WorldWideScience

Sample records for repeated human intrusion

  1. 10 CFR 63.321 - Individual protection standard for human intrusion.

    Science.gov (United States)

    2010-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Postclosure Public Health and Environmental Standards Human Intrusion Standard § 63.321 Individual protection standard for human intrusion. (a) DOE...

  2. HUMAN CANCER IS A PARASITE SPREAD VIA INTRUSION IN GENOME

    Directory of Open Access Journals (Sweden)

    Sergey N. Rumyantsev

    2013-03-01

    Full Text Available The present article is devoted to further development of new paradigm about the biology of human cancer: the hypothesis of parasitic nature, origin and evolution of the phenomenon. The study included integrative reconsidering, and reinterpretation of the make-ups, traits and processes existing both in human and animal cancers. It was demonstrated that human cancer possesses nearly analogous set of traits characteristic of transmissible animal cancer. Undoubted analogies are seen in the prevalence, clinical exposure, progression of disease, origin of causative agents, immune response against invasion and especially in the intrinsic deviations of the leading traits of cancerous cells. Both human and animal cancers are highly exceptional pathogens. But in contrast to contagious animal cancers the cells of of human cancer can not pass between individuals as usual infectious agents. Exhaustive evidence of the parasitic nature and evolutionary origin of human cancer was revealed and interpreted. In contrast to animal cancer formed of solitary cell lineage, human cancer consists of a couple of lineages constructed under different genetic regulations and performed different structural and physiological functions. The complex make-up of cancer composition remains stable over sequential propagation. The subsistence of human cancer regularly includes obligatory interchange of its successive forms. Human cancer possesses its own biological watch and the ability to gobble its victim, transmit via the intrusion of the genome, perform intercommunications within the tumor components and between the dispersed subunits of cancer. Such intrinsic traits characterize human cancer as a primitively structured parasite that can be classified in Class Mammalians, Species Genomeintruder malevolent (G.malevolent.

  3. Relationship between vapor intrusion and human exposure to trichloroethylene

    OpenAIRE

    ARCHER, NATALIE P.; BRADFORD, CARRIE M.; VILLANACCI, JOHN F.; CRAIN, NEIL E.; Corsi, Richard L; Chambers, David M.; BURK, TONIA; Blount, Benjamin C.

    2015-01-01

    Trichloroethylene (TCE) in groundwater has the potential to volatilize through soil into indoor air where it can be inhaled. The purpose of this study was to determine whether individuals living above TCE-contaminated groundwater are exposed to TCE through vapor intrusion. We examined associations between TCE concentrations in various environmental media and TCE concentrations in residents. For this assessment, indoor air, outdoor air, soil gas, and tap water samples were collected in and aro...

  4. Relationship between vapor intrusion and human exposure to trichloroethylene.

    Science.gov (United States)

    Archer, Natalie P; Bradford, Carrie M; Villanacci, John F; Crain, Neil E; Corsi, Richard L; Chambers, David M; Burk, Tonia; Blount, Benjamin C

    2015-01-01

    Trichloroethylene (TCE) in groundwater has the potential to volatilize through soil into indoor air where it can be inhaled. The purpose of this study was to determine whether individuals living above TCE-contaminated groundwater are exposed to TCE through vapor intrusion. We examined associations between TCE concentrations in various environmental media and TCE concentrations in residents. For this assessment, indoor air, outdoor air, soil gas, and tap water samples were collected in and around 36 randomly selected homes; blood samples were collected from 63 residents of these homes. Additionally, a completed exposure survey was collected from each participant. Environmental and blood samples were analyzed for TCE. Mixed model multiple linear regression analyses were performed to determine associations between TCE in residents' blood and TCE in indoor air, outdoor air, and soil gas. Blood TCE concentrations were above the limit of quantitation (LOQ; ≥ 0.012 µg L(-1)) in 17.5% of the blood samples. Of the 36 homes, 54.3%, 47.2%, and >84% had detectable concentrations of TCE in indoor air, outdoor air, and soil gas, respectively. Both indoor air and soil gas concentrations were statistically significantly positively associated with participants' blood concentrations (P = 0.0002 and P = 0.04, respectively). Geometric mean blood concentrations of residents from homes with indoor air concentrations of >1.6 µg m(-3) were approximately 50 times higher than geometric mean blood TCE concentrations in participants from homes with no detectable TCE in indoor air (P < .0001; 95% CI 10.4-236.4). This study confirms the occurrence of vapor intrusion and demonstrates the magnitude of exposure from vapor intrusion of TCE in a residential setting.

  5. Non-intrusive human fatigue monitoring in command centers

    Science.gov (United States)

    Alsamman, A.; Ratecki, T.

    2011-04-01

    An inexpensive, non-intrusive, vision-based, active fatigue monitoring system is presented. The system employs a single consumer webcam that is modified to operate in the near-IR range. An active IR LED system is developed to facilitate the quick localization of the eye pupils. Imaging software tracks the eye features by analyzing intensity areas and their changes in the vicinity of localization. To quantify the level of fatigue the algorithm measures the opening of the eyelid, PERCLOS. The software developed runs on the workstation and is designed to draw limited computational power, so as to not interfere with the user task. To overcome low-frame rate and improve real-time monitoring, a two-phase detection and tacking algorithm is implemented. The results presented show that the system successfully monitors the level of fatigue at a low rate of 8 fps. The system is well suited to monitor users in command centers, flight control centers, airport traffic dispatchers, military operation and command centers, etc., but the work can be extended to wearable devices and other environments.

  6. The evolution process of seawater intrusion in Laizhou Bay, and its linkage to climate change and human activity

    Science.gov (United States)

    xu, X.

    2013-12-01

    Seawater Intrusion is that seawater or saltwater intrude into the continent along the aquifer.Under the effects of the natural and artificial factors, the hydrodynamic conditions of aquifer in the coastal area has been changed ,which break the equilibrium between the seawater and the freshwater, hence the salt-fresh interface moves on the continent. Sea-level rise due to climate change and the paleoseawater hosting in marine strata combined with a rising population density in the Laizhou Bay have led to higher stresses on coastal water resources, and the risk of seawater intrusion has increased. Despite comprehensive seawater intrusion research and prevention measures are developed, the effects of climate change and human activity on seawater intrusion is still unclear. Therefore to reveal how climate change and human activity impact on seawater intrusion and to mathematical quantify it is important to establish reasonable prevention and control of seawater intrusion measures. Laizhou Bay is the region suffering from the geo-hazard of sea (saline) water intrusion most seriously in China, and is divided into seawater intrusion area, saline water (paleo-sea water) intrusion area and sea-saline water intrusion area The area of seawter intrusion in Laizhou Bay nearly 4,000 km2. And the seawater intrusion disasters in Laizhou bay can be divided into five stage from 1976 to now, which is Initial stage (1976-1979),Developing stage (1980-1985), Deterioration stage(1987-1989), Release stage (1990-2000)and Differentiation stage (2000-). The impact of human activities is shown as seawater intrusion in the linear growth trend. With the rapid economic development, the increase in abstraction from aquifers results in a serious imbalance between the seawater and freshwater interface, and the risk of seawater intrusion has increased. Taking into account of the climate change and human activity factors and seawater intrusion evaluation factors, such as the intensity of Cl

  7. Polymorphic GGC repeat differentially regulates human reelin gene expression levels.

    Science.gov (United States)

    Persico, A M; Levitt, P; Pimenta, A F

    2006-10-01

    The human gene encoding Reelin (RELN), a pivotal protein in neurodevelopment, includes a polymorphic GGC repeat in its 5' untranslated region (UTR). CHO cells transfected with constructs encompassing the RELN 5'UTR with 4-to-13 GGC repeats upstream of the luciferase reporter gene show declining luciferase activity with increasing GGC repeat number (P autism.

  8. Expert judgment on markers to deter inadvertent human intrusion into the Waste Isolation Pilot Plant

    Energy Technology Data Exchange (ETDEWEB)

    Trauth, K.M. [Sandia National Labs., Albuquerque, NM (United States); Hora, S.C. [Hawaii Univ., Hilo, HI (United States); Guzowski, R.V. [Science Applications International Corp., San Diego, CA (United States)

    1993-11-01

    The expert panel identified basic principles to guide current and future marker development efforts: (1) the site must be marked, (2) message(s) must be truthful and informative, (3) multiple components within a marker system, (4) multiple means of communication (e.g., language, pictographs, scientific diagrams), (5) multiple levels of complexity within individual messages on individual marker system elements, (6) use of materials with little recycle value, and (7) international effort to maintain knowledge of the locations and contents of nuclear waste repositories. The efficacy of the markers in deterring inadvertent human intrusion was estimated to decrease with time, with the probability function varying with the mode of intrusion (who is intruding and for what purpose) and the level of technological development of the society. The development of a permanent, passive marker system capable of surviving and remaining interpretable for 10,000 years will require further study prior to implementation.

  9. Specifying the neurobiological basis of human attachment: brain, hormones, and behavior in synchronous and intrusive mothers.

    Science.gov (United States)

    Atzil, Shir; Hendler, Talma; Feldman, Ruth

    2011-12-01

    The mother-infant bond provides the foundation for the infant's future mental health and adaptation and depends on the provision of species-typical maternal behaviors that are supported by neuroendocrine and motivation-affective neural systems. Animal research has demonstrated that natural variations in patterns of maternal care chart discrete profiles of maternal brain-behavior relationships that uniquely shape the infant's lifetime capacities for stress regulation and social affiliation. Such patterns of maternal care are mediated by the neuropeptide Oxytocin and by stress- and reward-related neural systems. Human studies have similarly shown that maternal synchrony--the coordination of maternal behavior with infant signals--and intrusiveness--the excessive expression of maternal behavior--describe distinct and stable maternal styles that bear long-term consequences for infant well-being. To integrate brain, hormones, and behavior in the study of maternal-infant bonding, we examined the fMRI responses of synchronous vs intrusive mothers to dynamic, ecologically valid infant videos and their correlations with plasma Oxytocin. In all, 23 mothers were videotaped at home interacting with their infants and plasma OT assayed. Sessions were micro-coded for synchrony and intrusiveness. Mothers were scanned while observing several own and standard infant-related vignettes. Synchronous mothers showed greater activations in the left nucleus accumbens (NAcc) and intrusive mothers exhibited higher activations in the right amygdala. Functional connectivity analysis revealed that among synchronous mothers, left NAcc and right amygdala were functionally correlated with emotion modulation, theory-of-mind, and empathy networks. Among intrusive mothers, left NAcc and right amygdala were functionally correlated with pro-action areas. Sorting points into neighborhood (SPIN) analysis demonstrated that in the synchronous group, left NAcc and right amygdala activations showed clearer

  10. Mechanisms of trinucleotide repeat instability during human development.

    Science.gov (United States)

    McMurray, Cynthia T

    2010-11-01

    Trinucleotide expansion underlies several human diseases. Expansion occurs during multiple stages of human development in different cell types, and is sensitive to the gender of the parent who transmits the repeats. Repair and replication models for expansions have been described, but we do not know whether the pathway involved is the same under all conditions and for all repeat tract lengths, which differ among diseases. Currently, researchers rely on bacteria, yeast and mice to study expansion, but these models differ substantially from humans. We need now to connect the dots among human genetics, pathway biochemistry and the appropriate model systems to understand the mechanism of expansion as it occurs in human disease.

  11. Analyses of natural resources in 10 CFR Part 60 as related to inadvertent human intrusion

    Energy Technology Data Exchange (ETDEWEB)

    Miklas, M.P. [Center for Nuclear Waste Regulatory Analyses, San Antonio, TX (United States); Lefevre, H.E. [Nuclear Regulatory Commission, Rockville, MD (United States)

    1993-12-31

    The purpose of this paper is to examine the intent of the regulatory language of the portions of 10 CFR Part 60 which deal with considerations of the natural resources of a proposed geologic repository for high-level radioactive wastes as they relate to inadvertent human intrusion. Four Potentially Adverse Conditions (PAC) the requirements of 10 CFR 60.21(c)(13) are shown to be related to natural resources. Groundwater is identified as a natural resource known to be present at Yucca Mountain, Nevada. For economic considerations of natural resources, the {open_quotes}foreseeable future{close_quotes} is thought to be no more than 50 years. Two of the topics addressed by the PACs, subsurface mining and drilling at a proposed repository site, are pre-site-characterization activities which must be evaluated in the context of repository performance criteria set by the US EPA standard, 40 CFR Part 191. An alternative US DOE compliance demonstration to another PAC, 10 CFR 60.122(c)(17), might be to use an {open_quotes}explorationist perspective{close_quotes} of natural resource assessment. The Commission intends for DOE to evaluate the likelihood and consequence of inadvertent human intrusion into a geologic repository as a result of exploration or exploitation of natural resources within or near a proposed high-level radioactive waste geologic repository.

  12. Repeated vitrification/warming of human sperm gives better results than repeated slow programmable freezing

    Institute of Scientific and Technical Information of China (English)

    Teraporn Vutyavanich; Worashorn Lattiwongsakorn; Waraporn Piromlertamorn; Sudarat Samchimchom

    2012-01-01

    In this study,we compared the effects of repeated freezing/thawing of human sperm by our in-house method of rapid freezing with slow programmable freezing.Sperm samples from 11 normozoospermic subjects were processed through density gradients and divided into three aliquots:non-frozen,rapid freezing and slow programmable freezing.Sperm in the rapid freezing group had better motility and viability than those in the slow freezing group (P<O.01) after the first,second and third cycles of freezing/thawing,but there was no difference in morphology.In the second experiment,rapid freezing was repeated three times in 20 subjects.The samples from each thawing cycle were evaluated for DNA fragmentation using the alkaline comet assay.DNA fragmentation began to increase considerably after the second cycle of freezing/thawing,but to a level that was not clinically important.In the third experiment,rapid freezing was done repeatedly in 10 subjects,until no motile sperm were observed after thawing.The median number of repeated freezing/thawing that yielded no motile sperm was seven (range:5-8,mean:6.8).In conclusion,we demonstrated that repeated freezing/thawing of processed semen using our rapid freezing method gave better results than standard slow programmable freezing.This method can help maximize the usage of precious cryopreserved sperm samples in assisted reproduction technology.

