniques that expand opportunistic analysis to a broader class of networks, proposes new opportunistic methods for several network geometries, and analyzes them in the high-SNR regime. For each of the geometries studied in the paper, we analyze the opportunistic DMT of several relay protocols, including amplify-and-forward, decode-and-forward, compress-and-forward, non-orthogonal amplify-forward, and dynamic decode-forward. Among the highlights of the results: in a variety of multi-user single-relay networks, simple selection strategies are developed and shown to be DMT-optimal. It is shown that compress-forward relaying achieves the DMT upper bound in the opportunistic multiple-access relay channel as well as in the opportunistic nxn user network with relay. Other protocols, e.g. dynamic decode-forward, are shown to be near optimal in several cas...

  8. Host-pathogen interactions in epidermolysis bullosa patients colonized with Staphylococcus aureus

    NARCIS (Netherlands)

    van der Kooi - Pol, Magdalena M.; Duipmans, Jose C.; Jonkman, Marcel F.; van Dijl, Jan Maarten

    Patients with the genetic blistering disease epidermolysis bullosa (EB) often have chronic wounds that can become colonized by different bacteria, especially the opportunistic pathogen Staphylococcus aureus. We therefore determined the S. aureus colonization rates in EB patients from the Netherlands

  9. Chaetomium-like fungi causing opportunistic infections in humans: a possible role for extremotolerance

    NARCIS (Netherlands)

    Ahmed, Sarah A.; Khan, Ziauddin; Wang, Xue-wei; Moussa, Tarek A. A.; Al-Zahrani, Hassan S.; Almaghrabi, Omar A.; Sutton, Deanna A.; Ahmad, S.; Groenewald, Johannes Z.; Alastruey-Izquierdo, A.; Diepeningen, Anne; Menken, S. B. J.; Najafzadeh, M. J.; Crous, Pedro W.; Cornely, Oliver; Hamprecht, Axel; Vehreschild, Maria J. G. T.; Kindo, A. J.; de Hoog, G. Sybren

    2016-01-01

    Members of the family Chaetomiaceae are ubiquitous ascosporulating fungi commonly, which reside in soil enriched with manure or cellulosic materials. Their role as human pathogens is largely ignored. However, the ability of some species to grow at high temperature enables them to play an important r

  10. Chaetomium-like fungi causing opportunistic infections in humans: a possible role for extremotolerance

    NARCIS (Netherlands)

    Ahmed, Sarah A.; Khan, Ziauddin; Wang, Xue-wei; Moussa, Tarek A. A.; Al-Zahrani, Hassan S.; Almaghrabi, Omar A.; Sutton, Deanna A.; Ahmad, S.; Groenewald, Johannes Z.; Alastruey-Izquierdo, A.; Diepeningen, Anne; Menken, S. B. J.; Najafzadeh, M. J.; Crous, Pedro W.; Cornely, Oliver; Hamprecht, Axel; Vehreschild, Maria J. G. T.; Kindo, A. J.; de Hoog, G. Sybren

    Members of the family Chaetomiaceae are ubiquitous ascosporulating fungi commonly, which reside in soil enriched with manure or cellulosic materials. Their role as human pathogens is largely ignored. However, the ability of some species to grow at high temperature enables them to play an important

  11. Chaetomium-like fungi causing opportunistic infections in humans: a possible role for extremotolerance

    NARCIS (Netherlands)

    Ahmed, S.A.; Khan, Z.; Wang, X.; Moussa, T.A.A.; Al-Zahrani, H.S.; Almaghrabi, O.A.; Sutton, D.A.; Ahmad, S.; Groenewald, J.Z.; Alastruey-Izquierdo, A.; van Diepeningen, A.; Menken, S.B.J.; Najafzadeh, M.J.; Crous, P.W.; Cornely, O.; Hamprecht, A.; Vehreschild, M.J.G.T.; Kindo, A.J.; de Hoog, G.S.

    2015-01-01

    Members of the family Chaetomiaceae are ubiquitous ascosporulating fungi commonly, which reside in soil enriched with manure or cellulosic materials. Their role as human pathogens is largely ignored. However, the ability of some species to grow at high temperature enables them to play an important

  12. Trichoderma: the genomics of opportunistic success

    Energy Technology Data Exchange (ETDEWEB)

    Druzhinina, Irina S.; Seiboth, Verena Seidl; Estrella, Alfredo Herrera; Horwitz, Benjamin A.; Kenerley, Charles M.; Monte, Enrique; Mukherjee, Prasun K.; Zeilinger, Susanne; Grigoriev, Igor V.; Kubicek, Christian P.

    2011-01-01

    Trichoderma is a genus of common filamentous fungi that display a remarkable range of lifestyles and interactions with other fungi, animals and plants. Because of their ability to antagonize plant-pathogenic fungi and to stimulate plant growth and defence responses, some Trichoderma strains are used for biological control of plant diseases. In this Review, we discuss recent advances in molecular ecology and genomics which indicate that the interactions of Trichoderma spp. with animals and plants may have evolved as a result of saprotrophy on fungal biomass (mycotrophy) and various forms of parasitism on other fungi (mycoparasitism), combined with broad environmental opportunism.

  13. SPECTRUM OF OPPORTUNISTIC INFECTIONS IN HIV-AIDS PATIENTS

    Directory of Open Access Journals (Sweden)

    S S Madkar

    2012-10-01

    Full Text Available Aim: AIDS is characterized by a number of opportunistic infections which are responsible for high morbidity and mortality. The spectrum and distribution of opportunistic infections (OIs in AIDS patients is ever-expanding. This spectrum varies from continent to continent. The aim of the present study was to document the spectrum of OIs in HIV-infected patients in Ambajogai. Material and Method: 178 HIV positive symptomatic patients, either hospitalized or coming to ART (Antiretroviral Therapy centre in S.R.T.R. Medical College, Ambajogai, were included in the study for finding the spectrum of opportunistic infections. Result: The commonest opportunistic infection seen was tuberculosis (59% of patients, followed by oral candidiasis (37.6% of patients and parasitic diarrhea due to Cryptosporidium parvum(18 % of patients. It was observed that out of 178 patients, maximum 53.3% were in the age group of 29-38 years followed by 21% in the age group of 39-48 years. It was found that 77% were males and 23% were females, with male to female ratio is 3.3:1. Conclusion: This study demonstrates that tuberculosis is the commonest opportunistic infection seen in HIV patients. Clinicians should consider HIV in the differential diagnosis and management of all persons with tuberculosis.

  14. On the Capacity of Hybrid Wireless Networks with Opportunistic Routing

    Directory of Open Access Journals (Sweden)

    Tan Le

    2010-01-01

    Full Text Available This paper studies the capacity of hybrid wireless networks with opportunistic routing (OR. We first extend the opportunistic routing algorithm to exploit high-speed data transmissions in infrastructure network through base stations. We then develop linear programming models to calculate the end-to-end throughput bounds from multiple source nodes to single as well as multiple destination nodes. The developed models are applied to study several hybrid wireless network examples. Through case studies, we investigate several factors that have significant impacts on the hybrid wireless network capacity under opportunistic routing, such as node transmission range, density and distribution pattern of base stations (BTs, and number of wireless channels on wireless nodes and base stations. Our numerical results demonstrate that opportunistic routing could achieve much higher throughput on both ad hoc and hybrid networks than traditional unicast routing (UR. Moreover, opportunistic routing can efficiently utilize base stations and achieve significantly higher throughput gains in hybrid wireless networks than in pure ad hoc networks especially with multiple-channel base stations.

  15.  Mycolic acids – potential biomarkers of opportunistic infections caused by bacteria of the suborder Corynebacterineae

    Directory of Open Access Journals (Sweden)

    Konrad Kowalski

    2012-06-01

    Full Text Available  Mycolic acids are one of the basic elements of the cell wall structure of bacteria belonging to the suborder Corynebacterineae, constituting from 20�0to 40�0of dry weight. Additionally, they show high structural diversity within each family and species. Nowadays, profiles of mycolic acids are widely described for the genus Mycobacterium, the causative agent of tuberculosis. However, the suborder Corynebacterineae also includes many representatives of opportunistic human pathogens, e.g. Dietzia, Gordonia, Nocardia and Rhodococcus. Currently, an increased infection risk caused by this group of microorganisms especially in immunocompromised patients has been observed. Better knowledge of mycolic acid profiles for Corynebacterineae may allow identification of mycolic acids as diagnostic markers in the detection of opportunistic bacterial infections. Modern techniques of chemical analysis, including mass spectrometry, may enable the development of new chemotaxonomic methods for the detection and differentiation of bacteria within the suborder Corynebacterineae.

  16. Efficient scheduling request algorithm for opportunistic wireless access

    KAUST Repository

    Nam, Haewoon

    2011-08-01

    An efficient scheduling request algorithm for opportunistic wireless access based on user grouping is proposed in this paper. Similar to the well-known opportunistic splitting algorithm, the proposed algorithm initially adjusts (or lowers) the threshold during a guard period if no user sends a scheduling request. However, if multiple users make requests simultaneously and therefore a collision occurs, the proposed algorithm no longer updates the threshold but narrows down the user search space by splitting the users into multiple groups iteratively, whereas the opportunistic splitting algorithm keeps adjusting the threshold until a single user is found. Since the threshold is only updated when no user sends a request, it is shown that the proposed algorithm significantly alleviates the burden of the signaling for the threshold distribution to the users by the scheduler. More importantly, the proposed algorithm requires a less number of mini-slots to make a user selection given a certain scheduling outage probability. © 2011 IEEE.

  17. Joint opportunistic scheduling and network coding for bidirectional relay channel

    KAUST Repository

    Shaqfeh, Mohammad

    2013-07-01

    In this paper, we consider a two-way communication system in which two users communicate with each other through an intermediate relay over block-fading channels. We investigate the optimal opportunistic scheduling scheme in order to maximize the long-term average transmission rate in the system assuming symmetric information flow between the two users. Based on the channel state information, the scheduler decides that either one of the users transmits to the relay, or the relay transmits to a single user or broadcasts to both users a combined version of the two users\\' transmitted information by using linear network coding. We obtain the optimal scheduling scheme by using the Lagrangian dual problem. Furthermore, in order to characterize the gains of network coding and opportunistic scheduling, we compare the achievable rate of the system versus suboptimal schemes in which the gains of network coding and opportunistic scheduling are partially exploited. © 2013 IEEE.

  18. Scale-Free Opportunistic Networks: is it Possible?

    CERN Document Server

    Ferretti, Stefano

    2011-01-01

    The coupling of scale-free networks with mobile unstructured networks is certainly unusual. In mobile networks, connections active at a given instant are constrained by the geographical distribution of mobile nodes, and by the limited signal strength of the wireless technology employed to build the ad-hoc overlay. This is in contrast with the presence of hubs, typical of scale-free nets. However, opportunistic (mobile) networks possess the distinctive feature to be delay tolerant; mobile nodes implement a store, carry and forward strategy that permits to disseminate data based on a multi-hop route, which is built in time, when nodes encounter other ones while moving. In this paper, we consider opportunistic networks as evolving graphs where links represent contacts among nodes arising during a (non-instantaneous) time interval. We discuss a strategy to control the way nodes manage contacts and build "opportunistic overlays". Based on such an approach, interesting overlays can be obtained, shaped following giv...

  19. Opportunistic Collaborative Beamforming with One-Bit Feedback

    CERN Document Server

    Pun, Man-On; Poor, H Vincent

    2008-01-01

    An energy-efficient opportunistic collaborative beamformer with one-bit feedback is proposed for ad hoc sensor networks over Rayleigh fading channels. In contrast to conventional collaborative beamforming schemes in which each source node uses channel state information to correct its local carrier offset and channel phase, the proposed beamforming scheme opportunistically selects a subset of source nodes whose received signals combine in a quasi-coherent manner at the intended receiver. No local phase-precompensation is performed by the nodes in the opportunistic collaborative beamformer. As a result, each node requires only one-bit of feedback from the destination in order to determine if it should or shouldn't participate in the collaborative beamformer. Theoretical analysis shows that the received signal power obtained with the proposed beamforming scheme scales linearly with the number of available source nodes. Since the the optimal node selection rule requires an exhaustive search over all possible subs...

  20. MOSDEN: A Scalable Mobile Collaborative Platform for Opportunistic Sensing Applications

    Directory of Open Access Journals (Sweden)

    Prem Prakash Jayaraman

    2014-05-01

    Full Text Available Mobile smartphones along with embedded sensors have become an efficient enabler for various mobile applications including opportunistic sensing. The hi-tech advances in smartphones are opening up a world of possibilities. This paper proposes a mobile collaborative platform called MOSDEN that enables and supports opportunistic sensing at run time. MOSDEN captures and shares sensor data acrossmultiple apps, smartphones and users. MOSDEN supports the emerging trend of separating sensors from application-specific processing, storing and sharing. MOSDEN promotes reuse and re-purposing of sensor data hence reducing the efforts in developing novel opportunistic sensing applications. MOSDEN has been implemented on Android-based smartphones and tablets. Experimental evaluations validate the scalability and energy efficiency of MOSDEN and its suitability towards real world applications. The results of evaluation and lessons learned are presented and discussed in this paper.

  1. Pathogenic agents in freshwater resources

    Science.gov (United States)

    Geldreich, Edwin E.

    1996-02-01

    Numerous pathogenic agents have been found in freshwaters used as sources for water supplies, recreational bathing and irrigation. These agents include bacterial pathogens, enteric viruses, several protozoans and parasitic worms more common to tropical waters. Although infected humans are a major source of pathogens, farm animals (cattle, sheep, pigs), animal pets (dogs, cats) and wildlife serve as significant reservoirs and should not be ignored. The range of infected individuals within a given warm-blooded animal group (humans included) may range from 1 to 25%. Survival times for pathogens in the water environment may range from a few days to as much as a year (Ascaris, Taenia eggs), with infective dose levels varying from one viable cell for several primary pathogenic agents to many thousands of cells for a given opportunistic pathogen.As pathogen detection in water is complex and not readily incorporated into routine monitoring, a surrogate is necessary. In general, indicators of faecal contamination provide a positive correlation with intestinal pathogen occurrences only when appropriate sample volumes are examined by sensitive methodology.Pathways by which pathogens reach susceptible water users include ingestion of contaminated water, body contact with polluted recreational waters and consumption of salad crops irrigated by polluted freshwaters. Major contributors to the spread of various water-borne pathogens are sewage, polluted surface waters and stormwater runoff. All of these contributions are intensified during periods of major floods. Several water-borne case histories are cited as examples of breakdowns in public health protection related to water supply, recreational waters and the consumption of contaminated salad crops. In the long term, water resource management must focus on pollution prevention from point sources of waste discharges and the spread of pathogens in watershed stormwater runoff.

  2. Adhesiveness of opportunistic Staphylococcus aureus to materials used in dental office: In vitro study.

    Science.gov (United States)

    Merghni, Abderrahmen; Bekir, Karima; Kadmi, Yassine; Dallel, Ines; Janel, Sébastien; Bovio, Simone; Barois, Nicolas; Lafont, Frank; Mastouri, Maha

    2017-02-01

    Staphylococcus aureus (S. aureus) is one of several opportunistic microbial pathogens associated with many healthcare problems. In the present study, S. aureus was assessed for its biofilm-forming ability on materials routinely used in dental offices, including stainless steel (SS), polyethylene (PE), and polyvinyl chloride (PVC). Materials that were tested were characterized for roughness (Ra) and surface free energy (SFE). The adhesion forces exerted by S. aureus to each substratum were investigated using atomic force microscopy (AFM), and biofilm formation was quantitatively assessed by crystal violet staining assay. AFM measurements demonstrated that the strongest adhesion forces (20 nN) were exerted on the PE surfaces (P materials when compared to the other materials (P materials used in dental practices is of crucial importance for preventing biofilm formation on dental materials to be used for patients' dental care. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Iterative group splitting algorithm for opportunistic scheduling systems

    KAUST Repository

    Nam, Haewoon

    2014-05-01

    An efficient feedback algorithm for opportunistic scheduling systems based on iterative group splitting is proposed in this paper. Similar to the opportunistic splitting algorithm, the proposed algorithm adjusts (or lowers) the feedback threshold during a guard period if no user sends a feedback. However, when a feedback collision occurs at any point of time, the proposed algorithm no longer updates the threshold but narrows down the user search space by dividing the users into multiple groups iteratively, whereas the opportunistic splitting algorithm keeps adjusting the threshold until a single user is found. Since the threshold is only updated when no user sends a feedback, it is shown that the proposed algorithm significantly alleviates the signaling overhead for the threshold distribution to the users by the scheduler. More importantly, the proposed algorithm requires a less number of mini-slots than the opportunistic splitting algorithm to make a user selection with a given level of scheduling outage probability or provides a higher ergodic capacity given a certain number of mini-slots. © 2013 IEEE.

  4. AIRBORNE HYPERSPECTRAL IDENTIFICATION OF INVASIVE AND OPPORTUNISTIC WETLANDS PLANT SPECIES

    Science.gov (United States)

    Coastal wetlands are among the most fragmented and disturbed ecosystems and the Great Lakes are no exception. One possible result is the observed increase in the presence and dominance of invasive and other opportunistic plant species, such as the common reed (Phragmites australi...

  5. a survey of opportunistic infections in hiv seropositive patients ...

    African Journals Online (AJOL)

    DR. AMINU

    The screening for the HIV/AID was done using the Genic II HIV-1/HIV – 2 Test and the screening for opportunistic infections was done using thin and thick blood films, direct wet mount, ... infections include bacterial diseases such as those.

  6. Analysis of full-duplex relay networks with opportunistic scheduling

    Directory of Open Access Journals (Sweden)

    Lei Shao

    2015-05-01

    Full Text Available This Letter addresses a two-hop decode-and-forward relay system with full-duplex relaying and opportunistic scheduling. Exact expressions for outage probability, average capacity and symbol error rate are presented in an independent identically distributed Rayleigh fading environment. Numerical and simulated results show the validity of the analytical results.

  7. Opportunistic Beacon Networks: Information Dissemination via Wireless Network Identifiers

    NARCIS (Netherlands)

    Türkes, Okan; Scholten, Johan; Havinga, Paul J.M.

    2016-01-01

    This paper presents OBN, a universal opportunistic ad hoc networking model particularly intended for smart mobile devices. It enables fast and lightweight data dissemination in wireless community networks through the utilization of universally-available wireless network identifiers. As a ubiquitous

  8. Opportunistic Beacon Networks: Information Dissemination via Wireless Network Identifiers

    NARCIS (Netherlands)

    Türkes, Okan; Scholten, Hans; Havinga, Paul J.M.

    2016-01-01

    This paper presents OBN, a universal opportunistic ad hoc networking model particularly intended for smart mobile devices. It enables fast and lightweight data dissemination in wireless community networks through the utilization of universally-available wireless network identifiers. As a ubiquitous

  9. Passive Multistatic Detection of Maritime Targets using Opportunistic Radars

    Science.gov (United States)

    2014-03-01

    optimal configuration using MATLAB simulation. The simulation results are obtained using actual system parameters extracted from civil marine radar ...Bistatic Radar . Norwood, MA: Artech House, Technology Service Corporation, p. 1, 1995. [2] D. C. Jenn, Radar and Laser Cross Section Engineering...MULTISTATIC DETECTION OF MARITIME TARGETS USING OPPORTUNISTIC RADARS by Chong Sze Sing March 2014 Thesis Advisor: Herschel H. Loomis Co-Advisor

  10. Culture enriched molecular profiling of the cystic fibrosis airway microbiome.

    Science.gov (United States)

    Sibley, Christopher D; Grinwis, Margot E; Field, Tyler R; Eshaghurshan, Christina S; Faria, Monica M; Dowd, Scot E; Parkins, Michael D; Rabin, Harvey R; Surette, Michael G

    2011-01-01

    The microbiome of the respiratory tract, including the nasopharyngeal and oropharyngeal microbiota, is a dynamic community of microorganisms that is highly diverse. The cystic fibrosis (CF) airway microbiome refers to the polymicrobial communities present in the lower airways of CF patients. It is comprised of chronic opportunistic pathogens (such as Pseudomonas aeruginosa) and a variety of organisms derived mostly from the normal microbiota of the upper respiratory tract. The complexity of these communities has been inferred primarily from culture independent molecular profiling. As with most microbial communities it is generally assumed that most of the organisms present are not readily cultured. Our culture collection generated using more extensive cultivation approaches, reveals a more complex microbial community than that obtained by conventional CF culture methods. To directly evaluate the cultivability of the airway microbiome, we examined six samples in depth using culture-enriched molecular profiling which combines culture-based methods with the molecular profiling methods of terminal restriction fragment length polymorphisms and 16S rRNA gene sequencing. We demonstrate that combining culture-dependent and culture-independent approaches enhances the sensitivity of either approach alone. Our techniques were able to cultivate 43 of the 48 families detected by deep sequencing; the five families recovered solely by culture-independent approaches were all present at very low abundance (<0.002% total reads). 46% of the molecular signatures detected by culture from the six patients were only identified in an anaerobic environment, suggesting that a large proportion of the cultured airway community is composed of obligate anaerobes. Most significantly, using 20 growth conditions per specimen, half of which included anaerobic cultivation and extended incubation times we demonstrate that the majority of bacteria present can be cultured.

  11. Culture enriched molecular profiling of the cystic fibrosis airway microbiome.

    Directory of Open Access Journals (Sweden)

    Christopher D Sibley

    Full Text Available The microbiome of the respiratory tract, including the nasopharyngeal and oropharyngeal microbiota, is a dynamic community of microorganisms that is highly diverse. The cystic fibrosis (CF airway microbiome refers to the polymicrobial communities present in the lower airways of CF patients. It is comprised of chronic opportunistic pathogens (such as Pseudomonas aeruginosa and a variety of organisms derived mostly from the normal microbiota of the upper respiratory tract. The complexity of these communities has been inferred primarily from culture independent molecular profiling. As with most microbial communities it is generally assumed that most of the organisms present are not readily cultured. Our culture collection generated using more extensive cultivation approaches, reveals a more complex microbial community than that obtained by conventional CF culture methods. To directly evaluate the cultivability of the airway microbiome, we examined six samples in depth using culture-enriched molecular profiling which combines culture-based methods with the molecular profiling methods of terminal restriction fragment length polymorphisms and 16S rRNA gene sequencing. We demonstrate that combining culture-dependent and culture-independent approaches enhances the sensitivity of either approach alone. Our techniques were able to cultivate 43 of the 48 families detected by deep sequencing; the five families recovered solely by culture-independent approaches were all present at very low abundance (<0.002% total reads. 46% of the molecular signatures detected by culture from the six patients were only identified in an anaerobic environment, suggesting that a large proportion of the cultured airway community is composed of obligate anaerobes. Most significantly, using 20 growth conditions per specimen, half of which included anaerobic cultivation and extended incubation times we demonstrate that the majority of bacteria present can be cultured.

  12. Pathogens spectrum of deep human mycosis

    Directory of Open Access Journals (Sweden)

    A. B. Kulko

    2012-01-01

    Full Text Available The article describes characteristics of two different etiology groups of deep human mycosis — extremely dangerous endemic deep mycoses (histoplasmosis, coccidioidomycosis, blastomycosis, paracoccidioidomycosis, penicilliosis due to Penicillium marneffei and opportunistic deep mycosis (candidiasis, cryptococcosis, aspergillosis, mucormycosis. Information on fungal pathogens and antifungal agents is presented. The own results of cultural studies obtained during pneumomycosis diagnosis in patients with tuberculosis are shown.

  13. Pathogens spectrum of deep human mycosis

    Directory of Open Access Journals (Sweden)

    A. B. Kulko

    2014-07-01

    Full Text Available The article describes characteristics of two different etiology groups of deep human mycosis — extremely dangerous endemic deep mycoses (histoplasmosis, coccidioidomycosis, blastomycosis, paracoccidioidomycosis, penicilliosis due to Penicillium marneffei and opportunistic deep mycosis (candidiasis, cryptococcosis, aspergillosis, mucormycosis. Information on fungal pathogens and antifungal agents is presented. The own results of cultural studies obtained during pneumomycosis diagnosis in patients with tuberculosis are shown.

  14. Who needs the assumption of opportunistic behavior? Transaction cost economics does not!

    DEFF Research Database (Denmark)

    Koch, Carsten Allan

    2000-01-01

    The assumption of opportunistic behavior, familiar from transaction cost economics, has been and remains highly controversial. But opportunistic behavior, albeit undoubtedly an extremely important form of motivation, is not a necessary condition for the contractual problems studied by transaction...

  15. Opportunistic feeding on various organic food sources by the cold-water coral Lophelia pertusa

    Directory of Open Access Journals (Sweden)

    C. E. Mueller

    2013-07-01

    Full Text Available The ability of the cold-water coral Lophelia pertusa to exploit different food sources was investigated under standardized conditions in a flume. All tested food sources, dissolved organic matter (DOM, added as dissolved free amino acids, bacteria, algae, and zooplankton (Artemia were deliberately enriched in 13C and 15N. The incorporation of 13C and 15N was traced into bulk tissue, fatty acids, hydrolysable amino acids, and the skeleton (13C only of L. pertusa. Incorporation rates of carbon (ranging from 0.8–2.4 µg C g–1 DW d–1 and nitrogen (0.2–0.8 µg N g–1 DW d–1 into coral tissue did not differ significantly among food sources indicating an opportunistic feeding strategy. Although total food assimilation was comparable among sources, subsequent food processing was dependent on the type of food source ingested and recovery of assimilated C in tissue compounds ranged from 17% (algae to 35% (Artemia. De novo synthesis of individual fatty acids by L. pertusa occurred in all treatments as indicated by the 13C enrichment of individual phospholipid-derived fatty acids (PLFAs in the coral that were absent in the added food sources. This indicates that the coral might be less dependent on its diet as a source of specific fatty acids than expected, with direct consequences for the interpretation of in situ observations on coral nutrition based on lipid profiles.

  16. Opportunistic feeding on various organic food sources by the cold-water coral Lophelia pertusa

    Science.gov (United States)

    Mueller, C. E.; Larsson, A. I.; Veuger, B.; Middelburg, J. J.; van Oevelen, D.

    2014-01-01

    The ability of the cold-water coral Lophelia pertusa to exploit different food sources was investigated under standardized conditions in a flume. The tested food sources, dissolved organic matter (DOM, added as dissolved free amino acids), bacteria, algae, and zooplankton (Artemia) were deliberately enriched in 13C and 15N. The incorporation of 13C and 15N was traced into bulk tissue, fatty acids, hydrolysable amino acids, and the skeleton (13C only) of L. pertusa. Incorporation rates of carbon (ranging from 0.8-2.4 μg C g-1 DW d-1) and nitrogen (0.2-0.8 μg N g-1 DW d-1) into coral tissue did not differ significantly among food sources indicating an opportunistic feeding strategy. Although total food assimilation was comparable among sources, subsequent food processing was dependent on the type of food source ingested and recovery of assimilated C in tissue compounds ranged from 17% (algae) to 35% (Artemia). De novo synthesis of individual fatty acids by L. pertusa occurred in all treatments as indicated by the 13C enrichment of individual phospholipid-derived fatty acids (PLFAs) in the coral that were absent in the added food sources. This indicates that the coral might be less dependent on its diet as a source of specific fatty acids than expected, with direct consequences for the interpretation of in situ observations on coral nutrition based on lipid profiles.

  17. Compositions and methods for pathogen transport

    Energy Technology Data Exchange (ETDEWEB)

    El-Etr, Sahar; Farquar, George R.

    2016-01-26

    This disclosure provides a method for transporting a pathogen under ambient conditions, by culturing the pathogen with an amoeba under conditions that favor the incorporation of the pathogen into a trophozoite, starving the amoeba until it encysts, then culturing under conditions that favor conversion of the amoeba back to a trophozoite. In one aspect, the conditions that favor incorporation of the pathogen into the cyst of the amoeba comprises contacting the pathogen with the amoeba in an iron rich environment. Virus and/or bacteria are pathogens that can be transported by the disclosed method. Amoeba that are useful in the disclosed methods include, without limitation Acanthamoeba castellanii, Hartmannella vermiformis and Naegleria gruberi. The disclosed methods have utility in: transporting pathogens from military field hospitals and clinics to the laboratory; transporting pathogens from global satellite laboratories to clinical laboratories; long term storage of pathogens; enriching contaminated patient samples for pathogens of interest; biosurveillance and detection efforts.

  18. Opportunistic filamentous mycoses: aspergillosis, mucormycosis, phaeohyphomycosis and hyalohyphomycosis.

    Science.gov (United States)

    Perusquía-Ortiz, Ana María; Vázquez-González, Denisse; Bonifaz, Alexandro

    2012-09-01

    Opportunistic filamentous mycoses are widely distributed all over the world. They are rarely observed in Europe but are common in developing countries. The most common are the aspergilloses (due to Aspergillus spp.) mostly in neutropenia and immunosuppression; the mucormycoses characterized by rapid progression in patients with diabetic ketoacidosis; the phaeohyphomycoses due to pigmented fungi causing either a mild superficial or a very serious deep disease and the hyalohyphomycoses due to hyaline filamentous fungi (Fusarium spp., Pseudallescheria spp., Scopulariopsis spp.). Cutaneous manifestations are usually secondary to dissemination from pulmonary or visceral disease; primary cases are less frequent and due to direct inoculation into the skin. We review epidemiological, clinical, diagnostic, and therapeutic data on the four most important opportunistic filamentous mycoses: aspergillosis, mucormycosis, phaeohyphomycosis and hyalohyphomycosis.

  19. Opportunistic spectrum access in cognitive radio based on channel switching

    KAUST Repository

    Gaaloul, Fakhreddine

    2012-01-01

    This paper investigates the performance of a cognitive radio transceiver that can monitor multiple channels and opportunistically use any one of them should it be available. In our work, we propose and compare two different opportunistic channel access schemes. The first scheme applies when the secondary user (SU) has access to only one channel. The second scheme applies when the SU has access to multiple channels but can at a given time monitor and access only one channel. Two switching strategies, namely the switch and examine and the switch and stay strategies, are proposed. For these proposed access schemes, we investigate their performance by deriving the analytical expression of the novel metric of the average access duration and the average waiting time and based on these two metrics a time average SU throughput formula is proposed to predict the performance of the secondary cognitive system. © 2012 ICST.

  20. Accurate Performance Analysis of Opportunistic Decode-and-Forward Relaying

    CERN Document Server

    Tourki, Kamel; Alouni, Mohamed-Slim

    2011-01-01

    In this paper, we investigate an opportunistic relaying scheme where the selected relay assists the source-destination (direct) communication. In our study, we consider a regenerative opportunistic relaying scheme in which the direct path can be considered unusable, and takes into account the effect of the possible erroneously detected and transmitted data at the best relay. We first derive statistics based on exact probability density function (PDF) of each hop. Then, the PDFs are used to determine accurate closed form expressions for end-to-end bit-error rate (BER) of binary phase-shift keying (BPSK) modulation. Furthermore, we evaluate the asymptotical performance analysis and the diversity order is deduced. Finally, we validate our analysis by showing that performance simulation results coincide with our analytical results over different network architectures.

  1. Error-rate performance analysis of opportunistic regenerative relaying

    KAUST Repository

    Tourki, Kamel

    2011-09-01

    In this paper, we investigate an opportunistic relaying scheme where the selected relay assists the source-destination (direct) communication. In our study, we consider a regenerative opportunistic relaying scheme in which the direct path can be considered unusable, and takes into account the effect of the possible erroneously detected and transmitted data at the best relay. We first derive the exact statistics of each hop, in terms of probability density function (PDF). Then, the PDFs are used to determine accurate closed form expressions for end-to-end bit-error rate (BER) of binary phase-shift keying (BPSK) modulation where the detector may use maximum ration combining (MRC) or selection combining (SC). Finally, we validate our analysis by showing that performance simulation results coincide with our analytical results over linear network (LN) architecture and considering Rayleigh fading channels. © 2011 IEEE.

  2. Opportunistic Channel Scheduling for Ad Hoc Networks with Queue Stability

    Science.gov (United States)

    Dong, Lei; Wang, Yongchao

    2015-03-01

    In this paper, a distributed opportunistic channel access strategy in ad hoc network is proposed. We consider the multiple sources contend for the transmission opportunity, the winner source decides to transmit or restart contention based on the current channel condition. Owing to real data assumption at all links, the decision still needs to consider the stability of the queues. We formulate the channel opportunistic scheduling as a constrained optimization problem which maximizes the system average throughput with the constraints that the queues of all links are stable. The proposed optimization model is solved by Lyapunov stability in queueing theory. The successive channel access problem is decoupled into single optimal stopping problem at every frame and solved with Lyapunov algorithm. The threshold for every frame is different, and it is derived based on the instantaneous queue information. Finally, computer simulations are conducted to demonstrate the validity of the proposed strategy.

  3. New results on performance analysis of opportunistic regenerative relaying

    KAUST Repository

    Tourki, Kamel

    2013-12-01

    In this paper, we investigate an opportunistic relaying scheme where the selected relay assists the source-destination (direct) communication. In our study, we consider a regenerative opportunistic relaying scheme in which the direct path may be unusable, and takes into account the effect of the possible erroneously detected and transmitted data at the selected relay. We first derive the signal-to-noise (SNR) statistics for each hop, which are used to determine accurate closed form expressions for end-to-end bit-error rate (BER) of binary phase-shift keying (BPSK) modulation and end-to-end outage probability for a transmission rate R over Rayleigh fading channels. Furthermore, we evaluate the asymptotical performance and deduce the diversity order. Finally, we validate our analysis by showing that performance simulation results coincide with our analytical results over linear network architecture. © 2013 Elsevier B.V.

  4. Optimality of Myopic Sensing in Multi-Channel Opportunistic Access

    CERN Document Server

    Ahmad, Sahand H A; Javidi, Tara; Zhao, Qing; Krishnamachari, Bhaskar

    2008-01-01

    We consider opportunistic communications over multiple channels where the state ("good" or "bad") of each channel evolves as independent and identically distributed Markov processes. A user, with limited sensing and access capability, chooses one channel to sense and subsequently access (based on the sensed channel state) in each time slot. A reward is obtained when the user senses and accesses a "good" channel. The objective is to design the optimal channel selection policy that maximizes the expected reward accrued over time. This problem can be generally cast as a Partially Observable Markov Decision Process (POMDP) or a restless multi-armed bandit process, to which optimal solutions are often intractable. We show in this paper that the myopic policy, with a simple and robust structure, achieves optimality under certain conditions. This result finds applications in opportunistic communications in fading environment, cognitive radio networks for spectrum overlay, and resource-constrained jamming and anti-ja...

  5. Accurate performance analysis of opportunistic decode-and-forward relaying

    KAUST Repository

    Tourki, Kamel

    2011-07-01

    In this paper, we investigate an opportunistic relaying scheme where the selected relay assists the source-destination (direct) communication. In our study, we consider a regenerative opportunistic relaying scheme in which the direct path may be considered unusable, and the destination may use a selection combining technique. We first derive the exact statistics of each hop, in terms of probability density function (PDF). Then, the PDFs are used to determine accurate closed form expressions for end-to-end outage probability for a transmission rate R. Furthermore, we evaluate the asymptotical performance analysis and the diversity order is deduced. Finally, we validate our analysis by showing that performance simulation results coincide with our analytical results over different network architectures. © 2011 IEEE.

  6. A Game Theoretic Approach to Distributed Opportunistic Scheduling

    CERN Document Server

    Banchs, Albert; Serrano, Pablo; Widmer, Joerg

    2011-01-01

    Distributed Opportunistic Scheduling (DOS) is inherently harder than conventional opportunistic scheduling due to the absence of a central entity that has knowledge of all the channel states. With DOS, stations contend for the channel using random access; after a successful contention, they measure the channel conditions and only transmit in case of a good channel, while giving up the transmission opportunity when the channel conditions are poor. The distributed nature of DOS systems makes them vulnerable to selfish users: by deviating from the protocol and using more transmission opportunities, a selfish user can gain a greater share of the wireless resources at the expense of the well-behaved users. In this paper, we address the selfishness problem in DOS from a game theoretic standpoint. We propose an algorithm that satisfies the following properties: (i) when all stations implement the algorithm, the wireless network is driven to the optimal point of operation, and (ii) one or more selfish stations cannot...

  7. Node-Dependence-Based Dynamic Incentive Algorithm in Opportunistic Networks

    Directory of Open Access Journals (Sweden)

    Ruiyun Yu

    2014-01-01

    Full Text Available Opportunistic networks lack end-to-end paths between source nodes and destination nodes, so the communications are mainly carried out by the “store-carry-forward” strategy. Selfish behaviors of rejecting packet relay requests will severely worsen the network performance. Incentive is an efficient way to reduce selfish behaviors and hence improves the reliability and robustness of the networks. In this paper, we propose the node-dependence-based dynamic gaming incentive (NDI algorithm, which exploits the dynamic repeated gaming to motivate nodes relaying packets for other nodes. The NDI algorithm presents a mechanism of tolerating selfish behaviors of nodes. Reward and punishment methods are also designed based on the node dependence degree. Simulation results show that the NDI algorithm is effective in increasing the delivery ratio and decreasing average latency when there are a lot of selfish nodes in the opportunistic networks.