  13. Repeat Sequences and Base Correlations in Human Y Chromosome Palindromes

    Institute of Scientific and Technical Information of China (English)

    Neng-zhi Jin; Zi-xian Liu; Yan-jiao Qi; Wen-yuan Qiu

    2009-01-01

    On the basis of information theory and statistical methods, we use mutual information, n-tuple entropy and conditional entropy, combined with biological characteristics, to analyze the long range correlation and short range correlation in human Y chromosome palindromes. The magnitude distribution of the long range correlation which can be reflected by the mutual information is P5>P5a>P5b (P5a and P5b are the sequences that replace solely Alu repeats and all interspersed repeats with random uncorrelated sequences in human Y chromosome palindrome 5, respectively); and the magnitude distribution of the short range correlation which can be reflected by the n-tuple entropy and the conditional entropy is P5>P5a>P5b>random uncorrelated sequence. In other words, when the Alu repeats and all interspersed repeats replace with random uncorrelated sequence, the long range and short range correlation decrease gradually. However, the random uncorrelated sequence has no correlation. This research indicates that more repeat sequences result in stronger correlation between bases in human Y chromosome. The analyses may be helpful to understand the special structures of human Y chromosome palindromes profoundly.

  14. Non-intrusive optical study of gas and its exchange in human maxillary sinuses

    Science.gov (United States)

    Persson, L.; Andersson, M.; Svensson, T.; Cassel-Engquist, M.; Svanberg, K.; Svanberg, S.

    2007-07-01

    We demonstrate a novel non-intrusive technique based on tunable diode laser absorption spectroscopy to investigate human maxillary sinuses in vivo. The technique relies on the fact that free gases have much sharper absorption features (typical a few GHz) than the surrounding tissue. Molecular oxygen was detected at 760 nm. Volunteers have been investigated by injecting near-infrared light fibre-optically in contact with the palate inside the mouth. The multiply scattered light was detected externally by a handheld probe on and around the cheek bone. A significant signal difference in oxygen imprint was observed when comparing volunteers with widely different anamnesis regarding maxillary sinus status. Control measurements through the hand and through the cheek below the cheekbone were also performed to investigate any possible oxygen offset in the setup. These provided a consistently non-detectable signal level. The passages between the nasal cavity and the maxillary sinuses were also non-intrusively optically studied, to the best of our knowledge for the first time. These measurements provide information on the channel conductivity which may prove useful in facial sinus diagnostics. The results suggest that a clinical trial together with an ear-nose-throat (ENT) clinic should be carried out to investigate the clinical use of the new technique.

  15. Alu repeats as markers for human population genetics

    Energy Technology Data Exchange (ETDEWEB)

    Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Bazan, H. [Louisiana State Univ., New Orleans, LA (United States). Medical Center] [and others

    1993-09-01

    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 97.9% nucleotide identity with each other and an average of 98.9% nucleotide identity with the HS subfamily consensus sequence. HS Alu family members are thought to be derived from a single source ``master`` gene, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 in. and 3 in. unique flanking DNA sequences from each HS Alu that allows the locus to be assayed for the presence or absence of an Alu repeat. Individual HS Alu sequences were found to be either monomorphic or dimorphic for the presence or absence of each repeat. The monomorphic HS Alu family members inserted in the human genome after the human/great ape divergence (which is thought to have occurred 4--6 million years ago), but before the radiation of modem man. The dimorphic HS Alu sequences inserted in the human genome after the radiation of modem man (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project as well. HS Alu family member insertion dimorphism differs from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) because individuals share HS Alu family member insertions based upon identity by descent from a common ancestor as a result of a single event which occurred one time within the human population. The VNTR and RFLP polymorphisms may arise multiple times within a population and are identical by state only.

  16. Trinucleotide repeat expansions catalyzed by human cell-free extracts

    Institute of Scientific and Technical Information of China (English)

    Jennifer R Stevens; Elaine E Lahue; Guo-Min Li; Robert S Lahue

    2013-01-01

    Trinucleotide repeat expansions cause 17 heritable human neurological disorders.In some diseases,somatic expansions occur in non-proliferating tissues such as brain where DNA replication is limited.This finding stimulated significant interest in replication-independent expansion mechanisms.Aberrant DNA repair is a likely source,based in part on mouse studies showing that somatic expansions are provoked by the DNA repair protein MutSβ (Msh2-Msh3complex).Biochemical studies to date used cell-free extracts or purified DNA repair proteins to yield partial reactions at triplet repeats.The findings included expansions on one strand but not the other,or processing of DNA hairpin structures thought to be important intermediates in the expansion process.However,it has been difficult to recapitulate complete expansions in vitro,and the biochemical role of MutSβ remains controversial.Here,we use a novel in vitro assay to show that human cell-free extracts catalyze expansions and contractions of trinucleotide repeats without the requirement for DNA replication.The extract promotes a size range of expansions that is similar to certain diseases,and triplet repeat length and sequence govern expansions in vitro as in vivo.MutSβ stimulates expansions in the extract,consistent with aberrant repair of endogenous DNA damage as a source of expansions.Overall,this biochemical system retains the key characteristics of somatic expansions in humans and mice,suggesting that this important mutagenic process can be restored in the test tube.

  17. Safety assessment on the human intrusion scenarios of near surface disposal facility for low and very low level radioactive waste

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Sung Wook; Park, Jin Baek [Korea Radioactive Waste Agency, Daejeon (Korea, Republic of); Park, Sang Ho [Chungnam National University, Daejeon (Korea, Republic of)

    2016-03-15

    The second-stage near surface disposal facility for low and very low level radioactive waste's permanent disposal is to be built. During the institutional control period, the inadvertent intrusion of the general public is limited. But after the institutional control period, the access to the general public is not restricted. Therefore human who has purpose of residence and resource exploration can intrude the disposal facility. In this case, radioactive effects to the intruder should be limited within regulatory dose limits. This study conducted the safety assessment of human intrusion on the second-stage surface disposal facility through drilling and post drilling scenario. Results of drilling and post drilling scenario were satisfied with regulatory dose limits. The result showed that post-drilling scenario was more significant than drilling scenario. According to the human intrusion time and behavior after the closure of the facility, dominant radionuclide contributing to the intruder was different. Sensitivity analyses on the parameters about the human behavior were also satisfied with regulatory dose limits. Especially, manual redistribution factor was the most sensitive parameter on exposure dose. A loading plan of spent filter waste and dry active waste was more effective than a loading plan of spent filter waste and other wastes for the radiological point of view. These results can be expected to provide both robustness and defense in depth for the development of safety case further.

  18. Decadal changes in bathymetry of the Yangtze River Estuary: Human impacts and potential saltwater intrusion

    Science.gov (United States)

    Wu, Shuaihu; Cheng, Heqin; Xu, Y. Jun; Li, Jiufa; Zheng, Shuwei

    2016-12-01

    This study analyzed bathymetric changes of the 77-km Yangtze River Estuary in China over the past ten years in order to understand the impacts of recent human activities on the estuary of a large alluvial river. Morphological changes were assessed by analyzing digitized bathymetric data of the estuarine channels from 2002 to 2013. Additionally, multi-beam bathymetric measurements made in 2012, 2014 and 2015 were utilized to investigate microtophographic bedforms of the lower reach of the estuary. Our results showed that the middle and upper reaches of the Yangtze River Estuary experienced substantial channel bed erosion in the past 10 years, and that the recent human activities have contributed to the change. These included the construction of a 70 km2 reservoir along the Yangtze River Estuary, the Qingcaosha Reservoir, for drinking water supply for the City of Shanghai, which has caused progressive bed erosion in the North Channel. The net volume of channel erosion in the Hengsha Passage from 2002 to 2013 was 0.86 × 108 m3. A large amount of the eroded sediment was trapped downstream, causing overall accretion in the upper reach of the North Passage. The middle and upper reaches of the South Passage also experienced intense erosion (0.45 × 108 m3) in the past ten years, while high accretion occurred in the lower reach because of the Deepening Waterway Project. The channel dredging left a large range of dredging marks and hollows in the North Passage. The increasing saltwater intrusion found in the Yangtze River Estuary may have been a consequence of either dredging or erosion, or both combined.

  19. Zinc-finger directed double-strand breaks within CAG repeat tracts promote repeat instability in human cells.

    Science.gov (United States)

    Mittelman, David; Moye, Christopher; Morton, Jason; Sykoudis, Kristen; Lin, Yunfu; Carroll, Dana; Wilson, John H

    2009-06-16

    Expanded triplet repeats have been identified as the genetic basis for a growing number of neurological and skeletal disorders. To examine the contribution of double-strand break repair to CAG x CTG repeat instability in mammalian systems, we developed zinc finger nucleases (ZFNs) that recognize and cleave CAG repeat sequences. Engineered ZFNs use a tandem array of zinc fingers, fused to the FokI DNA cleavage domain, to direct double-strand breaks (DSBs) in a site-specific manner. We first determined that the ZFNs cleave CAG repeats in vitro. Then, using our previously described tissue culture assay for identifying modifiers of CAG repeat instability, we found that transfection of ZFN-expression vectors induced up to a 15-fold increase in changes to the CAG repeat in human and rodent cell lines, and that longer repeats were much more sensitive to cleavage than shorter ones. Analysis of individual colonies arising after treatment revealed a spectrum of events consistent with ZFN-induced DSBs and dominated by repeat contractions. We also found that expressing a dominant-negative form of RAD51 in combination with a ZFN, dramatically reduced the effect of the nuclease, suggesting that DSB-induced repeat instability is mediated, in part, through homology directed repair. These studies identify a ZFN as a useful reagent for characterizing the effects of DSBs on CAG repeats in cells.

  20. Statistical analysis of simple repeats in the human genome

    Science.gov (United States)

    Piazza, F.; Liò, P.

    2005-03-01

    The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo- and di-nucleotide repeats, while middle repetitive DNA is rich of families of interspersed, mobile elements hundreds of base pairs (bp) long, among which belong the Alu families. A link between homo- and di-polymeric tracts and mobile elements has been recently highlighted. In particular, the mobility of Alu repeats, which form 10% of the human genome, has been correlated with the length of poly(A) tracts located at one end of the Alu. These tracts have a rigid and non-bendable structure and have an inhibitory effect on nucleosomes, which normally compact the DNA. We performed a statistical analysis of the genome-wide distribution of lengths and inter-tract separations of poly(X) and poly(XY) tracts in the human genome. Our study shows that in humans the length distributions of these sequences reflect the dynamics of their expansion and DNA replication. By means of general tools from linguistics, we show that the latter play the role of highly-significant content-bearing terms in the DNA text. Furthermore, we find that such tracts are positioned in a non-random fashion, with an apparent periodicity of 150 bases. This allows us to extend the link between repetitive, highly mobile elements such as Alus and low-complexity words in human DNA. More precisely, we show that Alus are sources of poly(X) tracts, which in turn affect in a subtle way the combination and diversification of gene expression and the fixation of multigene families.

  1. Repeatability and reliability of human eye in visual shade selection.

    Science.gov (United States)

    Özat, P B; Tuncel, İ; Eroğlu, E

    2013-12-01

    Deficiencies in the human visual percep-tion system have challenged the efficiency of the visual shade-matching protocol. The aim of this study was to evaluate the repeatability and reliability of human eye in visual shade selection. Fifty-four volunteering dentists were asked to match the shade of an upper right central incisor tooth of a single subject. The Vita 3D-Master shade guide was used for the protocol. Before each shade-matching procedure, the definitive codes of the shade tabs were hidden by an opaque strip and the shade tabs were placed into the guide randomly. The procedure was repeated 1 month later to ensure that visual memory did not affect the results. The L*, a* and b* values of the shade tabs were measured with a dental spectrophotometer (Vita Easyshade) to produce quantitative values to evaluate the protocol. The paired samples t-test and Pearson correlation test were used to compare the 1st and 2nd selections. The Yates-corrected chi-square test was use to compare qualitative values. Statistical significance was accepted at P shade matching, but they are able to select clinically acceptable shades.

  2. The chromatin remodeller ATRX: a repeat offender in human disease.

    Science.gov (United States)

    Clynes, David; Higgs, Douglas R; Gibbons, Richard J

    2013-09-01

    The regulation of chromatin structure is of paramount importance for a variety of fundamental nuclear processes, including gene expression, DNA repair, replication, and recombination. The ATP-dependent chromatin-remodelling factor ATRX (α thalassaemia/mental retardation X-linked) has emerged as a key player in each of these processes. Exciting recent developments suggest that ATRX plays a variety of key roles at tandem repeat sequences within the genome, including the deposition of a histone variant, prevention of replication fork stalling, and the suppression of a homologous recombination-based pathway of telomere maintenance. Here, we provide a mechanistic overview of the role of ATRX in each of these processes, and propose how they may be connected to give rise to seemingly disparate human diseases.

  3. GFP-based fluorescence assay for CAG repeat instability in cultured human cells.

    Directory of Open Access Journals (Sweden)

    Beatriz A Santillan

    Full Text Available Trinucleotide repeats can be highly unstable, mutating far more frequently than point mutations. Repeats typically mutate by addition or loss of units of the repeat. CAG repeat expansions in humans trigger neurological diseases that include myotonic dystrophy, Huntington disease, and several spinocerebellar ataxias. In human cells, diverse mechanisms promote CAG repeat instability, and in mice, the mechanisms of instability are varied and tissue-dependent. Dissection of mechanistic complexity and discovery of potential therapeutics necessitates quantitative and scalable screens for repeat mutation. We describe a GFP-based assay for screening modifiers of CAG repeat instability in human cells. The assay exploits an engineered intronic CAG repeat tract that interferes with expression of an inducible GFP minigene. Like the phenotypes of many trinucleotide repeat disorders, we find that GFP function is impaired by repeat expansion, in a length-dependent manner. The intensity of fluorescence varies inversely with repeat length, allowing estimates of repeat tract changes in live cells. We validate the assay using transcription through the repeat and engineered CAG-specific nucleases, which have previously been reported to induce CAG repeat instability. The assay is relatively fast and should be adaptable to large-scale screens of chemical and shRNA libraries.

  4. Improved set of short-tandem-repeat polymorphisms for screening the human genome

    Energy Technology Data Exchange (ETDEWEB)

    Yuan, Bo; Vaske, D.; Weber, J.L. [Marshfield Medical Research Foundation, WI (United States)] [and others

    1997-02-01

    Short-tandem-repeat (microsatellite) DNA polymorphisms are widely used for screening the human and other genomes in initial linkage mapping. Since the average spacing between polymorphisms in genome screens is usually {ge}10 cM and since many thousands of human short-tandem-repeat polymorphisms (STRPs) are now available, optimal subsets of STRPs must be selected for screening. Two screening sets of STRPs for humans have been described in the literature, both of which are based primarily on dinucleotide-repeat polymorphisms. Here we describe our eighth and most recent human screening set, which is based almost entirely on trinucleotide-and tetranucleotide-repeat polymorphisms. 7 refs., 1 tab.

  5. Evaluation of intrusive mechanics of the type "segmented arch" on a macerated human skull using the laser reflection technique and holographic interferometry.

    Science.gov (United States)

    Dermaut, L R; Vanden Bulcke, M M

    1986-03-01

    Twelve different systems of intrusion, based on the principle of the "segmented arch," were evaluated on a macerated human skull. The number of teeth involved in the anterior unit and the location of the application points of intrusive force were considered to be variables. Initial displacements of the anterior teeth after loading were registered by means of the laser reflection technique and double exposure holographic recordings. An attempt was made to define "this" intrusive system, achieving the most genuine intrusion (for definition, see text) without flaring of the teeth. When two central incisors were incorporated in the sectional wire, strong torque forces appeared, especially when the intrusive forces seized more distally. When four or six anterior teeth were pinned in the sectional wire, tooth movement seemed to be under better control. When the six front teeth were incorporated in the sectional wire, the center of resistance (for definition, see text) was located more to the distal side of the canines. It seemed more difficult, however, to define the center of resistance of the four incisors; it was situated approximately distal to the lateral incisors. In some of the intrusive systems, the teeth underwent independent mesial or distal rotations. This was easily observed with the laser measuring techniques used.

  6. Identification of the porcine homologous of human disease causing trinucleotide repeat sequences

    DEFF Research Database (Denmark)

    Madsen, Lone Bruhn; Thomsen, Bo; Sølvsten, Christina Ane Elisabeth

    2007-01-01

    expansion in the repeat number of intragenic trinucleotide repeats (TNRs) is associated with a variety of inherited human neurodegenerative diseases. To study the compositionof TNRs in a mammalian species representing an evolutionary intermediate between humans and arodents, we describe in this p...

  7. Systematic exchanges between nucleotides: Genomic swinger repeats and swinger transcription in human mitochondria.

    Science.gov (United States)

    Seligmann, Hervé

    2015-11-07

    Chargaff׳s second parity rule, quasi-equal single strand frequencies for complementary nucleotides, presumably results from insertion of repeats and inverted repeats during sequence genesis. Vertebrate mitogenomes escape this rule because repeats are counterselected: their hybridization produces loop bulges whose deletion is deleterious. Some DNA/RNA sequences match mitogenomes only after assuming one among 23 systematic nucleotide exchanges (swinger DNA/RNA: nine symmetric, e.g. A ↔ C; and 14 asymmetric, e.g. A → C → G → A). Swinger-transformed repeats do not hybridize, escaping selection against deletions due to bulge formation. Blast analyses of the human mitogenome detect swinger repeats for all 23 swinger types, more than in randomized sequences with identical length and nucleotide contents. Mean genomic swinger repeat lengths increase with observed human swinger RNA frequencies: swinger repeat and swinger RNA productions appear linked, perhaps by swinger RNA retrotranscription. Mean swinger repeat lengths are proportional to reading frame retrievability, post-swinger transformation, by the natural circular code. Genomic swinger repeats confirm at genomic level, independently of swinger RNA detection, occurrence of swinger polymerizations. They suggest that repeats, and swinger repeats in particular, contribute to genome genesis.

  8. Coupled human-water system dynamics of saltwater intrusion in the low coastal plain of the Po River, Ravenna, Italy

    Science.gov (United States)

    Lauriola, Ilaria; Ciriello, Valentina; Antonellini, Marco; Pande, Saket

    2017-04-01

    Human activities affect the whole hydrological cycle with possible severe consequences on ecosystem services. Human-water interaction follows complex dynamics that can't be addressed only through the analysis of water withdrawals and contamination processes. As such, comprehensive analysis strategies based on a socio-hydrology approach may allow to deeply understand the co-evolution of human and water systems. Here, we focus on the low coastal plain of the Po river in the south of Ravenna (Italy), which is adjacent to the North Adriatic sea. In particular, our study regards a basin characterized by a land reclamation drainage system, given the low topography which reaches in some places 1 m below sea level. In this area, the thin phreatic coastal aquifer is affected by a relevant salinization process and characterized by the presence of valuable water-dependent ecosystems such as pine forests and wetlands. Groundwater salinization is mainly caused by seawater intrusion due to the hydraulic gradient landwards that is enhanced by land subsidence, land use and drainage allowing for agriculture and settlements. Such a complex scenario involves environmental, social and economic interests. We study the intricate system of relationships occurring between a set of socio-hydrological state variables of interest based on the dynamic analysis of land use changes in the study area that mainly affect groundwater recharge and the availability of freshwater for ecosystem and agriculture activities.

  9. Repeated dose pharmacokinetics of pancopride in human volunteers.

    Science.gov (United States)

    Salva, P; Costa, J; Pérez-Campos, A; Martínez-Tobed, A

    1994-11-01

    The aim of this study was to assess the pharmacokinetic profile of pancopride after repeated oral dose administration of 20 mg pancopride in tablet form once a day for 5 d in 12 healthy male volunteers. Plasma levels were measured by HPLC using a solid phase extraction method and automated injection. The minimum quantification limit of pancopride in plasma was 2 ng mL-1. The maximum plasma concentration (mean +/- SD) after the first dose was 92.5 +/- 41.5 ng ML-1 and tmax was 1.7 +/- 0.9 h. The elimination half-life (t1/2) was 14.3 +/- 6.9 h. The area under the concentration-time curve from zero to infinity (AUC) was 997 +/- 396 ng h mL-1. The maximum plasma concentration (mean +/- SD) at steady state (day 5) was 101.8 +/- 36.9 ng mL-1 and tmax was 2.2 +/- 1.2 h. The elimination half-life (t1/2) was 16.3 +/- 2.7 h and the minimum plasma concentration (Cssmin) was 16.6 +/- 6.9 ng mL-1. The area under the concentration-time curve during the dosing interval (AUCss tau) was 995 +/- 389 ng h mL-1. The average plasma concentration at steady state (Cssav) was 43.3 +/- 16.1 ng mL-1 and the experimental accumulation ratio (RAUC) was 1.34 +/- 0.19, whereas the mean theoretical value (R) was 1.40 +/- 0.29. The results obtained showed a good correlation between the experimental plasma levels and the expected values calculated using a repeated dose two-compartment model assessed by means of the Akaike value. It is concluded that the pharmacokinetics of pancopride are not modified after repeated dose administration.(ABSTRACT TRUNCATED AT 250 WORDS)

  10. Dose estimation for repeated phosphorus-32 ingestion in human subjects

    Energy Technology Data Exchange (ETDEWEB)

    Chao, J.H.; Tseng, C.L.; Hsieh, W.A.; Hung, D.Z.; Chang, W.P. E-mail: wpc94@mailsrv.ym.edu.tw

    2001-01-15

    Dose estimation was conducted for internal phosphorus-32 exposure in one young male subject from repeated oral mis-ingestion for >1 year. Since disclosure for previous continuous contamination, a series of urine samples were collected from this individual weekly for a period of >2 months. P-32 radioactivity in urine samples were measured by the acid precipitation method. Estimation for retrospective total effective dose equivalent received by this subject was conducted for cumulative internal dose estimation. A minimum of 9.4 mSv was estimated for an assumed single ingestion. As this was a rare case in radiation protection and internal radiation dosimetry, its implications were of considerable significance.

  11. A common-sense probabilistic approach to assessing inadvertent human intrusion into low-level radioactive waste at the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Black, P.; Hooten, M.; Black, K. [Neptune and Co., Inc., Los Alamos, NM (United States); Moore, B. [Dept. of Energy, Las Vegas, NV (United States). Nevada Operations Office; Crowe, B. [Los Alamos National Lab., NM (United States); Rawlinson, S.; Barker, L. [Bechtel Nevada Corp., Las Vegas, NV (United States)

    1997-05-01

    Each site disposing of low-level radioactive waste is required to prepare and maintain a site-specific performance assessment (1) to determine potential risks posed by waste management systems to the public, and the environment, and (2) to compare these risks to established performance objectives. The DOE Nevada Operations Office, Waste Management Program recently completed a one-year study of site-specific scenarios for inadvertent human intrusion by drilling into buried low-level radioactive waste sites, as part of ongoing performance assessment studies. Intrusion scenarios focus on possible penetration of buried waste through drilling for sources of groundwater. The probability of drilling penetration into waste was judged to be driven primarily by two settlement scenarios: (1) scattered individual homesteaders, and (2) a community scenario consisting of a cluster of settlers that share drilling and distribution systems for groundwater. Management control factors include institutional control, site knowledge, placards and markers, surface barriers, and subsurface barriers. The Subject Matter Experts concluded that institutional control and site knowledge may be important factors for the first few centuries, but are not significant over the evaluation period of 10,000 years. Surface barriers can be designed that would deter the siting of a drill rig over the waste site to an effectiveness of 95%. Subsurface barriers and placards and markers will not as effectively prevent inadvertent human intrusion. Homestead and community scenarios were considered by the panel to render a site-specific probability of around 10% for inadvertent human intrusion. If management controls are designed and implemented effectively, then the probability of inadvertent human intrusion can be reduced to less than 1%.

  12. Isolation and characterization of human cerebellum cDNAs containing polymorphic CAG trinucleotide repeats

    Energy Technology Data Exchange (ETDEWEB)

    Igarashi, S.; Onodera, O.; Tanaka, H. [Niigata Univ. (Japan)] [and others

    1994-09-01

    It has been discovered that neurologic diseases such as X linked spinal and bulbar muscular atrophy, Huntington`s disease, spinocerebellar ataxia type 1 (SCA1), and dentatorubral-pallidoluysian atrophy (DRPLA) are caused by unstable expansions of CAG repeats, which shed a light on a new mechanism of human hereditary diseases. The genetic anticipation, a common genetic feature in these diseases, can be explained by the trinucleotide repeat expansions, and an inverse correlation between the ages of onset and the numbers of trinucleotide repeats is demonstrated in these diseases. Furthermore, there have been diseases such as spinocerebellar ataxia 2 (SCA2) and Machado-Joseph disease showing similar genetic anticipation, which suggests that their causative mutations are unstable expansions of trinucleotide repeats. To identify candidate genes for neurodegenerative diseases which are expressed in human cerebellum and contain CAG repeats, we screened a human cerebellum cDNA library with an oligonucleotide (CAG){sub 10}, labelled with [{gamma}{sup 32}P]ATP. Out of 78 clones we have isolated, 43 clones were partially sequenced and 31 clones were shown to contain CAG or CTG tinucleotide repeats. From homology searches, 12 of the 59 clones were identified to contain known sequences including human MAR/SAR DNA binding protein, human glial fibrillary acidic protein, human myelin transcription factor 1, human neuronal growth protein 43 and human myocyte-specific enhancer 2. From 6 clones out of the 43 novel genes, we were able to develop primer pairs flanking CAG repeats and determined chromosomal localizations with human and rodent hybrid mapping panels. These CAG repeats were shown to be polymorphic and mapped to 1, 15, 17 and 18. These novel cDNAs will be useful as candidate genes for hereditary neurologic diseases showing genetic anticipation.

  13. Genetics and epigenetics of repeat derepression in human disease

    NARCIS (Netherlands)

    Thijssen, P.E.

    2016-01-01

    A large part of the human genome consists of repetitive DNA. In this thesis two human diseases have been studied in which deregulation of repetitive DNA is a central feature: facioscapulohumeral muscular dystrophy (FSHD) and immunodeficiency, centromere instability and facial anomalies (ICF) syndrom

  14. GAA triplet-repeats cause nucleosome depletion in the human genome.

    Science.gov (United States)

    Zhao, Hongyu; Xing, Yongqiang; Liu, Guoqing; Chen, Ping; Zhao, Xiujuan; Li, Guohong; Cai, Lu

    2015-08-01

    Although there have been many investigations into how trinucleotide repeats affect nucleosome formation and local chromatin structure, the nucleosome positioning of GAA triplet-repeats in the human genome has remained elusive. In this work, the nucleosome occupancy around GAA triplet-repeats across the human genome was computed statistically. The results showed a nucleosome-depleted region in the vicinity of GAA triplet-repeats in activated and resting CD4(+) T cells. Furthermore, the A-tract was frequently adjacent to the upstream region of GAA triplet-repeats and could enhance the depletion surrounding GAA triplet-repeats. In vitro chromatin reconstitution assays with GAA-containing plasmids also demonstrated that the inserted GAA triplet-repeats destabilized the ability of recombinant plasmids to assemble nucleosomes. Our results suggested that GAA triplet-repeats have lower affinity to histones and can change local nucleosome positioning. These findings may be helpful for understanding the mechanism of Friedreich's ataxia, which is associated with GAA triplet-repeats at the chromatin level.

  15. Large-scale analysis of tandem repeat variability in the human genome.

    Science.gov (United States)

    Duitama, Jorge; Zablotskaya, Alena; Gemayel, Rita; Jansen, An; Belet, Stefanie; Vermeesch, Joris R; Verstrepen, Kevin J; Froyen, Guy

    2014-05-01

    Tandem repeats are short DNA sequences that are repeated head-to-tail with a propensity to be variable. They constitute a significant proportion of the human genome, also occurring within coding and regulatory regions. Variation in these repeats can alter the function and/or expression of genes allowing organisms to swiftly adapt to novel environments. Importantly, some repeat expansions have also been linked to certain neurodegenerative diseases. Therefore, accurate sequencing of tandem repeats could contribute to our understanding of common phenotypic variability and might uncover missing genetic factors in idiopathic clinical conditions. However, despite long-standing evidence for the functional role of repeats, they are largely ignored because of technical limitations in sequencing, mapping and typing. Here, we report on a novel capture technique and data filtering protocol that allowed simultaneous sequencing of thousands of tandem repeats in the human genomes of a three generation family using GS-FLX-plus Titanium technology. Our results demonstrated that up to 7.6% of tandem repeats in this family (4% in coding sequences) differ from the reference sequence, and identified a de novo variation in the family tree. The method opens new routes to look at this underappreciated type of genetic variability, including the identification of novel disease-related repeats.