  8. Benefits and performance of ATLAS approaches to utilizing opportunistic resources

    CERN Document Server

    Filip\\v{c}i\\v{c}, Andrej; The ATLAS collaboration

    2016-01-01

    ATLAS has been extensively exploring possibilities of using computing resources extending beyond conventional grid sites in the WLCG fabric to deliver as many computing cycles as possible and thereby enhance the significance of the Monte-Carlo samples to deliver better physics results. The difficulties of using such opportunistic resources come from architectural differences such as unavailability of grid services, the absence of network connectivity on worker nodes or inability to use standard authorization protocols. Nevertheless, ATLAS has been extremely successful in running production payloads on a variety of sites, thanks largely to the job execution workflow design in which the job assignment, input data provisioning and execution steps are clearly separated and can be offloaded to custom services. To transparently include the opportunistic sites in the ATLAS central production system, several models with supporting services have been developed to mimic the functionality of a full WLCG site. Some are e...

  9. Congestion aware forwarding in delay tolerant and social opportunistic networks

    OpenAIRE

    Radenkovic, Milena; Grundy, Andrew

    2011-01-01

    We propose an approach for opportunistic forwarding that supports optimization of multipoint high volume data flow transfer while maintaining high buffer availability and low delays. This paper explores a number of social, buffer and delay heuristics to offload the traffic from congested parts of the network and spread it over less congested parts of the network in order to keep low delays, high success ratios and high availability of nodes. We conduct an extensive set of experiments for asse...

  10. Opportunistic Third-Party Backhaul for Cellular Wireless Networks

    OpenAIRE

    Ford, Russell; Kim, Changkyu; Rangan, Sundeep

    2013-01-01

    With high capacity air interfaces and large numbers of small cells, backhaul -- the wired connectivity to base stations -- is increasingly becoming the cost driver in cellular wireless networks. One reason for the high cost of backhaul is that capacity is often purchased on leased lines with guaranteed rates provisioned to peak loads. In this paper, we present an alternate \\emph{opportunistic backhaul} model where third parties provide base stations and backhaul connections and lease out exce...

  11. Pathogens and host immunity in the ancient human oral cavity

    DEFF Research Database (Denmark)

    Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak

    2014-01-01

    cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction...... of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental...... calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past....

  12. Location-Aided Reliable Routing for Opportunistic Networks

    Institute of Scientific and Technical Information of China (English)

    Yong Yang; Zhi Ren; Jibi Li

    2012-01-01

    In our study, we investigate the problem of location-based routing in opportunistic networks. Due to the uncertainty of end-to-end paths between sources and destinations, the classical location-based ad hoc routing protocols cannot adapt to the environment of opportunistic networks, which leads to the decrease of the delivery rate of data. To address it, we propose in this paper a novel location-aided routing protocol which is suitable for opportunistic networks. In our protocol, a node can send location information on demand by using prediction mechanism, and when sending a data packet, the node chooses multiple neighbors which are closer to the destination as next hops. If the candidate neighbors do not exist, the node carries the data till it meets a proper neighbor or the destination. Theoretical analysis and simulation results show that our proposed protocol outperforms DREAM (Distance Routing Effect Protocol Mobility) and one of its improved versions, BFDREAM (Boundary Forwarding DREAM), in terms of the delivery rate and overhead.

  13. Leapfrog: Optimal opportunistic Routing in Probabilistically Contacted Delay Tolerant Networks

    Institute of Scientific and Technical Information of China (English)

    Ming-Jun Xiao; Liu-Sheng Huang; Qun-Feng Dong; An Liu; Zhen-Guo Yang

    2009-01-01

    Delay tolerant networks (DTNs)experience frequent and long lasting network disconnection due to various reasons such as mobility.power management.and scheduling.One primary concern in DTNs is to route messages to keep the end-to-end delivery delay as low as possible.In this paper,we study the single-copy message routing problem and propose an optimal opportunistic routing strategy--Leapfrog Routing--for probabilistically contacted DTNs where nodes encounter or contact in some fixed probabilities.We deduce the iterative computation formulate of minimum expected opportunistic delivery delay from each node to the destination and discover that under the optimal opportunistic routing strategy,messages would be delivered from high-delay node to low-delay node in the leapfrog manner.Rigorous theoretical analysis shows that such a routing strategy is exactly the optimal among all possible ones.Moreover,we apply the idea of Reverse Dijkstra algorithm to design an algorithm.When a destination iS given,this algorithm can determine for each node the routing selection function under the Leapfrog Routing strategy.The computation overhead of this algorithm is only O(n~2) where n is the number of nodes in the network.In addition,through extensive simulations based on real DTN traces,we demonstrate that our algorithm can significantly outperform the previous ones.

  14. Cooperative Opportunistic Pressure Based Routing for Underwater Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Nadeem Javaid

    2017-03-01

    Full Text Available In this paper, three opportunistic pressure based routing techniques for underwater wireless sensor networks (UWSNs are proposed. The first one is the cooperative opportunistic pressure based routing protocol (Co-Hydrocast, second technique is the improved Hydrocast (improved-Hydrocast, and third one is the cooperative improved Hydrocast (Co-improved Hydrocast. In order to minimize lengthy routing paths between the source and the destination and to avoid void holes at the sparse networks, sensor nodes are deployed at different strategic locations. The deployment of sensor nodes at strategic locations assure the maximum monitoring of the network field. To conserve the energy consumption and minimize the number of hops, greedy algorithm is used to transmit data packets from the source to the destination. Moreover, the opportunistic routing is also exploited to avoid void regions by making backward transmissions to find reliable path towards the destination in the network. The relay cooperation mechanism is used for reliable data packet delivery, when signal to noise ratio (SNR of the received signal is not within the predefined threshold then the maximal ratio combining (MRC is used as a diversity technique to improve the SNR of the received signals at the destination. Extensive simulations validate that our schemes perform better in terms of packet delivery ratio and energy consumption than the existing technique; Hydrocast.

  15. Cooperative Opportunistic Pressure Based Routing for Underwater Wireless Sensor Networks.

    Science.gov (United States)

    Javaid, Nadeem; Muhammad; Sher, Arshad; Abdul, Wadood; Niaz, Iftikhar Azim; Almogren, Ahmad; Alamri, Atif

    2017-03-19

    In this paper, three opportunistic pressure based routing techniques for underwater wireless sensor networks (UWSNs) are proposed. The first one is the cooperative opportunistic pressure based routing protocol (Co-Hydrocast), second technique is the improved Hydrocast (improved-Hydrocast), and third one is the cooperative improved Hydrocast (Co-improved Hydrocast). In order to minimize lengthy routing paths between the source and the destination and to avoid void holes at the sparse networks, sensor nodes are deployed at different strategic locations. The deployment of sensor nodes at strategic locations assure the maximum monitoring of the network field. To conserve the energy consumption and minimize the number of hops, greedy algorithm is used to transmit data packets from the source to the destination. Moreover, the opportunistic routing is also exploited to avoid void regions by making backward transmissions to find reliable path towards the destination in the network. The relay cooperation mechanism is used for reliable data packet delivery, when signal to noise ratio (SNR) of the received signal is not within the predefined threshold then the maximal ratio combining (MRC) is used as a diversity technique to improve the SNR of the received signals at the destination. Extensive simulations validate that our schemes perform better in terms of packet delivery ratio and energy consumption than the existing technique; Hydrocast.

  16. Fungal Opportunistic Pneumonias in HIV/AIDS Patients: An Indian Tertiary Care Experience

    Science.gov (United States)

    Mehra, Bhanu; Dhakad, Megh Singh; Goyal, Ritu; Bhalla, Preena; Dewan, Richa

    2017-01-01

    . Of these, sputa of 21 patients yielded single fungal isolates, while mixed fungal isolates were reported in four patients. Pneumocystis carinii was the predominant fungal pathogen isolated in our study and was reported in 14 (19.7%) patients. Pulmonary aspergillosis was reported in 7 (9.9%) patients, with Aspergillus flavus (4), Aspergillus fumigatus (2) and Aspergillus niger (1) being the commonly recovered Aspergillus species. Candida pneumonia was documented in 6 (8.5%) patients and the Candida species isolated included Candida albicans in four, Candida glabrata in one and Candida tropicalis in one of these six patients respectively. Pulmonary cryptococcosis was diagnosed in 2 (2.8%) patients; a coexisting cryptococcal meningitis was documented in one of them. Furthermore, antibodies against Histoplasma species were detected in 21 (29.6%) cases suggesting its possible aetiological role. Conclusion Fungal opportunistic pneumonias are common in HIV reactive patients in Indian setting and warrant a prompt and accurate diagnostic evaluation in the form of a combination of microbiological, serological and histopathological techniques, for an effective prophylactic and therapeutic management.

  17. Involvement of the opportunistic pathogen Aspergillus tubingensis in osteomyelitis of the maxillary bone : a case report

    NARCIS (Netherlands)

    Bathoorn, Erik; Salazar, Natalia Escobar; Sepehrkhouy, Shahrzad; Meijer, Martin; de Cock, Hans; Haas, Pieter-Jan

    2013-01-01

    Background: Aspergillus tubingensis is a black Aspergillus belonging to the Aspergillus section Nigri, which includes species that morphologically resemble Aspergillus niger. Recent developments in species determination have resulted in clinical isolates presumed to be Aspergillus niger being reclas

  18. Involvement of the opportunistic pathogen Aspergillus tubingensis in osteomyelitis of the maxillary bone: A case report

    NARCIS (Netherlands)

    Bathoorn, E.; Escobar Salazar, N.; Sepehrkhouy, S.; Meijer, M.; de Cock, H.; Haas, P.J.

    2013-01-01

    Background: Aspergillus tubingensis is a black Aspergillus belonging to the Aspergillus section Nigri, which includes species that morphologically resemble Aspergillus niger. Recent developments in species determination have resulted in clinical isolates presumed to be Aspergillus niger being

  19. The opportunistic pathogen Enterococcus faecalis resists phagosome acidification and autophagy to promote intracellular survival in macrophages.

    Science.gov (United States)

    Zou, Jun; Shankar, Nathan

    2016-06-01

    While many strains of Enterococcus faecalis have been reported to be capable of surviving within macrophages for extended periods, the exact mechanisms involved are largely unknown. In this study, we found that after phagocytosis by macrophages, enterococci-containing vacuoles resist acidification, and E. faecalis is resistant to low pH. Ultrastructural examination of the enterococci-containing vacuole by transmission electron microscopy revealed a single membrane envelope, with no evidence of the classical double-membraned autophagosomes. Western blot analysis further confirmed that E. faecalis could trigger inhibition of the production of LC3-II during infection. By employing cells transfected with RFP-LC3 plasmid and infected with GFP-labelled E. faecalis, we also observed that E. faecalis was not delivered into autophagosomes during macrophage infection. While these observations indicated no role for autophagy in elimination of intracellular E. faecalis, enhanced production of reactive oxygen species and nitric oxide were keys to this process. Stimulation of autophagy suppressed the intracellular survival of E. faecalis in macrophages in vitro and decreased the burden of E. faecalis in vivo. In summary, the results from this study offer new insights into the interaction of E. faecalis with host cells and may provide a new approach to treatment of enterococcal infections.

  20. Discovery of an opportunistic starfish pathogen, Orchitophrya stellarum, in captive blue crabs, Callinectes sapidus.

    Science.gov (United States)

    Small, H J; Miller, T L; Coffey, A H; Delaney, K L; Schott, E; Shields, J D

    2013-10-01

    Histophagous scuticociliate infections were discovered in blue crabs, Callinectes sapidus, held in research facilities at the Virginia Institute of Marine Science. Ciliates were observed infecting every tissue examined including the gills, heart, muscle, hepatopancreas, and epidermis. Hemolymph smears and histological tissue sections indicated a morphological similarity to Mesanophrys chesapeakensis, the only recorded histophagous ciliate infecting blue crabs. However, subsequent analysis of the ribosomal ITS region (ITS1-5.8S-ITS2) of the ciliate indicated the parasite was Orchitophrya stellarum, a parasitic ciliate previously reported infecting sea stars from Europe, Australia, and North America. A simple Polymerase Chain Reaction (PCR-RFLP) assay was developed to detect and differentiate between O. stellarum and M. chesapeakensis. Its application confirmed the presence of O. stellarum infecting blue crabs held in an additional research facility in Maryland. For growth studies, cultures of O. stellarum grew optimally on 10% blue crab serum in crustacean saline held at 10-20°C. A field survey of blue crabs collected during the winters of 2011-2012 and sea stars (Asterias forbesi) during the winter of 2010 from the Chesapeake Bay and eastern shore of Virginia did not identify additional infected individuals.

  1. Head and neck intensity modulated radiation therapy leads to an increase of opportunistic oral pathogens

    NARCIS (Netherlands)

    Schuurhuis, Jennifer M.; Stokman, Monique A.; Witjes, Max J. H.; Langendijk, Johannes A.; van Winkelhoff, Arie J.; Vissink, Arjan; Spijkervet, Frederik K. L.

    2016-01-01

    Objectives: The introduction of intensity modulated radiation therapy (IMRT) has led to new possibilities in the treatment of head and neck cancer (HNC). Limited information is available on how this more advanced radiation technique affects the oral microflora. In a prospective study we assessed the

  2. Monoclonal Antibodies to Hyphal Exoantigens Derived from the Opportunistic Pathogen Aspergillus terreus

    Science.gov (United States)

    Aspergillus terreus has been difficult to identify in cases of aspergillosis, and clinical identification has been restricted to the broad identification of aspergillosis lesions in affected organs or the detection of fungal carbohydrates. As a result, there is a clinical need to...

  3. Thiol compounds from a free-living pathogenic opportunistic amoeba, Acanthamoeba polyphaga.

    Science.gov (United States)

    Ondarza, Raúl N; Iturbe, Angélica; Hernández, Eva; Hurtado, Gerardo

    2002-12-01

    New bimane-reacting compounds from perchloric acid extracts have been detected by HPLC from Acanthamoeba polyphaga. The main compounds detected are cysteine, glutathione and other novel thiol compounds. All of these compounds must be thiols, since they disappear or decrease substantially when treated by N -ethylmaleimide prior to acetonitrile/bimane derivatization. Cysteine and glutathione increase in quantity when dithiothreitol reduction is applied to the fresh extract. This means that they are likely to be present in their oxidized and reduced form and indicates the possible presence of a corresponding thiol/disulphide enzymic system. There are other compounds that have a different behaviour, since although they can react with bimane, they do not disappear if treated previously by N -ethylmaleimide. This shows that they are not thiols but can react with bimane. The main thiol compounds found to be present, in both the parasite and the host lymphocyte cells, were cysteine and glutathione. We were unable to detect ovothiol A in Acanthamoeba but instead we found another thiol compound that could be structurally related to trypanothione. The new thiol compounds unique to this parasite and not present in lymphocytes will permit the study of disulphide-reducing enzymes as potential drug targets.

  4. An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice

    National Research Council Canada - National Science Library

    Fei, Na; Zhao, Liping

    2013-01-01

    Lipopolysaccharide endotoxin is the only known bacterial product which, when subcutaneously infused into mice in its purified form, can induce obesity and insulin resistance via an inflammation-mediated pathway...

  5. Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola

    Science.gov (United States)

    Looi, Hong Keat; Toh, Yue Fen; Yew, Su Mei; Na, Shiang Ling; Tan, Yung-Chie; Chong, Pei-Sin; Khoo, Jia-Shiun; Yee, Wai-Yan; Ng, Kee Peng

    2017-01-01

    Corynespora cassiicola is a common plant pathogen that causes leaf spot disease in a broad range of crop, and it heavily affect rubber trees in Malaysia (Hsueh, 2011; Nghia et al., 2008). The isolation of UM 591 from a patient’s contact lens indicates the pathogenic potential of this dematiaceous fungus in human. However, the underlying factors that contribute to the opportunistic cross-infection have not been fully studied. We employed genome sequencing and gene homology annotations in attempt to identify these factors in UM 591 using data obtained from publicly available bioinformatics databases. The assembly size of UM 591 genome is 41.8 Mbp, and a total of 13,531 (≥99 bp) genes have been predicted. UM 591 is enriched with genes that encode for glycoside hydrolases, carbohydrate esterases, auxiliary activity enzymes and cell wall degrading enzymes. Virulent genes comprising of CAZymes, peptidases, and hypervirulence-associated cutinases were found to be present in the fungal genome. Comparative analysis result shows that UM 591 possesses higher number of carbohydrate esterases family 10 (CE10) CAZymes compared to other species of fungi in this study, and these enzymes hydrolyses wide range of carbohydrate and non-carbohydrate substrates. Putative melanin, siderophore, ent-kaurene, and lycopene biosynthesis gene clusters are predicted, and these gene clusters denote that UM 591 are capable of protecting itself from the UV and chemical stresses, allowing it to adapt to different environment. Putative sterigmatocystin, HC-toxin, cercosporin, and gliotoxin biosynthesis gene cluster are predicted. This finding have highlighted the necrotrophic and invasive nature of UM 591. PMID:28149676

  6. Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola

    Directory of Open Access Journals (Sweden)

    Hong Keat Looi

    2017-01-01

    Full Text Available Corynespora cassiicola is a common plant pathogen that causes leaf spot disease in a broad range of crop, and it heavily affect rubber trees in Malaysia (Hsueh, 2011; Nghia et al., 2008. The isolation of UM 591 from a patient’s contact lens indicates the pathogenic potential of this dematiaceous fungus in human. However, the underlying factors that contribute to the opportunistic cross-infection have not been fully studied. We employed genome sequencing and gene homology annotations in attempt to identify these factors in UM 591 using data obtained from publicly available bioinformatics databases. The assembly size of UM 591 genome is 41.8 Mbp, and a total of 13,531 (≥99 bp genes have been predicted. UM 591 is enriched with genes that encode for glycoside hydrolases, carbohydrate esterases, auxiliary activity enzymes and cell wall degrading enzymes. Virulent genes comprising of CAZymes, peptidases, and hypervirulence-associated cutinases were found to be present in the fungal genome. Comparative analysis result shows that UM 591 possesses higher number of carbohydrate esterases family 10 (CE10 CAZymes compared to other species of fungi in this study, and these enzymes hydrolyses wide range of carbohydrate and non-carbohydrate substrates. Putative melanin, siderophore, ent-kaurene, and lycopene biosynthesis gene clusters are predicted, and these gene clusters denote that UM 591 are capable of protecting itself from the UV and chemical stresses, allowing it to adapt to different environment. Putative sterigmatocystin, HC-toxin, cercosporin, and gliotoxin biosynthesis gene cluster are predicted. This finding have highlighted the necrotrophic and invasive nature of UM 591.

  7. [Microbiological results of bronchoalveolar lavage that was performed for opportunistic pulmonary infections].

    Science.gov (United States)

    Gülcü, Aylin; Sevinç, Can; Esen, Nuran; Kilinç, Oğuz; Uçan, Eyüp Sabri; Itil, Oya; Cimrin, Arif Hikmet; Kömüs, Nuray; Sener, Gülper; Akkoçlu, Atila; Gülay, Zeynep; Yücesoy, Mine

    2006-01-01

    Between 2001-2002; in 62 cases, 33 (53%) male, 29 (47%) female, mean age 51.4 +/- 18.1 years) bronchoalveolar lavage (BAL) was performed for diagnosis of opportunistic pulmonary infection and specimens were evaluated for results of microbiological examinations. There was hematological malignancy in 18 (29%) and solid organ malignancy in 13 (21%) cases. Thirty-one (50%) cases were immunocompromised for reasons other than malignancy. By endoscopic evaluation endobronchial lesion was seen in 2 (3%) cases, indirect tumor signs were seen in 2 (3%) cases and signs of infection were seen in 11 (18%) cases. Forty-even (76%) cases were endoscopically normal. Acid-fast bacilli (AFB) direct examination was positive in 3 (5%) cases. In 4 (6%) cases mycobacterial culture was positive, Mycobacterium tuberculosis-polymerase chain reaction (PCR) was also positive in these four cases. Examination of gram-stained smears for bacteria was associated with infection in 14 (23%) cases. Bacteriologic cultures were positive for single potential pathogen in 10 (16%) cases, and for mixed pathogens in 7 (11%) cases for a total number of 17 (27%). Fungal cultures were positive in 3 (5%) cases all of which had hematological malignancy. As a result in 24 (39%) cases microbiological agent of infection is determined: in four mycobacteria, in 17 bacteria other than mycobacteria and in three fungi.

  8. Gingival Epithelial Cell Transcriptional Responses to Commensal and Opportunistic Oral Microbial Species▿ †

    Science.gov (United States)

    Hasegawa, Yoshiaki; Mans, Jeffrey J.; Mao, Song; Lopez, M. Cecilia; Baker, Henry V.; Handfield, Martin; Lamont, Richard J.

    2007-01-01

    Transcriptional profiling and ontology tools were utilized to define the biological pathways of gingival epithelial cells modulated by coculture with the oral commensal Streptococcus gordonii and the opportunistic commensal Fusobacterium nucleatum. Overall, F. nucleatum and S. gordonii perturbed the gingival epithelial cell transcriptome much less significantly than the oral pathogens Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans perturbed the transcriptome, indicating that there was a greater degree of host adaptation by the commensal species (M. Handfield, J. J. Mans, G. Zheng, M. C. Lopez, S. Mao, A. Progulske-Fox, G. Narasimhan, H. V. Baker, and R. J. Lamont, Cell. Microbiol. 7:811-823, 2005). The biological pathways significantly impacted by F. nucleatum and S. gordonii included the mitogen-activated protein kinase (MAPK) and Toll-like receptor signaling pathways. Differential regulation of GADD45 and DUSP4, key components of the MAPK pathway, was confirmed at the protein level by Western blotting. Modulation of the MAPK pathway is likely to affect host cell proliferation and differentiation. In addition, both the MAPK and Toll-like receptor pathways ultimately converge on cytokine gene expression. An enzyme-linked immunosorbent assay of secreted interleukin-6 (IL-6) and IL-8 demonstrated that F. nucleatum induced production of these cytokines, whereas S. gordonii inhibited secretion from the epithelial cells. Stimulation of secretion of proinflammatory cytokines from epithelial cells may reflect the invasive phenotype of F. nucleatum and contribute to the greater pathogenic potential of F. nucleatum than of S. gordonii. PMID:17307939

  9. Gingival epithelial cell transcriptional responses to commensal and opportunistic oral microbial species.

    Science.gov (United States)

    Hasegawa, Yoshiaki; Mans, Jeffrey J; Mao, Song; Lopez, M Cecilia; Baker, Henry V; Handfield, Martin; Lamont, Richard J

    2007-05-01

    Transcriptional profiling and ontology tools were utilized to define the biological pathways of gingival epithelial cells modulated by coculture with the oral commensal Streptococcus gordonii and the opportunistic commensal Fusobacterium nucleatum. Overall, F. nucleatum and S. gordonii perturbed the gingival epithelial cell transcriptome much less significantly than the oral pathogens Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans perturbed the transcriptome, indicating that there was a greater degree of host adaptation by the commensal species (M. Handfield, J. J. Mans, G. Zheng, M. C. Lopez, S. Mao, A. Progulske-Fox, G. Narasimhan, H. V. Baker, and R. J. Lamont, Cell. Microbiol. 7:811-823, 2005). The biological pathways significantly impacted by F. nucleatum and S. gordonii included the mitogen-activated protein kinase (MAPK) and Toll-like receptor signaling pathways. Differential regulation of GADD45 and DUSP4, key components of the MAPK pathway, was confirmed at the protein level by Western blotting. Modulation of the MAPK pathway is likely to affect host cell proliferation and differentiation. In addition, both the MAPK and Toll-like receptor pathways ultimately converge on cytokine gene expression. An enzyme-linked immunosorbent assay of secreted interleukin-6 (IL-6) and IL-8 demonstrated that F. nucleatum induced production of these cytokines, whereas S. gordonii inhibited secretion from the epithelial cells. Stimulation of secretion of proinflammatory cytokines from epithelial cells may reflect the invasive phenotype of F. nucleatum and contribute to the greater pathogenic potential of F. nucleatum than of S. gordonii.

  10. CLINICAL SPECTRUM OF OPPORTUNISTIC INFECTIONS IN HIV POSITIVE PATIENTS

    Directory of Open Access Journals (Sweden)

    Usmani

    2015-03-01

    Full Text Available The human immunodeficiency virus (HIV infection leading to Acquired Immunodeficiency Syndrome (AIDS causes progressive decline in immunological response in people living with HIV/AIDS, making them susceptible to a variety opportunistic infections (OIs which are responsible for morbidity and mortality. Therefore early diagnosis and management of opportunistic infections reduce the mortality and morbidity in HIV positive patients. CONTEXT : AIMS : To study the demographic variables; spectrum of opportunist ic infections and its correlation with CD4 count in HIV patients. SETTING AND DESIGN : The study was conducted on 200 HIV patients either admitted to Sanjay Gandhi Memorial Hospital or attending ART Center, Sh y am Shah Medical College, Rewa (M.P from Januar y 2013 to October 2014. METHODS AND MATERIAL : A detailed history was recorded with emphasis on personal history, high risk behavior, history of migration, mode of transmission of infection and complete thorough clinical examination was done. Data analysis was done by calculating P value using Chi Square test. RESULTS : Out of 200 HIV patients, most of them (88% belonged to the age group 20 - 49 years, 66% were males and 34% were females. 45% were illiterates, 62% were from low socioeconomic class. Majority of patients were married (79% and 72.2% had seropositive spouse. Unprotected sexual route was the most common (85% mode of transmission; among which heterosexual route was the only mode of transmission. 59.4% of males contracted infection through unprotect ed sex with either commercial sex workers (44.8% or multiple sex partners (14.6%. 61% of patients had history of emigration. Tuberculosis was the most common opportunistic infection (51%, followed by oral candidiasis 30% and chronic diarrhea (9%.Pulmon ary Tuberculosis was the most common form of Tuberculosis (64.7%, followed by tubercular lymphadenopathy (15.7%. CONCLUSION : HIV/AIDS has no vaccine or cure, so prevention is the only

  11. Pathogenic free-living amoebae: epidemiology and clinical review.

    Science.gov (United States)

    Trabelsi, H; Dendana, F; Sellami, A; Sellami, H; Cheikhrouhou, F; Neji, S; Makni, F; Ayadi, A

    2012-12-01

    Free-living amoebae are widely distributed in soil and water. Small number of them was implicated in human disease: Acanthamoeba spp., Naegleria fowleri, Balamuthia mandrillaris and Sappinia diploidea. Some of the infections were opportunistic, occurring mainly in immunocompromised hosts (Acanthamoeba and Balamuthia encephalitis) while others are non opportunistic (Acanthamoeba keratitis, Naegleria meningoencephalitis and some cases of Balamuthia encephalitis). Although, the number of infections caused by these amoebae is low, their diagnosis was still difficult to confirm and so there was a higher mortality, particularly, associated with encephalitis. In this review, we present some information about epidemiology, ecology and the types of diseases caused by these pathogens amoebae.

  12. Cost-effectiveness of opportunistic salpingectomy for ovarian cancer prevention.

    Science.gov (United States)

    Dilley, Sarah E; Havrilesky, Laura J; Bakkum-Gamez, Jamie; Cohn, David E; Michael Straughn, J; Caughey, Aaron B; Rodriguez, Maria I

    2017-08-01

    Data suggesting a link between the fallopian tube and ovarian cancer have led to an increase in rates of salpingectomy at the time of pelvic surgery, a practice known as opportunistic salpingectomy (OS). However, the potential benefits, risks and costs for this new practice are not well established. Our objective was to assess the cost-effectiveness of opportunistic salpingectomy at the time of laparoscopic permanent contraception or hysterectomy for benign indications. We created two models to compare the cost-effectiveness of salpingectomy versus usual care. The hypothetical study population is 50,000 women aged 45 undergoing laparoscopic hysterectomy with ovarian preservation for benign indications, and 300,000 women aged 35 undergoing laparoscopic permanent contraception. SEER data were used for probabilities of ovarian cancer cases and deaths. The ovarian cancer risk reduction, complication rates, utilities and associated costs were obtained from published literature. Sensitivity analyses and Monte Carlo simulation were performed, and incremental cost-effectiveness ratios (ICERs) were calculated to determine the cost per quality adjusted life year (QALY) gained. In the laparoscopic hysterectomy cohort, OS is cost saving and would yield $23.9 million in health care dollars saved. In the laparoscopic permanent contraception cohort, OS is cost-effective with an ICER of $31,432/QALY compared to tubal ligation, and remains cost-effective as long as it reduces ovarian cancer risk by 54%. Monte Carlo simulation demonstrated cost-effectiveness with hysterectomy and permanent contraception in 62.3% and 55% of trials, respectively. Opportunistic salpingectomy for low-risk women undergoing pelvic surgery may be a cost-effective strategy for decreasing ovarian cancer risk at time of hysterectomy or permanent contraception. In our model, salpingectomy was cost-effective with both procedures, but the advantage greater at time of hysterectomy. Copyright © 2017. Published by

  13. AnonySense: Opportunistic and Privacy-Preserving Context Collection

    DEFF Research Database (Denmark)

    Triandopoulos, Nikolaos; Kapadia, Apu; Cornelius, Cory

    2008-01-01

    Opportunistic sensing allows applications to "task" mobile devices to measure context in a target region. For example, one could leverage sensor-equipped vehicles to measure traffic or pollution levels on a particular street, or users' mobile phones to locate (Bluetooth-enabled) objects....... We propose AnonySense, a general-purpose architecture for leveraging users' mobile devices for measuring context, while maintaining the privacy of the users.AnonySense features multiple layers of privacy protection-a framework for nodes to receive tasks anonymously, a novel blurring mechanism based...... tessellation and clustering algorithm against real mobility traces....

  14. Survey on Opportunistic Networks in Delay Tolerant Mobile Sensor Networks

    Directory of Open Access Journals (Sweden)

    Koushik.C.P

    2016-02-01

    Full Text Available Delay Tolerant Network is an emerging research field in Mobile sensor network. It use forwarding technique to transmit the message from source to destination, there is no complete path between sources to destination. Due to mobility of nodes there is frequent change in node paten and difficult to find the path, there is chance that message keep on forwarded inside the network. In this paper we made detail survey on Opportunistic Routing Protocol in mobile network, and in that node getting the message form neighbor node and moving away from Sink. We proposed a technique in Gradient based Routing Protocol to solve node moving away from sink with message.

  15. CORMEN: Coding-Aware Opportunistic Routing in Wireless Mess Network

    CERN Document Server

    Islam, Jeherul

    2010-01-01

    These Network Coding improves the network operation beyond the traditional routing or store-and-forward, by mixing of data stream within a network. Network coding techniques explicitly minimizes the total no of transmission in wireless network. The Coding-aware routing maximizes the coding opportunity by finding the coding possible path for every packet in the network. Here we propose CORMEN: a new coding-aware routing mechanism based on opportunistic routing. In CORMEN, every node independently can take the decision whether to code packets or not and forwarding of packets is based on the coding opportunity available.

  16. Heterogeneous Epidemic Model for Assessing Data Dissemination in Opportunistic Networks

    DEFF Research Database (Denmark)

    Rozanova, Liudmila; Alekseev, Vadim; Temerev, Alexander

    2014-01-01

    In this paper we apply a susceptible-infected-susceptible (SIS) epidemic model to analyse data dissemination in opportunistic networks with heterogeneous setting of transmission parameters, as established in author's previous paper? . We obtained the estimation of the final epidemic size assuming...... that amount of data transferred between network nodes possesses a Pareto distribution, implying scale-free properties. In this context, more heterogeneity in susceptibility means the less severe epidemic progression, and, on the contrary, more heterogeneity in infectivity leads to more severe epidemics...

  17. Opportunistic Ports and Spaces of Exchange in Late Roman Cyprus

    Science.gov (United States)

    Leidwanger, Justin

    2013-12-01

    Ports served not only as interfaces between land and sea, but as central gathering spaces for economic and cultural exchange. Drawing on case studies from the eastern Mediterranean island of Cyprus, this paper situates opportunistic ports lacking built facilities within a broader socioeconomic context of diverse maritime communications, expanding rural settlement, and increased agricultural productivity during late antiquity. Though simple, these sites served as active agents in the development of new maritime networks as well as local markets throughout their hinterlands, adding flexibility and dynamism to the economic ties between city, countryside, and the wider late Roman world.

  18. Hybrid-ARQ in Multihop Networks with Opportunistic Relay Selection

    CERN Document Server

    Lo, Caleb K; Vishwanath, Sriram

    2007-01-01

    This paper develops a contention-based opportunistic feedback technique towards relay selection in a dense wireless network. This technique enables the forwarding of additional parity information from the selected relay to the destination. For a given network, the effects of varying key parameters such as the feedback probability are presented and discussed. A primary advantage of the proposed technique is that relay selection can be performed in a distributed way. Simulation results find its performance to closely match that of centralized schemes that utilize GPS information, unlike the proposed method. The proposed relay selection method is also found to achieve throughput gains over a point-to-point transmission strategy.

  19. Probability of recovering pathogenic Escherichia coli from foods.

    OpenAIRE

    Hill, W E; Ferreira, J. L; Payne, W L; Jones, V.M.

    1985-01-01

    The probability of recovering pathogenic Escherichia coli from food by the Bacteriological Analytical Manual method was determined by the effects of several factors: the number of strains per food, the ability of pathogenic strains to survive enrichment, and the frequency of plasmid loss during enrichment. Biochemical patterns indicated the presence of about six E. coli strains per food sample. About half of the strains isolated from humans did not survive enrichment. Among those which grew, ...

  20. Co-occurrence of free-living protozoa and foodborne pathogens on dishcloths: implications for food safety.

    Science.gov (United States)

    Chavatte, N; Baré, J; Lambrecht, E; Van Damme, I; Vaerewijck, M; Sabbe, K; Houf, K

    2014-11-17

    In the present study, the occurrence of free-living protozoa (FLP) and foodborne bacterial pathogens on dishcloths was investigated. Dishcloths form a potentially important source of cross-contamination with FLP and foodborne pathogens in food-related environments. First various protocols for recovering and quantifying FLP from dishcloths were assessed. The stomacher technique is recommended to recover flagellates and amoebae from dishcloths. Ciliates, however, were more efficiently recovered using centrifugation. For enumeration of free-living protozoa on dishcloths, the Most Probable Number method is a convenient method. Enrichment was used to assess FLP diversity on dishcloths (n=38). FLP were found on 89% of the examined dishcloths; 100% of these tested positive for amoebae, 71% for flagellates and 47% for ciliates. Diversity was dominated by amoebae: vahlkampfiids, vannellids, Acanthamoeba spp., Hyperamoeba sp. and Vermamoeba vermiformis were most common. The ciliate genus Colpoda was especially abundant on dishcloths while heterotrophic nanoflagellates mainly belonged to the genus Bodo, the glissomonads and cercomonads. The total number of FLP in used dishcloths ranged from 10 to 10(4) MPN/cm(2). Flagellates were the most abundant group, and ciliates the least abundant. Detergent use was identified as a prime determinant of FLP concentrations on used dishcloths. Bacterial load on dishcloths was high, with a mean total of aerobic bacteria of 7.47 log 10 cfu/cm(2). Escherichia coli was detected in 68% (26/38) of the used dishcloths, with concentrations up to 4 log 10 cfu/cm(2). Foodborne pathogens including Staphylococcus aureus (19/38), Arcobacter butzleri (5/38) and Salmonella enterica subsp. enterica ser. Halle (1/38) were also present. This study showed for the first time that FLP, including some opportunistic pathogens, are a common and diverse group on dishcloths. Moreover, important foodborne pathogens are also regularly recovered. This simultaneous

  1. Opportunistic spectrum sharing in software defined wireless network

    Institute of Scientific and Technical Information of China (English)

    Mao Yang; Yong Li; Depeng Jin; Li Su; Lieguang Zeng

    2014-01-01

    Over the past few decades, the world has witnessed a rapid growth in mobile and wireless networks (MWNs) which significantly change human life. However, proliferating mobile de-mands lead to several intractable chal enges that MWN has to face. Software-defined network is expected as a promising way for future network and has captured growing attention. Network virtualization is an essential feature in software-defined wireless network (SDWN), and it brings two new entities, physical networks and virtual networks. Accordingly, efficiently assigning spectrum resource to virtual networks is one of the fundamental problems in SDWN. Directly orienting towards the spectrum resource al o-cation problem, firstly, the fluctuation features of virtual network requirements in SDWN are researched, and the opportunistic spectrum sharing method is introduced to SDWN. Then, the prob-lem is proved as NP-hardness. After that, a dynamic programming and graph theory based spectrum sharing algorithm is proposed. Simulations demonstrate that the opportunistic spectrum sharing method conspicuously improves the system performance up to around 20%–30%in SDWN, and the proposed algorithm achieves more efficient performance.