  16. Isolation and characterization of human brain genes with (CCA){sub n} trinucleotide repeats

    Energy Technology Data Exchange (ETDEWEB)

    Longshore, J.W.; Finley, W.H.; Descartes, M. [Univ. of Alabama, Birmingham, AL (United States)] [and others

    1994-09-01

    Expansion of trinucleotide repeats has been described as a new form of mutation. To date, only the expansion of (CGG){sub n} and (CAG){sub n} repeats have been associated with disease. Expansion of (CAG){sub n} repeats has been found to cause Huntington`s disease, Kennedy`s disease, myotonic dystrophy, spinocerebellar ataxia type 1, and dentatorubral pallidoluysian atrophy. (CGG){sub n} repeat expansion has been implicated in the fragile X syndrome and FRAXE mental retardation. In an effort to identify other potential repeats as candidates for expansion, a DNA linguistics approach was used to study 10 Mb of human DNA sequences in GenBank. Our study found the (CCA){sub n} repeat and the disease-associated (CGG){sub n} and (CAG){sub n} repeats to be over-represented in the human genome. The (CCA){sub n} repeat also shares other characteristics with (CGG){sub n} and (CAG){sub n}, making it a good candidate for expansion. Trinucleotide repeat numbers in disease-associated genes are normally polymorphic in a population. Therefore, by studying genes for polymorphisms, candidate genes may be identified. Twelve sequences previously deposited in GenBank with at least five tandem copies of (CCA) were studied and no polymorphisms were found. To identify other candidate genes, a human hippocampus cDNA library was screened with a (CCA){sub 8} probe. This approach identified 19 novel expressed sequences having long tandem (CCA){sub n} repeats which are currently under investigation for polymorphisms. Genes with polymorphic repeats may serve as markers for linkage studies or as candidate genes for genetic diseases showing anticipation.

  17. Considerations Related To Human Intrusion In The Context Of Disposal Of Radioactive Waste-The IAEA HIDRA Project

    Energy Technology Data Exchange (ETDEWEB)

    Seitz, Roger; Kumano, Yumiko; Bailey, Lucy; Markley, Chris; Andersson, Eva; Beuth, Thomas

    2014-01-09

    The principal approaches for management of radioactive waste are commonly termed ‘delay and decay’, ‘concentrate and contain’ and ‘dilute and disperse’. Containing the waste and isolating it from the human environment, by burying it, is considered to increase safety and is generally accepted as the preferred approach for managing radioactive waste. However, this approach results in concentrated sources of radioactive waste contained in one location, which can pose hazards should the facility be disrupted by human action in the future. The International Commission on Radiological Protection (ICRP), International Atomic Energy Agency (IAEA), and Organization for Economic Cooperation and Development/Nuclear Energy Agency (OECD/NEA) agree that some form of inadvertent human intrusion (HI) needs to be considered to address the potential consequences in the case of loss of institutional control and loss of memory of the disposal facility. Requirements are reflected in national regulations governing radioactive waste disposal. However, in practice, these requirements are often different from country to country, which is then reflected in the actual implementation of HI as part of a safety case. The IAEA project on HI in the context of Disposal of RadioActive waste (HIDRA) has been started to identify potential areas for improved consistency in consideration of HI. The expected outcome is to provide recommendations on how to address human actions in the safety case in the future, and how the safety case may be used to demonstrate robustness and optimize siting, design and waste acceptance criteria within the context of a safety case.

  18. Tandem Repeat Analysis for Surveillance of Human Salmonella Typhimurium Infections

    DEFF Research Database (Denmark)

    Torpdahl, Mia; Sørensen, Gitte; Lindstedt, Bjørn-Arne

    2007-01-01

    In Denmark, as part of the national laboratory-based surveillance system of human enteric infections, all Salmonella enterica serotype Typhimurium isolates are currently subtyped by using phage typing, antimicrobial resistance profiles, and pulsed-field gel electrophoresis (PFGE). We evaluated th...

  19. Short Tandem Repeats in Human Exons: A Target for Disease Mutations

    Directory of Open Access Journals (Sweden)

    Villesen Palle

    2008-09-01

    Full Text Available Abstract Background In recent years it has been demonstrated that structural variations, such as indels (insertions and deletions, are common throughout the genome, but the implications of structural variations are still not clearly understood. Long tandem repeats (e.g. microsatellites or simple repeats are known to be hypermutable (indel-rich, but are rare in exons and only occasionally associated with diseases. Here we focus on short (imperfect tandem repeats (STRs which fall below the radar of conventional tandem repeat detection, and investigate whether STRs are targets for disease-related mutations in human exons. In particular, we test whether they share the hypermutability of the longer tandem repeats and whether disease-related genes have a higher STR content than non-disease-related genes. Results We show that validated human indels are extremely common in STR regions compared to non-STR regions. In contrast to longer tandem repeats, our definition of STRs found them to be present in exons of most known human genes (92%, 99% of all STR sequences in exons are shorter than 33 base pairs and 62% of all STR sequences are imperfect repeats. We also demonstrate that STRs are significantly overrepresented in disease-related genes in both human and mouse. These results are preserved when we limit the analysis to STRs outside known longer tandem repeats. Conclusion Based on our findings we conclude that STRs represent hypermutable regions in the human genome that are linked to human disease. In addition, STRs constitute an obvious target when screening for rare mutations, because of the relatively low amount of STRs in exons (1,973,844 bp and the limited length of STR regions.

  20. Mutagenic effect of cadmium on tetranucleotide repeats in human cells

    Energy Technology Data Exchange (ETDEWEB)

    Slebos, Robbert J.C. [Department of Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 (United States) and Department of Otolaryngology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 (United States)]. E-mail: r.slebos@vanderbilt.edu; Li Ming [Department of Biostatistics, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 (United States); Evjen, Amy N. [Department of Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 (United States); Coffa, Jordy [Department of Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 (United States); Shyr, Yu [Department of Biostatistics, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 (United States); Yarbrough, Wendell G. [Department of Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 (United States); Department of Otolaryngology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 (United States)

    2006-12-01

    Cadmium is a human carcinogen that affects cell proliferation, apoptosis and DNA repair processes that are all important to carcinogenesis. We previously demonstrated that cadmium inhibits DNA mismatch repair (MMR) in yeast cells and in human cell-free extracts (H.W. Jin, A.B. Clark, R.J.C. Slebos, H. Al-Refai, J.A. Taylor, T.A. Kunkel, M.A. Resnick, D.A. Gordenin, Cadmium is a mutagen that acts by inhibiting mismatch repair, Nat. Genet. 34 (3) (2003) 326-329), but cadmium also inhibits DNA excision repair. For this study, we selected a panel of three hypermutable tetranucleotide markers (MycL1, D7S1482 and DXS981) and studied their suitability as readout for the mutagenic effects of cadmium. We used a clonal derivative of the human fibrosarcoma cell line HT1080 to assess mutation levels in microsatellites after cadmium and/or N-methyl-N-nitro-N-nitrosoguanidine (MNNG) exposure to study effects of cadmium in the presence or absence of base damage. Mutations were measured in clonally expanded cells obtained by limiting dilution after exposure to zero dose, 0.5 {mu}M cadmium, 5 nM MNNG or a combination of 0.5 {mu}M cadmium and 5 nM MNNG. Exposure of HT1080-C1 to cadmium led to statistically significant increases in microsatellite mutations, either with or without concurrent exposure to MNNG. A majority of the observed mutant molecules involved 4-nucleotide shifts consistent with DNA slippage mutations that are normally repaired by MMR. These results provide evidence for the mutagenic effects of low, environmentally relevant levels of cadmium in intact human cells and suggest that inhibition of DNA repair is involved.

  1. Evolutionarily different alphoid repeat DNA on homologous chromosomes in human and chimpanzee.

    OpenAIRE

    Jørgensen, A L; Laursen, H B; Jones, C; Bak, A L

    1992-01-01

    Centromeric alphoid DNA in primates represents a class of evolving repeat DNA. In humans, chromosomes 13 and 21 share one subfamily of alphoid DNA while chromosomes 14 and 22 share another subfamily. We show that similar pairwise homogenizations occur in the chimpanzee (Pan troglodytes), where chromosomes 14 and 22, homologous to human chromosomes 13 and 21, share one partially homogenized alphoid DNA subfamily and chromosomes 15 and 23, homologous to human chromosomes 14 and 22, share anothe...

  2. Selection pressure on human STR loci and its relevance in repeat expansion disease

    KAUST Repository

    Shimada, Makoto K.

    2016-06-11

    Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases. © 2016, Springer-Verlag Berlin Heidelberg.

  3. Genome-wide identification of human- and primate-specific core promoter short tandem repeats.

    Science.gov (United States)

    Bushehri, A; Barez, M R Mashhoudi; Mansouri, S K; Biglarian, A; Ohadi, M

    2016-08-01

    Recent reports of a link between human- and primate-specific genetic factors and human/primate-specific characteristics and diseases necessitate genome-wide identification of those factors. We have previously reported core promoter short tandem repeats (STRs) of extreme length (≥6-repeats) that have expanded exceptionally in primates vs. non-primates, and may have a function in adaptive evolution. In the study reported here, we extended our study to the human STRs of ≥3-repeats in the category of penta and hexaucleotide STRs, across the entire human protein coding gene core promoters, and analyzed their status in several superorders and orders of vertebrates, using the Ensembl database. The ConSite software was used to identify the transcription factor (TF) sets binding to those STRs. STR specificity was observed at different levels of human and non-human primate (NHP) evolution. 73% of the pentanucleotide STRs and 68% of the hexanucleotide STRs were found to be specific to human and NHPs. AP-2alpha, Sp1, and MZF were the predominantly selected TFs (90%) binding to the human-specific STRs. Furthermore, the number of TF sets binding to a given STR was found to be a selection factor for that STR. Our findings indicate that selected STRs, the cognate binding TFs, and the number of TF set binding to those STRs function as switch codes at different levels of human and NHP evolution and speciation.

  4. Molecular cloning and expression of a novel human cDNA containing CAG repeats.

    Science.gov (United States)

    Takeuchi, T; Chen, B K; Qiu, Y; Sonobe, H; Ohtsuki, Y

    1997-12-19

    A novel human cDNA containing CAG repeats, designated B120, was cloned by PCR amplification. An approximately 300-bp 3' untranslated region in this cDNA was followed by a 3426-bp coding region containing the CAG repeats. A computer search failed to find any significant homology between this cDNA and previously reported genes. The number of CAG trinucleotide repeats appeared to vary from seven to 12 in analyses of genomic DNA from healthy volunteers. An approximately 8-kb band was detected in brain, skeletal muscle and thymus by Northern blot analysis. The deduced amino-acid sequence had a polyglutamine chain encoded by CAG repeats as well as glutamine- and tyrosine-rich repeats, which has also been reported for several RNA binding proteins. We immunized mice with recombinant gene product and established a monoclonal antibody to it. On Western immunoblotting, this antibody detected an approximately 120-kDa protein in human brain tissue. In addition, immunohistochemical staining showed that the cytoplasm of neural cells was stained with this antibody. These findings indicated that B120 is a novel cDNA with a CAG repeat length polymorphism and that its gene product is a cytoplasmic protein with a molecular mass of 120 kDa.

  5. Chromatin structure of repeating CTG/CAG and CGG/CCG sequences in human disease.

    Science.gov (United States)

    Wang, Yuh-Hwa

    2007-05-01

    In eukaryotic cells, chromatin structure organizes genomic DNA in a dynamic fashion, and results in regulation of many DNA metabolic processes. The CTG/CAG and CGG/CCG repeating sequences involved in several neuromuscular degenerative diseases display differential abilities for the binding of histone octamers. The effect of the repeating DNA on nucleosome assembly could be amplified as the number of repeats increases. Also, CpG methylation, and sequence interruptions within the triplet repeats exert an impact on the formation of nucleosomes along these repeating DNAs. The two most common triplet expansion human diseases, myotonic dystrophy 1 and fragile X syndrome, are caused by the expanded CTG/CAG and CGG/CCG repeats, respectively. In addition to the expanded repeats and CpG methylation, histone modifications, chromatin remodeling factors, and noncoding RNA have been shown to coordinate the chromatin structure at both myotonic dystrophy 1 and fragile X loci. Alterations in chromatin structure at these two loci can affect transcription of these disease-causing genes, leading to disease symptoms. These observations have brought a new appreciation that a full understanding of disease gene expression requires a knowledge of the structure of the chromatin domain within which the gene resides.

  6. The human TTAGGG repeat factors 1 and 2 bind to a subset of interstitial telomeric sequences and satellite repeats

    Institute of Scientific and Technical Information of China (English)

    Thomas Simonet; Elena Giulotto; Frederique Magdinier; Béatrice Horard; Pascal Barbry; Rainer Waldmann; Eric Gison; Laure-Emmanuelle Zaragosi; Claude Philippe; Kevin Lebrigand; Clémentine Schouteden; Adeline Augereau; Serge Bauwens; Jing Ye; Marco Santagostino

    2011-01-01

    The study of the proteins that bind to telomeric DNA in mammals has provided a deep understanding of the mech anisms involved in chromosome-end protection. However, very little is known on the binding of these proteins to nontelomeric DNA sequences. The TTAGGG DNA repeat proteins 1 and 2 (TRF1 and TRF2) bind to mammalian telomeres as part of the shelterin complex and are essential for maintaining chromosome end stability. In this study, we combined chromatin immunoprecipitation with high-throughput sequencing to map at high sensitivity and resolution the human chromosomal sites to which TRF1 and TRF2 bind. While most of the identified sequences correspond to telomeric regions, we showed that these two proteins also bind to extratelomeric sites. The vast majority of these extratelomeric sites contains interstitial telomeric sequences (or ITSs). However, we also identified non-iTS sites, which correspond to centromeric and pericentromeric satellite DNA. Interestingly, the TRF-binding sites are often located in the proximity of genes or within introns. We propose that TRF1 and TRF2 couple the functional state of telomeres to the long-range organization of chromosomes and gene regulation networks by binding to extratelomeric sequences.

  7. A novel tandem repeat sequence located on human chromosome 4p: isolation and characterization.

    Science.gov (United States)

    Kogi, M; Fukushige, S; Lefevre, C; Hadano, S; Ikeda, J E

    1997-06-01

    In an effort to analyze the genomic region of the distal half of human chromosome 4p, to where Huntington disease and other diseases have been mapped, we have isolated the cosmid clone (CRS447) that was likely to contain a region with specific repeat sequences. Clone CRS447 was subjected to detailed analysis, including chromosome mapping, restriction mapping, and DNA sequencing. Chromosome mapping by both a human-CHO hybrid cell panel and FISH revealed that CRS447 was predominantly located in the 4p15.1-15.3 region. CRS447 was shown to consist of tandem repeats of 4.7-kb units present on chromosome 4p. A single EcoRI unit was subcloned (pRS447), and the complete sequence was determined as 4752 nucleotides. When pRS447 was used as a probe, the number of copies of this repeat per haploid genome was estimated to be 50-70. Sequence analysis revealed that it contained two internal CA repeats and one putative ORF. Database search established that this sequence was unreported. However, two homologous STS markers were found in the database. We concluded that CRS447/pRS447 is a novel tandem repeat sequence that is mainly specific to human chromosome 4p.

  8. Evolutionary trend of exceptionally long human core promoter short tandem repeats.

    Science.gov (United States)

    Ohadi, M; Mohammadparast, S; Darvish, H

    2012-10-01

    Short tandem repeats (STRs) are variable elements that play a significant role in genome evolution by creating and maintaining quantitative genetic variation. Because of their proximity to the +1 transcription start site (TSS) and polymorphic nature, core promoter STRs may be considered a novel source of variation across species. In a genome-scale analysis of the entire human protein-coding genes annotated in the GeneCards database (19,927), we analyze the prevalence and repeat numbers of different classes of core promoter STRs in the interval between -120 and +1 to the TSS. We also analyze the evolutionary trend of exceptionally long core promoter STRs of ≥6-repeats. 133 genes (~2%) had core promoter STRs of ≥6-repeats. In the majority of those genes, the STR motifs were found to be conserved across evolution. Di-nucleotide repeats had the highest representation in the human core promoter long STRs (72 genes). Tri- (52 genes), tetra-, penta-, and hexa-nucleotide STRs (9 genes) were also present in the descending prevalence. The majority of those genes (84 genes) revealed directional expansion of core promoter STRs from mouse to human. However, in a number of genes, the difference in average allele size across species was sufficiently small that there might be a constraint on the evolution of average allele size. Random drift of STRs from mouse to human was also observed in a minority of genes. Future work on the genes listed in the current study may further our knowledge into the potential importance of core promoter STRs in human evolution.

  9. Petroleum Vapor Intrusion

    Science.gov (United States)

    One type of vapor intrusion is PVI, in which vapors from petroleum hydrocarbons such as gasoline, diesel, or jet fuel enter a building. Intrusion of contaminant vapors into indoor spaces is of concern.

  10. Human Short Tandem Repeat (STR Markers for Paternity Testing in Pig-Tailed Macaques

    Directory of Open Access Journals (Sweden)

    DYAH PERWITASARI-FARAJALLAH

    2007-06-01

    Full Text Available This study investigated the use of human short tandem repeat (STR or microsatellite loci markers for assessing paternity and genetic structure of pig-tailed macaques (Macaca nemestrina breeding colony. Four human microsatellite primer pairs located at human map position D1S548, D3S1768, D5S820, and D2S1777, were amplified by polymerase chain reaction (PCR for pig-tailed macaques. Four loci were found to be clearly and reliably amplified, and three loci exhibited high levels of genetic heterogeneity. These loci were sufficiently informative to differentiate discretely between related and unrelated pairs.

  11. Marked variation in predicted and observed variability of tandem repeat loci across the human genome

    Directory of Open Access Journals (Sweden)

    Shields Denis C

    2008-04-01

    Full Text Available Abstract Background Tandem repeat (TR variants in the human genome play key roles in a number of diseases. However, current models predicting variability are based on limited training sets. We conducted a systematic analysis of TRs of unit lengths 2–12 nucleotides in Whole Genome Shotgun (WGS sequences to define the extent of variation of 209,214 unique repeat loci throughout the genome. Results We applied a multivariate statistical model to predict TR variability. Predicted heterozygosity correlated with heterozygosity in the CEPH polymorphism database (correlation ρ = 0.29, p Conclusion Variability among 2–12-mer TRs in the genome can be modeled by a few parameters, which do not markedly differ according to unit length, consistent with a common mechanism for the generation of variability among such TRs. Analysis of the distributions of observed and predicted variants across the genome showed a general concordance, indicating that the repeat variation dataset does not exhibit strong regional ascertainment biases. This revealed a deficit of variant repeats in chromosomes 19 and Y – likely to reflect a reduction in 2-mer repeats in the former and a reduced level of recombination in the latter – and excesses in chromosomes 6, 13, 20 and 21.

  12. Building Intrusion Tolerant Software System

    Institute of Scientific and Technical Information of China (English)

    PENG Wen-ling; WANG Li-na; ZHANG Huan-guo; CHEN Wei

    2005-01-01

    In this paper, we describe and analyze the hypothesis about intrusion tolerance software system, so that it can provide an intended server capability and deal with the impacts caused by the intruder exploiting the inherent security vulnerabilities. We present some intrusion tolerance technology by exploiting N-version module threshold method in constructing multilevel secure software architecture, by detecting with hash value, by placing an "antigen" word next to the return address on the stack that is similar to human immune system, and by adding "Honey code" nonfunctional code to disturb intruder, so that the security and the availability of the software system are ensured.

  13. Repeated high-intensity exercise modulates Ca(2+) sensitivity of human skeletal muscle fibers

    DEFF Research Database (Denmark)

    Gejl, K D; Hvid, L G; Willis, S J;

    2016-01-01

    The effects of short-term high-intensity exercise on single fiber contractile function in humans are unknown. Therefore, the purposes of this study were: (a) to access the acute effects of repeated high-intensity exercise on human single muscle fiber contractile function; and (b) to examine whether...... the fourth sprint with respect to Ca(2+) sensitivity and maximal Ca(2+) -activated force. To investigate the oxidative effects of exercise on single fiber contractile function, a subset of fibers was incubated with dithiothreitol (DTT) before analysis. Ca(2+) sensitivity was enhanced by exercise in both MHC...... I (17%, P exercise. In conclusion, repeated high-intensity exercise increased Ca(2+) sensitivity in both MHC I and MHC II...

  14. Human immunodeficiency virus type 2 long terminal repeat: analysis of regulatory elements.

    OpenAIRE

    Arya, S. K.; Gallo, R C

    1988-01-01

    The long terminal repeats (LTRs) of the human immunodeficiency virus type 2 (HIV-2) and a related simian immunodeficiency virus (SIVmac) contain cis-acting positive regulatory elements upstream and the major transactivator gene (tat) response element and a possible negative regulatory element downstream of the transcriptional initiation site. The tat response element of HIV-2 and of SIVmac was more complex than that of HIV-1. Two structurally similar subelements within the HIV-2 tat response ...

  15. Human mitochondrial mTERF wraps around DNA through a left-handed superhelical tandem repeat.

    Science.gov (United States)

    Jiménez-Menéndez, Nereida; Fernández-Millán, Pablo; Rubio-Cosials, Anna; Arnan, Carme; Montoya, Julio; Jacobs, Howard T; Bernadó, Pau; Coll, Miquel; Usón, Isabel; Solà, Maria

    2010-07-01

    The regulation of mitochondrial DNA (mtDNA) processes is slowly being characterized at a structural level. We present here crystal structures of human mitochondrial regulator mTERF, a transcription termination factor also implicated in replication pausing, in complex with double-stranded DNA oligonucleotides containing the tRNA(Leu)(UUR) gene sequence. mTERF comprises nine left-handed helical tandem repeats that form a left-handed superhelix, the Zurdo domain.

  16. Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome

    Directory of Open Access Journals (Sweden)

    Chadwick Brian P

    2010-11-01

    Full Text Available Abstract Background Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease facioscapulohumeral muscular dystrophy. Nevertheless, many other macrosatellite arrays in the human genome remain poorly characterized. Results Here we describe the organization, tandem repeat copy number variation, transmission stability and expression of four macrosatellite arrays in the human genome: the TAF11-Like array located on chromosomes 5p15.1, the SST1 arrays on 4q28.3 and 19q13.12, the PRR20 array located on chromosome 13q21.1, and the ZAV array at 9q32. All are polymorphic macrosatellite arrays that at least for TAF11-Like and SST1 show evidence of meiotic instability. With the exception of the SST1 array that is ubiquitously expressed, all are expressed at high levels in the testis and to a lesser extent in the brain. Conclusions Our results extend the number of characterized macrosatellite arrays in the human genome and provide the foundation for formulation of hypotheses to begin assessing their functional role in the human genome.

  17. Resistance of human spermatozoa to cryoinjury in repeated cycles of thaw-refreezing

    Directory of Open Access Journals (Sweden)

    Sidney Verza Jr.

    2009-10-01

    Full Text Available Objective: To study the resistance of human spermatozoa to cryoinjury in repeated cycles of thaw-refreezing by using the fast liquid nitrogen vapor method. Material and Methods: Semen specimens were obtained from sixteen normal and oligozoospermic individuals who required disposal at the sperm bank. Five of them had testicular cancer. Specimens were thawed and an aliquot was removed for analysis. The remaining specimens were refrozen without removing the cryomedia. Repeated freeze-thaw cycles were performed until no motile sperm were observed. Sperm motility, number of motile spermatozoa and viability were determined after thawing. Resistance to cryoinjury was compared between groups and also after each refreezing cycle within groups. Results: Motile spermatozoa were recovered after five and two refreeze-thawing cycles in normozoospermic and oligozoospermic specimens, respectively. There were no significant differences in the recovery of motile spermatozoa between thaws within each group of normal and oligozoospermic specimens, but percentage motility and total number of motile spermatozoa were significantly lower in the oligozoospermic one. Specimens from men with cancer were exposed to six refreeze-thawing cycles. Although recovery of motile spermatozoa was significantly impaired after each thawing, there were no significant differences in the recovery of motile sperm between thaws in cancer and non-cancer groups. Conclusions: Human spermatozoa resist repeated cryopreservation using the fast liquid nitrogen vapor method. Normozoospermic specimens withstand refreezing for an average two cycles longer than oligozoospermic ones. Specimens from cancer patients seem to resist repeated cryoinjury similarly to non-cancer counterparts. Resistance to repeated cryoinjury was related to the initial semen quality.

  18. Grey-theory based intrusion detection model

    Institute of Scientific and Technical Information of China (English)

    Qin Boping; Zhou Xianwei; Yang Jun; Song Cunyi

    2006-01-01

    To solve the problem that current intrusion detection model needs large-scale data in formulating the model in real-time use, an intrusion detection system model based on grey theory (GTIDS) is presented. Grey theory has merits of fewer requirements on original data scale, less limitation of the distribution pattern and simpler algorithm in modeling.With these merits GTIDS constructs model according to partial time sequence for rapid detect on intrusive act in secure system. In this detection model rate of false drop and false retrieval are effectively reduced through twice modeling and repeated detect on target data. Furthermore, GTIDS framework and specific process of modeling algorithm are presented. The affectivity of GTIDS is proved through emulated experiments comparing snort and next-generation intrusion detection expert system (NIDES) in SRI international.

  19. Impact of Alu repeats on the evolution of human p53 binding sites

    Directory of Open Access Journals (Sweden)

    Sirotin Michael V

    2011-01-01

    Full Text Available Abstract Background The p53 tumor suppressor protein is involved in a complicated regulatory network, mediating expression of ~1000 human genes. Recent studies have shown that many p53 in vivo binding sites (BSs reside in transposable repeats. The relationship between these BSs and functional p53 response elements (REs remains unknown, however. We sought to understand whether the p53 REs also reside in transposable elements and particularly in the most-abundant Alu repeats. Results We have analyzed ~160 functional p53 REs identified so far and found that 24 of them occur in repeats. More than half of these repeat-associated REs reside in Alu elements. In addition, using a position weight matrix approach, we found ~400,000 potential p53 BSs in Alu elements genome-wide. Importantly, these putative BSs are located in the same regions of Alu repeats as the functional p53 REs - namely, in the vicinity of Boxes A/A' and B of the internal RNA polymerase III promoter. Earlier nucleosome-mapping experiments showed that the Boxes A/A' and B have a different chromatin environment, which is critical for the binding of p53 to DNA. Here, we compare the Alu-residing p53 sites with the corresponding Alu consensus sequences and conclude that the p53 sites likely evolved through two different mechanisms - the sites overlapping with the Boxes A/A' were generated by CG → TG mutations; the other sites apparently pre-existed in the progenitors of several Alu subfamilies, such as AluJo and AluSq. The binding affinity of p53 to the Alu-residing sites generally correlates with the age of Alu subfamilies, so that the strongest sites are embedded in the 'relatively young' Alu repeats. Conclusions The primate-specific Alu repeats play an important role in shaping the p53 regulatory network in the context of chromatin. One of the selective factors responsible for the frequent occurrence of Alu repeats in introns may be related to the p53-mediated regulation of Alu

  20. (TG/CAn repeats in human gene families: abundance and selective patterns of distribution according to function and gene length

    Directory of Open Access Journals (Sweden)

    Ramachandran Srinivasan

    2005-06-01

    Full Text Available Abstract Background Creation of human gene families was facilitated significantly by gene duplication and diversification. The (TG/CAn repeats exhibit length variability, display genome-wide distribution, and are abundant in the human genome. Accumulation of evidences for their multiple functional roles including regulation of transcription and stimulation of recombination and splicing elect them as functional elements. Here, we report analysis of the distribution of (TG/CAn repeats in human gene families. Results The 1,317 human gene families were classified into six functional classes. Distribution of (TG/CAn repeats were analyzed both from a global perspective and from a stratified perspective based on their biological properties. The number of genes with repeats decreased with increasing repeat length and several genes (53% had repeats of multiple types in various combinations. Repeats were positively associated with the class of Signaling and communication whereas, they were negatively associated with the classes of Immune and related functions and of Information. The proportion of genes with (TG/CAn repeats in each class was proportional to the corresponding average gene length. The repeat distribution pattern in large gene families generally mirrored the global distribution pattern but differed particularly for Collagen gene family, which was rich in repeats. The position and flanking sequences of the repeats of Collagen genes showed high conservation in the Chimpanzee genome. However the majority of these repeats displayed length polymorphism. Conclusion Positive association of repeats with genes of Signaling and communication points to their role in modulation of transcription. Negative association of repeats in genes of Information relates to the smaller gene length, higher expression and fundamental role in cellular physiology. In genes of Immune and related functions negative association of repeats perhaps relates to the smaller gene

  1. Enzymatic amplification of synthetic oligodeoxyribonucleotides: implications for triplet repeat expansions in the human genome.