  2. Opportunistic Cognitive Relaying: A Win-Win Spectrum Sharing Scheme

    Directory of Open Access Journals (Sweden)

    Luo Haiyan

    2010-01-01

    Full Text Available A cost-effective spectrum sharing architecture is proposed to enable the legacy noncognitive secondary system to coexist with the primary system. Specifically, we suggest to install a few intermediate nodes, namely, the cognitive relays, to conduct the spectrum sensing and coordinate the spectrum access. To achieve the goal of win-win between primary and secondary systems, the cognitive relay may act as a cooperator for both of them, and an Opportunistic Cognitive Relaying (OCR scheme is specially devised. In this scheme, the cognitive relay opportunistically switches among three different working modes, that is, Relay for Primary Link (RPL, Relay for Secondary Link (RSL, or Relay for Neither of the Links (RNL, respectively, based on the channel-dependent observation of both systems. In addition, the transmit power for cognitive relay and secondary transmitter in each mode are optimally determined by maximizing the transmission rate of secondary system while keeping or even reducing the outage probability of primary system. Simulation results validate the efficiency of the proposed spectrum sharing scheme.

  3. Cyclostationary Beacon for Assisting Spectrum Sensing in Opportunistic Spectrum Access

    Directory of Open Access Journals (Sweden)

    Thomas Kaiser

    2011-03-01

    Full Text Available Cognitive radio is a promising solution to the problem of spectrum scarcity by means of allowing secondary radio networks access the spectrum opportunistically. One of the most important issues in cognitive radio is how to detect existing over-the-air signals reliably. Not a few literatures have reported that signals could be detected via their inherent or embedded properties. However, this approach may not be reliable and flexible enough for all kinds of signals with different modulation types. In this paper, we propose a type of multitone beacon signal carrying cyclostationary signatures, which is able to enhance the reliability and efficiency of signal detection at low cost of spectrum overhead. This beacon not only can indicate the presence or absence of user signal but also can reveal some other information helpful to opportunistic spectrum access through the information bits carried on its cyclostationary signatures. It could be applied to device/network identification, indication of spectrum allocation and spectrum rendezvous, both for primary and secondary users. Based on our previous work reported in [1], the generation and detection algorithm of the beacon signal are extended with improved spectral efficiency. Performance is discussed with both computer simulation and testbed validation.

  4. A Novel Cooperative Opportunistic Routing Scheme for Underwater Sensor Networks.

    Science.gov (United States)

    Ghoreyshi, Seyed Mohammad; Shahrabi, Alireza; Boutaleb, Tuleen

    2016-01-01

    Increasing attention has recently been devoted to underwater sensor networks (UWSNs) because of their capabilities in the ocean monitoring and resource discovery. UWSNs are faced with different challenges, the most notable of which is perhaps how to efficiently deliver packets taking into account all of the constraints of the available acoustic communication channel. The opportunistic routing provides a reliable solution with the aid of intermediate nodes' collaboration to relay a packet toward the destination. In this paper, we propose a new routing protocol, called opportunistic void avoidance routing (OVAR), to address the void problem and also the energy-reliability trade-off in the forwarding set selection. OVAR takes advantage of distributed beaconing, constructs the adjacency graph at each hop and selects a forwarding set that holds the best trade-off between reliability and energy efficiency. The unique features of OVAR in selecting the candidate nodes in the vicinity of each other leads to the resolution of the hidden node problem. OVAR is also able to select the forwarding set in any direction from the sender, which increases its flexibility to bypass any kind of void area with the minimum deviation from the optimal path. The results of our extensive simulation study show that OVAR outperforms other protocols in terms of the packet delivery ratio, energy consumption, end-to-end delay, hop count and traversed distance.

  5. Psychological predictors of opportunistic snacking in the absence of hunger.

    Science.gov (United States)

    Fay, Stephanie H; White, Melanie J; Finlayson, Graham; King, Neil A

    2015-08-01

    Increased frequency of eating in the absence of homeostatic need, notably through snacking, is an important contributor to overconsumption and may be facilitated by increased availability of palatable food in the obesogenic environment. Opportunistic initiation of snacking is likely to be subject to individual differences, although these are infrequently studied in laboratory-based research paradigms. This study examined psychological factors associated with opportunistic initiation of snacking, and predictors of intake in the absence of homeostatic need. Fifty adults (mean age 34.5years, mean BMI 23.9kg/m(2), 56% female) participated in a snack taste test in which they ate a chocolate snack to satiation, after which they were offered an unanticipated opportunity to initiate a second eating episode. Trait and behavioural measures of self control, sensitivity to reward, dietary restraint and disinhibited eating were taken. Results showed that, contrary to expectations, those who initiated snacking were better at inhibitory control compared with those who did not initiate. However, amongst participants who initiated snacking, intake (kcal) was predicted by higher food reward sensitivity, impulsivity and BMI. These findings suggest that snacking initiation in the absence of hunger is an important contributor to overconsumption. Consideration of the individual differences promoting initiation of eating may aid in reducing elevated eating frequency in at-risk individuals.

  6. HIV Protease Inhibitors: Effect on the Opportunistic Protozoan Parasites.

    Science.gov (United States)

    Alfonso, Yenisey; Monzote, Lianet

    2011-01-01

    The impact of highly active antiretroviral therapy (HAART) in the natural history of AIDS disease has been allowed to prolong the survival of people with HIV infection, particularly whose with increased HIV viral load. Additionally, the antiretroviral therapy could exert a certain degree of protection against parasitic diseases. A number of studies have been evidenced a decrease in the incidence of opportunistic parasitic infections in the era of HAART. Although these changes have been attributed to the restoration of cell-mediated immunity, induced by either non-nucleoside reverse transcriptase inhibitors or HIV protease inhibitors, in combination with at least two nucleoside reverse transcriptase inhibitors included in HAART, there are evidence that the control of these parasitic infections in HIV-positive persons under HAART, is also induced by the inhibition of the proteases of the parasites. This review focuses on the principal available data related with therapeutic HIV-protease inhibitors and their in vitro and in vivo effects on the opportunistic protozoan parasites.

  7. Cooperative HARQ with Poisson Interference and Opportunistic Routing

    KAUST Repository

    Kaveh, Mostafa

    2014-01-06

    This presentation considers reliable transmission of data from a source to a destination, aided cooperatively by wireless relays selected opportunistically and utilizing hybrid forward error correction/detection, and automatic repeat request (Hybrid ARQ, or HARQ). Specifically, we present a performance analysis of the cooperative HARQ protocol in a wireless adhoc multihop network employing spatial ALOHA. We model the nodes in such a network by a homogeneous 2-D Poisson point process. We study the tradeoff between the per-hop rate, spatial density and range of transmissions inherent in the network by optimizing the transport capacity with respect to the network design parameters, HARQ coding rate and medium access probability. We obtain an approximate analytic expression for the expected progress of opportunistic routing and optimize the capacity approximation by convex optimization. By way of numerical results, we show that the network design parameters obtained by optimizing the analytic approximation of transport capacity closely follows that of Monte Carlo based exact transport capacity optimization. As a result of the analysis, we argue that the optimal HARQ coding rate and medium access probability are independent of the node density in the network.

  8. "A PCR-RFLP Method to Identification of the Important Opportunistic Fungi: Candida Species, Cryptococcus neoformans, Aspergillus famigatus and Fusarium solani"

    Directory of Open Access Journals (Sweden)

    SH Mirhendi

    2001-09-01

    Full Text Available Deep-seated fungal infection present with non specific symptoms and involove a large number of different organisms. DNA-based technology offers for eariler detection of fungal pathogens and then earlier initiation of antifungal therapy. In this study universal primers common to almost all fungi were used to amplification of internal transcribe spacer 1 and 2 region. Subsequent restriction enzyme analysis of PCR products, using HpaII allows us to identify the most medically opportunistic important fungi: Candida albicans, C. glabrata, C. tropicalis, C. kruzei, C. guilliermondi, Cryptococcus neoformans, Aspergillus fumigatus and Fusarium solani, according to sizely different bands in polyacrilamid gel electrophoresis. It seems that this panel of PCR-RFLP could be a rapid and useful molecular approach in diagnostic studies of invasive opportunistic fungal infections.

  9. A molecular biological protocol to distinguish potentially human pathogenic Stenotrophomonas maltophilia from plant-associated Stenotrophomonas rhizophila

    NARCIS (Netherlands)

    Ribbeck-Busch, K.; Roder, A.; Hasse, D.; De Boer, W.; Martinez, J.L.; Hagemann, M.; Berg, G.

    2005-01-01

    In recent years, the importance of the Gram-negative bacterium Stenotrophomonas as an opportunistic pathogen as well as in biotechnology has increased. The aim of the present study was to develop new methods for distinguishing between strains closely related to the potentially human pathogenic Steno

  10. Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa

    Science.gov (United States)

    Pseudomonas aeruginosa pathogenicity island 1 (PAPI-1) is one of the largest genomic islands of this important opportunistic human pathogen. Previous studies have shown that PAPI-1 encodes several putative virulence factors, a major regulator of biofilm formation, and antibiotic-resistance traits, a...

  11. Intracellular pathogens within alveolar macrophages in a patient with HIV infection: diagnostic challenge

    Directory of Open Access Journals (Sweden)

    Takashi Shinha

    2015-03-01

    Full Text Available In HIV-infected individuals, macrophages, the key defense effector cells, manifest defective activity in their interactions with a wide variety of opportunistic pathogens, including fungi and protozoa. Understanding the morphological characteristics of intracellular opportunistic pathogens in addition to their pathogenesis is of critical importance to provide optimal therapy, thereby decreasing morbidity and mortality in HIV-infected patients. We herein present a case of disseminated histoplasmosis confused with disseminated visceral leishmaniasis in an HIV-infected individual from Guyana who developed intracellular organisms within alveolar macrophages

  12. The Opportunistic House for Tehran: A Design Prototype

    Directory of Open Access Journals (Sweden)

    Sara Khorshidifard

    2015-12-01

    Full Text Available This article is an advocacy research for Tehran, promoting an implication of architectural design as a tool for citizen empowerment and positive environmental change. In the article, I am offering a fresh look at Tehran’s housing problems by speculating an “opportunistic house” typology as a residential style that would serve much more than just shelter. I am making a case for a new house prototype that applies socially-equitable solutions in design. My study finds applications and significance beyond plain housing design and, mainly, onto the design of ad hoc urban public realm spaces. This is in accord with my overarching mission of supporting new way of thinking about, and ultimately offering, welcoming, safe, and energized places for Tehran’s citizens. These will additionally have important implications for inhospitable public spaces worldwide. This research is grounded in my prior, multidisciplinary doctoral studies. The article itself is an initial step in my ongoing research design, of helping to build and revitalize a wide range of urban communities by nurturing their relationship to their built and natural environments. The article is a discussion around the following questions. How can housing design inventions empower citizens? In what manner can design offer progressive living place options whose services go beyond shelter needs? Particularly, in what ways can domestic spaces be designed to also embody other-than-living capacities, for example, for new kinds of public spaces? And eventually, what could a prototype of the opportunistic house look like in the context of a city like Tehran? The article is structured to first present a brief survey of how Tehran house forms and functions have developed historically, with more emphasis on their current state. It will then offer examples of opportunistic uses of domestic spaces in Tehran. This notion is communicated through narrative analysis and photographic vignettes from a few

  13. Fusarium ramigenum, a novel human opportunist in a patient with common variable immunodeficiency and cellular immune defects: case report.

    Science.gov (United States)

    Moroti, Ruxandra V; Gheorghita, Valeriu; Al-Hatmi, Abdullah M S; de Hoog, G Sybren; Meis, Jacques F; Netea, Mihai G

    2016-02-15

    Fusarium species are ubiquitous environmental fungi that occasionally provoke serious invasive infections in immunocompromised hosts. Among Fusarium species, Fusarium ramigenum, belonging to the Fusarium fujikuroi species complex, has thus far never been found to cause human infections. Here we describe the first case of invasive fusariosis caused by Fusarium ramigenum in a human and also identify immunological deficiencies that most likely contributed to invasiveness. A 32-year-old Caucasian male with a seemingly insignificant medical history of mild respiratory illness during the preceding two years, developed invasive pulmonary fusariosis. Detailed immunological assessment revealed the presence of common variable immunodeficiency, complicated by a severe impairment of the capacity of T-cells to produce both gamma-interferon and interleukin-17. In-depth microbiological assessment identified the novel human opportunistic pathogen Fusarium ramigenum as cause of the infection. This report demonstrated that an opportunistic invasive fungal infection may indicate an underlying cellular immune impairment of the host. The unexpected invasive infection with Fusarium ramigenum in this case unmasked a complex combined humoral and cellular immunological deficiency.

  14. Urine Stasis Predisposes to Urinary Tract Infection by an Opportunistic Uropathogen in the Megabladder (Mgb) Mouse.

    Science.gov (United States)

    Becknell, Brian; Mohamed, Ahmad Z; Li, Birong; Wilhide, Michael E; Ingraham, Susan E

    2015-01-01

    Urinary stasis is a risk factor for recurrent urinary tract infection (UTI). Homozygous mutant Megabladder (Mgb-/-) mice exhibit incomplete bladder emptying as a consequence of congenital detrusor aplasia. We hypothesize that this predisposes Mgb-/- mice to spontaneous and experimental UTI. Mgb-/-, Mgb+/-, and wild-type female mice underwent serial ultrasound and urine cultures at 4, 6, and 8 weeks to detect spontaneous UTI. Urine bacterial isolates were analyzed by Gram stain and speciated. Bladder stones were analyzed by x-ray diffractometry. Bladders and kidneys were subject to histologic analysis. The pathogenicity of coagulase-negative Staphylococcus (CONS) isolated from Mgb-/- urine was tested by transurethral administration to culture-negative Mgb-/- or wild-type animals. The contribution of urinary stasis to CONS susceptibility was evaluated by cutaneous vesicostomy in Mgb-/- mice. Mgb-/- mice develop spontaneous bacteriuria (42%) and struvite bladder stones (31%) by 8 weeks, findings absent in Mgb+/- and wild-type controls. CONS was cultured as a solitary isolate from Mgb-/- bladder stones. Bladders and kidneys from mice with struvite stones exhibit mucosal injury, inflammation, and fibrosis. These pathologic features of cystitis and pyelonephritis are replicated by transurethral inoculation of CONS in culture-negative Mgb-/- females, whereas wild-type animals are less susceptible to CONS colonization and organ injury. Cutaneous vesicostomy prior to CONS inoculation significantly reduces the quantity of CONS recovered from Mgb-/- urine, bladders, and kidneys. CONS is an opportunistic uropathogen in the setting of urinary stasis, leading to enhanced UTI incidence and severity in Mgb-/- mice.

  15. Shared Physiological Traits of Exophiala Species in Cold-Blooded Vertebrates, as Opportunistic Black Yeasts.

    Science.gov (United States)

    do Nascimento, Mariana Machado Fidelis; de Hoog, G Sybren; Gomes, Renata Rodrigues; Furuie, Jason Lee; Gelinski, Jane Mary Lafayette; Najafzadeh, Mohammad Javad; Boeger, Walter Antonio Pereira; Vicente, Vania Aparecida

    2016-06-01

    Several species of the genus Exophiala are found as opportunistic pathogens on humans, while others cause infections in cold-blooded waterborne vertebrates. Opportunism of these fungi thus is likely to be multifactorial. Ecological traits [thermotolerance and pH tolerance, laccase activity, assimilation of mineral oil, and decolorization of Remazol Brilliant Blue R (RBBR)] were studied in a set of 40 strains of mesophilic Exophiala species focused on the salmonis-clade mainly containing waterborne species. Thermophilic species and waterborne species outside the salmonis-clade were included for comparison. Strains were able to tolerate a wide range of pHs, although optimal growth was observed between pH 4.0 and 5.5. All strains tested were laccase positive. Strains were able to grow in the presence of the compounds (mineral oil and RBBR) with some differences in assimilation patterns between strains tested and also were capable of degrading the main chromophore of RBBR. The study revealed that distantly related mesophilic species behave similarly, and no particular trend in evolutionary adaptation was observed.

  16. Avian trichomonosis in spotted owls (Strix occidentalis): Indication of opportunistic spillover from prey.

    Science.gov (United States)

    Rogers, Krysta H; Girard, Yvette A; Woods, Leslie; Johnson, Christine K

    2016-12-01

    Avian trichomonosis, caused by the flagellated protozoan parasite Trichomonas gallinae, has variable pathogenicity among bird species ranging from asymptomatic infections to severe disease periodically manifesting in epidemic mortality. Traditionally, columbids are identified as highly susceptible to infection with occasional spillover into raptors that prey on infected birds. We identified avian trichomonosis in two dead California spotted owls (Strix occidentalis occidentalis) and three dead northern spotted owls (S. o. caurina) in California during 2011-2015; infection was confirmed in four owls by PCR. Pathologic lesions associated with trichomonosis in the owls included caseonecrotic lesions of the upper palate accompanied by oropharyngitis, cellulitis, myositis, and/or sinusitis. Spotted owls are known to mainly feed on small mammals; therefore, the source of infection as well as the significance of the disease in spotted owls is unclear. These owl trichomonosis cases coincided temporally and spatially with three trichomonosis epidemics in band-tailed pigeons (Patagioenas fasciata monilis). The same parasite, T. gallinae subtype A2, was isolated from the spotted owls and band-tailed pigeons, suggesting the owls became infected when opportunistically feeding on pigeons during mortality events. Avian trichomonosis is an important factor in the decline of the Pacific Coast band-tailed pigeon population with near-annual mortality events during the last 10 years and could have conservation implications for raptor species at risk, particularly those that are facing multiple threats.

  17. Avian trichomonosis in spotted owls (Strix occidentalis: Indication of opportunistic spillover from prey

    Directory of Open Access Journals (Sweden)

    Krysta H. Rogers

    2016-12-01

    Full Text Available Avian trichomonosis, caused by the flagellated protozoan parasite Trichomonas gallinae, has variable pathogenicity among bird species ranging from asymptomatic infections to severe disease periodically manifesting in epidemic mortality. Traditionally, columbids are identified as highly susceptible to infection with occasional spillover into raptors that prey on infected birds. We identified avian trichomonosis in two dead California spotted owls (Strix occidentalis occidentalis and three dead northern spotted owls (S. o. caurina in California during 2011–2015; infection was confirmed in four owls by PCR. Pathologic lesions associated with trichomonosis in the owls included caseonecrotic lesions of the upper palate accompanied by oropharyngitis, cellulitis, myositis, and/or sinusitis. Spotted owls are known to mainly feed on small mammals; therefore, the source of infection as well as the significance of the disease in spotted owls is unclear. These owl trichomonosis cases coincided temporally and spatially with three trichomonosis epidemics in band-tailed pigeons (Patagioenas fasciata monilis. The same parasite, T. gallinae subtype A2, was isolated from the spotted owls and band-tailed pigeons, suggesting the owls became infected when opportunistically feeding on pigeons during mortality events. Avian trichomonosis is an important factor in the decline of the Pacific Coast band-tailed pigeon population with near-annual mortality events during the last 10 years and could have conservation implications for raptor species at risk, particularly those that are facing multiple threats.

  18. Opportunistic splitting for scheduling using a score-based approach

    KAUST Repository

    Rashid, Faraan

    2012-06-01

    We consider the problem of scheduling a user in a multi-user wireless environment in a distributed manner. The opportunistic splitting algorithm is applied to find the best group of users without reporting the channel state information to the centralized scheduler. The users find the best among themselves while requiring just a ternary feedback from the common receiver at the end of each mini-slot. The original splitting algorithm is modified to handle users with asymmetric channel conditions. We use a score-based approach with the splitting algorithm to introduce time and throughput fairness while exploiting the multi-user diversity of the network. Analytical and simulation results are given to show that the modified score-based splitting algorithm works well as a fair scheduling scheme with good spectral efficiency and reduced feedback. © 2012 IEEE.

  19. Sinabro: A Smartphone-Integrated Opportunistic Electrocardiogram Monitoring System.

    Science.gov (United States)

    Kwon, Sungjun; Lee, Dongseok; Kim, Jeehoon; Lee, Youngki; Kang, Seungwoo; Seo, Sangwon; Park, Kwangsuk

    2016-03-11

    In our preliminary study, we proposed a smartphone-integrated, unobtrusive electrocardiogram (ECG) monitoring system, Sinabro, which monitors a user's ECG opportunistically during daily smartphone use without explicit user intervention. The proposed system also monitors ECG-derived features, such as heart rate (HR) and heart rate variability (HRV), to support the pervasive healthcare apps for smartphones based on the user's high-level contexts, such as stress and affective state levels. In this study, we have extended the Sinabro system by: (1) upgrading the sensor device; (2) improving the feature extraction process; and (3) evaluating extensions of the system. We evaluated these extensions with a good set of algorithm parameters that were suggested based on empirical analyses. The results showed that the system could capture ECG reliably and extract highly accurate ECG-derived features with a reasonable rate of data drop during the user's daily smartphone use.

  20. Outage analysis of opportunistic decode-and-forward relaying

    KAUST Repository

    Tourki, Kamel

    2010-09-01

    In this paper, we investigate a dual-hop opportunistic decode-and-forward relaying scheme where the source may or not be able to communicate directly with the destination. We first derive statistics based on exact probability density function (PDF) of each hop. Then, the PDFs are used to determine closed-form outage probability expression for a transmission rate R. Furthermore, we evaluate the asymptotic outage performance and the diversity order is deduced. Unlike existing works where the analysis focused on high signal-to-noise ratio (SNR) regime, such results are important to enable the designers to take decisions regarding practical systems that operate at low SNR regime. We show that performance simulation results coincide with our analytical results under practical assumption of unbalanced hops. © 2010 IEEE.

  1. Opportunistic microorganisms in individuals with lesions of denture stomatitis.

    Science.gov (United States)

    Pereira, Cristiane Aparecida; Toledo, Bruna Costa; Santos, Camila Teles; Pereira Costa, Anna Carolina Borges; Back-Brito, Graziella Nuernberg; Kaminagakura, Estela; Jorge, Antonio Olavo Cardoso

    2013-08-01

    The aim of this study was to isolate, quantify, identify, and compare opportunistic microorganisms (Candida and Staphylococcus genera and Enterobacteriaceae/Pseudomonadaceae families) from prosthesis-fitting surfaces, the hard palate, and mouth rinses of individuals wearing removable maxillary prosthesis with (50) and without (50) lesions of denture stomatitis (DS). The strains were collected and identified using phenotypic, biochemical and molecular tests. The counts of microorganisms were significantly higher in the group of individuals with DS (P < 0.05). C. albicans was the most frequently isolated yeast species in both groups, following by C. tropicalis and C. glabrata. Six isolates were identified as C. dubliniensis. S. aureus and S. epidermidis were the most frequent Staphylococcus species in both groups. Klebsiella pneumoniae was the predominant species in both groups. The association between Candida spp. and bacteria isolated in this study with DS suggests that these microorganisms may play important roles in the establishment and persistence of this disease.

  2. Optimistic Opportunistic Routing Techniques for Wireless Sensor Networks: -A Review

    Directory of Open Access Journals (Sweden)

    M.P. Anuradha

    2013-07-01

    Full Text Available Secure and optimistic routing is very important and significant task in Wireless Sensor Networks (WSN. In multi-hop communication, selection of routing path between the sensor nodes in the sensor field is essential and also important. Based on the coordination, time based, token based and network coding based techniques the data packets are forwarded from the source to the destination through the intermediate nodes in the network called Opportunistic Routing (OR. Compared with traditional routing, the OR uses the broadcast nature of transmission which greatly increases the wireless network throughput, reliability. In order to support higher node density in WSN, the selection of the most optimistic, flexible, dynamic and reliable OR mechanism and OR protocol are important. In this study the various OR mechanisms and OR protocol are identified and design issues like delivery ratio, packet transmission rate, communication pattern, reliability rate, throughput and fault tolerance are discussed and the comparative results are also tabulated.

  3. Sinabro: A Smartphone-Integrated Opportunistic Electrocardiogram Monitoring System

    Directory of Open Access Journals (Sweden)

    Sungjun Kwon

    2016-03-01

    Full Text Available In our preliminary study, we proposed a smartphone-integrated, unobtrusive electrocardiogram (ECG monitoring system, Sinabro, which monitors a user’s ECG opportunistically during daily smartphone use without explicit user intervention. The proposed system also monitors ECG-derived features, such as heart rate (HR and heart rate variability (HRV, to support the pervasive healthcare apps for smartphones based on the user’s high-level contexts, such as stress and affective state levels. In this study, we have extended the Sinabro system by: (1 upgrading the sensor device; (2 improving the feature extraction process; and (3 evaluating extensions of the system. We evaluated these extensions with a good set of algorithm parameters that were suggested based on empirical analyses. The results showed that the system could capture ECG reliably and extract highly accurate ECG-derived features with a reasonable rate of data drop during the user’s daily smartphone use.

  4. Congestion Control Strategy for Opportunistic Network Based on Message Values

    Directory of Open Access Journals (Sweden)

    Deng-yin Zhang

    2014-05-01

    Full Text Available To solve the congestion problem in opportunistic networks, a congestion control strategy based on message deleting and transferring(DATM is proposed. The congested node calculates the storage value of each message according to the forwarding probability and TTL of message, then deletes the message with the minimum storage value and transfers the message with the minimum forwarding probability to neighboring nodes. The neighboring nodes calculate the receiving value of the message according to the forwarding probability and free buffer capacity of this message. The congested node transfers the message to the neighboring node with the maximum receiving value. The message will be deleted when there is no neighboring node to receive it. The algorithm is more targeted at deleting messages. Besides, it combines the strategy of transferring message. Therefore, it can deal with the congestion more efficiently. The message arrival rate is improved significantly and the end-to-end delay is also reduced to some extent.

  5. Opportunistic Cooperative Reliable Transmission Protocol for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Hua Guo

    2014-04-01

    Full Text Available The high reliability requirement of data transmission in wireless sensor networks has been a large challenge due to the random mobility and network topoloy instability, as well as restriction of energy consumption and system life time. In this work, the relationship matirx of distance and speed was created at first. Then the binay tree of mobility and reliabiliy was proposed based on the distance relationship matrix. The optimal relay nodes with high reliabiliy were selected by seeking the binay tree. The high reliable opportunistic cooperative data transmission scheme was presnted finally. The outcome of both mathematical analysis and NS simulation indicate that the proposed mechanism is superior to the traditional data transmission mechnism such as the reliability, system throughput and energy efficiency and so on.

  6. Distributed opportunistic spectrum sharing in cognitive radio networks

    KAUST Repository

    Hawa, Mohammed

    2016-05-19

    In cases where the licensed radio spectrum is underutilized, cognitive radio technology enables cognitive devices to sense and then dynamically access this scarce resource making the most out of it. In this work, we introduce a simple and intuitive, yet powerful and efficient, technique that allows opportunistic channel access in cognitive radio systems in a completely distributed fashion. Our proposed method achieves very high values of spectrum utilization and throughput. It also minimizes interference between cognitive base stations and the primary users licensed to use the spectrum. The algorithm responds quickly and efficiently to variations in the network parameters and also achieves a high degree of fairness between cognitive base stations. © 2016 John Wiley & Sons, Ltd.

  7. DATA FORWARDING IN OPPORTUNISTIC NETWORK USING MOBILE TRACES

    Directory of Open Access Journals (Sweden)

    B.Poonguzharselvi

    2012-10-01

    Full Text Available Opportunistic networks are usually formed spontaneously by mobile devices equipped with short range wireless communication interfaces. The idea is that an end-to-end connection may never be present. Designing and implementing a routing protocol to support both service discovery and delivery in such kinds of networks is a challenging problem on account of frequent disconnections and topology changes. In these networks one of the most important issues relies on the selection of the best intermediate node to forward the messages towards the destination. This paper presents a mobile trace based routing protocol that uses the location information of the nodes in the network. Using the trace information, next hop is selected to forward the packets to destination. Data forwarding is done via the selected nodes. The effectiveness is shown using simulation.

  8. Opportunistic Sensor Data Collection with Bluetooth Low Energy.

    Science.gov (United States)

    Aguilar, Sergio; Vidal, Rafael; Gomez, Carles

    2017-01-23

    Bluetooth Low Energy (BLE) has gained very high momentum, as witnessed by its widespread presence in smartphones, wearables and other consumer electronics devices. This fact can be leveraged to carry out opportunistic sensor data collection (OSDC) in scenarios where a sensor node cannot communicate with infrastructure nodes. In such cases, a mobile entity (e.g., a pedestrian or a vehicle) equipped with a BLE-enabled device can collect the data obtained by the sensor node when both are within direct communication range. In this paper, we characterize, both analytically and experimentally, the performance and trade-offs of BLE as a technology for OSDC, for the two main identified approaches, and considering the impact of its most crucial configuration parameters. Results show that a BLE sensor node running on a coin cell battery can achieve a lifetime beyond one year while transferring around 10 Mbit/day, in realistic OSDC scenarios.

  9. An Opportunistic Relaying Selection Scheme Based on Relay Fairness

    Directory of Open Access Journals (Sweden)

    Ting An

    2013-07-01

    Full Text Available Opportunistic relaying scheme is a single cooperative relay selection method based on Channel State Information. However, the failure probability of the best relay selection may become unacceptable when the number of relays increases. Although most of the existing solutions can reduce the failure probability of relay selection, they ignore the fairness of the relay selection. In order to improve the fairness of the relay selection without affecting the failure probability of the best relay selection, we propose a modified practical best relay selection scheme in this paper,  and by introducing proportional fair algorithm, the relay timer will be given a smaller correlation coefficient. The proposed method makes the probability of selection be improved. In the light of defined fairness factor, the relay fairness is represented. Simulation results show that the new algorithm can improve the fairness of the relay selection on the basis of maintaining the original failure probability of relay selection.

  10. Vaccination approaches against opportunistic fungal infections caused by Aspergillus fumigatus.

    Science.gov (United States)

    Reichard, Utz; Herrmann, Sahra; Asif, Abdul R

    2014-01-01

    Although innate immunity primarily combats systemic infections of opportunistic fungi such as Aspergillus and Candida spp., acquired and protective immunoreactions were observed long ago in animal trials following sublethal systemic infections caused by viable fungi or after challenging animals with inactivated fungal cells. Based on these observations, fungal antigens should exist which mediate such protective immunoreactions and have in part already been identified. In this context, this review focuses primarily on the various approaches that have been used to identify protection-mediating Aspergillus-antigens and their rationale. Emphasis is placed on screening methods that have exploited genetic or proteomic approaches on the basis of the corresponding fungal genome projects. Thereby, a survey and description is given of the antigens so far known to be capable of inducing immune responses that protect animals against acquiring lethal systemic aspergillosis.

  11. The Opportunistic Transmission of Wireless Worms between Mobile Devices

    CERN Document Server

    Rhodes, C J

    2008-01-01

    The ubiquity of portable wireless-enabled computing and communications devices has stimulated the emergence of malicious codes (wireless worms) that are capable of spreading between spatially proximal devices. The potential exists for worms to be opportunistically transmitted between devices as they move around, so human mobility patterns will have an impact on epidemic spread. The scenario we address in this paper is proximity attacks from fleetingly in-contact wireless devices with short-range communication range, such as Bluetooth-enabled smart phones. An individual-based model of mobile devices is introduced and the effect of population characteristics and device behaviour on the outbreak dynamics is investigated. We show through extensive simulations that in the above scenario the resulting mass-action epidemic models remain applicable provided the contact rate is derived consistently from the underlying mobility model. The model gives useful analytical expressions against which more refined simulations ...

  12. Opportunistic Neurologic Infections in Patients with Acquired Immunodeficiency Syndrome (AIDS).

    Science.gov (United States)

    Albarillo, Fritzie; O'Keefe, Paul

    2016-01-01

    Infections of the central nervous system (CNS) in individuals with human immunodeficiency virus (HIV) remain a substantial cause of morbidity and mortality despite the introduction of highly active antiretroviral therapy (HAART) especially in the resource-limited regions of the world. Diagnosis of these infections may be challenging because findings on cerebrospinal fluid (CSF) analysis and brain imaging are nonspecific. While brain biopsy provides a definitive diagnosis, it is an invasive procedure associated with a relatively low mortality rate, thus less invasive modalities have been studied in recent years. Diagnosis, therefore, can be established based on a combination of a compatible clinical syndrome, radiologic and CSF findings, and understanding of the role of HIV in these infections. The most common CNS opportunistic infections are AIDS-defining conditions; thus, treatment of these infections in combination with HAART has greatly improved survival.

  13. Opportunistic Sensor Data Collection with Bluetooth Low Energy

    Science.gov (United States)

    Aguilar, Sergio; Vidal, Rafael; Gomez, Carles

    2017-01-01

    Bluetooth Low Energy (BLE) has gained very high momentum, as witnessed by its widespread presence in smartphones, wearables and other consumer electronics devices. This fact can be leveraged to carry out opportunistic sensor data collection (OSDC) in scenarios where a sensor node cannot communicate with infrastructure nodes. In such cases, a mobile entity (e.g., a pedestrian or a vehicle) equipped with a BLE-enabled device can collect the data obtained by the sensor node when both are within direct communication range. In this paper, we characterize, both analytically and experimentally, the performance and trade-offs of BLE as a technology for OSDC, for the two main identified approaches, and considering the impact of its most crucial configuration parameters. Results show that a BLE sensor node running on a coin cell battery can achieve a lifetime beyond one year while transferring around 10 Mbit/day, in realistic OSDC scenarios. PMID:28124987

  14. Exact performance analysis of decode-and-forward opportunistic relaying

    KAUST Repository

    Tourki, Kamel

    2010-06-01

    In this paper, we investigate a dual-hop decode-and-forward opportunistic relaying scheme where the source may or may not be able to communicate directly with the destination. In our study, we consider a regenerative relaying scheme in which the decision to cooperate takes into account the effect of the possible erroneously detected and transmitted data at the best relay. We derive an exact closed-form expression for the end-to-end bit-error rate (BER) of binary phase-shift keying (BPSK) modulation based on the exact statistics of each hop. Unlike existing works where the analysis focused on high signal-to-noise ratio (SNR) regime, such results are important to enable the designers to take decisions regarding practical systems that operate at low SNR regime. We show that performance simulation results coincide with our analytical results.

  15. POWER CONTROL BASED COOPERATIVE OPPORTUNISTIC ROUTING IN WIRELESS SENSOR NETWORKS

    Institute of Scientific and Technical Information of China (English)

    Hu Haifeng; Zhu Qi

    2009-01-01

    This paper proposes an approach called PC-CORP (Power Control based Cooperative Opportunistic Routing Protocol) for WSN (Wireless Sensor Networks), providing robustness to the random variations in network connectivity while ensuring better data forwarding efficiency in an energy efficient manner. Based on the realistic radio model, we combine the region-based routing, rendezvous scheme, sleep discipline and cooperative communication together to model data forwarding by cross layer design in WSN. At the same time, a lightweight transmission power control algorithm called PC-AIMD (Power Control Additive Increase Multiplicative Decrease) is introduced to utilize the cooperation of relay nodes to improve the forwarding efficiency performance and increase the robustness of the routing protocol. In the simulation, the performance of PC-COPR is investigated in terms of the adaptation of variations in network connectivity and satisfying the QoS requirements of application.

  16. Optimizing Cooperative Cognitive Radio Networks with Opportunistic Access

    KAUST Repository

    Zafar, Ammar

    2012-09-16

    Optimal resource allocation for cooperative cognitive radio networks with opportunistic access to the licensed spectrum is studied. Resource allocation is based on minimizing the symbol error rate at the receiver. Both the cases of all-participate relaying and selective relaying are considered. The objective function is derived and the constraints are detailed for both scenarios. It is then shown that the objective functions and the constraints are nonlinear and nonconvex functions of the parameters of interest, that is, source and relay powers, symbol time, and sensing time. Therefore, it is difficult to obtain closed-form solutions for the optimal resource allocation. The optimization problem is then solved using numerical techniques. Numerical results show that the all-participate system provides better performance than its selection counterpart, at the cost of greater resources. © 2012 Ammar Zafar et al.

  17. Outage probability of opportunistic decode-and-forward relaying over Nakagami-m fading channels

    Institute of Scientific and Technical Information of China (English)

    CHUAI Gang; ZHANG Bao-zhi; LIU Xing-mei; GAO Li

    2009-01-01

    In this article, the outage probability behavior of a relay network over Nakagami-m fading channels is analyzed. Both reactive and proactive opportunistic decode-and-forward (DAF) strategies are considered. The closed-form solutions to the outage probabilities on both opportunistic DAF strategies are derived. Simulation results conf'Lrrn the presented mathematical analysis.

  18. Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important pathogenic phenotypes

    DEFF Research Database (Denmark)

    Jakobsen, Tim Holm; Hansen, Martin Asser; Jensen, Peter Østrup;

    2013-01-01

    that render it an opportunistic human pathogen, We found genes involved in anaerobic growth and the pgaABCD operon encoding the biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamin. Furthermore, the genome contains a range of antibiotic resistance genes coding efflux pump systems and antibiotic modifying enzymes...

  19. Cellular immune responses in HIV-negative immunodeficiency with anti-interferon-γ antibodies and opportunistic intracellular microorganisms.