    Science.gov (United States)

    Behn-Krappa, A; Doerfler, W

    1994-01-01

    The triplet repeat sequences (CGG)n, (GCT)n, and (CAG)n, which naturally occur in the human genome, can be autonomously expanded in human DNA by an as yet unknown mechanism. These in part excessive expansions have been causally related to human genetic diseases, the fragile X (Martin-Bell) syndrome, to myotonic dystrophy (Curschmann-Steinert), to spinal and bulbar muscular atrophy (Kennedy disease), and recently to Huntington disease. A GCC trinucleotide repeat was found to be expanded and methylated in the fragile site FRAXE on the human X chromosome. These findings were associated with mental retardation (Knight et al., 1993). In spinocerebellar ataxia type 1 (SCA1), a polymorphic CAG repeat was found to be unstable and expanded in individuals with that disease (Orr et al., 1993). We have demonstrated in in vitro experiments that the synthetic oligodeoxyribonucleotides (CGG)17, (CGG)12, (GCC)17, (CG)25, (CTG)17, or (CAG)17 plus (GTC)17, in the absence of added natural DNA, can be expanded with Taq polymerase in the polymerase chain reaction (PCR). Some expansion can already be detected after 4 PCR cycles. The E. coli Klenow DNA polymerase also functions in a similar amplification and expansion reaction performed at 37 degrees C without cycling. Other oligodeoxyribonucleotides, like, (CGG)7, (CGGT)13, or (TAA)17, are devoid of this property or have very low activity. The cytidine-methylated polymers (GCC)17 or (CG)25 yield expansion products of considerably reduced chain lengths. The expansion of the polymer (CGG)17 is affected by cytidine methylation to a lesser degree. A specific sequence and/or secondary structure and high CG content appear to be requirements for this expansion reaction by a possible slippage mechanism.(ABSTRACT TRUNCATED AT 250 WORDS)

  2. Interior intrusion detection systems

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, J.R.; Matter, J.C. (Sandia National Labs., Albuquerque, NM (United States)); Dry, B. (BE, Inc., Barnwell, SC (United States))

    1991-10-01

    The purpose of this NUREG is to present technical information that should be useful to NRC licensees in designing interior intrusion detection systems. Interior intrusion sensors are discussed according to their primary application: boundary-penetration detection, volumetric detection, and point protection. Information necessary for implementation of an effective interior intrusion detection system is presented, including principles of operation, performance characteristics and guidelines for design, procurement, installation, testing, and maintenance. A glossary of sensor data terms is included. 36 figs., 6 tabs.

  3. Interior intrusion detection systems

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, J.R.; Matter, J.C. (Sandia National Labs., Albuquerque, NM (United States)); Dry, B. (BE, Inc., Barnwell, SC (United States))

    1991-10-01

    The purpose of this NUREG is to present technical information that should be useful to NRC licensees in designing interior intrusion detection systems. Interior intrusion sensors are discussed according to their primary application: boundary-penetration detection, volumetric detection, and point protection. Information necessary for implementation of an effective interior intrusion detection system is presented, including principles of operation, performance characteristics and guidelines for design, procurement, installation, testing, and maintenance. A glossary of sensor data terms is included. 36 figs., 6 tabs.

  4. Summary of Natural Resources that Potentially Influence Human Intrusion at the Area 5 Radioactive Waste Management Site, Nevada Test Site, Nye County, Nevada

    Energy Technology Data Exchange (ETDEWEB)

    NSTec Environmental Management

    2007-06-01

    In 1993, Raytheon Services Nevada completed a review of natural resource literature and other sources to identify potentially exploitable resources and potential future land uses near the Area 5 Radioactive Waste Management Site (RWMS) of the Nevada Test Site (NTS), Nye County, Nevada, that could lead to future inadvertent human intrusion and subsequent release of radionuclides to the accessible environment. National Security Technologies, LLC, revised the original limited-distribution document to conform to current editorial standards and U.S. Department of Energy requirements for public release. The researchers examined the potential for future development of sand, gravel, mineral, petroleum, water resources, and rural land uses, such as agriculture, grazing, and hunting. The study was part of the performance assessment for Greater Confinement Disposal boreholes. Sand and gravel are not considered exploitable site resources because the materials are common throughout the area and the quality at the Area 5 RWMS is not ideal for typical commercial uses. Site information also indicates a very low mineral potential for the area. None of the 23 mining districts in southern Nye County report occurrences of economic mineral deposits in unconsolidated alluvium. The potential for oil and natural gas is low for southern Nye County. No occurrences of coal, tar sand, or oil shale on the NTS are reported in available literature. Several potential future uses of water were considered. Agricultural irrigation is impractical due to poor soils and existing water supply regulations. Use of water for geothermal energy development is unlikely because temperatures are too low for typical commercial applications using current technology. Human consumption of water has the most potential for cause of intrusion. The economics of future water needs may create a demand for the development of deep carbonate aquifers in the region. However, the Area 5 RWMS is not an optimal location for

  5. The coding region of the human c-mos pseudogene contains Alu repeat insertions.

    Science.gov (United States)

    Zabarovsky, E R; Chumakov, I M; Prassolov, V S; Kisselev, L L

    1984-10-01

    We have determined the nucleotide sequence of an 841-bp fragment derived from a segment of the human genome previously cloned by Chumakov et al. [Gene 17 (1982) 19-26] and Zabarovsky et al. [Gene 23 (1983) 379-384] and containing regions homologous to the viral mos gene probe. This sequence displays homology with part of the coding region of the human and murine c-mos genes, contains several termination codons, and is interrupted by two Alu-family elements flanked by short direct repeats. Probably, the progenitor of the human c-mos gene was duplicated approximately at the time of mammalian divergence, was converted to a pseudogene, and acquired insertions of two Alu elements.

  6. Transcription-induced CAG repeat contraction in human cells is mediated in part by transcription-coupled nucleotide excision repair.

    Science.gov (United States)

    Lin, Yunfu; Wilson, John H

    2007-09-01

    Expansions of CAG repeat tracts in the germ line underlie several neurological diseases. In human patients and mouse models, CAG repeat tracts display an ongoing instability in neurons, which may exacerbate disease symptoms. It is unclear how repeats are destabilized in nondividing cells, but it cannot involve DNA replication. We showed previously that transcription through CAG repeats induces their instability (Y. Lin, V. Dion, and J. H. Wilson, Nat. Struct. Mol. Biol. 13:179-180). Here, we present a genetic analysis of the link between transcription-induced repeat instability and nucleotide excision repair (NER) in human cells. We show that short interfering RNA-mediated knockdown of CSB, a component specifically required for transcription-coupled NER (TC-NER), and knockdowns of ERCC1 and XPG, which incise DNA adjacent to damage, stabilize CAG repeat tracts. These results suggest that TC-NER is involved in the pathway for transcription-induced CAG repeat instability. In contrast, knockdowns of OGG1 and APEX1, key components involved in base excision repair, did not affect repeat instability. In addition, repeats are stabilized by knockdown of transcription factor IIS, consistent with a requirement for RNA polymerase II (RNAPII) to backtrack from a transcription block. Repeats also are stabilized by knockdown of either BRCA1 or BARD1, which together function as an E3 ligase that can ubiquitinate arrested RNAPII. Treatment with the proteasome inhibitor MG132, which stabilizes repeats, confirms proteasome involvement. We integrate these observations into a tentative pathway for transcription-induced CAG repeat instability that can account for the contractions observed here and potentially for the contractions and expansions seen with human diseases.

  7. Repeated tongue lift movement induces neuroplasticity in corticomotor control of tongue and jaw muscles in humans

    DEFF Research Database (Denmark)

    Komoda, Yoshihiro; Lida, Takashi; Kothari, Mohit

    2015-01-01

    This study investigated the effect of repeated tongue lift training (TLT) on the excitability of the corticomotor representation of the human tongue and jaw musculature. Sixteen participants performed three series of TLT for 41min on each of 5 consecutive days. Each TLT series consisted of two....... EMG recordings from the left and right tongue dorsum and masseter muscles were made at three pressure levels (5kPa, 10kPa, 100% tongue lift), and tongue, masseter, and first dorsal interosseous (FDI) MEPs were measured. There were no significant day-to-day differences in the tongue pressure during...

  8. Positive Selection of a Pre-Expansion CAG Repeat of the Human SCA2 Gene.

    Directory of Open Access Journals (Sweden)

    2005-09-01

    Full Text Available A region of approximately one megabase of human Chromosome 12 shows extensive linkage disequilibrium in Utah residents with ancestry from northern and western Europe. This strikingly large linkage disequilibrium block was analyzed with statistical and experimental methods to determine whether natural selection could be implicated in shaping the current genome structure. Extended Haplotype Homozygosity and Relative Extended Haplotype Homozygosity analyses on this region mapped a core region of the strongest conserved haplotype to the exon 1 of the Spinocerebellar ataxia type 2 gene (SCA2. Direct DNA sequencing of this region of the SCA2 gene revealed a significant association between a pre-expanded allele [(CAG(8CAA(CAG(4CAA(CAG(8] of CAG repeats within exon 1 and the selected haplotype of the SCA2 gene. A significantly negative Tajima's D value (-2.20, p < 0.01 on this site consistently suggested selection on the CAG repeat. This region was also investigated in the three other populations, none of which showed signs of selection. These results suggest that a recent positive selection of the pre-expansion SCA2 CAG repeat has occurred in Utah residents with European ancestry.

  9. Positive selection of a pre-expansion CAG repeat of the human SCA2 gene.

    Directory of Open Access Journals (Sweden)

    Fuli Yu

    2005-09-01

    Full Text Available A region of approximately one megabase of human Chromosome 12 shows extensive linkage disequilibrium in Utah residents with ancestry from northern and western Europe. This strikingly large linkage disequilibrium block was analyzed with statistical and experimental methods to determine whether natural selection could be implicated in shaping the current genome structure. Extended Haplotype Homozygosity and Relative Extended Haplotype Homozygosity analyses on this region mapped a core region of the strongest conserved haplotype to the exon 1 of the Spinocerebellar ataxia type 2 gene (SCA2. Direct DNA sequencing of this region of the SCA2 gene revealed a significant association between a pre-expanded allele [(CAG8CAA(CAG4CAA(CAG8] of CAG repeats within exon 1 and the selected haplotype of the SCA2 gene. A significantly negative Tajima's D value (-2.20, p < 0.01 on this site consistently suggested selection on the CAG repeat. This region was also investigated in the three other populations, none of which showed signs of selection. These results suggest that a recent positive selection of the pre-expansion SCA2 CAG repeat has occurred in Utah residents with European ancestry.

  10. A model of human nasal epithelial cells adapted for direct and repeated exposure to airborne pollutants.

    Science.gov (United States)

    Bardet, Gaëlle; Achard, Sophie; Loret, Thomas; Desauziers, Valérie; Momas, Isabelle; Seta, Nathalie

    2014-08-17

    Airway epithelium lining the nasal cavity plays a pivotal role in respiratory tract defense and protection mechanisms. Air pollution induces alterations linked to airway diseases such as asthma. Only very few in vitro studies to date have succeeded in reproducing physiological conditions relevant to cellular type and chronic atmospheric pollution exposure. We therefore, set up an in vitro model of human Airway Epithelial Cells of Nasal origin (hAECN) close to real human cell functionality, specifically adapted to study the biological effects of exposure to indoor gaseous pollution at the environmental level. hAECN were exposed under air-liquid interface, one, two, or three-times at 24 h intervals for 1 h, to air or formaldehyde (200 μg/m(3)), an indoor air gaseous pollutant. All experiments were ended at day 4, when both cellular viability and cytokine production were assessed. Optimal adherence and confluence of cells were obtained 96 h after cell seeding onto collagen IV-precoated insert. Direct and repeated exposure to formaldehyde did not produce any cellular damage or IL-6 production change, although weak lower IL-8 production was observed only after the third exposure. Our model is significantly better than previous ones due to cell type and the repeated exposure protocol.

  11. Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.

    Directory of Open Access Journals (Sweden)

    Augix Guohua Xu

    Full Text Available Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20-28% of non-ribosomal transcripts correspond to annotated exons and 20-23% to introns. By contrast, transcripts originating within intronic and intergenic repetitive sequences constitute 40-48% of the total brain transcriptome. Notably, some repeat families show elevated transcription. In non-repetitive intergenic regions, we identify and characterize 1,093 distinct regions highly expressed in the human brain. These regions are conserved at the RNA expression level across primates studied and at the DNA sequence level across mammals. A large proportion of these transcripts (20% represents 3'UTR extensions of known genes and may play roles in alternative microRNA-directed regulation. Finally, we show that while transcriptome divergence between species increases with evolutionary time, intergenic transcripts show more expression differences among species and exons show less. Our results show that many yet uncharacterized evolutionary conserved transcripts exist in the human brain. Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits.

  12. Evidence for integration of retroviral vectors in a novel human repeat sequence

    Energy Technology Data Exchange (ETDEWEB)

    Kurdi-Haidar, B.; Friedmann, T. [USCD School of Medicine, La Jolla, CA (United States)

    1994-09-01

    Retroviruses have become attractive vehicles for the introduction of foreign genes into mammalian cells not only for gene therapy but also to serve as anchor points for long-range mapping purposes. The information relating to retroviral integration in mammalian cells is derived mostly from studies of rodent genomes. The absence of information regarding integration sites of murine-based retroviral vectors in human cells has prompted us to investigate the characteristics of integration sites in the human genome. We have constructed a Moloney murine leukemia virus-based retroviral vector that carries the pUC8 origin of replication and the chloramphenicol resistance gene to allow the rescue of the flanking genomic sequences in plasmid form. We have infected human primary fibroblasts and myoblasts with this retroviral vector and isolated independently transduced clones. Genomic DNA was obtained from independent clones and the genomic fragment carrying the provirus-host sequence boundary was isolated after digestion of the genomic DNA, circularization, and transformation by electroporation of E. coli C cells to chloramphenicol resistance. Restriction map and nucleotide sequence analysis of the rescued plasmids showed that a number of the clones shared the same integration site within the human genome. We have used the nucleotide sequence information about the human DNA adjacent to the 3{prime}LTR to design a PCR-based assay diagnostic for this common integration site. Analysis revealed the presence of the same integration site in four out of twelve human primary fibroblast clones infected with this specific retroviral vector, and in one out of twelve human primary myoblast clones infected with a second retroviral vector. Further analysis revealed the common integration site to be a previously unreported primate repeat present in monkey and human genomes and absent from rodent, bovine and avian genomes.