    Directory of Open Access Journals (Sweden)

    Jiraprapa Wipasa

    Full Text Available BACKGROUND: Cell-mediated immunity plays a crucial role in resistance to intracellular infection. We previously reported antibodies against interferon-gamma (IFN-γ in HIV- negative (HIV- patients with acquired immunodeficiency presenting with repeated episodes of disseminated infection caused by uncommon opportunistic intracellular fungal, bacterial, and viral pathogens. This follow-up study aimed to investigate cellular immune responses in these unusual patients. METHODS: Twenty HIV- patients presenting with ≥2 episodes of culture- or histopathologic-proven opportunistic infections were enrolled along with age- and sex-matched controls comprised of 20 HIV+ patients plus 20 healthy adults. Monocyte phenotyping and intracellular cytokine production were determined by staining with specific antibodies followed by flow cytometry. Anti-interferon-γ antibodies were measured by enzyme-linked immunosorbent assay, and inducible nitric oxide synthase by reverse-transcription polymerase chain reaction. RESULTS: There were no differences among cases, HIV+, and healthy controls in the percentage of monocytes, or CD68 and HLA-DR expression on their surfaces. FcR1 (CD119 expression on monocytes was significantly higher in cases than in HIV+ (p<0.05 and healthy controls (p<0.01, suggesting the presence of activated monocytes in the circulation. Interleukin (IL-2 and tumor necrosis factor (TNF-α production in CD4 cells were significantly lower in cases than in healthy controls (p<0.01 and p<0.001, respectively. CD8 production of TNF-α among cases was significantly lower than that of healthy controls (p<0.05. CONCLUSION: Immunodeficiency in HIV- individuals with repeated infections with intracellular pathogens may be associated with one or more of the abnormal immune responses reflected by the reduced production of both IL-2 by CD4 T cells and TNF-α by CD4 T cells and CD8 T cells, as well as presence of anti-IFN-γ antibody, as previously reported.

  20. Pathogen intelligence

    Science.gov (United States)

    Steinert, Michael

    2014-01-01

    Different species inhabit different sensory worlds and thus have evolved diverse means of processing information, learning and memory. In the escalated arms race with host defense, each pathogenic bacterium not only has evolved its individual cellular sensing and behavior, but also collective sensing, interbacterial communication, distributed information processing, joint decision making, dissociative behavior, and the phenotypic and genotypic heterogeneity necessary for epidemiologic success. Moreover, pathogenic populations take advantage of dormancy strategies and rapid evolutionary speed, which allow them to save co-generated intelligent traits in a collective genomic memory. This review discusses how these mechanisms add further levels of complexity to bacterial pathogenicity and transmission, and how mining for these mechanisms could help to develop new anti-infective strategies. PMID:24551600

  1. New trends in emerging pathogens.

    Science.gov (United States)

    Skovgaard, Niels

    2007-12-15

    The emergence of pathogens is the result of a number of impact in all parts of the food chain. The emerging technologies in food production explain how new pathogens can establish themselves in the food chain and compromise food safety. The impact of the food technology is analysed for several bacteria, such as Yersinia, Campylobacter, Arcobacter, Helicobacter pullorum, Enterobacter sakazakii, Mycobacterium avium spp. paratuberculosis, prions related to vCJD and others. The importance of the ability of many microbes to form VBNC forms is elaborated on. Research on culture independent methods may address this outstanding issue to the better understanding of emerging pathogens. The "demerging" of pathogens also occur, and examples of this are explained. The reaction of bacteria to stresses and sublethal treatments, and how exposure to one stress factor can confer resistance to other stresses, literally speaking causing contagious resistance, are explained. The implication of this e.g. in modern approaches of food preservation, such as Minimally processed Foods, is considerable. Intestinal colonization of EHEC may be regulated by Quorum sensing, and this ability of microbes plays an important role in the colonization of microbes in food and on food processing equipment, an important factor in the emergence of pathogens. The emergence of Saccharomyces cerevisiae, as an opportunistic human pathogen, used for centuries for food and production of alcoholic beverages, calls for research in molecular tools to distinguish between probiotic and clinical strains. Cyclospora cayetanensis and Norovirus outbreaks can no longer be designated as emerging pathogens, they share however one characteristic in the epidemiology of emerging nature, the importance of the hygiene in the primary production stage, including supply of potable water, and the application of GMP and the HACCP principles in the beginning of the food chain. Hepatitis E virus is a potential emerging food borne

  2. Recent advances in understanding Pseudomonas aeruginosa as a pathogen.

    Science.gov (United States)

    Klockgether, Jens; Tümmler, Burkhard

    2017-01-01

    The versatile and ubiquitous Pseudomonas aeruginosa is an opportunistic pathogen causing acute and chronic infections in predisposed human subjects. Here we review recent progress in understanding P. aeruginosa population biology and virulence, its cyclic di-GMP-mediated switches of lifestyle, and its interaction with the mammalian host as well as the role of the type III and type VI secretion systems in P. aeruginosa infection.

  3. Pathogens in drinking water: Are there any new ones

    Energy Technology Data Exchange (ETDEWEB)

    Reasoner, D.J.

    1993-01-01

    Since 1976 three newly recognized human pathogens have become familiar to the drinking water industry as waterborne disease agents. These are: the legionnaires disease agent, Legionella pneumophila and related species; and two protozoan pathogens, Giardia lamblia and Cryptosporidium parvum, both of which form highly disinfectant resistant cysts that are shed in the feces of infected individuals. The question frequently arises - are there other emerging waterborne pathogens that may pose a human health problem that the drinking water industry will have to deal with. The paper will review the current state of knowledge of the occurrence and incidence of pathogens and opportunistic pathogens other than Legionella, Giardia and Cryptosporidium in treated and untreated drinking water. Bacterial agents that will be reviewed include Aeromonas, Pseudomonas, Campylobacter, Mycobacterium, Yersinia and Plesiomonas. Aspects of detection of these agents including detection methods and feasibility of monitoring will be addressed.

  4. Location Based Opportunistic Routing Protocol for Mobile Ad Hoc Networks

    Directory of Open Access Journals (Sweden)

    Jubin Sebastian E

    2012-01-01

    Full Text Available : Most existing ad hoc routing protocols are susceptible to node mobility, especially for large-scale networks. This paper proposes a Location Based Opportunistic Routing Protocol (LOR to addresses the problem of delivering data packets for highly dynamic mobile ad hoc networks in a reliable and timely manner.This protocol takes advantage of the stateless property of geographic routing and the broadcast nature of wireless medium. When a data packet is sent out, some of the neighbor nodes that have overheard the transmission will serve as forwarding candidates, and take turn to forward the packet if it is not relayed by the specific best forwarder within a certain period of time. By utilizing such in-the-air backup, communication is maintained without being interrupted. The additional latency incurred by local route recovery is greatly reduced and the duplicate relaying caused by packet reroute is also decreased. Simulation results on NS2 verified the effectiveness of the proposed protocol with improvement in throughput by 28%.

  5. The opportunistic transmission of wireless worms between mobile devices

    Science.gov (United States)

    Rhodes, C. J.; Nekovee, M.

    2008-12-01

    The ubiquity of portable wireless-enabled computing and communications devices has stimulated the emergence of malicious codes (wireless worms) that are capable of spreading between spatially proximal devices. The potential exists for worms to be opportunistically transmitted between devices as they move around, so human mobility patterns will have an impact on epidemic spread. The scenario we address in this paper is proximity attacks from fleetingly in-contact wireless devices with short-range communication range, such as Bluetooth-enabled smart phones. An individual-based model of mobile devices is introduced and the effect of population characteristics and device behaviour on the outbreak dynamics is investigated. The model uses straight-line motion to achieve population, though it is recognised that this is a highly simplified representation of human mobility patterns. We show that the contact rate can be derived from the underlying mobility model and, through extensive simulation, that mass-action epidemic models remain applicable to worm spreading in the low density regime studied here. The model gives useful analytical expressions against which more refined simulations of worm spread can be developed and tested.

  6. Gastrointestinal opportunistic infections in human immunodeficiency virus disease

    Directory of Open Access Journals (Sweden)

    Al Anazi Awadh

    2009-01-01

    Full Text Available Gastrointestinal (GI opportunistic infections (OIs are commonly encountered at various stages of human immunodeficiency virus (HIV disease. In view of the suppressive nature of the virus and the direct contact with the environment, the GI tract is readily accessible and is a common site for clinical expression of HIV. The subject is presented based on information obtained by electronic searches of peer-reviewed articles in medical journals, Cochrane reviews and PubMed sources. The spectrum of GI OIs ranges from oral lesions of Candidiasis, various lesions of viral infections, hepatobiliary lesions, pancreatitis and anorectal lesions. The manifestations of the disease depend on the level of immunosuppression, as determined by the CD4 counts. The advent of highly active antiretroviral therapy has altered the pattern of presentation, resorting mainly to features of antimicrobial-associated colitis and side effects of antiretroviral drugs. The diagnosis of GI OIs in HIV/ acquired immunodeficiency syndrome patients is usually straightforward. However, subtle presentations require that the physicians should have a high index of suspicion when given the setting of HIV infection.

  7. Effect of threshold quantization in opportunistic splitting algorithm

    KAUST Repository

    Nam, Haewoon

    2011-12-01

    This paper discusses algorithms to find the optimal threshold and also investigates the impact of threshold quantization on the scheduling outage performance of the opportunistic splitting scheduling algorithm. Since this algorithm aims at finding the user with the highest channel quality within the minimal number of mini-slots by adjusting the threshold every mini-slot, optimizing the threshold is of paramount importance. Hence, in this paper we first discuss how to compute the optimal threshold along with two tight approximations for the optimal threshold. Closed-form expressions are provided for those approximations for simple calculations. Then, we consider linear quantization of the threshold to take the limited number of bits for signaling messages in practical systems into consideration. Due to the limited granularity for the quantized threshold value, an irreducible scheduling outage floor is observed. The numerical results show that the two approximations offer lower scheduling outage probability floors compared to the conventional algorithm when the threshold is quantized. © 2006 IEEE.

  8. Hide, Keep Quiet, and Keep Low : Properties That Make Aspergillus fumigatus a Successful Lung Pathogen

    NARCIS (Netherlands)

    Escobar, Natalia; Ordonez Alvarez, Soledad; Wosten, Han; Haas, Pieter-Jan A; de Cock, Hans; Haagsman, Henk P

    2016-01-01

    Representatives of the genus Aspergillus are opportunistic fungal pathogens. Their conidia can reach the alveoli by inhalation and can give rise to infections in immunocompromised individuals. Aspergillus fumigatus is the causal agent of invasive aspergillosis in nearly 90% of the cases. It is not y

  9. Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis

    DEFF Research Database (Denmark)

    Nosek, J.; Novotna, M.; Hlavatovicova, Z.

    2004-01-01

    The complete sequence of the mitochondrial DNA of the opportunistic yeast pathogen Candida parapsilosis was determined. The mitochondrial genome is represented by linear DNA molecules terminating with tandem repeats of a 738-bp unit. The number of repeats varies, thus generating a population...

  10. Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis

    DEFF Research Database (Denmark)

    Nosek, J.; Novotna, M.; Hlavatovicova, Z.

    2004-01-01

    The complete sequence of the mitochondrial DNA of the opportunistic yeast pathogen Candida parapsilosis was determined. The mitochondrial genome is represented by linear DNA molecules terminating with tandem repeats of a 738-bp unit. The number of repeats varies, thus generating a population...

  11. The role of quorum sensing in the pathogenicity of the cunning aggressor Pseudomonas aeruginosa

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Givskov, Michael Christian

    2007-01-01

    , and, particularly, higher organisms We have focused on Pseudomonas aeruginosa, an opportunistic pathogen producing more than 30 QS-regulated virulence factors. P. aeruginosa causes several types of nosocomial infection, and lung infection in cystic fibrosis (CF) patients. We review the role of QS...

  12. Probability of recovering pathogenic Escherichia coli from foods.

    Science.gov (United States)

    Hill, W E; Ferreira, J L; Payne, W L; Jones, V M

    1985-01-01

    The probability of recovering pathogenic Escherichia coli from food by the Bacteriological Analytical Manual method was determined by the effects of several factors: the number of strains per food, the ability of pathogenic strains to survive enrichment, and the frequency of plasmid loss during enrichment. Biochemical patterns indicated the presence of about six E. coli strains per food sample. About half of the strains isolated from humans did not survive enrichment. Among those which grew, plasmid loss, as determined by gel electrophoresis and DNA colony hybridization, ranged from 20 to 95%. The combined effects of failure to survive enrichment and plasmid loss decreased the relative numbers of these strains and reduced the chance of detecting pathogens. To counteract this tendency and obtain a 90 to 95% probability off recovering a given pathogenic strain, 40 to 50 colonies per food sample should be picked during the routine testing of foods. PMID:3893320

  13. Pathogen Sensors

    Directory of Open Access Journals (Sweden)

    Joseph Irudayaraj

    2009-10-01

    Full Text Available The development of sensors for detecting foodborne pathogens has been motivated by the need to produce safe foods and to provide better healthcare. However, in the more recent times, these needs have been expanded to encompass issues relating to biosecurity, detection of plant and soil pathogens, microbial communities, and the environment. The range of technologies that currently flood the sensor market encompass PCR and microarray-based methods, an assortment of optical sensors (including bioluminescence and fluorescence, in addition to biosensor-based approaches that include piezoelectric, potentiometric, amperometric, and conductometric sensors to name a few. More recently, nanosensors have come into limelight, as a more sensitive and portable alternative, with some commercial success. However, key issues affecting the sensor community is the lack of standardization of the testing protocols and portability, among other desirable elements, which include timeliness, cost-effectiveness, user-friendliness, sensitivity and specificity. [...

  14. Toward distributed relay selection for opportunistic amplify-and-forward transmission

    KAUST Repository

    Tourki, Kamel

    2011-05-01

    Opportunistic relaying in cooperative communication depends on careful relay selection. However the traditional centralized method used for opportunistic Amplify-and-Forward (OAF) protocols requires precise measurements of channel state information (CSI) at the destination (CSI-OAF). In this paper, we propose a distributed relay selection framework for opportunistic AF (D-OAF) cooperative communications and offer an accurate performance analysis based on exact statistics of the local signalto- noise ratios of the best relay. Furthermore, we validate our analysis by showing that performance simulation results coincide with our analytical results over different network architectures, and we compare our new results with their CSI-based counterparts. © 2011 IEEE.

  15. Why is HIV a pathogen?

    Science.gov (United States)

    Forsman, Anna; Weiss, Robin A

    2008-12-01

    The pathogenesis of HIV begins with a profound depletion of CD4+ T cells in the gut followed by a long period of clinically silent but dynamic virus replication and diversification with high host cell turnover before the onset of AIDS. The AIDS-defining opportunistic infections and tumors mark the end-point of a long balancing act between virus and host that occurs when CD4+ T cell numbers fall below a level that can sustain immunity. Comparative studies of lentivirus infections in other species show that AIDS is not an inevitable outcome of infection because simian immunodeficiency virus in natural hosts seldom causes disease. What distinguishes pathogenic from 'passenger' infection is a systemic activation of immune responses followed by destruction of the integrity of lymphoid follicles. Macrophage and dendritic cell infection also contribute to pathogenesis. Maedi-Visna virus infection in sheep, which targets these cells but not T lymphocytes, also leads to progressive disease and death that resembles the wasting and brain diseases of HIV without the T cell immunodeficiency. Thus, lessons from pathogenic and nonpathogenic lentivirus infections provide insight into the complex syndrome called AIDS.

  16. Urine Stasis Predisposes to Urinary Tract Infection by an Opportunistic Uropathogen in the Megabladder (Mgb) Mouse

    Science.gov (United States)

    Becknell, Brian; Mohamed, Ahmad Z.; Li, Birong; Wilhide, Michael E.; Ingraham, Susan E.

    2015-01-01

    Purpose Urinary stasis is a risk factor for recurrent urinary tract infection (UTI). Homozygous mutant Megabladder (Mgb-/-) mice exhibit incomplete bladder emptying as a consequence of congenital detrusor aplasia. We hypothesize that this predisposes Mgb-/- mice to spontaneous and experimental UTI. Methods Mgb-/-, Mgb+/-, and wild-type female mice underwent serial ultrasound and urine cultures at 4, 6, and 8 weeks to detect spontaneous UTI. Urine bacterial isolates were analyzed by Gram stain and speciated. Bladder stones were analyzed by x-ray diffractometry. Bladders and kidneys were subject to histologic analysis. The pathogenicity of coagulase-negative Staphylococcus (CONS) isolated from Mgb-/- urine was tested by transurethral administration to culture-negative Mgb-/- or wild-type animals. The contribution of urinary stasis to CONS susceptibility was evaluated by cutaneous vesicostomy in Mgb-/- mice. Results Mgb-/- mice develop spontaneous bacteriuria (42%) and struvite bladder stones (31%) by 8 weeks, findings absent in Mgb+/- and wild-type controls. CONS was cultured as a solitary isolate from Mgb-/- bladder stones. Bladders and kidneys from mice with struvite stones exhibit mucosal injury, inflammation, and fibrosis. These pathologic features of cystitis and pyelonephritis are replicated by transurethral inoculation of CONS in culture-negative Mgb-/- females, whereas wild-type animals are less susceptible to CONS colonization and organ injury. Cutaneous vesicostomy prior to CONS inoculation significantly reduces the quantity of CONS recovered from Mgb-/- urine, bladders, and kidneys. Conclusions CONS is an opportunistic uropathogen in the setting of urinary stasis, leading to enhanced UTI incidence and severity in Mgb-/- mice. PMID:26401845

  17. Opportunistic infections in relation to antiretroviral status among AIDS patients from south India

    Directory of Open Access Journals (Sweden)

    S Srirangaraj

    2011-01-01

    Full Text Available Background: There is a need to generate data from India on relative frequencies of specific opportunistic infections (OIs in different regions and their relation to the choice of commonly used generic highly active anti-retroviral therapy (HAART regimens. Objectives: To document the prevailing prevalence pattern of OIs both before and after HAART, to look for reduction in OIs following HAART, to assess the risk of developing new OIs within 6 months of HAART initiation and to see if there is any difference in the risk of developing a new OI within 6 months of HAART initiation, for those on Efavirenz (EFV-based regimens and Nevirapine (NVP-based regimens. Materials and Methods: In a prospective observational cohort study conducted in South India involving 108 ART-naive AIDS patients, different pathogens were isolated and identified using standard laboratory techniques. Data analysis was done using SPSS software (version 16.0. Risk of developing an OI after HAART initiation was assessed using the likelihood ratio test from Cox regression models. Results: Tuberculosis (53.4%, oral Candidiasis (27.2% and Herpes Zoster (14.7% were the common infections seen. There was a drastic reduction of 96.59% in OI events after 6 months of HAART. The risk of developing an OI within 6 months of HAART initiation was 5.56%. Time to development of an OI in the first 6 months of HAART was shorter for the NVP-based regimens than with EFV-based regimens, but this difference was not statistically significant (HR=0.891, 95% CI: 0.179-4.429; P=0.888. Conclusion: Tuberculosis is the most important OI before initiation of HAART. Both EFV and NVP-based regimens are equally efficacious in controlling OIs.

  18. Urine Stasis Predisposes to Urinary Tract Infection by an Opportunistic Uropathogen in the Megabladder (Mgb Mouse.

    Directory of Open Access Journals (Sweden)

    Brian Becknell

    Full Text Available Urinary stasis is a risk factor for recurrent urinary tract infection (UTI. Homozygous mutant Megabladder (Mgb-/- mice exhibit incomplete bladder emptying as a consequence of congenital detrusor aplasia. We hypothesize that this predisposes Mgb-/- mice to spontaneous and experimental UTI.Mgb-/-, Mgb+/-, and wild-type female mice underwent serial ultrasound and urine cultures at 4, 6, and 8 weeks to detect spontaneous UTI. Urine bacterial isolates were analyzed by Gram stain and speciated. Bladder stones were analyzed by x-ray diffractometry. Bladders and kidneys were subject to histologic analysis. The pathogenicity of coagulase-negative Staphylococcus (CONS isolated from Mgb-/- urine was tested by transurethral administration to culture-negative Mgb-/- or wild-type animals. The contribution of urinary stasis to CONS susceptibility was evaluated by cutaneous vesicostomy in Mgb-/- mice.Mgb-/- mice develop spontaneous bacteriuria (42% and struvite bladder stones (31% by 8 weeks, findings absent in Mgb+/- and wild-type controls. CONS was cultured as a solitary isolate from Mgb-/- bladder stones. Bladders and kidneys from mice with struvite stones exhibit mucosal injury, inflammation, and fibrosis. These pathologic features of cystitis and pyelonephritis are replicated by transurethral inoculation of CONS in culture-negative Mgb-/- females, whereas wild-type animals are less susceptible to CONS colonization and organ injury. Cutaneous vesicostomy prior to CONS inoculation significantly reduces the quantity of CONS recovered from Mgb-/- urine, bladders, and kidneys.CONS is an opportunistic uropathogen in the setting of urinary stasis, leading to enhanced UTI incidence and severity in Mgb-/- mice.

  19. Non-Orthogonal Opportunistic Beamforming: Performance Analysis and Implementation

    KAUST Repository

    Xia, Minghua

    2012-04-01

    Aiming to achieve the sum-rate capacity in multi-user multi-antenna systems where $N_t$ antennas are implemented at the transmitter, opportunistic beamforming (OBF) generates~$N_t$ orthonormal beams and serves $N_t$ users during each channel use, which results in high scheduling delay over the users, especially in densely populated networks. Non-orthogonal OBF with more than~$N_t$ transmit beams can be exploited to serve more users simultaneously and further decrease scheduling delay. However, the inter-beam interference will inevitably deteriorate the sum-rate. Therefore, there is a tradeoff between sum-rate and scheduling delay for non-orthogonal OBF. In this context, system performance and implementation of non-orthogonal OBF with $N>N_t$ beams are investigated in this paper. Specifically, it is analytically shown that non-orthogonal OBF is an interference-limited system as the number of users $K \\\\to \\\\infty$. When the inter-beam interference reaches its minimum for fixed $N_t$ and~$N$, the sum-rate scales as $N\\\\ln\\\\left(\\\\frac{N}{N-N_t}\\ ight)$ and it degrades monotonically with the number of beams $N$ for fixed $N_t$. On the contrary, the average scheduling delay is shown to scale as $\\\\frac{1}{N}K\\\\ln{K}$ channel uses and it improves monotonically with $N$. Furthermore, two practical non-orthogonal beamforming schemes are explicitly constructed and they are demonstrated to yield the minimum inter-beam interference for fixed $N_t$ and $N$. This study reveals that, if user traffic is light and one user can be successfully served within a single transmission, non-orthogonal OBF can be applied to obtain lower worst-case delay among the users. On the other hand, if user traffic is heavy, non-orthogonal OBF is inferior to orthogonal OBF in terms of sum-rate and packet delay.

  20. The Effect of the Acetone Extract of Arctotis arctotoides (Asteraceae on the Growth and Ultrastructure of Some Opportunistic Fungi Associated with HIV/AIDS

    Directory of Open Access Journals (Sweden)

    Wilfred M. Otang

    2011-12-01

    Full Text Available In this study, the effect of the acetone extract of Arctotis arctotoides (L.f. O. Hoffm. (Asteraceae on the growth and ultrastructure of some opportunistic fungi associated with HIV/AIDS was analyzed by means of scanning electron microscope (SEM. Remarkable morphological alterations in the fungal mycelia which were attributed to the loss of cell wall strength ranged from loss of turgidity and uniformity, collapse of entire hyphae to evident destruction of the hyphae. The elements responsible for giving the fungi their characteristic virulence were detected and quantified by energy dispersive X-ray microanalysis techniques. X-ray microanalysis showed the specific spectra of sodium, potassium and sulfur as the principal intersection of the four pathogenic fungi studied. Since these ions have the potential of fostering fungal invasion by altering the permeability of hosts’ membranes, their presence was considered inherent to the pathogenicity of the opportunistic fungi. Hence, these findings indicate the potential of the crude extract of A. arctotoides in preventing fungal invasion and subsequent infection of host’s membranes.

  1. An ad-hoc opportunistic dissemination protocol for smartphone-based participatory traffic monitoring

    NARCIS (Netherlands)

    Türkes, Okan; Seraj, Fatjon; Scholten, Hans; Meratnia, Nirvana; Havinga, Paul J.M.

    2015-01-01

    This study introduces an ad-hoc opportunistic data dissemination protocol, called VADISS, that facilitates participatory traffic monitoring applications with smartphones. As a ubiquitous alternative to existing vehicular networking methods, VADISS uses the default WiFi interfaces universally adopted

  2. Cook Inlet Beluga Opportunistic Sightings, 1975 to 2015 (NCEI Accession 0142326)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — As a part of National Marine Fisheries Service (NMFS) management of the endangered Cook Inlet beluga whale population, a database of opportunistic beluga whale...

  3. Exploiting Opportunistic Resources for ATLAS with ARC CE and the Event Service

    CERN Document Server

    Cameron, David; The ATLAS collaboration

    2016-01-01

    With ever-greater computing needs and fixed budgets, big scientific experiments are turning to opportunistic resources as a means to add much-needed extra computing power. These resources can be very different in design from the resources that comprise the Grid computing of most experiments, therefore exploiting these resources requires a change in strategy for the experiment. The resources may be highly restrictive in what can be run or in connections to the outside world, or tolerate opportunistic usage only on condition that tasks may be terminated without warning. The ARC CE with its non-intrusive architecture is designed to integrate resources such as High Performance Computing (HPC) systems into a computing Grid. The ATLAS experiment developed the Event Service primarily to address the issue of jobs that can be terminated at any point when opportunistic resources are needed by someone else. This paper describes the integration of these two systems in order to exploit opportunistic resources for ATLAS in...

  4. Exploiting Opportunistic Resources for ATLAS with ARC CE and the Event Service

    CERN Document Server

    Cameron, David; The ATLAS collaboration; Guan, Wen

    2017-01-01

    With ever-greater computing needs and fixed budgets, big scientific experiments are turning to opportunistic resources as a means to add much-needed extra computing power. These resources can be very different in design from the resources that comprise the Grid computing of most experiments, therefore exploiting these resources requires a change in strategy for the experiment. The resources may be highly restrictive in what can be run or in connections to the outside world, or tolerate opportunistic usage only on condition that tasks may be terminated without warning. The ARC CE with its non-intrusive architecture is designed to integrate resources such as High Performance Computing (HPC) systems into a computing Grid. The ATLAS experiment developed the Event Service primarily to address the issue of jobs that can be terminated at any point when opportunistic resources are needed by someone else. This paper describes the integration of these two systems in order to exploit opportunistic resources for ATLAS in...

  5. Scaling up ATLAS Event Service to production levels on opportunistic computing platforms

    Science.gov (United States)

    Benjamin, D.; Caballero, J.; Ernst, M.; Guan, W.; Hover, J.; Lesny, D.; Maeno, T.; Nilsson, P.; Tsulaia, V.; van Gemmeren, P.; Vaniachine, A.; Wang, F.; Wenaus, T.; ATLAS Collaboration

    2016-10-01

    Continued growth in public cloud and HPC resources is on track to exceed the dedicated resources available for ATLAS on the WLCG. Examples of such platforms are Amazon AWS EC2 Spot Instances, Edison Cray XC30 supercomputer, backfill at Tier 2 and Tier 3 sites, opportunistic resources at the Open Science Grid (OSG), and ATLAS High Level Trigger farm between the data taking periods. Because of specific aspects of opportunistic resources such as preemptive job scheduling and data I/O, their efficient usage requires workflow innovations provided by the ATLAS Event Service. Thanks to the finer granularity of the Event Service data processing workflow, the opportunistic resources are used more efficiently. We report on our progress in scaling opportunistic resource usage to double-digit levels in ATLAS production.

  6. AFSC/NMML: Cook Inlet Beluga Opportunistic Sightings, 1975 to 2015

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — As a part of National Marine Fisheries Service (NMFS) management of the endangered Cook Inlet beluga whale population, a database of opportunistic beluga whale...

  7. Scaling up ATLAS Event Service to production levels on opportunistic computing platforms

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00066086; The ATLAS collaboration; Caballero, Jose; Ernst, Michael; Guan, Wen; Hover, John; Lesny, David; Maeno, Tadashi; Nilsson, Paul; Tsulaia, Vakhtang; van Gemmeren, Peter; Vaniachine, Alexandre; Wang, Fuquan; Wenaus, Torre

    2016-01-01

    Continued growth in public cloud and HPC resources is on track to exceed the dedicated resources available for ATLAS on the WLCG. Examples of such platforms are Amazon AWS EC2 Spot Instances, Edison Cray XC30 supercomputer, backfill at Tier 2 and Tier 3 sites, opportunistic resources at the Open Science Grid (OSG), and ATLAS High Level Trigger farm between the data taking periods. Because of specific aspects of opportunistic resources such as preemptive job scheduling and data I/O, their efficient usage requires workflow innovations provided by the ATLAS Event Service. Thanks to the finer granularity of the Event Service data processing workflow, the opportunistic resources are used more efficiently. We report on our progress in scaling opportunistic resource usage to double-digit levels in ATLAS production.

  8. Scaling up ATLAS Event Service to production levels on opportunistic computing platforms

    CERN Document Server

    Benjamin, Douglas; The ATLAS collaboration; Ernst, Michael; Guan, Wen; Hover, John; Lesny, David; Maeno, Tadashi; Nilsson, Paul; Tsulaia, Vakhtang; van Gemmeren, Peter; Vaniachine, Alexandre; Wang, Fuquan; Wenaus, Torre

    2016-01-01

    Continued growth in public cloud and HPC resources is on track to overcome the dedicated resources available for ATLAS on the WLCG. Example of such platforms are Amazon AWS EC2 Spot Instances, Edison Cray XC30 supercomputer, backfill at the Tier-2 and Tier-3 sites, opportunistic resources at the Open Science Grid, and ATLAS High Level Trigger farm between the data taking periods. Because of opportunistic resources specifics such as preemptive job scheduling and data I/O, their efficient usage requires workflow innovations provided by the ATLAS Event Service. Thanks to the finer granularity of the Event Service data processing workflow, the opportunistic resources are used more efficiently. We report on our progress in scaling opportunistic resource usage to double-digit levels in ATLAS production.

  9. Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important pathogenic phenotypes.

    Science.gov (United States)

    Jakobsen, Tim Holm; Hansen, Martin Asser; Jensen, Peter Østrup; Hansen, Lars; Riber, Leise; Cockburn, April; Kolpen, Mette; Rønne Hansen, Christine; Ridderberg, Winnie; Eickhardt, Steffen; Hansen, Marlene; Kerpedjiev, Peter; Alhede, Morten; Qvortrup, Klaus; Burmølle, Mette; Moser, Claus; Kühl, Michael; Ciofu, Oana; Givskov, Michael; Sørensen, Søren J; Høiby, Niels; Bjarnsholt, Thomas

    2013-01-01

    Achromobacter xylosoxidans is an environmental opportunistic pathogen, which infects an increasing number of immunocompromised patients. In this study we combined genomic analysis of a clinical isolated A. xylosoxidans strain with phenotypic investigations of its important pathogenic features. We present a complete assembly of the genome of A. xylosoxidans NH44784-1996, an isolate from a cystic fibrosis patient obtained in 1996. The genome of A. xylosoxidans NH44784-1996 contains approximately 7 million base pairs with 6390 potential protein-coding sequences. We identified several features that render it an opportunistic human pathogen, We found genes involved in anaerobic growth and the pgaABCD operon encoding the biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamin. Furthermore, the genome contains a range of antibiotic resistance genes coding efflux pump systems and antibiotic modifying enzymes. In vitro studies of A. xylosoxidans NH44784-1996 confirmed the genomic evidence for its ability to form biofilms, anaerobic growth via denitrification, and resistance to a broad range of antibiotics. Our investigation enables further studies of the functionality of important identified genes contributing to the pathogenicity of A. xylosoxidans and thereby improves our understanding and ability to treat this emerging pathogen.

  10. Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important pathogenic phenotypes.

    Directory of Open Access Journals (Sweden)

    Tim Holm Jakobsen

    Full Text Available Achromobacter xylosoxidans is an environmental opportunistic pathogen, which infects an increasing number of immunocompromised patients. In this study we combined genomic analysis of a clinical isolated A. xylosoxidans strain with phenotypic investigations of its important pathogenic features. We present a complete assembly of the genome of A. xylosoxidans NH44784-1996, an isolate from a cystic fibrosis patient obtained in 1996. The genome of A. xylosoxidans NH44784-1996 contains approximately 7 million base pairs with 6390 potential protein-coding sequences. We identified several features that render it an opportunistic human pathogen, We found genes involved in anaerobic growth and the pgaABCD operon encoding the biofilm adhesin poly-β-1,6-N-acetyl-D-glucosamin. Furthermore, the genome contains a range of antibiotic resistance genes coding efflux pump systems and antibiotic modifying enzymes. In vitro studies of A. xylosoxidans NH44784-1996 confirmed the genomic evidence for its ability to form biofilms, anaerobic growth via denitrification, and resistance to a broad range of antibiotics. Our investigation enables further studies of the functionality of important identified genes contributing to the pathogenicity of A. xylosoxidans and thereby improves our understanding and ability to treat this emerging pathogen.

  11. Uranium Conversion & Enrichment

    Energy Technology Data Exchange (ETDEWEB)

    Karpius, Peter Joseph [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-02-06

    The isotopes of uranium that are found in nature, and hence in ‘fresh’ Yellowcake’, are not in relative proportions that are suitable for power or weapons applications. The goal of conversion then is to transform the U3O8 yellowcake into UF6. Conversion and enrichment of uranium is usually required to obtain material with enough 235U to be usable as fuel in a reactor or weapon. The cost, size, and complexity of practical conversion and enrichment facilities aid in nonproliferation by design.

  12. Lower Bound of Energy-Latency Tradeoff of Opportunistic Routing in Multihop Networks

    Directory of Open Access Journals (Sweden)

    Gorce Jean-Marie

    2011-01-01

    Full Text Available Opportunistic networking aims at exploiting sporadic radio links to improve the connectivity of multihop networks and to foster data transmissions. The broadcast nature of wireless channels is an important feature that can be exploited to improve transmissions by using several potential receivers. Opportunistic relaying is thus the first brick for opportunistic networking. However, the advantage of opportunistic relaying may be degraded due to energy increase related to having multiple active receivers. This paper proposes a thorough analysis of opportunistic relaying efficiency under different realistic radio channel conditions. The study is intended to find the best tradeoff between two objectives: energy and latency minimizations, with a hard reliability constraint. We derive an optimal bound, namely, the Pareto front of the related optimization problem, which offers a good insight into the benefits of opportunistic routings compared with classical multihop routing schemes. Meanwhile, the lower bound provides a framework to optimize the parameters at the physical layer, MAC layer, and routing layer from the viewpoint of cross layer during the design or planning phase of a network.

  13. Pathogens and host immunity in the ancient human oral cavity.

    Science.gov (United States)

    Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y; Tito, Raul Y; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-García, Domingo C; Eppler, Elisabeth; Seiler, Roger; Hansen, Lars H; Castruita, José Alfredo Samaniego; Barkow-Oesterreicher, Simon; Teoh, Kai Yik; Kelstrup, Christian D; Olsen, Jesper V; Nanni, Paolo; Kawai, Toshihisa; Willerslev, Eske; von Mering, Christian; Lewis, Cecil M; Collins, Matthew J; Gilbert, M Thomas P; Rühli, Frank; Cappellini, Enrico

    2014-04-01

    Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past.

  14. Enriching the Catalog

    Science.gov (United States)

    Tennant, Roy

    2004-01-01

    After decades of costly and time-consuming effort, nearly all libraries have completed the retrospective conversion of their card catalogs to electronic form. However, bibliographic systems still are really not much more than card catalogs on wheels. Enriched content that Amazon.com takes for granted--such as digitized tables of contents, cover…

  15. 改良 TT 增菌液在分离肠道致病菌沙门菌和志贺菌的应用评价%Application evaluation of modified TT enrichment broth in separation of intestinal pathogenic Salmonella and Shigella bacteria

    Institute of Scientific and Technical Information of China (English)

    罗宇鹏

    2016-01-01

    目的:分析改良T T增菌液在分离肠道致病中沙门菌和志贺菌的效果评价。方法采用常规接种麦康凯平板及SS平板,同时另外加种改良TT增菌液(硫代硫酸钠碳酸钙增菌液)两种不同方法筛查沙门志贺菌,并参考该院历年菌株分离情况进行血清凝聚。采用 SPSS18.0统计软件包处理数据,比较两种不同粪便培养方法对沙门菌和志贺菌的分离率之间差异。结果2013~2015年纳入统计分析粪便培养标本790例,采用常规方法分离出沙门菌属30例,阳性率3.80%;志贺菌属5例,阳性率0.63%;而采用改良T T增菌培养方法分离出沙门菌属77例,阳性率9.75%,志贺菌属7例,阳性率0.89%;采用改良T T增菌液培养方法沙门菌检出率是常规培养方法2.57倍,志贺菌属是1.41倍,两种方法对沙门志贺菌属的分离差异均有统计学意义( P<0.05)。结论改良TT增菌液能够显著地提高粪便培养沙门菌和志贺菌的阳性分离率,为临床医生正确诊治患者提供较大帮助。%Objective To analyze the effect evaluation of modified TT enrichment broth in the separation of intestinal pathogenic Salmonella and Shigella bacteria .Methods The routine inoculation of Macconkey agar and SS agar were adopted ,meanwhile two different methods for adding the modified TT enrichment broth(sodium thiosulfate and calcium carbonate) were used to screen Sal‐monella and Shigella bacteria .Serum coagulation was performed by referring to the bacterial isolation situation over the years .The SPSS 18 .0 software was adopted to process the data .Then the difference in the separation rate of Salmonella and Shigella bacteria between the two different stool culture methods was compared .Results Totally 790 stool culture samples during 2013-2015 were included into the statistical analysis ,30 cases of Salmonella bacteria were isolated by adopting the routine method ,the

  16. Myxobolus sp., Another Opportunistic Parasite in Immunosuppressed Patients?

    Science.gov (United States)

    Moncada, Ligia I.; López, Myriam C.; Murcia, Martha I.; Nicholls, Santiago; León, Frecia; Guío, Olga Lucia; Corredor, Augusto

    2001-01-01

    During a study of intestinal parasitic infections in human immunodeficiency virus-positive patients, a parasite belonging to the phylum Myxozoa, recently described from human samples, was identified in one sample. When this parasite was stained by the modified Ziehl-Neelsen staining method, the features of the spores were identified: they were pyriform in shape, had thick walls, and had one suture and two polar capsules, with each one having four or five coils. The suture and two polar capsules were observed with the chromotrope-modified stain. The number of stools passed was more than 30 per day, but oocysts of Isospora belli were also found. Upon reexamination of some formalin- or merthiolate-iodine-formaldehyde-preserved samples an identical parasite was found in another sample from a patient presenting with diarrhea. Strongyloides stercoralis larvae and eggs of Hymenolepis nana and Ascaris lumbricoides were also found in this sample. Given that both patients were also infected with other pathogens that cause diarrhea, the possible pathogenic role of this parasite could not be established. The probable route of infection also could not be established. PMID:11326017

  17. Dietary cholesterol modulates pathogen blocking by Wolbachia.

    Directory of Open Access Journals (Sweden)

    Eric P Caragata

    Full Text Available The bacterial endosymbiont Wolbachia pipientis protects its hosts from a range of pathogens by limiting their ability to form infections inside the insect. This "pathogen blocking" could be explained by innate immune priming by the symbiont, competition for host-derived resources between pathogens and Wolbachia, or the direct modification of the cell or cellular environment by Wolbachia. Recent comparative work in Drosophila and the mosquito Aedes aegypti has shown that an immune response is not required for pathogen blocking, implying that there must be an additional component to the mechanism. Here we have examined the involvement of cholesterol in pathogen blocking using a system of dietary manipulation in Drosophila melanogaster in combination with challenge by Drosophila C virus (DCV, a common fly pathogen. We observed that flies reared on cholesterol-enriched diets infected with the Wolbachia strains wMelPop and wMelCS exhibited reduced pathogen blocking, with viral-induced mortality occurring 2-5 days earlier than flies reared on Standard diet. This shift toward greater virulence in the presence of cholesterol also corresponded to higher viral copy numbers in the host. Interestingly, an increase in dietary cholesterol did not have an effect on Wolbachia density except in one case, but this did not directly affect the strength of pathogen blocking. Our results indicate that host cholesterol levels are involved with the ability of Wolbachia-infected flies to resist DCV infections, suggesting that cholesterol contributes to the underlying mechanism of pathogen blocking.

  18. Acinetobacter baumannii: evolution of a global pathogen.

    Science.gov (United States)

    Antunes, Luísa C S; Visca, Paolo; Towner, Kevin J

    2014-08-01

    Acinetobacter baumannii is an opportunistic nosocomial pathogen and one of the six most important multidrug-resistant microorganisms in hospitals worldwide. This human pathogen is responsible for a vast array of infections, of which ventilator-associated pneumonia and bloodstream infections are the most common, and mortality rates can reach 35%. Community-acquired infections have also been reported, but few strains have been recovered from environmental sources and infection reservoirs external to the hospital have not been identified. The majority of A. baumannii infections are caused by two main population clones with worldwide distribution. Infection outbreaks are often associated with multidrug resistance, including the recent emergence of strains resistant to all available antibiotics. Nevertheless, A. baumannii virulence traits and pathogenic potential have mostly remained elusive. The recent expansion of A. baumannii sequenced genomes has permitted the development of large-array phylogenomic and phenotypic analyses, which can offer valuable insights into the evolution and adaptation of A. baumannii as a human pathogen. This review summarises these recent advances, with particular focus on A. baumannii evolutionary and genomic aspects, and proposes new avenues of research.

  19. Opportunistic illnesses in Brazilian children with AIDS: results from two national cohort studies, 1983-2007

    Directory of Open Access Journals (Sweden)

    Heukelbach Jorg

    2011-07-01

    Full Text Available Abstract Background HAART has significantly reduced AIDS-related morbidity in children. However, limited evidence is available from developing countries regarding patterns of opportunistic illnesses. We describe these events and their associated factors in children with AIDS in Brazil. Methods This study is based on two representative retrospective multi-center cohorts including a total 1,859 children with AIDS, infected via mother-to-child transmission (MTCT, between 1983-2002. Opportunistic illnesses were described and analyzed over time. The association of demographic, clinical and operational data with the occurrence of opportunistic diseases was assessed. Results In total, 1,218 (65.5% had at least one event of an opportunistic disease. Variables significantly associated with occurrence of these events included: region of residence (OR 2.68-11.33, as compared to the Northern region, age Pneumocystis jirovecii pneumonia (21.9 vs. 13.2%; p Conclusions Despite the significant reduction in recent years, opportunistic illnesses are still common in Brazilian children with AIDS in the HAART era, especially bacterial diseases. The data reinforce the need for scaling up prevention of MTCT, early diagnosis of infection, and improvement of comprehensive pediatric care.

  20. Analysing the Behaviour and Performance of Opportunistic Routing Protocols in Highly Mobile Wireless Ad Hoc Networks

    Directory of Open Access Journals (Sweden)

    Varun G Menon

    2016-10-01

    Full Text Available Recent advances in wireless networks have enabled us to deploy and use mobile ad hoc networks for communication between the rescue officers in disaster recovery and reconstruction operations. This highly dynamic network does not require any infrastructure or centralized control. As the topology of the network remain dynamic, severe performance limitations incur with traditional routing strategies. Recently a new routing paradigm known as opportunistic routing protocols have been proposed to overcome these limitations and to provide efficient delivery of data in these highly dynamic ad hoc networks. Using the broadcasting nature of the wireless medium, this latest routing technique tries to address two major issues of varying link quality and unpredictable node mobility in ad hoc networks. Unlike conventional IP forwarding, where an intermediate node looks up a forwarding table for a suitable next hop, opportunistic routing brings in opportunistic data forwarding that allows multiple candidate nodes in the forwarding area to act on the broadcasted data packet. This increases the reliability of data delivery in the network with reduced delay. One of the most important issues that have not been studied so far is the varying performance of opportunistic routing protocols in wireless networks with highly mobile nodes. This research paper analyses and compares the various advantages, disadvantages and the performance of the latest opportunistic routing protocols in wireless ad hoc networks with highly mobile nodes.

  1. Complete Genome Sequence of Cronobacter turicensis LMG 23827, a Food-Borne Pathogen Causing Deaths in Neonates ▿

    OpenAIRE

    2010-01-01

    Here, we report the complete and annotated genome sequence of Cronobacter turicensis, an opportunistic food-borne pathogen, which is known as a rare but important cause of life-threatening neonatal infections. Among all proteins of C. turicensis, 223 have been annotated as virulence- and disease-related proteins.

  2. Complete genome sequence of Cronobacter turicensis LMG 23827, a food-borne pathogen causing deaths in neonates.

    Science.gov (United States)

    Stephan, Roger; Lehner, Angelika; Tischler, Patrick; Rattei, Thomas

    2011-01-01

    Here, we report the complete and annotated genome sequence of Cronobacter turicensis, an opportunistic food-borne pathogen, which is known as a rare but important cause of life-threatening neonatal infections. Among all proteins of C. turicensis, 223 have been annotated as virulence- and disease-related proteins.

  3. Effects of Low-Level Laser Irradiation on the Pathogenicity of Candida albicans: In Vitro and in Vivo Study

    NARCIS (Netherlands)

    Seyedmousavi Tasieh, S.; Hashemi, S.J.; Rezaie, S.; Fateh, M.; Djavid, G.E.; Zibafar, E.; Morsali, F.; Zand, N.; Alinaghizadeh, M.; Ataie-Fashtami, L.

    2014-01-01

    Abstract Objective: The purpose of this study was to evaluate the effects of low-level laser irradiation (LLLI) on the in vitro growth characteristics and in vivo pathogenicity of Candida albicans in a murine model in the absence of a photosensitizer. Background data: C. albicans is an opportunistic

  4. Effects of Low-Level Laser Irradiation on the Pathogenicity of Candida albicans: In Vitro and in Vivo Study

    NARCIS (Netherlands)

    Seyedmousavi Tasieh, S.; Hashemi, S.J.; Rezaie, S.; Fateh, M.; Djavid, G.E.; Zibafar, E.; Morsali, F.; Zand, N.; Alinaghizadeh, M.; Ataie-Fashtami, L.

    2014-01-01

    Abstract Objective: The purpose of this study was to evaluate the effects of low-level laser irradiation (LLLI) on the in vitro growth characteristics and in vivo pathogenicity of Candida albicans in a murine model in the absence of a photosensitizer. Background data: C. albicans is an opportunistic

  5. Cloning and characterization of a pectin lyase gene from Colletotrichum lindemuthianum and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms.

    Science.gov (United States)

    Lara-Márquez, Alicia; Zavala-Páramo, María G; López-Romero, Everardo; Calderón-Cortés, Nancy; López-Gómez, Rodolfo; Conejo-Saucedo, Ulises; Cano-Camacho, Horacio

    2011-12-09

    Microorganisms produce cell-wall-degrading enzymes as part of their strategies for plant invasion/nutrition. Among these, pectin lyases (PNLs) catalyze the depolymerization of esterified pectin by a β-elimination mechanism. PNLs are grouped together with pectate lyases (PL) in Family 1 of the polysaccharide lyases, as they share a conserved structure in a parallel β-helix. The best-characterized fungal pectin lyases are obtained from saprophytic/opportunistic fungi in the genera Aspergillus and Penicillium and from some pathogens such as Colletotrichum gloeosporioides.The organism used in the present study, Colletotrichum lindemuthianum, is a phytopathogenic fungus that can be subdivided into different physiological races with different capacities to infect its host, Phaseolus vulgaris. These include the non-pathogenic and pathogenic strains known as races 0 and 1472, respectively. Here we report the isolation and sequence analysis of the Clpnl2 gene, which encodes the pectin lyase 2 of C. lindemuthianum, and its expression in pathogenic and non-pathogenic races of C. lindemuthianum grown on different carbon sources. In addition, we performed a phylogenetic analysis of the deduced amino acid sequence of Clpnl2 based on reported sequences of PNLs from other sources and compared the three-dimensional structure of Clpnl2, as predicted by homology modeling, with those of other organisms. Both analyses revealed an early separation of bacterial pectin lyases from those found in fungi and oomycetes. Furthermore, two groups could be distinguished among the enzymes from fungi and oomycetes: one comprising enzymes from mostly saprophytic/opportunistic fungi and the other formed mainly by enzymes from pathogenic fungi and oomycetes. Clpnl2 was found in the latter group and was grouped together with the pectin lyase from C. gloeosporioides. The Clpnl2 gene of C. lindemuthianum shares the characteristic elements of genes coding for pectin lyases. A time-course analysis

  6. Cloning and characterization of a pectin lyase gene from Colletotrichum lindemuthianum and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms

    Directory of Open Access Journals (Sweden)

    Lara-Márquez Alicia

    2011-12-01

    Full Text Available Abstract Background Microorganisms produce cell-wall-degrading enzymes as part of their strategies for plant invasion/nutrition. Among these, pectin lyases (PNLs catalyze the depolymerization of esterified pectin by a β-elimination mechanism. PNLs are grouped together with pectate lyases (PL in Family 1 of the polysaccharide lyases, as they share a conserved structure in a parallel β-helix. The best-characterized fungal pectin lyases are obtained from saprophytic/opportunistic fungi in the genera Aspergillus and Penicillium and from some pathogens such as Colletotrichum gloeosporioides. The organism used in the present study, Colletotrichum lindemuthianum, is a phytopathogenic fungus that can be subdivided into different physiological races with different capacities to infect its host, Phaseolus vulgaris. These include the non-pathogenic and pathogenic strains known as races 0 and 1472, respectively. Results Here we report the isolation and sequence analysis of the Clpnl2 gene, which encodes the pectin lyase 2 of C. lindemuthianum, and its expression in pathogenic and non-pathogenic races of C. lindemuthianum grown on different carbon sources. In addition, we performed a phylogenetic analysis of the deduced amino acid sequence of Clpnl2 based on reported sequences of PNLs from other sources and compared the three-dimensional structure of Clpnl2, as predicted by homology modeling, with those of other organisms. Both analyses revealed an early separation of bacterial pectin lyases from those found in fungi and oomycetes. Furthermore, two groups could be distinguished among the enzymes from fungi and oomycetes: one comprising enzymes from mostly saprophytic/opportunistic fungi and the other formed mainly by enzymes from pathogenic fungi and oomycetes. Clpnl2 was found in the latter group and was grouped together with the pectin lyase from C. gloeosporioides. Conclusions The Clpnl2 gene of C. lindemuthianum shares the characteristic elements of

  7. Optimising social information by game theory and ant colony method to enhance routing protocol in opportunistic networks

    Directory of Open Access Journals (Sweden)

    Chander Prabha

    2016-09-01

    Full Text Available The data loss and disconnection of nodes are frequent in the opportunistic networks. The social information plays an important role in reducing the data loss because it depends on the connectivity of nodes. The appropriate selection of next hop based on social information is critical for improving the performance of routing in opportunistic networks. The frequent disconnection problem is overcome by optimising the social information with Ant Colony Optimization method which depends on the topology of opportunistic network. The proposed protocol is examined thoroughly via analysis and simulation in order to assess their performance in comparison with other social based routing protocols in opportunistic network under various parameters settings.

  8. Joint Network Coding and Opportunistic Scheduling for the Bidirectional Relay Channel

    KAUST Repository

    Shaqfeh, Mohammad

    2013-05-27

    In this paper, we consider a two-way communication system in which two users communicate with each other through an intermediate relay over block-fading channels. We investigate the optimal opportunistic scheduling scheme in order to maximize the long-term average transmission rate in the system assuming symmetric information flow between the two users. Based on the channel state information, the scheduler decides that either one of the users transmits to the relay, or the relay transmits to a single user or broadcasts to both users a combined version of the two users’ transmitted information by using linear network coding. We obtain the optimal scheduling scheme by using the Lagrangian dual problem. Furthermore, in order to characterize the gains of network coding and opportunistic scheduling, we compare the achievable rate of the system versus suboptimal schemes in which the gains of network coding and opportunistic scheduling are partially exploited.

  9. Improved Power-Delay Trade-off in Wireless Networks Using Opportunistic Routing

    CERN Document Server

    Shin, Won-Yong; Lee, Yong H

    2009-01-01

    We study the benefits of opportunistic routing in wireless networks by examining how the power and delay scale as the number of source-destination (S-D) pairs in the network increases. The scaling behavior of conventional multi-hop transmission that does not employ opportunistic routing is also examined for comparison. Our results indicate that opportunistic routing can exhibit a better power--delay trade-off than that of conventional routing by providing up to a logarithmic boost in the scaling law. Such a gain is possible since the receivers can tolerate more interference due to the increased received signal power provided by the multi-user diversity (MUD) gain, which means having more simultaneous transmissions is possible. Computer simulations for both routing schemes are also performed, which show trends consistent with our analytical predictions.

  10. Opportunistic Routing with Congestion Diversity in Wireless Ad-hoc Networks

    CERN Document Server

    Bhorkar, Abhijeet; Javidi, Tara

    2012-01-01

    We consider the problem of routing packets across a multi-hop network consisting of multiple sources of traffic and wireless links while ensuring bounded expected delay. Each packet transmission can be overheard by a random subset of receiver nodes among which the next relay is selected opportunistically. The main challenge in the design of minimum-delay routing policies is balancing the trade-off between routing the packets along the shortest paths to the destination and distributing traffic according to the maximum backpressure. Combining important aspects of shortest path and backpressure routing, this paper provides a systematic development of a distributed opportunistic routing policy with congestion diversity ({D-ORCD}). {D-ORCD} uses a measure of draining time to opportunistically identify and route packets along the paths with an expected low overall congestion. {D-ORCD} is proved to ensure a bounded expected delay for all networks and under any admissible traffic. Furthermore, this paper proposes a p...

  11. Performance analysis of adaptive modulation for cognitive radios with opportunistic access

    KAUST Repository

    Chen, Yunfei

    2011-06-01

    The performance of adaptive modulation for cognitive radio with opportunistic access is analyzed by considering the effects of spectrum sensing and primary user traffic for Nakagami-m fading channels. Both the adaptive continuous rate scheme and the adaptive discrete rate scheme are considered. Numerical results show that spectrum sensing and primary user traffic cause considerable degradation to the bit error rate performance of adaptive modulation in a cognitive radio system with opportunistic access to the licensed channel. They also show that primary user traffic does not affect the link spectral efficiency performance of adaptive modulation, while the spectrum sensing degrades the link spectral efficiency performance. © 2011 IEEE.

  12. Switch Based Opportunistic Spectrum Access for General Primary User Traffic Model

    KAUST Repository

    Gaaloul, Fakhreddine

    2012-06-18

    This letter studies cognitive radio transceiver that can opportunistically use the available channels of primary user (PU). Specifically, we investigate and compare two different opportunistic channel access schemes. The first scheme applies when the secondary user (SU) has access to only one channel. The second scheme, based on channel switching mechanism, applies when the SU has access to multiple channels but can at a given time monitor and access only one channel. For these access schemes, we derive the exact analytical results for the novel performance metrics of average access time and average waiting time under general PU traffic models.

  13. Opportunistic relaying in multipath and slow fading channel: Relay selection and optimal relay selection period

    KAUST Repository

    Sungjoon Park,

    2011-11-01

    In this paper we present opportunistic relay communication strategies of decode and forward relaying. The channel that we are considering includes pathloss, shadowing, and fast fading effects. We find a simple outage probability formula for opportunistic relaying in the channel, and validate the results by comparing it with the exact outage probability. Also, we suggest a new relay selection algorithm that incorporates shadowing. We consider a protocol of broadcasting the channel gain of the previously selected relay. This saves resources in slow fading channel by reducing collisions in relay selection. We further investigate the optimal relay selection period to maximize the throughput while avoiding selection overhead. © 2011 IEEE.

  14. Context sensitive trust based geographic opportunistic routing in mobile ad hoc networks

    Indian Academy of Sciences (India)

    A RAJESH; N MOHAN KUMAR

    2016-11-01

    Position based opportunistic routing (POR) is a stateless, robust, and reliable geographic routing protocol in Mobile AdHoc NETwork (MANET). The opportunistic routing embraces broadcast property of wireless channels and utilizes it for opportunistic forwarding. Both the malicious node behavior and the backupnodes’ behavior are equally treated as malicious in the existing misbehavior detection mechanisms. Hence, incorporating a general trust model in POR is not combative with routing attacks. It is necessary to determine whether the misbehavior is likely a result of malicious activity or due to the backup scenario of opportunistic forwarding. On the other hand, if context-sensitive trust information is available on every node, it ensures a fair decision making and also supports secured routing in an opportunistic approach. This work investigates the utilization of context attributes along with generic trust model to allow POR for secure and reliable data forwarding. This paper introduces context-sensitive trust for choosing the data forwarding node in POR (CPOR) to assist opportunistic routing in selecting the trusted optimal data forwarding node and to cope with both security and reliability of communications. The proposed work exercises both coarse- and fine-grained trust evaluation to strengthen the trustworthiness. The coarse-grained trust measure includes positive progress per hop and behavioral attribute of the nodes in terms of routing service. The fine-grained trust evaluation differs the opportunistic routing environment from the adverse scenarios and aids the source node such that it builds a highly trusted positive progress set using contextual attributes. The fine-grained trust evaluation deduces the ideal contextual information such as the link quality, battery energy, and the backup service to determine the accurate trust value of nodes. As a result, it involves optimal routes and enables CPOR to maintain the routingperformance equal to the POR even

  15. Pathogens and host immunity in the ancient human oral cavity

    DEFF Research Database (Denmark)

    Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak

    2014-01-01

    cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction......Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral...... of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental...

  16. Identification of putative plant pathogenic determinants from a draft genome sequence of an opportunistic klebsiella pneumoniae strain

    Science.gov (United States)

    Klebsiella pneumoniae has been known historically as a causal agent of bacterial pneumonia. More recently, K. pneumoniaerepresentatives have been shown to have a broad ecological distribution and are recognized nitrogen-fixers. Previously, we demonstrated the capacity of K. pneumoniae strain Kp 5-1R...

  17. Comparative effects of micafungin, caspofungin, and anidulafungin against a difficult-to-treat fungal opportunistic pathogen, Candida glabrata.

    Science.gov (United States)

    Spreghini, Elisabetta; Orlando, Fiorenza; Sanguinetti, Maurizio; Posteraro, Brunella; Giannini, Daniele; Manso, Esther; Barchiesi, Francesco

    2012-03-01

    The aim of this study was to compare the in vitro and in vivo activities of micafungin, caspofungin, and anidulafungin against Candida glabrata. The MICs against 28 clinical isolates showed that the overall susceptibilities to caspofungin and to micafungin were not statistically different in the absence of human serum, whereas the isolates were less susceptible to micafungin than to caspofungin in its presence. Minimum fungicidal concentrations, as well as time-kill experiments, showed that caspofungin was more active than anidulafungin, while micafungin was superior to either caspofungin or anidulafungin without serum; its addition rendered caspofungin and micafungin equally effective. A murine model of systemic candidiasis against a C. glabrata-susceptible isolate was performed to study the effects of all three echinocandins, and kidney burden counts showed that caspofungin, micafungin, and anidulafungin were active starting from 0.25, 1, and 5 mg/kg of body weight/day, respectively. Two echinocandin-resistant strains of C. glabrata were selected: C. glabrata 30, a laboratory strain harboring the mutation Fks2p-P667T, and C. glabrata 51, a clinical isolate harboring the mutation Fks2p-D666G. Micafungin activity was shown to be as effective as or more effective than that of caspofungin or anidulafungin in terms of MICs. In vivo studies against these resistant strains showed that micafungin was active starting from 1 mg/kg/day, while caspofungin was effective only when administrated at higher doses of 5 or 10 mg/kg/day. Although a trend toward colony reduction was observed with the highest doses of anidulafungin, a significant statistical difference was never reached.

  18. Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20T)

    Energy Technology Data Exchange (ETDEWEB)

    Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lu, Megan [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Ivanova, N [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Microbial Monitoring of Common Opportunistic Pathogens by Comparing Multiple Real-time PCR Platforms for Potential Space Applications

    Science.gov (United States)

    Roman, Monserrate C.; Jones, Kathy U.; Oubre, Cherie M.; Castro, Victoria; Ott, Mark C.; Birmele, Michele; Venkateswaran, Kasthuri J.; Vaishampayan, Parag A.

    2013-01-01

    Current methods for microbial detection: a) Labor & time intensive cultivation-based approaches that can fail to detect or characterize all cells present. b) Requires collection of samples on orbit and transportation back to ground for analysis. Disadvantages to current detection methods: a) Unable to perform quick and reliable detection on orbit. b) Lengthy sampling intervals. c) No microbe identification.

  20. Isolation and characterization of numerous novel phages targeting diverse strains of the ubiquitous and opportunistic pathogen Achromobacter xylosoxidans.

    Science.gov (United States)

    Wittmann, Johannes; Dreiseikelmann, Brigitte; Rohde, Christine; Rohde, Manfred; Sikorski, Johannes

    2014-01-01

    The clinical relevance of nosocomially acquired infections caused by multi-resistant Achromobacter strains is rapidly increasing. Here, a diverse set of 61 Achromobacter xylosoxidans strains was characterized by MultiLocus Sequence Typing and Phenotype MicroArray technology. The strains were further analyzed in regard to their susceptibility to 35 antibiotics and to 34 different and newly isolated bacteriophages from the environment. A large proportion of strains were resistant against numerous antibiotics such as cephalosporines, aminoglycosides and quinolones, whereas piperacillin-tazobactam, ticarcillin, mezlocillin and imipenem were still inhibitory. We also present the first expanded study on bacteriophages of the genus Achromobacter that has been so far a blank slate with respect to phage research. The phages were isolated mainly from several waste water treatment plants in Germany. Morphological analysis of all of these phages by electron microscopy revealed a broad diversity with different members of the order Caudovirales, including the families Siphoviridae, Myoviridae, and Podoviridae. A broad spectrum of different host ranges could be determined for several phages that lysed up to 24 different and in part highly antibiotic resistant strains. Molecular characterisation by DNA restriction analysis revealed that all phages contain linear double-stranded DNA. Their restriction patterns display distinct differences underlining their broad diversity.

  1. Safe interruption of maintenance therapy against previous infection with four common HIV-associated opportunistic pathogens during potent antiretroviral therapy

    DEFF Research Database (Denmark)

    Kirk, Ole; Reiss, Peter; Uberti-Foppa, Caterina;

    2002-01-01

    maintenance therapy for cytomegalovirus (CMV) end-organ disease, disseminated Mycobacterium avium complex (MAC) infection, cerebral toxoplasmosis, and extrapulmonary cryptococcosis in patients receiving antiretroviral therapy. DESIGN: Observational study. SETTING: Seven European HIV cohorts. PATIENTS: 358...... identified: 162 for CMV disease, 103 for MAC infection, 75 for toxoplasmosis, and 39 for cryptococcosis. During 781 person-years of follow-up, five patients had relapse. Two relapses (one of CMV disease and one of MAC infection) were diagnosed after maintenance therapy was interrupted when the CD4 lymphocyte....... One relapse (toxoplasmosis) was diagnosed after maintenance therapy interruption at a CD4 lymphocyte count greater than 200 x 10(6) cells/L for 15 months. The overall incidences of recurrent CMV disease, MAC infection, toxoplasmosis, and cryptococcosis were 0.54 per 100 person-years (95% CI, 0.07 to 1...

  2. Microbial Monitoring of Common Opportunistic Pathogens by Comparing Multiple Real-Time PCR Platforms for Potential Space Applications

    Science.gov (United States)

    Oubre, Cherie M.; Birmele, Michele N.; Castro, Victoria A.; Venkateswaran, Kasthuri J.; Vaishampayan, Parag A.; Jones, Kathy U.; Singhal, Adesh; Johnston, Angela S.; Roman, Monserrate C.; Ozbolt, Tamra A.; Jett, Daniel X.; Roberts, Michael S.; Ott, C. Mark

    2013-01-01

    Because the International Space Station is a closed environment with rotations of astronauts and equipment that each introduce their own microbial flora, it is necessary to monitor the air, surfaces, and water for microbial contamination. Current microbial monitoring includes labor- and time-intensive methods to enumerate total bacterial and fungal cells, with limited characterization, during in-flight testing. Although this culture-based method is sufficient for monitoring the International Space Station, on future long-duration missions more detailed characterization will need to be performed during flight, as sample return and ground characterization may not be available. At a workshop held in 2011 at NASA's Johnson Space Center to discuss alternative methodologies and technologies suitable for microbial monitoring for these long-term exploration missions, molecular-based methodologies such as polymerase chain reaction (PCR) were recommended. In response, a multi-center (Marshall Space Flight Center, Johnson Space Center, Jet Propulsion Laboratory, and Kennedy Space Center) collaborative research effort was initiated to explore novel commercial-off-the-shelf hardware options for space flight environmental monitoring. The goal was to evaluate quantitative or semi-quantitative PCR approaches for low-cost in-flight rapid identification of microorganisms that could affect crew safety. The initial phase of this project identified commercially available platforms that could be minimally modified to perform nominally in microgravity. This phase was followed by proof-of-concept testing of the highest qualifying candidates with a universally available challenge organism, Salmonella enterica. The analysis identified two technologies that were able to perform sample-to-answer testing with initial cell sample concentrations between 50 and 400 cells. In addition, the commercial systems were evaluated for initial flight safety and readiness.

  3. A Double-Edged Sword: The Role of VEGF in Wound Repair and Chemoattraction of Opportunist Pathogens

    Directory of Open Access Journals (Sweden)

    Eric Birkenhauer

    2015-03-01

    Full Text Available Wound healing is a complex process essential to repairing damaged tissues and preventing infection. Skin is the first line of defense, a chief physical barrier to microbe entry. Wound healing is a physical rebuilding process, but at the same time it is an inflammatory event. In turn, molecules for wound repair are secreted by fibroblasts and others present at the wound site. Vascular endothelial growth factor (VEGF is a critical cytokine that exhibits chemoattractant properties, recruiting other immune cells to the site. Although generally beneficial, VEGF may also act as a chemoattractant for invading microorganisms, such as Pseudomonas aeruginosa. P. aeruginosa is problematic during wound infection due to its propensity to form biofilms and exhibit heightened antimicrobial resistance. Here, we explored the influence of VEGF gradients (in a microfluidic device wound model on the motility and chemotactic properties of P. aeruginosa. At lower concentrations, VEGF had little effect on motility, but as the maximal concentration within the gradient increased, P. aeruginosa cells exhibited directed movement along the gradient. Our data provide evidence that while beneficial, VEGF, in excess, may aid colonization by P. aeruginosa. This highlights the necessity for the efficient resolution of inflammation. Understanding the dynamics of wound colonization may lead to new/enhanced therapeutics to hasten recovery.

  4. Anti-biofilm and antibacterial activities of zinc oxide nanoparticles against the oral opportunistic pathogens Rothia dentocariosa and Rothia mucilaginosa.

    Science.gov (United States)

    Khan, Shams T; Ahamed, Maqusood; Musarrat, Javed; Al-Khedhairy, Abdulaziz A

    2014-12-01

    Species of the genus Rothia that inhabit the oral cavity have recently been implicated in a number of diseases. To minimize their role in oral infections, it is imperative to reduce and/or control the growth and biofilm formation activity of Rothia spp. In this study, two bacterial isolates, Ora-7 and Ora-16, were obtained from the oral cavity of a healthy male subject and identified as Rothia dentocariosa and Rothia mucilaginosa, respectively, using a polyphasic taxonomic approach. Antimicrobial and anti-biofilm formation activities of zinc oxide nanoparticles (ZnO-NPs), of average size 35 nm, were assessed in in vitro assays using Crystal Violet and live and dead staining techniques. The ZnO-NPs exhibited an IC50 value of 53 and 76 μg ml(-1) against R. dentocariosa and R. mucilaginosa, respectively. Biofilm-formation assays, performed on the surfaces of polystyrene plates, artificial teeth, and dental prostheses, revealed the efficacy of ZnO-NPs as a potential antibacterial agent for controlling the growth of Rothia isolates in both planktonic form and biofilm.

  5. Draft Genome Sequences of Vibrio alginolyticus Strains V1 and V2, Opportunistic Marine Pathogens

    DEFF Research Database (Denmark)

    Castillo, Daniel; D'Alvise, Paul; Kalatzis, Panos G.

    2015-01-01

    We announce the draft genome sequences of Vibrio alginolyticus strains V1 and V2, isolated from juvenile Sparus aurata and Dentex dentex, respectively, during outbreaks of vibriosis. The genome sequences are 5,257,950 bp with a G+C content of 44.5% for V. alginolyticus V1 and 5,068,299 bp with a ...

  6. Isolation and characterization of numerous novel phages targeting diverse strains of the ubiquitous and opportunistic pathogen Achromobacter xylosoxidans.

    Directory of Open Access Journals (Sweden)

    Johannes Wittmann

    Full Text Available The clinical relevance of nosocomially acquired infections caused by multi-resistant Achromobacter strains is rapidly increasing. Here, a diverse set of 61 Achromobacter xylosoxidans strains was characterized by MultiLocus Sequence Typing and Phenotype MicroArray technology. The strains were further analyzed in regard to their susceptibility to 35 antibiotics and to 34 different and newly isolated bacteriophages from the environment. A large proportion of strains were resistant against numerous antibiotics such as cephalosporines, aminoglycosides and quinolones, whereas piperacillin-tazobactam, ticarcillin, mezlocillin and imipenem were still inhibitory. We also present the first expanded study on bacteriophages of the genus Achromobacter that has been so far a blank slate with respect to phage research. The phages were isolated mainly from several waste water treatment plants in Germany. Morphological analysis of all of these phages by electron microscopy revealed a broad diversity with different members of the order Caudovirales, including the families Siphoviridae, Myoviridae, and Podoviridae. A broad spectrum of different host ranges could be determined for several phages that lysed up to 24 different and in part highly antibiotic resistant strains. Molecular characterisation by DNA restriction analysis revealed that all phages contain linear double-stranded DNA. Their restriction patterns display distinct differences underlining their broad diversity.

  7. Transmission of the opportunistic cotton (Gossypium hirsutum L.) boll pathogen Pantoea agglomerans by the brown stink bug (Euschistus servus Say)

    Science.gov (United States)

    Damage to developing cotton bolls by piercing-sucking insects such as stink bugs has traditionally been attributed solely to pest feeding. Previously, we showed clear differences in severity of boll damage resulting from southern green stink bug (Nezara viridula L.) fed sterile food compared to thos...

  8. Microbiology and foodborne pathogens in honey.

    Science.gov (United States)

    Grabowski, N T; Klein, G

    2017-06-13

    Honey has been considered a relatively safe foodstuff due to its compositional properties, with infant botulism caused by Clostridium botulinum being the most prominent health risk associated with it. Our review is focused on the honey microflora along the food chain and evaluates the pathogenic potential of those microorganisms found in honey. This product may contain a great variety of bacteria and, particularly, fungi that eventually entered the food chain at an early stage (e.g., via pollen). For many of these microorganisms, opportunistic infections in humans have been recorded (e.g., infections by Staphylococcus spp., Citrobacter spp., Escherichia coli, Hafnia alvei, Aspergillus spp., Fusarium spp., Trichoderma spp., Chaetomium spp.), although direct infections via honey were not registered.

  9. Emerging Pathogens Initiative (EPI)

    Data.gov (United States)

    Department of Veterans Affairs — The Emerging Pathogens Initiative (EPI) database contains emerging pathogens information from the local Veterans Affairs Medical Centers (VAMCs). The EPI software...

  10. Potency and selectivity indices of acetone leaf extracts of nine selected South African trees against six opportunistic Enterobacteriaceae isolates from commercial chicken eggs.