  13. Repeated tongue lift movement induces neuroplasticity in corticomotor control of tongue and jaw muscles in humans.

    Science.gov (United States)

    Komoda, Yoshihiro; Iida, Takashi; Kothari, Mohit; Komiyama, Osamu; Baad-Hansen, Lene; Kawara, Misao; Sessle, Barry; Svensson, Peter

    2015-11-19

    This study investigated the effect of repeated tongue lift training (TLT) on the excitability of the corticomotor representation of the human tongue and jaw musculature. Sixteen participants performed three series of TLT for 41 min on each of 5 consecutive days. Each TLT series consisted of two pressure levels (5 kPa and 10 kPa). All participants underwent transcranial magnetic stimulation (TMS) and electromyographic (EMG) recordings of motor evoked potentials (MEPs) in four sessions: (1) before TLT on Day 1 (baseline), (2) after TLT on Day 1, (3) before TLT on Day 5, and (4) after TLT on Day 5. EMG recordings from the left and right tongue dorsum and masseter muscles were made at three pressure levels (5 kPa, 10 kPa, 100% tongue lift), and tongue, masseter, and first dorsal interosseous (FDI) MEPs were measured. There were no significant day-to-day differences in the tongue pressure during maximum voluntary contractions. The amplitudes and thresholds of tongue and masseter MEPs after TLT on Day 5 were respectively higher and lower than before TLT on Day 1 (Ptongue and masseter MEP areas; no significant changes occurred in MEP onset latencies. FDI MEP parameters (amplitude, threshold, area, latency) were not significantly different between the four sessions. Our findings suggest that repeated TLT can trigger neuroplasticity reflected in increased excitability of the corticomotor representation of not only the tongue muscles but also the masseter muscles.

  14. Autonomous Rule Creation for Intrusion Detection

    Energy Technology Data Exchange (ETDEWEB)

    Todd Vollmer; Jim Alves-Foss; Milos Manic

    2011-04-01

    Many computational intelligence techniques for anomaly based network intrusion detection can be found in literature. Translating a newly discovered intrusion recognition criteria into a distributable rule can be a human intensive effort. This paper explores a multi-modal genetic algorithm solution for autonomous rule creation. This algorithm focuses on the process of creating rules once an intrusion has been identified, rather than the evolution of rules to provide a solution for intrusion detection. The algorithm was demonstrated on anomalous ICMP network packets (input) and Snort rules (output of the algorithm). Output rules were sorted according to a fitness value and any duplicates were removed. The experimental results on ten test cases demonstrated a 100 percent rule alert rate. Out of 33,804 test packets 3 produced false positives. Each test case produced a minimum of three rule variations that could be used as candidates for a production system.

  15. Autonomous Rule Creation for Intrusion Detection

    Energy Technology Data Exchange (ETDEWEB)

    Todd Vollmer; Jim Alves-Foss; Milos Manic

    2011-04-01

    Many computational intelligence techniques for anomaly based network intrusion detection can be found in literature. Translating a newly discovered intrusion recognition criteria into a distributable rule can be a human intensive effort. This paper explores a multi-modal genetic algorithm solution for autonomous rule creation. This algorithm focuses on the process of creating rules once an intrusion has been identified, rather than the evolution of rules to provide a solution for intrusion detection. The algorithm was demonstrated on anomalous ICMP network packets (input) and Snort rules (output of the algorithm). Output rules were sorted according to a fitness value and any duplicates were removed. The experimental results on ten test cases demonstrated a 100 percent rule alert rate. Out of 33,804 test packets 3 produced false positives. Each test case produced a minimum of three rule variations that could be used as candidates for a production system.

  16. Repeat use of human recombinant bone morphogenetic protein-2 for second level lumbar arthrodesis.

    Science.gov (United States)

    Singh, Kern; Dumonski, Mark; Stanley, Tom; Ponnappan, Ravi; Phillips, Frank M

    2011-02-01

    Prospective randomized controlled animal model. The purpose of this study is to determine whether the readministration of human recombinant bone morphogenetic protein-2 (rhBMP-2) induces an immune response and inhibits successful fusion in repeat posterolateral spinal surgery. Little research has been performed on the effectiveness or immunoreactivity of rhBMP-2 (Infuse, Medtronic, Memphis, TN) in the context of its reuse in posterolateral fusion spinal surgery at adjacent levels. A total of 34 New Zealand White rabbits underwent posterior intertransverse process fusion with the use of rhBMP-2 delivered on an absorbable collagen sponge (rhBMP-2/ACS). Two rabbits were killed early leaving 32 total rabbits. Serologic studies (Type I bovine collagen and rhBMP-2 antibodies) were obtained at 2-week intervals throughout the experiment. At 10 weeks, posteroanterior radiographs confirmed solid fusion masses in all rabbits. The 32 rabbits were randomly separated into 2 groups of 16, and each group underwent an adjacent level, bilateral intertransverse process fusion with either rhBMP-2/ACS or iliac crest. There was no statistical difference in fusion rates with repeat use of rhBMP-2 (n = 15/16, 94%) or iliac crest (n = 11/16, 69%) (P = 0.17) at the adjacent level. Four rabbits (n = 4/32, 13%) developed rhBMP-2 antibodies. Of these 4 rabbits, 1 developed anti-rhBMP antibodies after the first exposure and 3 developed antibodies after the second surgery. Eight rabbits (n = 8/32, 25%) developed collagen antibodies with 7 rabbits developing antibodies after the first exposure and 1 rabbit developing antibodies after the second exposure. The development of antibodies did not effect fusion rates. No rabbit demonstrated evidence of a systemic or anaphylactic reaction to repeat exposure to rhBMP-2. rhBMP-2 appears to be successful in promoting intertransverse fusions when used in both primary and repeat fusion environments. The infrequent development of antibodies to rhBMP-2 after

  17. Improved haplotype analysis of human myelin basic protein short tandem repeat loci.

    Science.gov (United States)

    Watanabe, G; Umetsu, K; Yuasa, I; Suzuki, T

    2000-06-01

    We report an improved haplotype analysis of the human myelin basic protein gene (MBP) short tandem repeat (STR) polymorphism. The polymorphic G-->A transition and 2 conventional STR polymorphisms, MBPA and MBPB, were simultaneously determined by an amplified product length polymorphism technique. After the MBPC fragments containing MBPA and MBPB were amplified, the linkage of these 2 STR loci was determined by a second amplification, using polymerase chain reaction (PCR) technique, of the isolated MBPC fragments. The present haplotype analysis dispensed with family studies for the haplotyping of MBPA and MBPB. Polymorphisms of the MBP loci studied in German and Japanese populations showed a high genomic variation. Haplotype analysis of the MBP loci showed distinct differences between the German and the Japanese populations. Consequently, haplotype analysis of the MBP loci promises to be useful in forensic identification and paternity testing.

  18. The response of human nasal and bronchial organotypic tissue cultures to repeated whole cigarette smoke exposure.

    Science.gov (United States)

    Talikka, Marja; Kostadinova, Radina; Xiang, Yang; Mathis, Carole; Sewer, Alain; Majeed, Shoaib; Kuehn, Diana; Frentzel, Stefan; Merg, Celine; Geertz, Marcel; Martin, Florian; Ivanov, Nikolai V; Peitsch, Manuel C; Hoeng, Julia

    2014-01-01

    Exposure to cigarette smoke (CS) is linked to the development of respiratory diseases, and there is a need to understand the mechanisms whereby CS causes damage. Although animal models have provided valuable insights into smoking-related respiratory tract damage, modern toxicity testing calls for reliable in vitro models as alternatives for animal experimentation. We report on a repeated whole mainstream CS exposure of nasal and bronchial organotypic tissue cultures that mimic the morphological, physiological, and molecular attributes of the human respiratory tract. Despite the similar cellular staining and cytokine secretion in both tissue types, the transcriptomic analyses in the context of biological network models identified similar and diverse biological processes that were impacted by CS-exposed nasal and bronchial cultures. Our results demonstrate that nasal and bronchial tissue cultures are appropriate in vitro models for the assessment of CS-induced adverse effects in the respiratory system and promising alternative to animal experimentation.

  19. Purification of proteins specifically binding human endogenous retrovirus K long terminal repeat by affinity elution chromatography.

    Science.gov (United States)

    Trubetskoy, D O; Zavalova, L L; Akopov, S B; Nikolaev, L G

    2002-11-01

    A novel affinity elution procedure for purification of DNA-binding proteins was developed and employed to purify to near homogeneity the proteins recognizing a 21 base pair sequence within the long terminal repeat of human endogenous retroviruses K. The approach involves loading the initial protein mixture on a heparin-agarose column and elution of protein(s) of interest with a solution of double-stranded oligonucleotide containing binding sites of the protein(s). The affinity elution has several advantages over conventional DNA-affinity chromatography: (i) it is easier and faster, permitting to isolate proteins in a 1 day-one stage procedure; (ii) yield of a target protein is severalfold higher than that in DNA-affinity chromatography; (iii) it is not necessary to prepare a special affinity support for each factor to be isolated. Theaffinity elution could be a useful alternative to conventional DNA-affinity chromatography.

  20. Pulp-dentine complex changes and root resorption during intrusive orthodontic tooth movement in patients prescribed nabumetone.

    Science.gov (United States)

    Villa, Paula A; Oberti, Giovanni; Moncada, Cesar A; Vasseur, Olga; Jaramillo, Alejandro; Tobón, Diego; Agudelo, Jaime A

    2005-01-01

    Pulpitis, external root resorption, and pain may be experienced during orthodontic movement. The use of nonsteroidal anti-inflammatory drugs (NSAIDs) has been suggested to control these changes. The purpose of this study was to observe pulp-dentinal reactions, root resorption, tooth pain, and tooth movement after the application of a 4-ounce intrusive orthodontic force to human maxillary first premolars in patients given the NSAID nabumetone. Thirty-four maxillary first premolars were evaluated. A placebo was prescribed to 17 patients after an intrusive force was activated and reactivated for an 8-week period on the right side. The same procedure was repeated on the left side after patients were given nabumetone. Pulp-dentinal reactions and external root resorption were evaluated by histology. Pain and movement were also evaluated. Nabumetone was found to be useful in reducing pulpitis, external root resorption, and pain caused by intrusive orthodontic movement, without altering tooth movement in response to the application of orthodontic force.

  1. Triplet repeat sequences in human DNA can be detected by hybridization to a synthetic (5'-CGG-3')17 oligodeoxyribonucleotide

    DEFF Research Database (Denmark)

    Behn-Krappa, A; Mollenhauer, J; Doerfler, W

    1993-01-01

    The seemingly autonomous amplification of naturally occurring triplet repeat sequences in the human genome has been implicated in the causation of human genetic disease, such as the fragile X (Martin-Bell) syndrome, myotonic dystrophy (Curshmann-Steinert), spinal and bulbar muscular atrophy...

  2. Computer Intrusions and Attacks.

    Science.gov (United States)

    Falk, Howard

    1999-01-01

    Examines some frequently encountered unsolicited computer intrusions, including computer viruses, worms, Java applications, trojan horses or vandals, e-mail spamming, hoaxes, and cookies. Also discusses virus-protection software, both for networks and for individual users. (LRW)

  3. Repeatedly positive human immunodeficiency virus type 1 DNA polymerase chain reaction in human immunodeficiency virus-exposed seroreverting infants.

    Science.gov (United States)

    Bakshi, S S; Tetali, S; Abrams, E J; Paul, M O; Pahwa, S G

    1995-08-01

    Three human immunodeficiency virus type 1 (HIV-1)-exposed children who had repeatedly positive DNA polymerase chain reaction (PCR) tests for HIV in > or = 5 samples before seroreversion to HIV-negative status are reported. The children belong to a cohort of 210 infants who were born to HIV-infected mothers and were tested at intervals of 1 to 3 months by HIV viral culture, PCR, and p24 antigen; only the PCR was positive in > or = 5 samples in the children reported here. Their clinical features were indistinguishable from other seroreverters. All three children had a transient drop in CD4:CD8 ratio to < 1.0. The transiently positive DNA PCR in HIV-exposed infants may indicate either that HIV infection was eliminated by a strong host immune response or that infection was caused by an attenuated/defective strain of virus.

  4. Analysis of the trinucleotide CAG repeat from the human mitochondrial DNA polymerase gene in healthy and diseased individuals.

    Science.gov (United States)

    Rovio, A; Tiranti, V; Bednarz, A L; Suomalainen, A; Spelbrink, J N; Lecrenier, N; Melberg, A; Zeviani, M; Poulton, J; Foury, F; Jacobs, H T

    1999-01-01

    The human nuclear gene (POLG) for the catalytic subunit of mitochondrial DNA polymerase (DNA polymerase gamma) contains a trinucleotide CAG microsatellite repeat within the coding sequence. We have investigated the frequency of different repeat-length alleles in populations of diseased and healthy individuals. The predominant allele of 10 CAG repeats was found at a very similar frequency (approximately 88%) in both Finnish and ethnically mixed population samples, with homozygosity close to the equilibrium prediction. Other alleles of between 5 and 13 repeat units were detected, but no larger, expanded alleles were found. A series of 51 British myotonic dystrophy patients showed no significant variation from controls, indicating an absence of generalised CAG repeat instability. Patients with a variety of molecular lesions in mtDNA, including sporadic, clonal deletions, maternally inherited point mutations, autosomally transmitted mtDNA depletion and autosomal dominant multiple deletions showed no differences in POLG trinucleotide repeat-length distribution from controls. These findings rule out POLG repeat expansion as a common pathogenic mechanism in disorders characterised by mitochondrial genome instability.