    Science.gov (United States)

    Elisha, Ishaku L; Jambalang, Alexander R; Botha, Francien S; Buys, Elna M; McGaw, Lyndy J; Eloff, Jacobus N

    2017-02-02

    The rise in antimicrobial resistance in a plethora of nosocomial and opportunistic bacterial pathogens often isolated from commercial eggs, poses a serious public health concern. The existence of these contaminants may also serve as a drawback in the current efforts of improving the well-being of immunocompromised patients. The aim of this study was to determine the efficacy of plant extracts that had good activity on Escherichia coli in previous word on pathogens isolated from eggs for possible use in combating pathogens from eggs. Acetone leaf extracts of nine trees with good activities against Escherichia coli were tested for their in vitro antibacterial activity against six opportunistic bacterial isolates from commercial eggs (Stenotrophomonas maltophilia, Klebsiella pneumoniae, Salmonella serotype Typhimurium, Proteus mirabilis, Enterobacter cloacae and Escherichia coli) using a serial microdilution method with tetrazolium violet as indicator of growth. Cytotoxicity was determined using a tetrazolium-based colorimetric assay against Vero kidney cells, and selectivity index calculated. The MIC values range of the different extracts against Stenotrophomonas maltophilia was 0.08-0.31 mg/ml, Klebsiella pneumonia 0.08-0.63 mg/ml, Salmonella ser. Typhimurium 0.08-0.63 mg/ml, Proteus mirabilis 0.02-1.25 mg/ml, Enterobacter cloacae 0.08-0.31 mg/ml and Escherichia coli 0.08-0.16 mg/ml respectively. Escherichia coli was the most sensitive while Proteus mirabilis was most resistant pathogen to the different test extracts, with mean MIC values of 0.08 mg/ml and 0.46 mg/ml respectively. Cremaspora triflora extracts had good activity against all the pathogenic egg isolates, with the exception of Proteus mirabilis. Maesa lanceolata and Elaeodendron croceum had the best total antibacterial activity (TAA), while generally the selectivity index of the extract was low (SI activity of C. triflora extracts suggests that the plant has potential as a therapeutic agent

  11. Red knots scavenging on large, dying cockles : Opportunistic feeding by a sensory specialized mollusc-crushing shorebird

    NARCIS (Netherlands)

    Poot, Martin J M; Roelen, Bernard A J; Piersma, Theunis

    2014-01-01

    Despite their specializations, shorebirds can be opportunistic foragers during the non-breeding season. We describe how a highly specialized probe-feeding shorebird, the Red Knot Calidris canutus, suddenly ignored its shallow buried hard-shelled mollusc prey and opportunistically shifted to an unusu

  12. Red knots scavenging on large, dying cockles : Opportunistic feeding by a sensory specialized mollusc-crushing shorebird

    NARCIS (Netherlands)

    Poot, Martin J M; Roelen, Bernard A J; Piersma, Theunis

    2014-01-01

    Despite their specializations, shorebirds can be opportunistic foragers during the non-breeding season. We describe how a highly specialized probe-feeding shorebird, the Red Knot Calidris canutus, suddenly ignored its shallow buried hard-shelled mollusc prey and opportunistically shifted to an

  13. Opportunistic mobile air pollution monitoring: A case study with city wardens in Antwerp

    Science.gov (United States)

    Van den Bossche, Joris; Theunis, Jan; Elen, Bart; Peters, Jan; Botteldooren, Dick; De Baets, Bernard

    2016-09-01

    The goal of this paper is to explore the potential of opportunistic mobile monitoring to map the exposure to air pollution in the urban environment at a high spatial resolution. Opportunistic mobile monitoring makes use of existing mobile infrastructure or people's common daily routines to move measurement devices around. Opportunistic mobile monitoring can also play a crucial role in participatory monitoring campaigns as a typical way to gather data. A case study to measure black carbon was set up in Antwerp, Belgium, with the collaboration of city employees (city wardens). The Antwerp city wardens are outdoors for a large part of the day on surveillance tours by bicycle or on foot, and gathered a total of 393 h of measurements. The data collection is unstructured both in space and time, leading to sampling bias. A temporal adjustment can only partly counteract this bias. Although a high spatial coverage was obtained, there is still a rather large uncertainty on the average concentration levels at a spatial resolution of 50 m due to a limited number of measurements and sampling bias. Despite of this uncertainty, large spatial patterns within the city are clearly captured. This study illustrates the potential of campaigns with unstructured opportunistic mobile monitoring, including participatory monitoring campaigns. The results demonstrate that such an approach can indeed be used to identify broad spatial trends over a wider area, enabling applications including hotspot identification, personal exposure studies, regression mapping, etc. But, they also emphasize the need for repeated measurements and careful processing and interpretation of the data.

  14. Opportunistic feeding behaviour of rough-toothed dolphins Steno bredanensis off Mauritania

    NARCIS (Netherlands)

    Addink, M.J.; Smeenk, C.

    2001-01-01

    A small group of rough-toothed dolphins Steno bredanensis was observed at the outer edge of the Banc d’Arguin, Mauritania. The animals were feeding opportunistically around a trawling research vessel. Hunting behaviour and mother-calf interactions are described

  15. Non-Orthogonal Random Access in MIMO Cognitive Radio Networks: Beamforming, Power Allocation, and Opportunistic Transmission.

    Science.gov (United States)

    Lin, Huifa; Shin, Won-Yong

    2017-01-01

    We study secondary random access in multi-input multi-output cognitive radio networks, where a slotted ALOHA-type protocol and successive interference cancellation are used. We first introduce three types of transmit beamforming performed by secondary users, where multiple antennas are used to suppress the interference at the primary base station and/or to increase the received signal power at the secondary base station. Then, we show a simple decentralized power allocation along with the equivalent single-antenna conversion. To exploit the multiuser diversity gain, an opportunistic transmission protocol is proposed, where the secondary users generating less interference are opportunistically selected, resulting in a further reduction of the interference temperature. The proposed methods are validated via computer simulations. Numerical results show that increasing the number of transmit antennas can greatly reduce the interference temperature, while increasing the number of receive antennas leads to a reduction of the total transmit power. Optimal parameter values of the opportunistic transmission protocol are examined according to three types of beamforming and different antenna configurations, in terms of maximizing the cognitive transmission capacity. All the beamforming, decentralized power allocation, and opportunistic transmission protocol are performed by the secondary users in a decentralized manner, thus resulting in an easy implementation in practice.

  16. Cocoon: A lightweight opportunistic networking middleware for community-oriented smart mobile applications

    NARCIS (Netherlands)

    Türkes, Okan; Scholten, Hans; Havinga, Paul J.M.

    2016-01-01

    Modern society is surrounded by an ample spectrum of smart mobile devices. This ubiquity forms a high potential for community-oriented opportunistic ad hoc networking applications. Nevertheless, today’s smart mobile devices such as smartphones, tablets, and wristbands are still onerous to automatica

  17. Opportunistic Interference Mitigation Achieves Optimal Degrees-of-Freedom in Cellular Networks

    CERN Document Server

    Jung, Bang Chul; Shin, Won-Yong

    2010-01-01

    We introduce an opportunistic interference mitigation (OIM) for cellular networks, where a user scheduling strategy is utilized in uplink $K$-cell environments with time-invariant channel coefficients and base stations (BSs) having $M$ receive antennas. In the OIM scheme, each BS opportunistically selects a set of users who generate the minimum interference to the other BSs. We consider two OIM protocols according to the number $S$ of simultaneously transmitting users per cell: an opportunistic interference nulling (OIN) and an opportunistic interference alignment (OIA). Then, their performance is analyzed in terms of degrees-of-freedom (DoFs). It is shown that $KM$ DoFs are achievable under the OIN protocol with $M$ selected users per cell, while the OIA scheme with $S$ selected users (smaller than $M$) achieves $KS$ DoFs. Assuming that $N$ denotes the total number of users in a cell, we also analyze the scaling condition between system parameters $K$, $M$, $N$, $S$, and the received signal-to-noise ratio su...

  18. From Spectrum Pooling to Space Pooling: Opportunistic Interference Alignment in MIMO Cognitive Networks

    CERN Document Server

    Perlaza, S M; Lasaulce, S; Debbah, M

    2009-01-01

    We describe a non-cooperative interference alignment (IA) technique which allows an opportunistic multiple input multiple output (MIMO) link (secondary) to harmlessly coexist with another MIMO link (primary) in the same frequency band. We assume perfect channel knowledge in the primary receiver and transmitter such that capacity is achieved by transmiting along the spatial directions (SD) associated with the singular values of its channel matrix using a water-filling power allocation (PA) scheme. Often, power limitations lead the primary transmitter to leave some of its SD unused. We show that the opportunistic link can transmit its own data if it is possible to align the interference produced on the primary link with such unused SDs. We provide both a processing scheme to perform IA and a PA scheme which maximizes the transmission rate of the opportunistic link. We determine the asymptotes of the achievable transmission rates of the opportunistic link in the regime of large numbers of antennas to show that d...

  19. Public policy and regulatory implications for the implementation of Opportunistic Cloud Computing Services for Enterprises

    DEFF Research Database (Denmark)

    Kuada, Eric; Olesen, Henning; Henten, Anders

    2012-01-01

    Opportunistic Cloud Computing Services (OCCS) is a social network approach to the provisioning and management of cloud computing services for enterprises. This paper discusses how public policy and regulations will impact on OCCS implementation. We rely on documented publicly available government...

  20. Danish General Practitioners' Use of Prostate-Specific Antigen in Opportunistic Screening for Prostate Cancer

    DEFF Research Database (Denmark)

    Jessen, Kasper; Søndergaard, Jens; Larsen, Pia Veldt;

    2013-01-01

    Background. The use of prostate-specific antigen test has markedly increased in Danish general practice in the last decade. Despite the national guidelines advice against PSA screening, opportunistic screening is supposed to be the primary reason for this increased number of PSA tests performed. ...

  1. Performance of systematic and non-systematic ('opportunistic') screening mammography: a comparative study from Denmark

    DEFF Research Database (Denmark)

    Bihrmann, Kristine; Jensen, Allan; Olsen, Anne Helene;

    2008-01-01

    OBJECTIVES: Evaluation and comparison of the performance of organized and opportunistic screening mammography. METHODS: Women attending screening mammography in Denmark in 2000. The study included 37,072 women attending organized screening. Among these, 320 women were diagnosed with breast cancer...

  2. Opportunistic error correction for mimo-ofdm: from theory to practice

    NARCIS (Netherlands)

    Shao, Xiaoying; Slump, Cornelis H.

    2013-01-01

    Opportunistic error correction based on fountain codes is especially designed for the MIMOOFDM system. The key point of this new method is the tradeoff between the code rate of error correcting codes and the number of sub-carriers in the channel vector to be discarded. By transmitting one fountain-e

  3. Yield of opportunistic targeted screening for type 2 diabetes in primary care: the diabscreen study.

    NARCIS (Netherlands)

    Klein Woolthuis, E.P.; Grauw, W.J.C. de; Gerwen, W.H.E.M. van; Hoogen, H.J.M. van den; Lisdonk, E.H. van de; Metsemakers, J.F.M.; Weel, C. van

    2009-01-01

    PURPOSE: In screening for type 2 diabetes, guidelines recommend targeting high-risk individuals. Our objectives were to assess the yield of opportunistic targeted screening for type 2 diabetes in primary care and to assess the diagnostic value of various risk factors. METHODS: In 11 family practices

  4. Opportunistic feeding behaviour of rough-toothed dolphins Steno bredanensis off Mauritania

    NARCIS (Netherlands)

    Addink, M.J.; Smeenk, C.

    2001-01-01

    A small group of rough-toothed dolphins Steno bredanensis was observed at the outer edge of the Banc d’Arguin, Mauritania. The animals were feeding opportunistically around a trawling research vessel. Hunting behaviour and mother-calf interactions are described

  5. Channel access delay and buffer distribution of two-user opportunistic scheduling schemes in wireless networks

    KAUST Repository

    Hossain, Md Jahangir

    2010-07-01

    In our earlier works, we proposed rate adaptive hierarchical modulation-assisted two-best user opportunistic scheduling (TBS) and hybrid two-user scheduling (HTS) schemes. The proposed schemes are innovative in the sense that they include a second user in the transmission opportunistically using hierarchical modulations. As such the frequency of information access of the users increases without any degradation of the system spectral efficiency (SSE) compared to the classical opportunistic scheduling scheme. In this paper, we analyze channel access delay of an incoming packet at the base station (BS) buffer when our proposed TBS and HTS schemes are employed at the BS. Specifically, using a queuing analytic model we derive channel access delay as well as buffer distribution of the packets that wait at BS buffer for down-link (DL) transmission. We compare performance of the TBS and HTS schemes with that of the classical single user opportunistic schemes namely, absolute carrier-to-noise ratio (CNR)-based single user scheduling (ASS) and normalized CNR-based single user scheduling (NSS). For an independent and identically distributed (i.i.d.) fading environment, our proposed scheme can improve packet\\'s access delay performance compared to the ASS. Selected numerical results in an independent but non-identically distributed (i.n.d.) fading environment show that our proposed HTS achieves overall good channel access delay performance. © 2010 IEEE.

  6. Research of opportunistic behavior in the market of non-standard products

    Directory of Open Access Journals (Sweden)

    Natalya Sergeyevna Grigoryeva

    2015-03-01

    Full Text Available Objective to study the characteristic features of opportunistic behavior in the markets of complex products not subject to standardization by the example of rendering services during constructionandassembling operations. Methods analysis synthesis collection and description of empirical data. Results a significant amount of theoretical material has been analyzed budgets of constructionandassembling operations have been analyzed normative documents have been studied. A poll of quantity surveyors supervisors of constructionandassembling operations consumers of services and works have been carried out. The differences were revealed in the kinds of opportunistic behavior in the nonstandard products markets compared to the standard products markets the results of those surveys were presented in the earlier works by the author. Scientific novelty it has been shown that in case of individual elaboration of each project due to the uniqueness of the result of economic activity as a single complex the opportunistic behavior has such prerequisites as high costs for measurements and control of the quantity and quality of the rendered services and used materials lack of professional competencies of the consumers in the sphere of activity of the producer. Practical value the key provisions and conclusions of the article can be used in the scientific and educational activity when viewing the issues of opportunistic revelations between economic subjects. nbsp

  7. Friend-to-friend short message service with opportunistic Wi-Fi beacons

    NARCIS (Netherlands)

    Türkes, Okan; Scholten, Johan; Havinga, Paul J.M.

    2016-01-01

    This study introduces Oppline, an ad hoc opportunistic short message service that can be collaboratively used by everyone who has a smart mobile device. The data exchange method of Oppline is built on top of the universal Wi-Fi standard, thus expedites platform-independent integration of related

  8. Thermal breeder fuel enrichment zoning

    Science.gov (United States)

    Capossela, Harry J.; Dwyer, Joseph R.; Luce, Robert G.; McCoy, Daniel F.; Merriman, Floyd C.

    1992-01-01

    A method and apparatus for improving the performance of a thermal breeder reactor having regions of higher than average moderator concentration are disclosed. The fuel modules of the reactor core contain at least two different types of fuel elements, a high enrichment fuel element and a low enrichment fuel element. The two types of fuel elements are arranged in the fuel module with the low enrichment fuel elements located between the high moderator regions and the high enrichment fuel elements. Preferably, shim rods made of a fertile material are provided in selective regions for controlling the reactivity of the reactor by movement of the shim rods into and out of the reactor core. The moderation of neutrons adjacent the high enrichment fuel elements is preferably minimized as by reducing the spacing of the high enrichment fuel elements and/or using a moderator having a reduced moderating effect.

  9. Predictor of Mortality in Acquired Immunodeficiency Syndrome Patients with Central Nervous System Opportunistic Infections

    Directory of Open Access Journals (Sweden)

    Agustina Lestari

    2016-12-01

    Full Text Available Background: Indonesia’s increase of acquired immunodeficiency syndrome (AIDS cases is one of the fastest. Mortality cases of AIDS also increase per year. Central nervous system (CNS opportunistic infection is one of the most likely manifestations on advanced stage of Human immunodeficiency virus (HIV/AIDS patients. Common CNS opportunistic infections are toxoplasma infection and tuberculous meningitis (TBM. The study aimed to analyze the predictor of mortality in AIDS patients with CNS opportunistic infections. Methods: This study reviewed 151 medical records from AIDS patients with CNS opportunistic infection admitted to the Department of Neurology, Dr. Hasan Sadikin General Hospital Bandung from 2007-2012. This study was conducted from April to November 2013. Patients’ clinical manifestations (seizure, headache, altered consciousness, laboratory examination (CD4+ level count and treatment history (antiretroviral or ART and cotrimoxazole were collected. Chi-square and logistic regression test were used to determine the mortality predictor in patients. Results: Mortality rate was 37.7%. Clinical manifestations from patients were seizure 29.8%, altered consciousness 66.2%, and headache 88.7%. Patients had cotrimoxazole treatment 44.4% and 38.4% patients had ART. CD4+ level count data from 86 patients were obtained, 94% had CD4+ level count ≤200. Bivariate analysis showed altered consciousness had significant mortality predictor (Odd ratio (OR: 29.944; 95% Confidence interval (CI 6.9–129.945; p<0,0. Multivariate analysis showed ART had highest predictive mortality value (OR: 2.968; 95% CI 1.236–7.126; p=0.015. Conclusions: Altered consciousness and no antiretroviral treatment are mortality predictors in AIDS patients with CNS opportunistic infections.

  10. A trip in the "New Microbiology" with the bacterial pathogen Listeria monocytogenes.

    OpenAIRE

    2014-01-01

    International audience; Listeria monocytogenes is a food-borne pathogen causing an opportunistic disease called listeriosis. This bacterium invades and replicates in most cell types, due to its multiple strategies to exploit host molecular mechanisms. Research aiming at unravelling Listeria invasion and intracellular lifestyle has led to a number of key discoveries in infection biology, cell biology and also microbiology. In this review, we report on our most recent advances in understanding ...

  11. Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment

    OpenAIRE

    Davin-Regli, Anne,; Pagès, Jean-Marie

    2015-01-01

    International audience; Enterobacter aerogenes and E. cloacae have been reported as important opportunistic and multiresistant bacterial pathogens for humans during the last three decades in hospital wards. These Gram-negative bacteria have been largely described during several outbreaks of hospital-acquired infections in Europe and particularly in France. The dissemination of Enterobacter sp. is associated with the presence of redundant regulatory cascades that efficiently control the membra...

  12. DNA topoisomerases from pathogenic fungi: targets for the discovery of antifungal drugs.

    OpenAIRE

    Shen, L L; Baranowski, J; Fostel, J.; Montgomery, D A; Lartey, P A

    1992-01-01

    DNA topoisomerases, a class of enzymes that change the topological structure of DNA, have been shown to be the target of many therapeutic agents, including antibacterial agents (quinolones) and anticancer agents. These drugs inhibit the enzyme in a unique way so that the enzyme is converted into a cellular poison. Candida albicans and Aspergillus niger are two major opportunistic fungal pathogens. Our results show that these fungi have high levels of both type I and type II topoisomerases (wi...

  13. ENRICHMENT OF OBO ONTOLOGIES

    Science.gov (United States)

    Bada, Michael; Hunter, Lawrence

    2006-01-01

    This paper describes a frame-based integration of the three GO subontologies, the Chemicals of Biological Interest ontology (ChEBI), and the Cell Type Ontology (CTO) in which relationships between elements of the ontologies are modeled in a way that better captures the relational semantics between biological concepts represented by the terms, rather than between the terms themselves, than previous frame-based efforts. We also describe a methodology for creating suggested enriching assertions of the form (subject, relationship, object) by identifying patterns in GO terms, mapping these patterns and subpatterns to relationships, matching concepts to these patterns and subpatterns, and integrating these assertions into the ontologies. Using this methodology, a large number of reliable assertions linking previously unlinked OBO terms using a wide variety of specific, hierarchically arranged relationships were created: A predicted assertion was made for 62% of GO terms that matched one of 31 patterns, and 97% of these predicted assertions were assessed to be valid; a further 429 assertions (corresponding to 6% of the matching terms) were manually created, resulting in an initial set of 4,497 assertions. Furthermore, this methodology programmatically integrates assertions into a base ontology such that each assertion is fully consistent with respect to higher (i.e., more general) relevant class and slot levels. Such an integration is absent from previous compositional efforts, and we argue its necessity for the creation of coherent biological ontologies when linking previously unlinked terms. PMID:17011833

  14. Earthquake forecast enrichment scores

    Directory of Open Access Journals (Sweden)

    Christine Smyth

    2012-03-01

    Full Text Available The Collaboratory for the Study of Earthquake Predictability (CSEP is a global project aimed at testing earthquake forecast models in a fair environment. Various metrics are currently used to evaluate the submitted forecasts. However, the CSEP still lacks easily understandable metrics with which to rank the universal performance of the forecast models. In this research, we modify a well-known and respected metric from another statistical field, bioinformatics, to make it suitable for evaluating earthquake forecasts, such as those submitted to the CSEP initiative. The metric, originally called a gene-set enrichment score, is based on a Kolmogorov-Smirnov statistic. Our modified metric assesses if, over a certain time period, the forecast values at locations where earthquakes have occurred are significantly increased compared to the values for all locations where earthquakes did not occur. Permutation testing allows for a significance value to be placed upon the score. Unlike the metrics currently employed by the CSEP, the score places no assumption on the distribution of earthquake occurrence nor requires an arbitrary reference forecast. In this research, we apply the modified metric to simulated data and real forecast data to show it is a powerful and robust technique, capable of ranking competing earthquake forecasts.

  15. City model enrichment

    Science.gov (United States)

    Smart, Philip D.; Quinn, Jonathan A.; Jones, Christopher B.

    The combination of mobile communication technology with location and orientation aware digital cameras has introduced increasing interest in the exploitation of 3D city models for applications such as augmented reality and automated image captioning. The effectiveness of such applications is, at present, severely limited by the often poor quality of semantic annotation of the 3D models. In this paper, we show how freely available sources of georeferenced Web 2.0 information can be used for automated enrichment of 3D city models. Point referenced names of prominent buildings and landmarks mined from Wikipedia articles and from the OpenStreetMaps digital map and Geonames gazetteer have been matched to the 2D ground plan geometry of a 3D city model. In order to address the ambiguities that arise in the associations between these sources and the city model, we present procedures to merge potentially related buildings and implement fuzzy matching between reference points and building polygons. An experimental evaluation demonstrates the effectiveness of the presented methods.

  16. Genome Sequencing and Comparative Genomics Analysis Revealed Pathogenic Potential in Penicillium capsulatum as a Novel Fungal Pathogen Belonging to Eurotiales

    Science.gov (United States)

    Yang, Ying; Chen, Min; Li, Zongwei; Al-Hatmi, Abdullah M. S.; de Hoog, Sybren; Pan, Weihua; Ye, Qiang; Bo, Xiaochen; Li, Zhen; Wang, Shengqi; Wang, Junzhi; Chen, Huipeng; Liao, Wanqing

    2016-01-01

    Penicillium capsulatum is a rare Penicillium species used in paper manufacturing, but recently it has been reported to cause invasive infection. To research the pathogenicity of the clinical Penicillium strain, we sequenced the genomes and transcriptomes of the clinical and environmental strains of P. capsulatum. Comparative analyses of these two P. capsulatum strains and close related strains belonging to Eurotiales were performed. The assembled genome sizes of P. capsulatum are approximately 34.4 Mbp in length and encode 11,080 predicted genes. The different isolates of P. capsulatum are highly similar, with the exception of several unique genes, INDELs or SNPs in the genes coding for glycosyl hydrolases, amino acid transporters and circumsporozoite protein. A phylogenomic analysis was performed based on the whole genome data of 38 strains belonging to Eurotiales. By comparing the whole genome sequences and the virulence-related genes from 20 important related species, including fungal pathogens and non-human pathogens belonging to Eurotiales, we found meaningful pathogenicity characteristics between P. capsulatum and its closely related species. Our research indicated that P. capsulatum may be a neglected opportunistic pathogen. This study is beneficial for mycologists, geneticists and epidemiologists to achieve a deeper understanding of the genetic basis of the role of P. capsulatum as a newly reported fungal pathogen. PMID:27761131

  17. Opportunistic diseases in HIV-infected patients in Gabon following the administration of highly active antiretroviral therapy: a retrospective study.

    Science.gov (United States)

    Okome-Nkoumou, Madeleine; Guiyedi, Vincent; Ondounda, Magloire; Efire, Nora; Clevenbergh, Philippe; Dibo, Mireille; Dzeing-Ella, Arnaud

    2014-02-01

    Opportunistic diseases cause substantial morbidity and mortality to human immunodeficiency virus (HIV)-infected patients. Highly active antiretroviral therapy (HAART) leading to immune reconstitution is the most effective treatment of preventing opportunistic diseases. This retrospective study established an epidemiologic profile of opportunistic diseases 10 years after the introduction of HAART. The HIV antiretroviral therapy-naive patients matching inclusion criteria were included. The primary outcome was the prevalence of opportunistic diseases. From January 1, 2002 to September 30, 2010, 654 opportunistic diseases were identified in 458 patients. Pulmonary tuberculosis, herpes zoster, cerebral toxoplasmosis, oral candidiasis, and severe pneumonia accounted for 22.05%, 15.94%, 14.19%, 14.19%, and 9.39%, respectively. Cryptococcal meningitis and pneumocystosis accounted for 0.44% and 0.21%, respectively. The prevalence of opportunistic diseases in Gabon remains high. New guidelines emphasize the importance of initiating antiretroviral therapy early to reconstitute the immune system, and reduce disease risk, and treat the primary opportunistic infection of pulmonary tuberculosis.

  18. Hydrogen-enriched fuels

    Energy Technology Data Exchange (ETDEWEB)

    Roser, R. [NRG Technologies, Inc., Reno, NV (United States)

    1998-08-01

    NRG Technologies, Inc. is attempting to develop hardware and infrastructure that will allow mixtures of hydrogen and conventional fuels to become viable alternatives to conventional fuels alone. This commercialization can be successful if the authors are able to achieve exhaust emission levels of less than 0.03 g/kw-hr NOx and CO; and 0.15 g/kw-hr NMHC at full engine power without the use of exhaust catalysts. The major barriers to achieving these goals are that the lean burn regimes required to meet exhaust emissions goals reduce engine output substantially and tend to exhibit higher-than-normal total hydrocarbon emissions. Also, hydrogen addition to conventional fuels increases fuel cost, and reduces both vehicle range and engine output power. Maintaining low emissions during transient driving cycles has not been demonstrated. A three year test plan has been developed to perform the investigations into the issues described above. During this initial year of funding research has progressed in the following areas: (a) a cost effective single-cylinder research platform was constructed; (b) exhaust gas speciation was performed to characterize the nature of hydrocarbon emissions from hydrogen-enriched natural gas fuels; (c) three H{sub 2}/CH{sub 4} fuel compositions were analyzed using spark timing and equivalence ratio sweeping procedures and finally; (d) a full size pick-up truck platform was converted to run on HCNG fuels. The testing performed in year one of the three year plan represents a baseline from which to assess options for overcoming the stated barriers to success.

  19. CLEAN: CLustering Enrichment ANalysis

    Directory of Open Access Journals (Sweden)

    Medvedovic Mario

    2009-07-01

    Full Text Available Abstract Background Integration of biological knowledge encoded in various lists of functionally related genes has become one of the most important aspects of analyzing genome-wide functional genomics data. In the context of cluster analysis, functional coherence of clusters established through such analyses have been used to identify biologically meaningful clusters, compare clustering algorithms and identify biological pathways associated with the biological process under investigation. Results We developed a computational framework for analytically and visually integrating knowledge-based functional categories with the cluster analysis of genomics data. The framework is based on the simple, conceptually appealing, and biologically interpretable gene-specific functional coherence score (CLEAN score. The score is derived by correlating the clustering structure as a whole with functional categories of interest. We directly demonstrate that integrating biological knowledge in this way improves the reproducibility of conclusions derived from cluster analysis. The CLEAN score differentiates between the levels of functional coherence for genes within the same cluster based on their membership in enriched functional categories. We show that this aspect results in higher reproducibility across independent datasets and produces more informative genes for distinguishing different sample types than the scores based on the traditional cluster-wide analysis. We also demonstrate the utility of the CLEAN framework in comparing clusterings produced by different algorithms. CLEAN was implemented as an add-on R package and can be downloaded at http://Clusteranalysis.org. The package integrates routines for calculating gene specific functional coherence scores and the open source interactive Java-based viewer Functional TreeView (FTreeView. Conclusion Our results indicate that using the gene-specific functional coherence score improves the reproducibility of the

  20. Experimentally-induced Placentitis in Late Gestation Ewes and Mares: Evaluation of Pathogen Progression Using Lux-modified Bacteria and Bioluminescence Imaging

    Science.gov (United States)

    Placental infection due to opportunistic pathogens such as Escherichia coli (E. coli) is the single most common cause of abortion, still birth and premature delivery in women and domestic animal species. The consequence of placentitis during late pregnancy increases the incidence of abortion, preter...

  1. Draft Genome Sequence Analysis of a Pseudomonas putida W15Oct28 Strain with Antagonistic Activity to Gram-Positive and Pseudomonas sp. Pathogens

    NARCIS (Netherlands)

    Ye, L.; Hildebrandt, F.; Ballet, S.; Laus, M.S.; Berendsen, Roeland; Cornelis, P.

    2014-01-01

    Pseudomonas putida is a member of the fluorescent pseudomonads known to produce the yellow-green fluorescent pyoverdine siderophore. P. putida W15Oct28, isolated from a stream in Brussels, was found to produce compound(s) with antimicrobial activity against the opportunistic pathogens Staphylococcus

  2. Optimality of Multichannel Myopic Sensing in the Presence of Sensing Error for Opportunistic Spectrum Access

    Directory of Open Access Journals (Sweden)

    Xiaofeng Jiang

    2013-01-01

    Full Text Available The optimization problem for the performance of opportunistic spectrum access is considered in this study. A user, with the limited sensing capacity, has opportunistic access to a communication system with multiple channels. The user can only choose several channels to sense and decides whether to access these channels based on the sensing information in each time slot. Meanwhile, the presence of sensing error is considered. A reward is obtained when the user accesses a channel. The objective is to maximize the expected (discounted or average reward accrued over an infinite horizon. This problem can be formulated as a partially observable Markov decision process. This study shows the optimality of the simple and robust myopic policy which focuses on maximizing the immediate reward. The results show that the myopic policy is optimal in the case of practical interest.

  3. Cloud Platform Based on Mobile Internet Service Opportunistic Drive and Application Aware Data Mining

    Directory of Open Access Journals (Sweden)

    Ge Zhou

    2015-01-01

    Full Text Available Because the static cloud platform cannot satisfy the diversity of mobile Internet service and inefficient data mining problems, we presented a reliable and efficient data mining cloud platform construction scheme based on the mobile Internet service opportunistic driving and application perception. In this scheme, first of all data selection mechanism was established based on mobile Internet service opportunistic drive. Secondly, through the cloud platform different cloud and channel aware, nonlinear mapping from the service to a data set of proposed perceptual model is applied. Finally, on the basis of the driving characteristics and extraction of perceptual features, the cloud platform would be constructed through the service opportunities of mobile Internet applications, which could provide robust and efficient data mining services. The experimental results show that the proposed mechanism, compared to the cloud platform based on distributed data mining, has obvious advantages in system running time, memory usage, and data clustering required time, as well as average clustering quality.

  4. An opportunistic routing mechanism combined with long-term and short-term metrics for WMN.

    Science.gov (United States)

    Sun, Weifeng; Wang, Haotian; Piao, Xianglan; Qiu, Tie

    2014-01-01

    WMN (wireless mesh network) is a useful wireless multihop network with tremendous research value. The routing strategy decides the performance of network and the quality of transmission. A good routing algorithm will use the whole bandwidth of network and assure the quality of service of traffic. Since the routing metric ETX (expected transmission count) does not assure good quality of wireless links, to improve the routing performance, an opportunistic routing mechanism combined with long-term and short-term metrics for WMN based on OLSR (optimized link state routing) and ETX is proposed in this paper. This mechanism always chooses the highest throughput links to improve the performance of routing over WMN and then reduces the energy consumption of mesh routers. The simulations and analyses show that the opportunistic routing mechanism is better than the mechanism with the metric of ETX.

  5. A Restless Bandit Formulation of Multi-channel Opportunistic Access: Indexablity and Index Policy

    CERN Document Server

    Liu, Keqin

    2008-01-01

    We focus on an opportunistic communication system consisting of multiple independent channels with time-varying states. With limited sensing, a user can only sense and access a subset of channels and accrue rewards determined by the states of the sensed channels. We formulate the problem of optimal sequential channel selection as a restless multi-armed bandit process, for which a powerful index policy--Whittle's index policy--can be implemented based on the indexability of the system. Exploiting the underlying structure of the multi-channel opportunistic access problem, we establish the indexability and obtain Whittle's index in closed-form for both discounted reward and average reward criteria. These results lead to the direct implementation of Whittle's index policy with remarkably low complexity. Furthermore, we develop a simple approach to evaluate the optimal performance under a relaxed constraint on sensing actions, which provides an upper bound of the optimal performance of the original restless multi-...

  6. Buffer Management and Hybrid Probability Choice Routing for Packet Delivery in Opportunistic Networks

    Directory of Open Access Journals (Sweden)

    Daru Pan

    2012-01-01

    Full Text Available Due to the features of long connection delays, frequent network partitions, and topology unsteadiness, the design of opportunistic networks faces the challenge of how to effectively deliver data based only on occasional encountering of nodes, where the conventional routing schemes do not work properly. This paper proposes a hybrid probability choice routing protocol with buffer management for opportunistic networks. A delivery probability function is set up based on continuous encounter duration time, which is used for selecting a better node to relay packets. By combining the buffer management utility and the delivery probability, a total utility is used to decide whether the packet should be kept in the buffer or be directly transmitted to the encountering node. Simulation results show that the proposed routing outperforms the existing one in terms of the delivery rate and the average delay.

  7. A non-digging zoobenthivorous fish attracts two opportunistic predatory fish associates

    Directory of Open Access Journals (Sweden)

    Cristina Sazima

    Full Text Available Following behaviour among reef fishes involves mostly a digging nuclear species while foraging, which attracts opportunistic followers preying on the exposed organisms. The flying gurnard Dactylopterus volitans preys on benthic animals, mostly crustaceans and small fishes, scratching and probing the bottom with the inner rays of its pectoral fins. We recorded the flying gurnard being followed by two opportunistic predators, the yellow jack Caranx bartholomaei and the coney Cephalopholis fulva at Fernando de Noronha, off northeast Brazil. Albeit not actually digging the substrate, the flying gurnard acts as a nuclear species by exploring algae tufts and by its wandering near the boulders and ledges, disturbing and flushing out hidden animals which thus become available to predation.

  8. Seasonal neuroplasticity of the song control system in tropical, flexibly, and opportunistically breeding birds.

    Science.gov (United States)

    Small, Thomas W; Moore, Ignacio T

    2009-09-01

    The avian song control system is one of the primary models used to study neuroplasticity and neurogenesis in the adult vertebrate brain. A great deal of progress has been made in understanding the mechanisms controlling seasonal neuroplasticity of the song control system. However, relatively little work has been done to identify how prevalent this phenomenon is and if a diversity of environmental cues can regulate it. Photoperiod is the primary environmental cue used by mid- to high-latitude seasonally breeding birds to time growth of the song control system but many birds display flexible or opportunistic breeding patterns that are less reliant on photoperiodic cues. In addition, approximately 75% of birds are tropical and in only one such species has neuroplasticity of the song control system been studied. Our goal is to outline some of what is known and expand on the ways that studying tropical, flexibly, and opportunistically breeding birds can advance our understanding of plasticity in the song bird brain.

  9. Opportunistic Scheduling and Beamforming for MIMO-OFDMA Downlink Systems with Reduced Feedback

    CERN Document Server

    Pun, Man-On; Poor, H Vincent

    2008-01-01

    Opportunistic scheduling and beamforming schemes with reduced feedback are proposed for MIMO-OFDMA downlink systems. Unlike the conventional beamforming schemes in which beamforming is implemented solely by the base station (BS) in a per-subcarrier fashion, the proposed schemes take advantages of a novel channel decomposition technique to perform beamforming jointly by the BS and the mobile terminal (MT). The resulting beamforming schemes allow the BS to employ only {\\em one} beamforming matrix (BFM) to form beams for {\\em all} subcarriers while each MT completes the beamforming task for each subcarrier locally. Consequently, for a MIMO-OFDMA system with $Q$ subcarriers, the proposed opportunistic scheduling and beamforming schemes require only one BFM index and $Q$ supportable throughputs to be returned from each MT to the BS, in contrast to $Q$ BFM indices and $Q$ supportable throughputs required by the conventional schemes. The advantage of the proposed schemes becomes more evident when a further feedback ...

  10. Cooperative Cloud Service Aware Mobile Internet Coverage Connectivity Guarantee Protocol Based on Sensor Opportunistic Coverage Mechanism

    Directory of Open Access Journals (Sweden)

    Qin Qin

    2015-01-01

    Full Text Available In order to improve the Internet coverage ratio and provide connectivity guarantee, based on sensor opportunistic coverage mechanism and cooperative cloud service, we proposed the coverage connectivity guarantee protocol for mobile Internet. In this scheme, based on the opportunistic covering rules, the network coverage algorithm of high reliability and real-time security was achieved by using the opportunity of sensor nodes and the Internet mobile node. Then, the cloud service business support platform is created based on the Internet application service management capabilities and wireless sensor network communication service capabilities, which is the architecture of the cloud support layer. The cooperative cloud service aware model was proposed. Finally, we proposed the mobile Internet coverage connectivity guarantee protocol. The results of experiments demonstrate that the proposed algorithm has excellent performance, in terms of the security of the Internet and the stability, as well as coverage connectivity ability.

  11. Molecular detection of foodborne pathogens

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann

    of these pathogens in the food chain, in order to improve intervention strategies and make more effective the control of production lines and single food items. To serve this purpose, rapid and reliable detection and quantification methods are imperative. The culture-based standard methods currently applied...... for detection and enumeration of Salmonella and Campylobacter are time-consuming and laborious. They lack specificity and do not enable detection of viable but non-culturable (VBNC) bacteria. The focus of the present thesis has been development and validation of PCR-based detection methods for Salmonella...... and Campylobacter. A conventional PCR-based method for detection of Campylobacter in chicken carcass rinse following 20 h of enrichment in Bolton broth was successfully compared to the ISO standard culture-based method (10272) on 68 naturally infected chickens. The method was subsequently validated on artificially...

  12. Indoor Positioning Using Opportunistic Multi-Frequency RSS With Foot-Mounted INS

    OpenAIRE

    Nilsson, Martin

    2014-01-01

    Reliable and accurate positioning systems are expected to significantly improve the safety for first responders and enhance their operational efficiency. To be effective, a first responder positioning systemmust provide room level accuracy during extended time periods of indoor operation. This thesis presents a system which combines a zero-velocity-update (ZUPT) aided inertial navigation system (INS), using a foot-mounted inertial measurement unit (IMU), with the use of opportunistic multi-fr...

  13. Heuristic Approach to Select Opportunistic Routing Forwarders (HASORF) to Enhance Throughput for Wireless Sensor Networks

    OpenAIRE

    Yousaf Bin Zikria; Summera Nosheen; Jin-Ghoo Choi; Sung Won Kim

    2015-01-01

    Biological schemes provide useful resources for designing adaptive routing protocols for wireless sensor networks (WSNs). The key idea behind using bioinspired routing is to find the optimal path to the destination. Similarly, the idea of opportunistic routing (OR) is to find the least number of hops to deliver the data to the destination. Numerous routing schemes have been proposed in WSNs while targeting various performance goals, such as throughput, delay, and link quality. Rec...

  14. Analytical evaluation of adaptive-modulation-based opportunistic cognitive radio in nakagami-m fading channels

    KAUST Repository

    Chen, Yunfei

    2012-09-01

    The performance of adaptive modulation for cognitive radio with opportunistic access is analyzed by considering the effects of spectrum sensing, primary user (PU) traffic, and time delay for Nakagami- m fading channels. Both the adaptive continuous rate scheme and the adaptive discrete rate scheme are considered. Numerical examples are presented to quantify the effects of spectrum sensing, PU traffic, and time delay for different system parameters. © 1967-2012 IEEE.

  15. Heavy Metal Distribution in Opportunistic Beach Nourishment: A Case Study in Greece

    OpenAIRE

    Spyros Foteinis; Kallithrakas-Kontos, Nikolaos G.; Costas Synolakis

    2013-01-01

    The existence and distribution of persistent pollutants, such as heavy metals, in coastal sediment used for opportunistic beach nourishment, is a problem that has not received much attention. Here, we assessed the coastal sediments in one restoration project for the occurrence and distribution of heavy metals, by utilizing an Energy Dispersive X-Ray Fluorescence (EDXRF) system. Heavy metal point sources included (i) the effluents of small industries (tanneries), (ii) wastewater treatment plan...

  16. Look-Ahead Techniques for Micro-Opportunistic Job Shop Scheduling

    Science.gov (United States)

    1991-03-01

    throughout all these years; My advisor, Mark Fox , for his guidance, enthusiasm and unfailing support; The other members of my thesis committee, Tom Mitchell...about the same time, the ISIS factory scheduling system developed by Mark Fox and his team first demonstrated the potential of AI modeling and...Katia Sycara, Steve Roth, and Mark Fox . LOOK-AHEAD TECHNIQUES FOR MICRO-OPPORTUNISTIC JOB SHOP SCHEDULING 155 Appendix A Counting the Number of

  17. Opportunistic Infections and Complications in Human Immunodeficiency Virus-1-Infected Children: Correlation with immune status

    Directory of Open Access Journals (Sweden)

    Jaivinder Yadav

    2014-10-01

    Full Text Available Objectives: The aim of this study was to ascertain the correlation between various opportunistic infections and complications in human immunodeficiency virus (HIV-1-infected children and the immune status of these patients, evaluated by absolute cluster of differentiation 4 (CD4 count and CD4 percentage. Methods: This study was conducted from January 2009 to June 2010 at the Antiretroviral Treatment Centre of the Pt. B.D. Sharma Post Graduate Institute of Medical Sciences, a tertiary care hospital in Rohtak, Haryana, in northern India. A total of 20 HIV-1-infected children aged 4–57 months were studied. Demographic and baseline investigations were performed prior to the start of highly active antiretroviral therapy (HAART. A fixed-dose combination of HAART was given based on the patient’s weight. Baseline investigations were repeated after six months of HAART. Results: There was a significant increase in the patients’ haemoglobin, weight, height and CD4 count after six months of HAART. Significant improvements (P <0.05 were also noted in the patients’ immune status, graded according to the World Health Organization. Conclusion: This study observed that the severity and frequency of opportunistic complications in paediatric patients with HIV-1 increased with a fall in the CD4 count. The treatment of opportunistic infections, along with antiretroviral therapy, may lead to both clinical and immunological recovery as well as a decreased incidence of future opportunistic infections. The CD4 count may give treating physicians an initial idea about the immune status of each child and could also be used as a biological marker of HAART efficacy. Patient compliance must be ensured during HAART as this is a key factor in improving outcomes.

  18. Low-Feedback Opportunistic Scheduling Schemes for Wireless Networks with Heterogenous Users

    KAUST Repository

    Rashid, Faraan

    2012-07-01

    Efficient implementation of resource sharing strategies in a multi-user wireless environment can improve the performance of a network significantly. In this thesis we study various scheduling strategies for wireless networks and handle the problem of opportunistically scheduling transmissions using channel aware schemes. First we propose a scheme that can handle users with asymmetric channel conditions and is opportunistic in the sense that it exploits the multi-user diversity of the network. The scheme requires the users to have a priori knowledge of their channel distributions. The associated overhead is limited meaning it offers reduced feedback load, that does not scale with the increasing number of users. The main technique used to shrink the feedback load is the contention based distributed implementation of a splitting algorithm that does not require explicit feedback to the scheduler from every user. The users find the best among themselves, in a distributed manner, while requiring just a ternary broadcast feedback from the scheduler at the end of each mini-slot. In addition, it can also handle fairness constraints in time and throughput to various degrees. Next we propose another opportunistic scheduler that offers most of the benefits of the previously proposed scheme but is more practical because it can also handle heterogenous users whose channel distributions are unknown. This new scheme actually reduces the complexity and is also more robust for changing traffic patterns. Finally we extend both these schemes to the scenario where there are fixed thresholds, this enables us to handle opportunistic scheduling in practical systems that can only transmit over finite number of discrete rates with the additional benefit that full feedback session, even from the selected user, is never required.

  19. Dermatophytes, related keratinophilic and opportunistic fungi in indoor dust of houses and hospitals

    OpenAIRE

    Singh I; Mishra A; Kushwaha RKS

    2009-01-01

    Dermatophytes, related keratinophilic and opportunistic fungi were isolated from indoor dust samples of 46 hospitals and 47 houses in Kanpur. A total of 19 fungi represented by 11 genera were isolated by the hair-baiting technique from 230 and 235 samples from hospitals and houses respectively. The isolated fungi are Acremonium implicatum (Indian Type Culture Collection) ITCC 5266 , A. strictum (Germplasm Centre for Keratinophilic Fungi) GPCK 1137 , Aphanoascus fulvescens GPCK 1081 , ...

  20. Exploration of an Opportunistic Overlaid Paradigm for Complex Networks via Stochastic Geometry

    Science.gov (United States)

    2012-03-01

    Cui, “A Selection Region Based Routing Protocol for Ran- dom Mobile ad hoc Networks,” Proceedings: IEEE GLOBECOM Workshop on Heterogeneous, Multi...opportunistically to limit the interference to the primary tier. Based on the assumption that the secondary tier is allowed to route the packets for the...the framework of distributed Kalman filtering. It is shown that, in a weakly connected communica- tion network, there exist (randomized) gossip based

  1. Oral-resident natural Th17 cells and γδ T cells control opportunistic Candida albicans infections.

    Science.gov (United States)

    Conti, Heather R; Peterson, Alanna C; Brane, Lucas; Huppler, Anna R; Hernández-Santos, Nydiaris; Whibley, Natasha; Garg, Abhishek V; Simpson-Abelson, Michelle R; Gibson, Gregory A; Mamo, Anna J; Osborne, Lisa C; Bishu, Shrinivas; Ghilardi, Nico; Siebenlist, Ulrich; Watkins, Simon C; Artis, David; McGeachy, Mandy J; Gaffen, Sarah L

    2014-09-22

    Oropharyngeal candidiasis (OPC) is an opportunistic fungal infection caused by Candida albicans. OPC is frequent in HIV/AIDS, implicating adaptive immunity. Mice are naive to Candida, yet IL-17 is induced within 24 h of infection, and susceptibility is strongly dependent on IL-17R signaling. We sought to identify the source of IL-17 during the early innate response to candidiasis. We show that innate responses to Candida require an intact TCR, as SCID, IL-7Rα(-/-), and Rag1(-/-) mice were susceptible to OPC, and blockade of TCR signaling by cyclosporine induced susceptibility. Using fate-tracking IL-17 reporter mice, we found that IL-17 is produced within 1-2 d by tongue-resident populations of γδ T cells and CD3(+)CD4(+)CD44(hi)TCRβ(+)CCR6(+) natural Th17 (nTh17) cells, but not by TCR-deficient innate lymphoid cells (ILCs) or NK cells. These cells function redundantly, as TCR-β(-/-) and TCR-δ(-/-) mice were both resistant to OPC. Whereas γδ T cells were previously shown to produce IL-17 during dermal candidiasis and are known to mediate host defense at mucosal surfaces, nTh17 cells are poorly understood. The oral nTh17 population expanded rapidly after OPC, exhibited high TCR-β clonal diversity, and was absent in Rag1(-/-), IL-7Rα(-/-), and germ-free mice. These findings indicate that nTh17 and γδ T cells, but not ILCs, are key mucosal sentinels that control oral pathogens.

  2. Emerging bacterial pathogens: the past and beyond.

    Science.gov (United States)

    Vouga, M; Greub, G

    2016-01-01

    Since the 1950s, medical communities have been facing with emerging and reemerging infectious diseases, and emerging pathogens are now considered to be a major microbiologic public health threat. In this review, we focus on bacterial emerging diseases and explore factors involved in their emergence as well as future challenges. We identified 26 major emerging and reemerging infectious diseases of bacterial origin; most of them originated either from an animal and are considered to be zoonoses or from water sources. Major contributing factors in the emergence of these bacterial infections are: (1) development of new diagnostic tools, such as improvements in culture methods, development of molecular techniques and implementation of mass spectrometry in microbiology; (2) increase in human exposure to bacterial pathogens as a result of sociodemographic and environmental changes; and (3) emergence of more virulent bacterial strains and opportunistic infections, especially affecting immunocompromised populations. A precise definition of their implications in human disease is challenging and requires the comprehensive integration of microbiological, clinical and epidemiologic aspects as well as the use of experimental models. It is now urgent to allocate financial resources to gather international data to provide a better understanding of the clinical relevance of these waterborne and zoonotic emerging diseases.

  3. Location Prediction-Based Data Dissemination Using Swarm Intelligence in Opportunistic Cognitive Networks

    Directory of Open Access Journals (Sweden)

    Jie Li

    2014-01-01

    Full Text Available Swarm intelligence is widely used in the application of communication networks. In this paper we adopt a biologically inspired strategy to investigate the data dissemination problem in the opportunistic cognitive networks (OCNs. We model the system as a centralized and distributed hybrid system including a location prediction server and a pervasive environment deploying the large-scale human-centric devices. To exploit such environment, data gathering and dissemination are fundamentally based on the contact opportunities. To tackle the lack of contemporaneous end-to-end connectivity in opportunistic networks, we apply ant colony optimization as a cognitive heuristic technology to formulate a self-adaptive dissemination-based routing scheme in opportunistic cognitive networks. This routing strategy has attempted to find the most appropriate nodes conveying messages to the destination node based on the location prediction information and intimacy between nodes, which uses the online unsupervised learning on geographical locations and the biologically inspired algorithm on the relationship of nodes to estimate the delivery probability. Extensive simulation is carried out on the real-world traces to evaluate the accuracy of the location prediction and the proposed scheme in terms of transmission cost, delivery ratio, average hops, and delivery latency, which achieves better routing performances compared to the typical routing schemes in OCNs.

  4. Opportunistic maintenance and adaptation of warranty maintenance tasks for Power Plant equipment

    Directory of Open Access Journals (Sweden)

    P. McGibney

    2016-08-01

    Full Text Available This paper makes a link between opportunistic maintenance literature and warranty analysis of a power plant. A new plant warranty maintenance tasks are observed over a two year period. The main aim is to see how opportunistic maintenance could be incorporated when the warranty period has elapsed. The paper examine the warranty period maintenance task list and propose adequate methods for assessing opportunistic maintenance as a preventive maintenance task in order to ensure reliability and availability of the plant equipment. Statistical approach is used to give an insight to the plant equipment status and a modeling approach is proposed to also assess maintenance information defined by experts in the context of actual operating regimes. This study focuses on the power plant‟s critical equipment. Failure Mode and Effect Analysis (FMEA is conducted on the power plant Booster Fans. This gives an insight about equipment failure mode patterns and maintenance requirements. A simulation example is presented based in the failure modes results obtained and a graphical display of optimum preventive maintenance schedule cost curves is also presented.

  5. Asymmetric competition prevents the outbreak of an opportunistic species after coral reef degradation.

    Science.gov (United States)

    González-Rivero, Manuel; Bozec, Yves-Marie; Chollett, Iliana; Ferrari, Renata; Schönberg, Christine H L; Mumby, Peter J

    2016-05-01

    Disturbance releases space and allows the growth of opportunistic species, excluded by the old stands, with a potential to alter community dynamics. In coral reefs, abundances of fast-growing, and disturbance-tolerant sponges are expected to increase and dominate as space becomes available following acute coral mortality events. Yet, an increase in abundance of these opportunistic species has been reported in only a few studies, suggesting certain mechanisms may be acting to regulate sponge populations. To gain insights into mechanisms of population control, we simulated the dynamics of the common reef-excavating sponge Cliona tenuis in the Caribbean using an individual-based model. An orthogonal hypothesis testing approach was used, where four candidate mechanisms-algal competition, stock-recruitment limitation, whole and partial mortality-were incorporated sequentially into the model and the results were tested against independent field observations taken over a decade in Belize, Central America. We found that releasing space after coral mortality can promote C. tenuis outbreaks, but such outbreaks can be curtailed by macroalgal competition. The asymmetrical competitive superiority of macroalgae, given by their capacity to pre-empt space and outcompete with the sponge in a size-dependant fashion, supports their capacity to steal the opportunity from other opportunists. While multiple system stages can be expected in coral reefs following intense perturbation macroalgae may prevent the growth of other space-occupiers, such as bioeroding sponges, under low grazing pressure.

  6. An Improved Spray and Wait with Probability Choice Routing for Opportunistic Networks

    Directory of Open Access Journals (Sweden)

    Daru Pan

    2012-09-01

    Full Text Available Opportunistic networks are sparse multi-hop ad hoc networks in which nodes exploit any pair-wise contact opportunities to share and forward messages. The main challenge for this environment is that conventional routing schemes do not work properly.  Among the existing Opportunistic Networks routing algorithms, the epidemic routing and probabilistic  routing could provide higher delivery  probability and shorter delays, but is with a large overhead, while the spay and wait routing could reduce the overhead, but is with low delivery probability and high delay.  This paper proposes the Spray and Wait with Probability Choice (SWPC routing, where continuous encounter time is used to describe the encounter opportunity; a delivery probability function is set up to direct the different number of copies to the destination during the spray phase; and a forwarding scheme is implemented in the wait phase. Simulation results show that proposed SWPC shows prominent superiority in the delivery rate, the average delay and the communication overhead, and adapted for the frequently disconnected opportunistic network.

  7. Postmortem findings and opportunistic infections in HIV-positive patients from a public hospital in Peru

    Science.gov (United States)

    Eza, Dominique; Cerrillo, Gustavo; Moore, David A.J.; Castro, Cecilia; Ticona, Eduardo; Morales, Domingo; Cabanillas, Jose; Barrantes, Fernando; Alfaro, Alejandro; Benavides, Alejandro; Rafael, Arturo; Valladares, Gilberto; Arevalo, Fernando; Evans, Carlton A.; Gilman, Robert H.

    2010-01-01

    There is a paucity of HIV autopsy data from South America and none that document the postmortem findings in patients with HIV/AIDS in Peru. The purpose of this autopsy study was to determine the spectrum of opportunistic infections and the causes of mortality in HIV-positive patients at a public hospital in Lima. Clinico-epidemiological information regarding HIV infection in Peru is also reviewed. Sixteen HIV-related hospital postmortems, performed between 1999 and 2004, were included in this retrospective analysis. The primary cause of death was established in 12 patients: one died of neoplasia and 11 of infectious diseases, including 3 from pulmonary infection, 7 from disseminated infection, and 2 from central nervous system infection (one case had dual pathology). Opportunistic infections were identified in 14 cases, comprising cytomegalovirus, histoplasmosis, cryptococcosis, toxoplasmosis, Pneumocystis pneumonia, aspergillosis, tuberculosis, varicella zoster virus, and cryptosporidiosis. Fourteen patients had at least one AIDS-related disease that had been neither clinically suspected nor diagnosed premortem. Moreover, 82% of the diagnoses considered to be of important clinical significance had not been suspected antemortem. The spectrum and frequency of certain opportunistic infections differed from other South American autopsy studies, highlighting the importance of performing HIV/AIDS postmortems in resource-limited countries where locally specific disease patterns may be observed. PMID:16979302

  8. Opportunistic Hybrid Transport Protocol (OHTP) for Cognitive Radio Ad Hoc Sensor Networks.

    Science.gov (United States)

    Bin Zikria, Yousaf; Nosheen, Summera; Ishmanov, Farruh; Kim, Sung Won

    2015-12-15

    The inefficient assignment of spectrum for different communications purposes, plus technology enhancements and ever-increasing usage of wireless technology is causing spectrum scarcity. To address this issue, one of the proposed solutions in the literature is to access the spectrum dynamically or opportunistically. Therefore, the concept of cognitive radio appeared, which opens up a new research paradigm. There is extensive research on the physical, medium access control and network layers. The impact of the transport layer on the performance of cognitive radio ad hoc sensor networks is still unknown/unexplored. The Internet's de facto transport protocol is not well suited to wireless networks because of its congestion control mechanism. We propose an opportunistic hybrid transport protocol for cognitive radio ad hoc sensor networks. We developed a new congestion control mechanism to differentiate true congestion from interruption loss. After such detection and differentiation, we propose methods to handle them opportunistically. There are several benefits to window- and rate-based protocols. To exploit the benefits of both in order to enhance overall system performance, we propose a hybrid transport protocol. We empirically calculate the optimal threshold value to switch between window- and rate-based mechanisms. We then compare our proposed transport protocol to Transmission Control Protocol (TCP)-friendly rate control, TCP-friendly rate control for cognitive radio, and TCP-friendly window-based control. We ran an extensive set of simulations in Network Simulator 2. The results indicate that the proposed transport protocol performs better than all the others.

  9. On the Optimality of Opportunistic Interference Alignment in 3-Transmitter MIMO Interference Channels

    CERN Document Server

    Lee, Jung Hoon; Love, David J

    2011-01-01

    In this paper, we propose opportunistic interference alignment (OIA) for three-transmitter multiple-input multiple-output (MIMO) interference channels (ICs). In the proposed OIA scheme, each transmitter has its own user group that consists of $K$ users, and each transmitter opportunistically selects the user whose received interference signals are most aligned. Thus, three-transmitter MIMO IC is opportunistically constructed by three transmitters and their selected users. Contrary to conventional IA, perfect channel information for all of the interference links is not required at the transmitter. Each user just needs to feed back one scalar value in the proposed OIA scheme. When the number of receive antennas is $N_R$ (with $N_R=2M$) and the number of transmit antennas is $N_T$ (with $N_T\\ge M$), we prove that each transmitter can achieve $M$ degrees of freedom (DoF) as the number of users in each group goes to infinity ($K\\to\\infty$), in comparison with the $\\frac{2M}{3}$ DoF known to be achievable in the th...

  10. Site-occupancy distribution modeling to correct population-trend estimates derived from opportunistic observations

    Science.gov (United States)

    Kery, M.; Royle, J. Andrew; Schmid, Hans; Schaub, M.; Volet, B.; Hafliger, G.; Zbinden, N.

    2010-01-01

    Species' assessments must frequently be derived from opportunistic observations made by volunteers (i.e., citizen scientists). Interpretation of the resulting data to estimate population trends is plagued with problems, including teasing apart genuine population trends from variations in observation effort. We devised a way to correct for annual variation in effort when estimating trends in occupancy (species distribution) from faunal or floral databases of opportunistic observations. First, for all surveyed sites, detection histories (i.e., strings of detection-nondetection records) are generated. Within-season replicate surveys provide information on the detectability of an occupied site. Detectability directly represents observation effort; hence, estimating detectablity means correcting for observation effort. Second, site-occupancy models are applied directly to the detection-history data set (i.e., without aggregation by site and year) to estimate detectability and species distribution (occupancy, i.e., the true proportion of sites where a species occurs). Site-occupancy models also provide unbiased estimators of components of distributional change (i.e., colonization and extinction rates). We illustrate our method with data from a large citizen-science project in Switzerland in which field ornithologists record opportunistic observations. We analyzed data collected on four species: the widespread Kingfisher (Alcedo atthis. ) and Sparrowhawk (Accipiter nisus. ) and the scarce Rock Thrush (Monticola saxatilis. ) and Wallcreeper (Tichodroma muraria. ). Our method requires that all observed species are recorded. Detectability was biodiversity monitoring and modeling of species distributions. ?? 2010 Society for Conservation Biology.

  11. Opportunistic Carrier Sensing for Energy-Efficient Information Retrieval in Sensor Networks

    Directory of Open Access Journals (Sweden)

    Zhao Qing

    2005-01-01

    Full Text Available We consider distributed information retrieval for sensor networks with cluster heads or mobile access points. The performance metric used in the design is energy efficiency defined as the ratio of the average number of bits reliably retrieved by the access point to the total amount of energy consumed. A distributed opportunistic transmission protocol is proposed using a combination of carrier sensing and backoff strategy that incorporates channel state information (CSI of individual sensors. By selecting a set of sensors with the best channel states to transmit, the proposed protocol achieves the upper bound on energy efficiency when the signal propagation delay is negligible. For networks with substantial propagation delays, a backoff function optimized for energy efficiency is proposed. The design of this backoff function utilizes properties of extreme statistics and is shown to have mild performance loss in practical scenarios. We also demonstrate that opportunistic strategies that use CSI may not be optimal when channel acquisition at individual sensors consumes substantial energy. We show further that there is an optimal sensor density for which the opportunistic information retrieval is the most energy efficient. This observation leads to the design of the optimal sensor duty cycle.

  12. Novel Opportunistic Network Routing Based on Social Rank for Device-to-Device Communication

    Directory of Open Access Journals (Sweden)

    Tong Wang

    2017-01-01

    Full Text Available In recent years, there has been dramatic proliferation of research concerned with fifth-generation (5G mobile communication networks, among which device-to-device (D2D communication is one of the key technologies. Due to the intermittent connection of nodes, the D2D network topology may be disconnected frequently, which will lead to failure in transmission of large data files. In opportunistic networks, in case of encountering nodes which never meet before a flood message blindly to cause tremendous network overhead, a novel opportunistic network routing protocol based on social rank and intermeeting time (SRIT is proposed in this paper. An improved utility approach applied in utility replication based on encounter durations and intermeeting time is put forward to enhance the routing efficiency. Meanwhile, in order to select better candidate nodes in the network, a social graph among people is established when they socially relate to each other in social rank replication. The results under the scenario show an advantage of the proposed opportunistic network routing based on social rank and intermeeting time (SRIT over the compared algorithms in terms of delivery ratio, average delivery latency, and overhead ratio.

  13. Antimicrobial active herbal compounds against Acinetobacter baumannii and other pathogens

    Directory of Open Access Journals (Sweden)

    Vishvanath eTiwari

    2015-06-01

    Full Text Available Bacterial pathogens cause a number of lethal diseases. Opportunistic bacterial pathogens grouped into ESKAPE pathogens that are linked to the high degree of morbidity, mortality and increased costs as described by Infectious Disease Society of America. Acinetobacter baumannii is one of the ESKAPE pathogens which cause respiratory infection, pneumonia and urinary tract infections. The prevalence of this pathogen increases gradually in the clinical setup where it can grow on artificial surfaces, utilize ethanol as a carbon source and resists desiccation. Carbapenems, a β-lactam, are the most commonly prescribed drugs against A. baumannii. The high level of acquired and intrinsic carbapenem resistance mechanisms acquired by these bacteria makes their eradication difficult. The pharmaceutical industry has no solution to this problem. Hence, it is an urgent requirement to find a suitable alternative to carbapenem, a commonly prescribed drug for Acinetobacter infection. In order to do this, here we have made an effort to review the active compounds of plants that have potent antibacterial activity against many bacteria including carbapenem resistant strain of A. baumannii. We have also briefly highlighted the separation and identification methods used for these active compounds. This review will help researchers involved in the screening of herbal active compounds that might act as a replacement for carbapenem.

  14. Aspergillus species: An emerging pathogen in onychomycosis among diabetics

    Directory of Open Access Journals (Sweden)

    T M Wijesuriya

    2015-01-01

    Full Text Available Introduction: Approximately, 33% patients with diabetes are afflicted with onychomycosis. In the past, nondermatophyte molds have been regarded as opportunistic pathogens; recently, Aspergillus species are considered as emerging pathogens of toenail infections. In Sri Lanka, the prevalence of Aspergillus species in onychomycosis among diabetics is not well documented. Objective: To determine the proportion of Aspergillus onychomycosis, risk factors and knowledge among diabetics. Materials and Methods: This was descriptive cross-sectional study. Three hundred diabetic patients were included. Clinical examinations of patients' toenails were performed by a clinical microbiologist. Laboratory identification was done, and pathogens were identified to the species level by morpho-physiological methods. All inferential statistics were tested at P age group. In men, Aspergillus onycomycosis was seen in 82%. Among patients who had Aspergillus nail infection, 114 (63% had diabetes for a period of > years. Among patients who were engaged in agricultural activities, 77% were confirmed to have infected nails due to Aspergillus species. Conclusion: Aspergillus niger was the most common pathogen isolated from toenail infection. Aspergillus species should be considered as an important pathogen in toenail onychomycosis in diabetic patients. Risk factors associated with Aspergillus onychomycosis were age, gender, duration of diabetes, length of exposure to fungi, and occupation.

  15. Antimicrobial active herbal compounds against Acinetobacter baumannii and other pathogens.

    Science.gov (United States)

    Tiwari, Vishvanath; Roy, Ranita; Tiwari, Monalisa

    2015-01-01

    Bacterial pathogens cause a number of lethal diseases. Opportunistic bacterial pathogens grouped into ESKAPE pathogens that are linked to the high degree of morbidity, mortality and increased costs as described by Infectious Disease Society of America. Acinetobacter baumannii is one of the ESKAPE pathogens which cause respiratory infection, pneumonia and urinary tract infections. The prevalence of this pathogen increases gradually in the clinical setup where it can grow on artificial surfaces, utilize ethanol as a carbon source and resists desiccation. Carbapenems, a β-lactam, are the most commonly prescribed drugs against A. baumannii. The high level of acquired and intrinsic carbapenem resistance mechanisms acquired by these bacteria makes their eradication difficult. The pharmaceutical industry has no solution to this problem. Hence, it is an urgent requirement to find a suitable alternative to carbapenem, a commonly prescribed drug for Acinetobacter infection. In order to do this, here we have made an effort to review the active compounds of plants that have potent antibacterial activity against many bacteria including carbapenem resistant strain of A. baumannii. We have also briefly highlighted the separation and identification methods used for these active compounds. This review will help researchers involved in the screening of herbal active compounds that might act as a replacement for carbapenem.

  16. Pathogenicity of Conidiobolus coronatus and Fusarium solani in mouse models.

    Science.gov (United States)

    Li, Yadi; Fang, Xiangang; Zhou, Xiaoqian; Geng, Suying; Wang, Yuxin; Yang, Xiumin

    2017-06-01

    To study the pathogenicity of Conidiobolus coronatus (C. coronatus) and Fusarium solani (F. solani) in animal models. Immunocompromised mice were treated with cyclophosphamide and prednisolone via intraperitoneal injection before and after inoculation. According to pathogenic characteristics of different fungi, C. coronatus was used to infect mice via intravenous inoculation, intraperitoneal inoculation, gastrointestinal infusion and intradermal inoculation methods. And F. solani was used to infect mice by inoculation via the abraded or normal skin. In the group of immunocompromised mice, C. coronatus was isolated from the lung tissues of one mouse on day 7 and another on day 10 respectively. The corresponding histopathology revealed infiltration of local inflammatory cells in the lung tissue. Pathogenic lesions were observed in all normal and immunocompromised mice infected with F. solani via abraded skin. The lesions in the immunocompromised mice were more severe and persisted longer than those in the normal mice. Moreover, hyphae were mostly observed in the histopathological examination and fungal culture from the immunocompromised mouse. The pathogenicity of C. coronatus was relatively weak as it did not induce local infections and did not disseminate the disease in immunocompetent and immunocompromised mice. Therefore, F. solani is a type of opportunistic pathogenic fungus, and abraded skin is one of the causative routes of infection. © 2017 Blackwell Verlag GmbH.

  17. Involvement of glycosphingolipid-enriched lipid rafts in inflammatory responses.

    Science.gov (United States)

    Iwabuchi, Kazuhisa

    2015-01-01

    Glycosphingolipids (GSLs) are membrane components consisting of hydrophobic ceramide and hydrophilic sugar moieties. GSLs cluster with cholesterol in cell membranes to form GSL-enriched lipid rafts. Biochemical analyses have demonstrated that GSL-enriched lipid rafts contain several kinds of transducer molecules, including Src family kinases. Among the GSLs, lactosylceramide (LacCer, CDw17) can bind to various microorganisms, is highly expressed on the plasma membranes of human phagocytes, and forms lipid rafts containing the Src family tyrosine kinase Lyn. LacCer-enriched lipid rafts mediate immunological and inflammatory reactions, including superoxide generation, chemotaxis, and non-opsonic phagocytosis. Therefore, LacCer-enriched membrane microdomains are thought to function as pattern recognition receptors (PRRs), which recognize pathogen-associated molecular patterns (PAMPs) expressed on microorganisms. LacCer also serves as a signal transduction molecule for functions mediated by CD11b/CD18-integrin (αM/β2-integrin, CR3, Mac-1), as well as being associated with several key cellular processes. LacCer recruits PCKα/ε and phospholipase A2 to stimulate PECAM-1 expression in human monocytes and their adhesion to endothelial cells, as well as regulating β1-integrin clustering and endocytosis on cell surfaces. This review describes the organizational and inflammation-related functions of LacCer-enriched lipid rafts.

  18. Autologous antibody capture to enrich immunogenic viruses for viral discovery.

    Science.gov (United States)

    Oude Munnink, Bas B; Jazaeri Farsani, Seyed Mohammad; Deijs, Martin; Jonkers, Jiri; Verhoeven, Joost T P; Ieven, Margareta; Goossens, Herman; de Jong, Menno D; Berkhout, Ben; Loens, Katherine; Kellam, Paul; Bakker, Margreet; Canuti, Marta; Cotten, Matthew; van der Hoek, Lia

    2013-01-01

    Discovery of new viruses has been boosted by novel deep sequencing technologies. Currently, many viruses can be identified by sequencing without knowledge of the pathogenicity of the virus. However, attributing the presence of a virus in patient material to a disease in the patient can be a challenge. One approach to meet this challenge is identification of viral sequences based on enrichment by autologous patient antibody capture. This method facilitates identification of viruses that have provoked an immune response within the patient and may increase the sensitivity of the current virus discovery techniques. To demonstrate the utility of this method, virus discovery deep sequencing (VIDISCA-454) was performed on clinical samples from 19 patients: 13 with a known respiratory viral infection and 6 with a known gastrointestinal viral infection. Patient sera was collected from one to several months after the acute infection phase. Input and antibody capture material was sequenced and enrichment was assessed. In 18 of the 19 patients, viral reads from immunogenic viruses were enriched by antibody capture (ranging between 1.5x to 343x in respiratory material, and 1.4x to 53x in stool). Enriched reads were also determined in an identity independent manner by using a novel algorithm Xcompare. In 16 of the 19 patients, 21% to 100% of the enriched reads were derived from infecting viruses. In conclusion, the technique provides a novel approach to specifically identify immunogenic viral sequences among the bulk of sequences which are usually encountered during virus discovery metagenomics.

  19. Prevalence of plant beneficial and human pathogenic bacteria isolated from salad vegetables in India.

    Science.gov (United States)

    Nithya, Angamuthu; Babu, Subramanian

    2017-03-14

    The study aimed at enumerating, identifying and categorizing the endophytic cultivable bacterial community in selected salad vegetables (carrot, cucumber, tomato and onion). Vegetable samples were collected from markets of two vegetable hot spot growing areas, during two different crop harvest seasons. Crude and diluted vegetable extracts were plated and the population of endophytic bacteria was assessed based on morphologically distinguishable colonies. The bacterial isolates were identified by growth in selective media, biochemical tests and 16S rRNA gene sequencing. The endophytic population was found to be comparably higher in cucumber and tomato in both of the sampling locations, whereas lower in carrot and onion. Bacterial isolates belonged to 5 classes covering 46 distinct species belonging to 19 genera. Human opportunistic pathogens were predominant in carrot and onion, whereas plant beneficial bacteria dominated in cucumber and tomato. Out of the 104 isolates, 16.25% are human pathogens and 26.5% are human opportunistic pathogens. Existence of a high population of plant beneficial bacteria was found to have suppressed the population of plant and human pathogens. There is a greater potential to study the native endophytic plant beneficial bacteria for developing them as biocontrol agents against human pathogens that are harboured by plants.

  20. Pathogen Phytosensing: Plants to Report Plant Pathogens

    Directory of Open Access Journals (Sweden)

    C. Neal Stewart

    2008-04-01

    Full Text Available Real-time systems that provide evidence of pathogen contamination in crops can be an important new line of early defense in agricultural centers. Plants possess defense mechanisms to protect against pathogen attack. Inducible plant defense is controlled by signal transduction pathways, inducible promoters and cis-regulatory elements corresponding to key genes involved in defense, and pathogen-specific responses. Identified inducible promoters and cis-acting elements could be utilized in plant sentinels, or ‘phytosensors’, by fusing these to reporter genes to produce plants with altered phenotypes in response to the presence of pathogens. Here, we have employed cis-acting elements from promoter regions of pathogen inducible genes as well as those responsive to the plant defense signal molecules salicylic acid, jasmonic acid, and ethylene. Synthetic promoters were constructed by combining various regulatory elements supplemented with the enhancer elements from the Cauliflower mosaic virus (CaMV 35S promoter to increase basal level of the GUS expression. The inducibility of each synthetic promoter was first assessed in transient expression assays using Arabidopsis thaliana protoplasts and then examined for efficacy in stably transgenic Arabidopsis and tobacco plants. Histochemical and fluorometric GUS expression analyses showed that both transgenic Arabidopsis and tobacco plants responded to elicitor and phytohormone treatments with increased GUS expression when compared to untreated plants. Pathogen-inducible phytosensor studies were initiated by analyzing the sensitivity of the synthetic promoters against virus infection. Transgenic tobacco plants infected with Alfalfa mosaic virus showed an increase in GUS expression when compared to mock-inoculated control plants, whereas Tobacco mosaic virus infection caused no changes in GUS expression. Further research, using these transgenic plants against a range of different

  1. Opportunistic Infections

    Science.gov (United States)

    ... National HIV/AIDS and Aging Awareness Day National Gay Men's HIV/AIDS Awareness Day National Latinx AIDS ... to be responsive to antiretroviral therapy. In some cases, the disease resolves without any ... Diagnosis of this condition often requires imaging studies (CT or MRI) of the brain and a ...

  2. opportunistic infections

    African Journals Online (AJOL)

    Winnie

    THE SOUTHERN AFRICAN JOURNAL OF HIV MEDICINE. 28 ... micronutrients and herbal concoctions have been advocated.4 But none has provided the survival benefit, freedom from ... trimoxazole (CTX) use in patients with advanced HIV infection became .... A further Zambian study noted birth outcomes in pregnant.

  3. DNA extraction protocol for rapid PCR detection of pathogenic bacteria

    Science.gov (United States)

    Virtually all current assays for foodborne pathogens, including PCR assays, are conducted after lengthy cultural enrichment of the sample to increase the concentration of the target organism. This delays detection by many hours, prevents quantitation, and limits the ability to detect multiple organ...

  4. Selective enrichment media bias the types of Salmonella enterica strains isolated from mixed strain cultures and complex enrichment broths.

    Science.gov (United States)

    Gorski, Lisa

    2012-01-01

    For foodborne outbreak investigations it can be difficult to isolate the relevant strain from food and/or environmental sources. If the sample is contaminated by more than one strain of the pathogen the relevant strain might be missed. In this study mixed cultures of Salmonella enterica were grown in one set of standard enrichment media to see if culture bias patterns emerged. Nineteen strains representing four serogroups and ten serotypes were compared in four-strain mixtures in Salmonella-only and in cattle fecal culture enrichment backgrounds using Salmonella enrichment media. One or more strain(s) emerged as dominant in each mixture. No serotype was most fit, but strains of serogroups C2 and E were more likely to dominate enrichment culture mixtures than strains of serogroups B or C1. Different versions of Rappaport-Vassiliadis (RV) medium gave different patterns of strain dominance in both Salmonella-only and fecal enrichment culture backgrounds. The fittest strains belonged to serogroups C1, C2, and E, and included strains of S. Infantis, S. Thompson S. Newport, S. 6,8:d:-, and S. Give. Strains of serogroup B, which included serotypes often seen in outbreaks such as S. Typhimurium, S. Saintpaul, and S. Schwarzengrund were less likely to emerge as dominant strains in the mixtures when using standard RV as part of the enrichment. Using a more nutrient-rich version of RV as part of the protocol led to a different pattern of strains emerging, however some were still present in very low numbers in the resulting population. These results indicate that outbreak investigations of food and/or other environmental samples should include multiple enrichment protocols to ensure isolation of target strains of Salmonella.

  5. Genomic transition to pathogenicity in chytrid fungi.

    Directory of Open Access Journals (Sweden)

    Suzanne Joneson

    2011-11-01

    Full Text Available Understanding the molecular mechanisms of pathogen emergence is central to mitigating the impacts of novel infectious disease agents. The chytrid fungus Batrachochytrium dendrobatidis (Bd is an emerging pathogen of amphibians that has been implicated in amphibian declines worldwide. Bd is the only member of its clade known to attack vertebrates. However, little is known about the molecular determinants of - or evolutionary transition to - pathogenicity in Bd. Here we sequence the genome of Bd's closest known relative - a non-pathogenic chytrid Homolaphlyctis polyrhiza (Hp. We first describe the genome of Hp, which is comparable to other chytrid genomes in size and number of predicted proteins. We then compare the genomes of Hp, Bd, and 19 additional fungal genomes to identify unique or recent evolutionary elements in the Bd genome. We identified 1,974 Bd-specific genes, a gene set that is enriched for protease, lipase, and microbial effector Gene Ontology terms. We describe significant lineage-specific expansions in three Bd protease families (metallo-, serine-type, and aspartyl proteases. We show that these protease gene family expansions occurred after the divergence of Bd and Hp from their common ancestor and thus are localized to the Bd branch. Finally, we demonstrate that the timing of the protease gene family expansions predates the emergence of Bd as a globally important amphibian pathogen.

  6. Pathogenic Network Analysis Predicts Candidate Genes for Cervical Cancer

    Directory of Open Access Journals (Sweden)

    Yun-Xia Zhang

    2016-01-01

    Full Text Available Purpose. The objective of our study was to predicate candidate genes in cervical cancer (CC using a network-based strategy and to understand the pathogenic process of CC. Methods. A pathogenic network of CC was extracted based on known pathogenic genes (seed genes and differentially expressed genes (DEGs between CC and normal controls. Subsequently, cluster analysis was performed to identify the subnetworks in the pathogenic network using ClusterONE. Each gene in the pathogenic network was assigned a weight value, and then candidate genes were obtained based on the weight distribution. Eventually, pathway enrichment analysis for candidate genes was performed. Results. In this work, a total of 330 DEGs were identified between CC and normal controls. From the pathogenic network, 2 intensely connected clusters were extracted, and a total of 52 candidate genes were detected under the weight values greater than 0.10. Among these candidate genes, VIM had the highest weight value. Moreover, candidate genes MMP1, CDC45, and CAT were, respectively, enriched in pathway in cancer, cell cycle, and methane metabolism. Conclusion. Candidate pathogenic genes including MMP1, CDC45, CAT, and VIM might be involved in the pathogenesis of CC. We believe that our results can provide theoretical guidelines for future clinical application.

  7. Comparative genomics and the evolution of pathogenicity in human pathogenic fungi.

    LENUS (Irish Health Repository)

    Moran, Gary P

    2011-01-01

    Because most fungi have evolved to be free-living in the environment and because the infections they cause are usually opportunistic in nature, it is often difficult to identify specific traits that contribute to fungal pathogenesis. In recent years, there has been a surge in the number of sequenced genomes of human fungal pathogens, and comparison of these sequences has proved to be an excellent resource for exploring commonalities and differences in how these species interact with their hosts. In order to survive in the human body, fungi must be able to adapt to new nutrient sources and environmental stresses. Therefore, genes involved in carbohydrate and amino acid metabolism and transport and genes encoding secondary metabolites tend to be overrepresented in pathogenic species (e.g., Aspergillus fumigatus). However, it is clear that human commensal yeast species such as Candida albicans have also evolved a range of specific factors that facilitate direct interaction with host tissues. The evolution of virulence across the human pathogenic fungi has occurred largely through very similar mechanisms. One of the most important mechanisms is gene duplication and the expansion of gene families, particularly in subtelomeric regions. Unlike the case for prokaryotic pathogens, horizontal transfer of genes between species and other genera does not seem to have played a significant role in the evolution of fungal virulence. New sequencing technologies promise the prospect of even greater numbers of genome sequences, facilitating the sequencing of multiple genomes and transcriptomes within individual species, and will undoubtedly contribute to a deeper insight into fungal pathogenesis.

  8. Opportunistic Hybrid Transport Protocol (OHTP for Cognitive Radio Ad Hoc Sensor Networks

    Directory of Open Access Journals (Sweden)

    Yousaf Bin Zikria

    2015-12-01

    Full Text Available The inefficient assignment of spectrum for different communications purposes, plus technology enhancements and ever-increasing usage of wireless technology is causing spectrum scarcity. To address this issue, one of the proposed solutions in the literature is to access the spectrum dynamically or opportunistically. Therefore, the concept of cognitive radio appeared, which opens up a new research paradigm. There is extensive research on the physical, medium access control and network layers. The impact of the transport layer on the performance of cognitive radio ad hoc sensor networks is still unknown/unexplored. The Internet’s de facto transport protocol is not well suited to wireless networks because of its congestion control mechanism. We propose an opportunistic hybrid transport protocol for cognitive radio ad hoc sensor networks. We developed a new congestion control mechanism to differentiate true congestion from interruption loss. After such detection and differentiation, we propose methods to handle them opportunistically. There are several benefits to window- and rate-based protocols. To exploit the benefits of both in order to enhance overall system performance, we propose a hybrid transport protocol. We empirically calculate the optimal threshold value to switch between window- and rate-based mechanisms. We then compare our proposed transport protocol to Transmission Control Protocol (TCP-friendly rate control, TCP-friendly rate control for cognitive radio, and TCP-friendly window-based control. We ran an extensive set of simulations in Network Simulator 2. The results indicate that the proposed transport protocol performs better than all the others.

  9. A Hierarchical Distance Sampling Approach to Estimating Mortality Rates from Opportunistic Carcass Surveillance Data.

    Science.gov (United States)

    Bellan, Steve E; Gimenez, Olivier; Choquet, Rémi; Getz, Wayne M

    2013-04-01

    Distance sampling is widely used to estimate the abundance or density of wildlife populations. Methods to estimate wildlife mortality rates have developed largely independently from distance sampling, despite the conceptual similarities between estimation of cumulative mortality and the population density of living animals. Conventional distance sampling analyses rely on the assumption that animals are distributed uniformly with respect to transects and thus require randomized placement of transects during survey design. Because mortality events are rare, however, it is often not possible to obtain precise estimates in this way without infeasible levels of effort. A great deal of wildlife data, including mortality data, is available via road-based surveys. Interpreting these data in a distance sampling framework requires accounting for the non-uniformity sampling. Additionally, analyses of opportunistic mortality data must account for the decline in carcass detectability through time. We develop several extensions to distance sampling theory to address these problems.We build mortality estimators in a hierarchical framework that integrates animal movement data, surveillance effort data, and motion-sensor camera trap data, respectively, to relax the uniformity assumption, account for spatiotemporal variation in surveillance effort, and explicitly model carcass detection and disappearance as competing ongoing processes.Analysis of simulated data showed that our estimators were unbiased and that their confidence intervals had good coverage.We also illustrate our approach on opportunistic carcass surveillance data acquired in 2010 during an anthrax outbreak in the plains zebra of Etosha National Park, Namibia.The methods developed here will allow researchers and managers to infer mortality rates from opportunistic surveillance data.

  10. Staff views of an opportunistic chlamydia testing pilot in a primary health organisation

    Directory of Open Access Journals (Sweden)

    McKernon S

    2013-12-01

    Full Text Available INTRODUCTION: The Auckland chlamydia pilot was one of three pilots funded by the Ministry of Health to trial implementation of the 2008 Chlamydia Management Guidelines prior to national roll-out. AIM: To assess what elements in the testing programme pilot worked best for staff and to determine how an opportunistic testing programme could be better configured to meet staff needs and preferences. METHODS: A staff survey listed key chlamydia testing tasks in chronological order, and service interventions supporting these tasks. Staff were asked to rate each task on its difficulty prior to the pilot, and then on the difference the pilot had made to each task. They were also asked to rate service interventions on their usefulness during the pilot implementation. RESULTS: The survey had a response rate of 94%. The testing tasks posing the greatest difficulties to staff were those involving patient interactions (41% and management of follow-up (52%. About 70% of staff felt tasks were improved by the pilot. Staff considered the three most useful service interventions to be a chlamydia-specific template created for the practice management system, provision of printed patient resources, and regular team discussions with other staff. DISCUSSION: A significant proportion of staff reported difficulties with routine tasks required for opportunistic testing for chlamydia, highlighting the need to involve staff during programme design. Practice nurse-led approaches to future opportunistic testing programmes should be considered as nurses had a more positive response to the pilot and nurse-led approaches have been shown to be successful overseas.

  11. Pharmacokinetic Studies in Neonates: The Utility of an Opportunistic Sampling Design.

    Science.gov (United States)

    Leroux, Stéphanie; Turner, Mark A; Guellec, Chantal Barin-Le; Hill, Helen; van den Anker, Johannes N; Kearns, Gregory L; Jacqz-Aigrain, Evelyne; Zhao, Wei

    2015-12-01

    The use of an opportunistic (also called scavenged) sampling strategy in a prospective pharmacokinetic study combined with population pharmacokinetic modelling has been proposed as an alternative strategy to conventional methods for accomplishing pharmacokinetic studies in neonates. However, the reliability of this approach in this particular paediatric population has not been evaluated. The objective of the present study was to evaluate the performance of an opportunistic sampling strategy for a population pharmacokinetic estimation, as well as dose prediction, and compare this strategy with a predetermined pharmacokinetic sampling approach. Three population pharmacokinetic models were derived for ciprofloxacin from opportunistic blood samples (SC model), predetermined (i.e. scheduled) samples (TR model) and all samples (full model used to previously characterize ciprofloxacin pharmacokinetics), using NONMEM software. The predictive performance of developed models was evaluated in an independent group of patients. Pharmacokinetic data from 60 newborns were obtained with a total of 430 samples available for analysis; 265 collected at predetermined times and 165 that were scavenged from those obtained as part of clinical care. All datasets were fit using a two-compartment model with first-order elimination. The SC model could identify the most significant covariates and provided reasonable estimates of population pharmacokinetic parameters (clearance and steady-state volume of distribution) compared with the TR and full models. Their predictive performances were further confirmed in an external validation by Bayesian estimation, and showed similar results. Monte Carlo simulation based on area under the concentration-time curve from zero to 24 h (AUC24)/minimum inhibitory concentration (MIC) using either the SC or the TR model gave similar dose prediction for ciprofloxacin. Blood samples scavenged in the course of caring for neonates can be used to estimate

  12. Two-user opportunistic scheduling using hierarchical modulations in wireless networks with heterogenous average link gains

    KAUST Repository

    Hossain, Md Jahangir

    2010-03-01

    Our contribution, in this paper, is two-fold. First, we analyze the performance of a hierarchical modulation-assisted two-best user opportunistic scheduling (TBS) scheme, which was proposed by the authors, in a fading environment where different users have different average link gains. Specifically, we present a new expression for the spectral efficiency (SE) of the users and using this expression, we compare the degrees of fairness (DOF) of the TBS scheme with that of classical single user opportunistic scheduling schemes, namely, absolute carrier-to-noise ratio (CNR) based single-best user scheduling (SBS) and normalized CNR based proportional fair scheduling (PFS) schemes. The second contribution is that we propose a new hybrid two-user opportunistic scheduling (HTS) scheme based on our earlier proposed TBS scheme. This HTS scheme selects the first user based on the largest absolute CNR value among all the users while the second user is selected based on the ratios of the absolute CNRs to the corresponding average CNRs of the remaining users. The total transmission rate i.e., the constellation size is selected according to the absolute CNR of the first best user. The total transmission rate is then allocated among these selected users by joint consideration of their absolute CNRs and allocated number of information bit(s) are transmitted to them using hierarchical modulations. Numerical results are presented for a fading environment where different users experience independent but non-identical (i.n.d.) channel fading. These selected numerical results show that the proposed HTS scheme can considerably increase the system\\'s fairness without any degradation of the link spectral efficiency (LSE) i.e., the multiuser diversity gain compared to the classical SBS scheme. These results also show that the proposed HTS scheme has a lower fairness in comparison to the PFS scheme which suffers from a considerable degradation in LSE. © 2010 IEEE.

  13. The Influence of Contrarians and Opportunists on the Stability of a Democracy in the Sznajd Model

    Science.gov (United States)

    Schneider, Johannes J.

    Sznajd-Weron and Sznajd introduced a model investigating the democratic development in a closed community. This model is based on the USDF-principle ("united we stand, divided we fall"). However, it faces the problem that the system tends either to a dictatorship (i.e., 100% pro or 100% contra) or to a stalemate state (i.e., exactly 50% pro, 50% contra). Based on their model, I will show that a democratic system keeps alive due to the existence of both opportunists and persons in opposition.

  14. Protocol for Message Forwarding in Cellular and Mobile Opportunistic Wireless Network (Oppnets

    Directory of Open Access Journals (Sweden)

    Lokendra Singh Songare

    2013-09-01

    Full Text Available We describes hybrid approach for routing in opportunistic networks. In such networks there is no guarantee that a fully connected path between source and destination exists at any time, rendering traditional routing protocols unable to deliver messages between hosts. Thus, there is a need for a way to route through such networks. We propose hybrid approach which combines Prioritized Epidemic Routing and Probabilistic Routing. This approach prioritizes bundles based on costs to destination, source, and expiry time. Costs are derived from per-link “average availability” information that is disseminated in an epidemic manner.

  15. Service time analysis of secondary packet transmission with opportunistic channel access

    KAUST Repository

    Usman, Muneer

    2014-09-01

    Cognitive radio transceiver can opportunistically access the underutilized channels of primary systems for new wireless services. The secondary transmission may be interrupted by the primary user\\'s transmission. To facilitate the delay analysis of such secondary packet transmission, we study the resulting extended delivery time for a fixed-size secondary packet that includes both transmission time and waiting time. In particular we derive the exact distribution functions of extended delivery time of secondary transmission for both continuous sensing and periodic sensing cases. Selected numerical results are presented for illustrating the mathematical formulation.

  16. Outage Analysis of Opportunistic Cooperative Ad Hoc Networks with Randomly Located Nodes

    Institute of Scientific and Technical Information of China (English)

    Cheng-Wen Xing; Hai-Chuan Ding; Guang-Hua Yang; Shao-Dan Ma; Ze-Song Fei

    2013-01-01

    In this paper,an opportunistic cooperative ad hoc sensor network with randomly located nodes is analyzed.The randomness of nodes' locations is captured by a homogeneous Poisson point process.The effect of imperfect interference cancellation is also taken into account in the analysis.Based on the theory of stochastic geometry,outage probability and cooperative gain are derived.It is demonstrated that explicit performance gain can be achieved through cooperation.The analyses are corroborated by extensive simulation results and the analytical results can thus serve as a guideline for wireless sensor network design.

  17. Methodology for the conceptual design of a robust and opportunistic system-of-systems

    Science.gov (United States)

    Talley, Diana Noonan

    Systems are becoming more complicated, complex, and interrelated. Designers have recognized the need to develop systems from a holistic perspective and design them as Systems-of-Systems (SoS). The design of the SoS, especially in the conceptual design phase, is generally characterized by significant uncertainty. As a result, it is possible for all three types of uncertainty (aleatory, epistemic, and error) and the associated factors of uncertainty (randomness, sampling, confusion, conflict, inaccuracy, ambiguity, vagueness, coarseness, and simplification) to affect the design process. While there are a number of existing SoS design methods, several gaps have been identified: the ability to modeling all of the factors of uncertainty at varying levels of knowledge; the ability to consider both the pernicious and propitious aspects of uncertainty; and, the ability to determine the value of reducing the uncertainty in the design process. While there are numerous uncertainty modeling theories, no one theory can effectively model every kind of uncertainty. This research presents a Hybrid Uncertainty Modeling Method (HUMM) that integrates techniques from the following theories: Probability Theory, Evidence Theory, Fuzzy Set Theory, and Info-Gap theory. The HUMM is capable of modeling all of the different factors of uncertainty and can model the uncertainty for multiple levels of knowledge. In the design process, there are both pernicious and propitious characteristics associated with the uncertainty. Existing design methods typically focus on developing robust designs that are insensitive to the associated uncertainty. These methods do not capitalize on the possibility of maximizing the potential benefit associated with the uncertainty. This research demonstrates how these deficiencies can be overcome by identifying the most robust and opportunistic design. In a design process it is possible that the most robust and opportunistic design will not be selected from the set

  18. New resource allocation scheme for cognitive relay networks with opportunistic access

    KAUST Repository

    Zafar, Ammar

    2012-06-01

    In this paper, a new resource allocation scheme to minimize Symbol Error rate (SER) for relay assisted cognitive radio networks is studied. A cognitive relay network with amplify-and-forward (AF) fixed gain relays and opportunistic access to the licensed spectrum is considered. The SER objective function and the optimization constraints are derived first. The resource allocation algorithm is then derived using the Langrangian multiplier method. Closed form expressions are derived for the source and relay powers and, symbol time. Analytical results show that the optimal power allocation follows an extended water-filling solution. © 2012 IEEE.

  19. Exact outage analysis of incremental decode-and-forward opportunistic relaying

    KAUST Repository

    Tourki, Kamel

    2010-11-01

    In this paper, we investigate a dual-hop decode-andforward opportunistic relaying scheme where the selected relay chooses to cooperate only if the source-destination channel is of an unacceptable quality. In our study, we derive exact closed-form expression for the outage probability based on the exact statistics of each hop. Furthermore, we perform asymptotic analysis and we deduce the diversity order of the scheme. We validate our analysis by showing that performance simulation results coincide with our analytical results over different network architectures. © 2010 IEEE.

  20. Specialized Fungal Parasites and Opportunistic Fungi in Gardens of Attine Ants

    Directory of Open Access Journals (Sweden)

    Fernando C. Pagnocca

    2012-01-01

    Full Text Available Ants in the tribe Attini (Hymenoptera: Formicidae comprise about 230 described species that share the same characteristic: all coevolved in an ancient mutualism with basidiomycetous fungi cultivated for food. In this paper we focused on fungi other than the mutualistic cultivar and their roles in the attine ant symbiosis. Specialized fungal parasites in the genus Escovopsis negatively impact the fungus gardens. Many fungal parasites may have small impacts on the ants' fungal colony when the colony is balanced, but then may opportunistically shift to having large impacts if the ants' colony becomes unbalanced.

  1. PlayNCool: Opportunistic Network Coding for Local Optimization of Routing in Wireless Mesh Networks

    DEFF Research Database (Denmark)

    Pahlevani, Peyman; Roetter, Daniel Enrique Lucani; Pedersen, Morten Videbæk;

    2013-01-01

    This paper introduces PlayNCool, an opportunistic protocol with local optimization based on network coding to increase the throughput of a wireless mesh network (WMN). PlayNCool aims to enhance current routing protocols by (i) allowing random linear network coding transmissions end-to-end, (ii...... in large scale mesh networks. We show that PlayNCool can provide gains of more than 3x in individual links, which translates into a large end-to-end throughput improvement, and that it provides higher gains when more nodes in the network contend for the channel at the MAC layer, making it particularly...... relevant for dense mesh networks....

  2. Outage and ser performance of an opportunistic multi-user underlay cognitive network

    KAUST Repository

    Khan, Fahd Ahmed

    2012-10-01

    Consider a multi-user underlay cognitive network where multiple cognitive users concurrently share the spectrum with a primary network and a single secondary user is selected for transmission. The channel is assumed to have independent but not identical Nakagami-m fading. Closed form expressions for the outage performance and the symbol-error-rate performance of the opportunistic multi-user secondary network are derived when a peak interference power constraint is imposed on the secondary network in addition to the limited peak transmit power of each secondary user. © 2012 IEEE.

  3. Structure and Optimality of Myopic Policy in Opportunistic Access with Noisy Observations

    CERN Document Server

    Zhao, Qing

    2008-01-01

    A restless multi-armed bandit problem that arises in multichannel opportunistic communications is considered, where channels are modeled as independent and identical Gilbert-Elliot channels and channel state observations are subject to errors. A simple structure of the myopic policy is established under a certain condition on the false alarm probability of the channel state detector. It is shown that myopic actions can be obtained with a simple counting procedure without knowing the underlying Markovian model. The optimality of the myopic policy is proved for the case of two channels and conjectured based on simulations for the general case.

  4. Macrozoobenthic community structure in two Portuguese estuaries: Relationship with organic enrichment and nutrient gradients

    Science.gov (United States)

    Mucha, Ana Paula; Costa, Maria Helena

    1999-07-01

    The aim of this work consists in the study of the structural and functional aspects of the macrozoobenthic communities and their relationships with the organic enrichment and nutrient gradients in water and sediment. The study was carried out in two coastal ecosystems under strong anthropogenic pressure: the Sado estuary and the Aveiro Lagoon. Samples were collected at four stations between October 1994 and April 1995. The results obtained allowed us to state that spatial variability, both horizontal and vertical, was higher than the temporal variability. This was due to local hydrodynamism, organic load and granulometric structure of the sediment. Comparing the community structure at the different stations, it was possible to observe the existence of disturbance cases not directly related to organic enrichment gradients. The interpretation of the functional role of the macrozoobenthic communities at the water-sediment interface was based on the trophodynamic group classification. This approach allowed us to state that the sensitivity of different groups to organic enrichment, confirming the role of burrower subsurface-deposit feeders as opportunists associated with organic enrichment and, on the other hand, the influence of certain trophodynamic groups in the nutrient transfer processes, particularly the association between tube-builder omnivores and burrower carnivore and nitrate content in interstitial water.

  5. Enrichment of light hydrocarbon mixture

    Science.gov (United States)

    Yang; Dali; Devlin, David; Barbero, Robert S.; Carrera, Martin E.; Colling, Craig W.

    2010-08-10

    Light hydrocarbon enrichment is accomplished using a vertically oriented distillation column having a plurality of vertically oriented, nonselective micro/mesoporous hollow fibers. Vapor having, for example, both propylene and propane is sent upward through the distillation column in between the hollow fibers. Vapor exits neat the top of the column and is condensed to form a liquid phase that is directed back downward through the lumen of the hollow fibers. As vapor continues to ascend and liquid continues to countercurrently descend, the liquid at the bottom of the column becomes enriched in a higher boiling point, light hydrocarbon (propane, for example) and the vapor at the top becomes enriched in a lower boiling point light hydrocarbon (propylene, for example). The hollow fiber becomes wetted with liquid during the process.

  6. 31 CFR 540.316 - Uranium enrichment.

    Science.gov (United States)

    2010-07-01

    ... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process...

  7. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms.

    Science.gov (United States)

    Mendes, Rodrigo; Garbeva, Paolina; Raaijmakers, Jos M

    2013-09-01

    Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  8. Interactive effects of metal contamination and pathogenic organisms on the introduced marine bivalve Ruditapes philippinarum in European populations

    Energy Technology Data Exchange (ETDEWEB)

    Paul-Pont, Ika, E-mail: i.paulpont@epoc.u-bordeaux1.f [Universite Bordeaux 1, UMR 5805 CNRS, Station Marine d' Arcachon, place du Dr. Peyneau, Arcachon 33120 (France); Montaudouin, Xavier de; Gonzalez, Patrice; Jude, Florence; Raymond, Natalie [Universite Bordeaux 1, UMR 5805 CNRS, Station Marine d' Arcachon, place du Dr. Peyneau, Arcachon 33120 (France); Paillard, Christine [Universite de Bretagne Occidentale-IUEM, LEMAR UMR 6539 CNRS, Place Nicolas Copernic, Technopole Brest Iroise, 29280 Plouzane (France); Baudrimont, Magalie [Universite Bordeaux 1, UMR 5805 CNRS, Station Marine d' Arcachon, place du Dr. Peyneau, Arcachon 33120 (France)

    2010-11-15

    In natural environment, marine organisms are concomitantly exposed to pollutants and multiple disease agents resulting in detrimental interactions. The present study evaluated interactive effects of metal contamination (cadmium) and pathogenic organisms (trematode parasites Himasthla elongata and pathogenic bacteria Vibrio tapetis) singularly and in combination on the bivalve Ruditapes philippinarum, an introduced species to Europe, under laboratory controlled conditions. After 7 days, metal bioaccumulation and pathogen load were analyzed as well as metallothionein (MT) response and hemocyte concentrations and activities. Results showed that infection by opportunistic pathogens affects metal accumulation, leading to maximal Cd accumulation in co-infected clams. Among stressors only V. tapetis induced significant effects on immune parameters whereas a particular interaction 'trematode-bacteria' was shown on MT responses. Despite low trematode infection in agreement with the resistant status of R. philippinarum to these macroparasites, significant interaction with bacteria and metal occurred. Such results highlight the necessity of taking pathogens into account in ecotoxicological studies. - Co-infection by opportunistic pathogens affects metal accumulation and some defense-related activities in the Manila clam Ruditapes philippinarum.

  9. [Unknown pathogens from the human oral microflora of interest for otorhinolaryngology].

    Science.gov (United States)

    Tets, V V; Tets, G V; Vikina, D S; Vecherovskaia, M F; Kharlamova, V V

    2014-01-01

    The identification of microorganisms from the human oral cavity is a topical problem in many clinical disciplines including otorhinolaryngology. Many bacterial species of oral microbiota are causative agents of ENT diseases, and poor conditions of the oral cavity, unhealthy teeth and gums increase the risk of the spread of infection. The objective of the present study was to distinguish and identify poorly explored and previously unknown aerobic opportunistic pathogenic microorganisms responsible for various ENT disorders. The normal microflora remains to be thoroughly studied with the use of the new culturing techniques that ensure the isolation of pure microbial cultures. The present publication reports for the first time isolation of the stable mixed microbial biofilms formed by unrelated bacterial species and containing the yet unknown microorganisms. The isolated bacteria were identified as previously unknown or poorly unexplored anaerobic opportunistic species capable of inducing ENT pathology; their sensitivity to antibiotics was evaluated.

  10. Potatoes, pathogens and pests

    NARCIS (Netherlands)

    Lazebnik, Jenny

    2017-01-01

    Currently, fungicides are necessary to protect potato crops against late blight, Phytophthora infestans, one of the world’s most damaging crop pathogens. The introgression of plant resistance genes from wild potato species targeted specifically to the late blight pathogen into susceptible

  11. Plant pathogen resistance

    Science.gov (United States)

    Greenberg, Jean T; Jung, Ho Won; Tschaplinski, Timothy

    2012-11-27

    Azelaic acid or its derivatives or analogs induce a robust and a speedier defense response against pathogens in plants. Azelaic acid treatment alone does not induce many of the known defense-related genes but activates a plant's defense signaling upon pathogen exposure.

  12. Plant pathogen resistance

    Energy Technology Data Exchange (ETDEWEB)

    Greenberg, Jean T.; Jung, Ho Won; Tschaplinski, Timothy

    2015-10-20

    Azelaic acid or its derivatives or analogs induce a robust and a speedier defense response against pathogens in plants. Azelaic acid treatment alone does not induce many of the known defense-related genes but activates a plant's defense signaling upon pathogen exposure.

  13. Enrichment of omnivorous cercozoan nanoflagellates from coastal Baltic Sea waters.

    Directory of Open Access Journals (Sweden)

    Kasia Piwosz

    Full Text Available Free-living nano-sized flagellates are important bacterivores in aquatic habitats. However, some slightly larger forms can also be omnivorous, i.e., forage upon both bacterial and eukaryotic resources. This hitherto largely ignored feeding mode may have pronounced implications for the interpretation of experiments about protistan bacterivory. We followed the response of an uncultured group of omnivorous cercozoan nanoflagellates from the Novel Clade 2 (Cerc_BAL02 to experimental food web manipulation in samples from the Gulf of Gdańsk (Southern Baltic Sea. Seawater was either prefiltered through 5 µm filters to exclude larger predators of nanoflagellates (F-treatment, or prefiltered and subsequently 1∶10 diluted with sterile seawater (F+D-treatment to stimulate the growth of both, flagellates and bacteria. Initially, Cerc_BAL02 were rapidly enriched under both conditions. They foraged on both, eukaryotic prey and bacteria, and were highly competitive at low concentrations of food. However, these omnivores were later only successful in the F+D treatment, where they eventually represented almost one fifth of all aplastidic nanoflagellates. By contrast, their numbers stagnated in the F-treatment, possibly due to top-down control by a concomitant bloom of other, unidentified flagellates. In analogy with observations about the enrichment of opportunistically growing bacteria in comparable experimental setups we suggest that the low numbers of omnivorous Cerc_Bal02 flagellates in waters of the Gulf of Gdańsk might also be related to their vulnerability to grazing pressure.

  14. Exploiting Channel Correlation and PU Traffic Memory for Opportunistic Spectrum Scheduling

    CERN Document Server

    Wang, Shanshan; Zhang, Junshan

    2012-01-01

    We consider a cognitive radio network with multiple primary users (PUs) and one secondary user (SU), where a spectrum server is utilized for spectrum sensing and scheduling the SU to transmit over one of the PU channels opportunistically. One practical yet challenging scenario is when \\textit{both} the PU occupancy and the channel fading vary over time and exhibit temporal correlations. Little work has been done for exploiting such temporal memory in the channel fading and the PU occupancy simultaneously for opportunistic spectrum scheduling. A main goal of this work is to understand the intricate tradeoffs resulting from the interactions of the two sets of system states - the channel fading and the PU occupancy, by casting the problem as a partially observable Markov decision process. We first show that a simple greedy policy is optimal in some special cases. To build a clear understanding of the tradeoffs, we then introduce a full-observation genie-aided system, where the spectrum server collects channel fa...

  15. [Opportunistic diseases in HIV-infected patients at the Jeanne Ebori Foundation in Libreville, Gabon].

    Science.gov (United States)

    Okome-Nkoumou, M; Boguikouma, J B; Kombila, M

    2006-04-01

    The purpose of this study was to determine the frequencies of opportunistic diseases among AIDS patients at the Jeanne Ebori Foundation (JEF) in Libreville, Gabon. A total 6313 file of patients treated in the internal medicine unit between 1994 and 1998 were analyzed. Findings showed that the main diseases related to AIDS classified according to seroprevalence were as follows: purigo (100%), cerebral toxoplasmosis (100%), oral candidiaisis (88%), bacteremia (87.8%), shingles (84.6%), minor salmonelosis (72%), and tuberclosis. The main diagnoses unrelated to AIDS at the JEF according to seroprevalene were typhoid (9.4%), common pneumonia (28%), bacterial meningitis (26.3%, hepatitis B (20.0%), and malaria (14%). In addition to these diseases there were nine cases of Kaposi's sarcoma, four cases of isosporosis, two cases of cryptococcosis, two cases of herpes Varicella, one case of cryptosporidiosis, and one case of isosporosis. The incidence of opportunistic disease was high in our study and must be taken in drug procurement.

  16. Allelopathic interactions between the opportunistic species Ulva prolifera and the native macroalga Gracilaria lichvoides.

    Science.gov (United States)

    Xu, Dong; Gao, Zhengquan; Zhang, Xiaowen; Fan, Xiao; Wang, Yitao; Li, Demao; Wang, Wei; Zhuang, Zhimeng; Ye, Naihao

    2012-01-01

    Allelopathy, one type of direct plant competition, can be a potent mechanism through which plant communities are structured. The aim of this study was to determine whether allelopathic interactions occur between the opportunistic green tide-forming species Ulva prolifera and the native macroalga Gracilaria lichvoides, both of which were collected from the coastline of East China sea. In laboratory experiments, the presence of G. lichvoides at 1.25 g wet weight L(-1) significantly inhibited growth and photosynthesis of U. prolifera at concentrations of 1.25, 2.50, and 3.75 g wet weight L(-1) (p0.05). Culture medium experiments further confirmed that some allelochemicals may be released by both of the tested macroalgae, and these could account for the observed physiological inhibition of growth and photosynthesis. Moreover, the native macroalgae G. lichvoides was a stronger competitor than the opportunistic species U. prolifera. Collectively, the results of the present study represent a significant advance in exploring ecological questions about the effects of green tide blooms on the macroalgal community.

  17. Opportunistic Energy-Aware Amplify-and-Forward Cooperative Systems with Imperfect CSI

    KAUST Repository

    Amin, Osama

    2015-07-29

    Recently, much attention has been paid to the green design of wireless communication systems using energy efficiency (EE) metrics that should capture all energy consumption sources to deliver the required data. In this paper, we design an energyefficient relay assisted communication system based on estimated channel state information (CSI). It employs amplify-andforward relaying and switches between different communication schemes, which are known as direct-transmission, two-hop and cooperative-transmission schemes, using the estimated CSI in order to maximize the EE. Two estimation strategies are assumed, namely disintegrated channel estimation and cascaded channel estimation. To formulate an accurate EE metric for the proposed opportunistic amplify-and-forward system, the channel estimation cost is reflected on the EE metric by including its impact in the signal-to-noise ratio term and in the energy consumption during the channels estimation phase. Based on the formulated EE metric, we propose an adaptive power allocation algorithm to maximize the EE of the proposed opportunistic amplify-andforward system with channel estimation. Furthermore, we study the impact of the estimation parameters on the proposed system via simulation examples.

  18. The diagnosis of HIV-associated central nervous system opportunistic infections

    Directory of Open Access Journals (Sweden)

    GONG Qi-ming

    2013-01-01

    Full Text Available Opportunistic infections of the central nervous system (CNS are very common and severe complications of advanced immunodeficiency in patients with human immunodeficiency virus type 1 (HIV-1 infection, which are included in the diagnostic criteria for acquired immunodeficiency syndrome (AIDS defining conditions according to 1993 Revised Classification System for HIV Infection and Expanded Surveillance Case Definition for AIDS among Adolescents and Adults published by USA Centers for Disease Control and Prevention (CDC. The etiologic microorganisms of CNS opportunistic infections include virus, bacteria, fungus, mycobacterium and parasite. The clinical symptoms, signs and laboratory examinations of these diseases are different from that of patients with non-immunodeficiency. Even in the era of highly active antiretroviral therapy (HAART, worsening conditions or new infections may occur. Therefore, prompt diagnosis and treatment of such disorders are critical. The immune reconstitution inflammatory syndrome (IRIS in HIV-1 infected patients in the initiating antiretroviral therapy results from restored immunity to specific infectious or non-infectious antigens. This study reviews the epidemiology, pathogenesis, clinical features, diagnosis of some common CNS disorders in HIV-1 infected patients. Physicians caring for such patients must be aware of the new diagnostic modalities and therapeutic options of these diseases.

  19. A Wireless Video Transmission Scheme Based on MAC-independent Opportunistic Routing &Encoding Protocol

    Directory of Open Access Journals (Sweden)

    Yong Liu

    2010-11-01

    Full Text Available It is a tremendous challenge to transmit real-time video streams over wireless sensor network because of the poor wireless communication conditions and the high requirements of video transmission. The opportunistic routing protocol can take advantage of the broadcast nature of wireless communication and can improve transfer throughput significantly. But the bigger size of transmission unit also increases the end-to-end delay at the same time. In order to overcome this problem and improve the real-time video transmission quality in wireless video sensor network, we propose a source adaptive frame discard algorithm for MAC-independent Opportunistic Routing & Encoding (MORE Protocol in this paper. In our approach, the historical transmission delay is recorded to estimate current network transmission rate. Based on the video deadline, frames predicted to be delayed are discarded adaptively in the source node to get better overall video quality. In some practice application scenarios, there are usually need to deliver multiple video streams over multi-hop wireless network. It can’t work effectively with the originally MORE protocol in such scenarios. Furthermore, we modify the MORE protocol and design an adaptive scheme to support multiple video streams over multi-hop wireless video sensor network in this paper. The simulation results show that our algorithm can reduce frame loss rate and improve video quality significantly.

  20. SPRINT-SELF: Social-Based Routing and Selfish Node Detection in Opportunistic Networks

    Directory of Open Access Journals (Sweden)

    Radu Ioan Ciobanu

    2015-01-01

    Full Text Available Since mobile devices nowadays have become ubiquitous, several types of networks formed over such devices have been proposed. One such approach is represented by opportunistic networking, which is based on a store-carry-and-forward paradigm, where nodes store data and carry it until they reach a suitable node for forwarding. The problem in such networks is how to decide what the next hop will be, since nodes do not have a global view of the network. We propose using the social network information of a node when performing routing, since a node is more likely to encounter members of its own social community than other nodes. In addition, we approximate a node’s contact as a Poisson distribution and show that we can predict its future behavior based on the contact history. Furthermore, since opportunistic network nodes may be selfish, we improve our solution by adding a selfish node detection and avoidance mechanism, which can help reduce the number of unnecessary messages sent in the network, and thus avoid congestion and decrease battery consumption. We show that our algorithm outperforms existing solutions such as BUBBLE Rap and Epidemic in terms of delivery cost and hit rate, as well as the rate of congestion introduced in the network, by testing in various realistic scenarios.