  5. Gene expression in human skeletal muscle: alternative normalization method and effect of repeated biopsies.

    Science.gov (United States)

    Lundby, Carsten; Nordsborg, Nikolai; Kusuhara, Keiko; Kristensen, Kristina Møller; Neufer, P Darrell; Pilegaard, Henriette

    2005-10-01

    The reverse transcriptase-polymerase chain reaction (RT-PCR) method has lately become widely used to determine transcription and mRNA content in rodent and human muscle samples. However, the common use of endogenous controls for correcting for variance in cDNA between samples is not optimal. Specifically, we investigated (1) a new normalization method based on determining the cDNA content by the flourophores PicoGreen and OliGreen, (2) effect of repeated muscle biopsies on mRNA gene expression, and (3) the spatial heterogeneity in mRNA expression across the muscle. Standard curves using oligo standards revealed a high degree of sensitivity and linearity (2.5-45 ng; R2>0.99) with OliGreen reagent, as was the case for OliGreen analyses with standard curves constructed from serial dilutions of representative RT samples (R2 >0.99 for a ten times dilution range of a representative reversed transcribed (RT) sample). Likewise, PicoGreen reagent detected the RNA:DNA hybrid content in RT samples with great sensitivity. Standard curves constructed from both double-stranded lambda DNA (1-10 ng) and from serial dilutions of representative RT samples consistently resulted in linearity with R2 >0.99. The present determination of cDNA content in reversed transcribed human skeletal muscle RNA samples by both PicoGreen and OliGreen analyses suggests that these fluorophores provide a potential alternative normalization procedure for human gene expression studies. In addition, the present study shows that multiple muscle biopsies obtained from the same muscle do not influence the mRNA response induced by an acute exercise bout for any of the genes examined.

  6. Network intrusion detection

    Institute of Scientific and Technical Information of China (English)

    Oboile Tirelo; YANG Chun-hua

    2003-01-01

    Nowadays, network computer systems play an increasingly important role in society and economy. They have become the targets of a wide array of malicious attacks that invariably turn into actual intrusions. This is why the computer security has become an essential concern for network administrators. Too often, intrusions wreak havoc inside LANs and the time and cost to repair the damage can grow to extreme proportions. Instead of using passive measures to fix and patch security holes once they have been exploited, it is more effective to adopt a protective approach to intrusions. In addition to the well-established intrusion prevention techniques such as data encryption and message integrity, user authentication and user authorization, as well as the avoidance of security flaws inherent to many off-the-shelf applications, intrusion detection techniques can be viewed as an addition safeguard for network computers. The paper discusses traditional and new security designs, the approach to implementing best-practice security measures and the method to trace the malicious computer attackers.

  7. Repeated Exposure to Dissection Does Not Influence Students’ Attitudes towards Human Body Donation for Anatomy Teaching

    Directory of Open Access Journals (Sweden)

    Philip Maseghe Mwachaka

    2016-01-01

    Full Text Available The use of unclaimed bodies for anatomical dissection has been the main method of instruction at our institution. There is however a shortage of cadavers for dissection given the increase in the number of medical schools as well as in the number of students enrolling in these schools. This shortage could be mitigated by having voluntary human body donation programs. This study aimed at assessing the attitudes of medical students and surgical residents towards body donation for anatomy learning. We conducted an online survey involving 72 first-year medical students and 41 surgical residents at University of Nairobi who had completed one year of anatomy dissection. For the medical students, this was their first dissection experience while it was the second exposure for the surgery trainees. Most of the surgical trainees (70.7% and medical students (68.1% were opposed to self-body donation. This was mainly due to cultural (37% and religious (20% barriers. Surprisingly, of those not willing to donate themselves, 67.9% (82.8% surgical trainees, 59.2% medical students would recommend the practice to other people. Exposure to repeated dissection does not change the perceptions towards body donation. It is noteworthy that culture and religion rank high as clear barriers amongst this “highly informed” group of potential donors.

  8. Homogeneity of fascicle architecture following repeated contractions in the human gastrocnemius medialis.

    Science.gov (United States)

    Thomas, Neil M; Dewhurst, Susan; Bampouras, Theodoros M

    2015-12-01

    This investigation sought to determine the effects of fatigue on fascicle architecture across the length of the human gastrocnemius medialis (GM). With institutional ethical approval, fifteen healthy males performed repeated isometric plantar flexion maximal voluntary contractions (MVC) until peak force fell 30% below baseline. Brightness-mode ultrasound was used to determine fascicle length and pennation angle at rest and during MVC prior to and following the fatiguing contractions. The results show a significant increase in fascicle length during MVC in the distal (2.8 mm, 8.1%) middle, (4.9 mm, 14.1%), and proximal (5.2 mm, 14.7%) regions post-fatigue compared to pre-fatigue (p MVC in the distal (3.3°, 8.8%), middle (3.9°, 9.4%), and proximal (2.9°, 6.9%) regions post-fatigue compared to pre-fatigue (p < 0.05). These changes, however, were not region specific. These are the first results to show that fascicle shortening within the GM remains homogeneous following fatigue, suggesting that the fascicles were fatigued in a similar pattern throughout the muscle. The significant reduction of fascicle shortening may reflect an additional strategy to maintain an optimal force output in fatigued conditions, although future work is needed to confirm this notion.

  9. Repeated Exposure to Dissection Does Not Influence Students' Attitudes towards Human Body Donation for Anatomy Teaching.

    Science.gov (United States)

    Mwachaka, Philip Maseghe; Mandela, Pamela; Saidi, Hassan

    2016-01-01

    The use of unclaimed bodies for anatomical dissection has been the main method of instruction at our institution. There is however a shortage of cadavers for dissection given the increase in the number of medical schools as well as in the number of students enrolling in these schools. This shortage could be mitigated by having voluntary human body donation programs. This study aimed at assessing the attitudes of medical students and surgical residents towards body donation for anatomy learning. We conducted an online survey involving 72 first-year medical students and 41 surgical residents at University of Nairobi who had completed one year of anatomy dissection. For the medical students, this was their first dissection experience while it was the second exposure for the surgery trainees. Most of the surgical trainees (70.7%) and medical students (68.1%) were opposed to self-body donation. This was mainly due to cultural (37%) and religious (20%) barriers. Surprisingly, of those not willing to donate themselves, 67.9% (82.8% surgical trainees, 59.2% medical students) would recommend the practice to other people. Exposure to repeated dissection does not change the perceptions towards body donation. It is noteworthy that culture and religion rank high as clear barriers amongst this "highly informed" group of potential donors.

  10. Serine-Rich Repeat Adhesins Contribute to Streptococcus gordonii-Induced Maturation of Human Dendritic Cells

    Science.gov (United States)

    Ko, Eun Byeol; Kim, Sun Kyung; Seo, Ho Seong; Yun, Cheol-Heui; Han, Seung Hyun

    2017-01-01

    Dendritic cells (DCs) play a pivotal role in the induction of immunity by recognition, capture, process, and presentation of antigens from infectious microbes. Streptococcus gordonii is able to cause life-threatening systemic diseases such as infective endocarditis. Serine-rich repeat (SRR) glycoproteins of S. gordonii are sialic acid-binding adhesins mediating the bacterial adherence to the host and the development of infective endocarditis. Thus, the SRR adhesins are potentially involved in the bacterial adherence to DCs and the maturation and activation of DCs required for the induction of immunity to S. gordonii. Here, we investigated the phenotypic and functional changes of human monocyte-derived DCs treated with wild-type S. gordonii or the SRR adhesin-deficient mutant. The mutant poorly bound to DCs and only weakly increased the expression of CD83, CD86, MHC class II, and PD-L1 on DCs compared with the wild-type. In addition, the mutant induced lower levels of TNF-α, IL-6, and IL-12 than the wild-type in DCs. When DCs sensitized with the mutant were co-cultured with autologous T cells, they induced weaker proliferation and activation of T cells than DCs stimulated with the wild-type. Blockade of SRR adhesin with 3′-sialyllactose markedly reduced S. gordonii binding and internalization, causing attenuation of the bacterial immunostimulatory potency in DC maturation. Collectively, our results suggest that SRR adhesins of S. gordonii are important for maturation and activation of DCs.

  11. Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines.

    Science.gov (United States)

    Zhang, Zhou; Zheng, Yinan; Zhang, Xu; Liu, Cong; Joyce, Brian Thomas; Kibbe, Warren A; Hou, Lifang; Zhang, Wei

    2016-02-01

    Inter-individual variation in cytosine modifications has been linked to complex traits in humans. Cytosine modification variation is partially controlled by single nucleotide polymorphisms (SNPs), known as modified cytosine quantitative trait loci (mQTL). However, little is known about the role of short tandem repeat polymorphisms (STRPs), a class of structural genetic variants, in regulating cytosine modifications. Utilizing the published data on the International HapMap Project lymphoblastoid cell lines (LCLs), we assessed the relationships between 721 STRPs and the modification levels of 283,540 autosomal CpG sites. Our findings suggest that, in contrast to the predominant cis-acting mode for SNP-based mQTL, STRPs are associated with cytosine modification levels in both cis-acting (local) and trans-acting (distant) modes. In local scans within the ±1 Mb windows of target CpGs, 21, 9, and 21 cis-acting STRP-based mQTL were detected in CEU (Caucasian residents from Utah, USA), YRI (Yoruba people from Ibadan, Nigeria), and the combined samples, respectively. In contrast, 139,420, 76,817, and 121,866 trans-acting STRP-based mQTL were identified in CEU, YRI, and the combined samples, respectively. A substantial proportion of CpG sites detected with local STRP-based mQTL were not associated with SNP-based mQTL, suggesting that STRPs represent an independent class of mQTL. Functionally, genetic variants neighboring CpG-associated STRPs are enriched with genome-wide association study (GWAS) loci for a variety of complex traits and diseases, including cancers, based on the National Human Genome Research Institute (NHGRI) GWAS Catalog. Therefore, elucidating these STRP-based mQTL in addition to SNP-based mQTL can provide novel insights into the genetic architectures of complex traits.

  12. Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma

    NARCIS (Netherlands)

    Lamprecht, Bjoern; Walter, Korden; Kreher, Stephan; Kumar, Raman; Hummel, Michael; Lenze, Dido; Koechert, Karl; Bouhlel, Mohamed Amine; Richter, Julia; Soler, Eric; Stadhouders, Ralph; Joehrens, Korinna; Wurster, Kathrin D.; Callen, David F.; Harte, Michael F.; Giefing, Maciej; Barlow, Rachael; Stein, Harald; Anagnostopoulos, Ioannis; Janz, Martin; Cockerill, Peter N.; Siebert, Reiner; Doerken, Bernd; Bonifer, Constanze; Mathas, Stephan

    2010-01-01

    Mammalian genomes contain many repetitive elements, including long terminal repeats (LTRs), which have long been suspected to have a role in tumorigenesis. Here we present evidence that aberrant LTR activation contributes to lineage-inappropriate gene expression in transformed human cells and that s

  13. Network Intrusion Dataset Assessment

    Science.gov (United States)

    2013-03-01

    Science, pages 576–585. Springer Berlin / Heidelberg, June 2010. • Jing Xiao-Pei and Wang Hou -Xiang. “A new immunity intrusion detection model based on...2008. • Hongying Zheng, Meiju Hou , and Yu Wang. “An efficient hybrid clustering-PSO algorithm for anomaly intrusion detection.” Journal of Software...Technology, 2(6):1790– 1799, 2010. [34] Lee, Suchul, Hyunchul Kim, Dhiman Barman, Sungryoul Lee, Chong -kwon Kim, Ted Kwon, and Yanghee Choi. “NeTraMark: a

  14. Instability of human TATA-binding protein CAG triplet repeats during amplification by PCR.

    Science.gov (United States)

    Holstege, F C; van der Vliet, P C; Timmers, H T

    1994-09-13

    Polymerase chain reaction (PCR) of a TATA-binding protein cDNA that contains CAG triplet repeats results in heterogeneous products. This is caused by a variable loss in the number of CAG triplets. Sequence analysis of PCR products suggests that instability increases with repeat length.

  15. Repeated increases in blood flow, independent of exercise, enhance conduit artery vasodilator function in humans

    NARCIS (Netherlands)

    Naylor, L.H.; Carter, H.; Fitzsimons, M.G.; Cable, N.T.; Thijssen, D.H.J.; Green, D.J.

    2011-01-01

    This study aimed to determine the importance of repeated increases in blood flow to conduit artery adaptation, using an exercise-independent repeated episodic stimulus. Recent studies suggest that exercise training improves vasodilator function of conduit arteries via shear stress-mediated

  16. Specification Mining for Intrusion Detection in Networked Control Systems

    NARCIS (Netherlands)

    Caselli, Marco; Zambon, Emmanuele; Amann, Johanna; Sommer, Robin; Kargl, Frank

    2016-01-01

    This paper discusses a novel approach to specification-based intrusion detection in the field of networked control systems. Our approach reduces the substantial human effort required to deploy a specification-based intrusion detection system by automating the development of its specification rules.

  17. Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA

    Indian Academy of Sciences (India)

    Richard R Sinden; Vladimir N Potaman; Elena A Oussatcheva; Christopher E Pearson; Yuri L Lyubchenko; Luda S Shlyakhtenko

    2002-02-01

    Fourteen genetic neurodegenerative diseases and three fragile sites have been associated with the expansion of (CTG)n•(CAG)n, (CGG)n•(CCG)n, or (GAA)n•(TTC)n repeat tracts. Different models have been proposed for the expansion of triplet repeats, most of which presume the formation of alternative DNA structures in repeat tracts. One of the most likely structures, slipped strand DNA, may stably and reproducibly form within triplet repeat sequences. The propensity to form slipped strand DNA is proportional to the length and homogeneity of the repeat tract. The remarkable stability of slipped strand DNA may, in part, be due to loop-loop interactions facilitated by the sequence complementarity of the loops and the dynamic structure of three-way junctions formed at the loop-outs.

  18. Human pharmacology of 3,4-methylenedioxymethamphetamine (MDMA, ecstasy) after repeated doses taken 4 h apart Human pharmacology of MDMA after repeated doses taken 4 h apart.

    Science.gov (United States)

    Farré, Magí; Tomillero, Angels; Pérez-Mañá, Clara; Yubero, Samanta; Papaseit, Esther; Roset, Pere-Nolasc; Pujadas, Mitona; Torrens, Marta; Camí, Jordi; de la Torre, Rafael

    2015-10-01

    3,4-Methylenedioxymethamphetamine (MDMA, ecstasy) is a popular psychostimulant, frequently associated with multiple administrations over a short period of time. Repeated administration of MDMA in experimental settings induces tolerance and metabolic inhibition. The aim is to determine the acute pharmacological effects and pharmacokinetics resulting from two consecutive 100mg doses of MDMA separated by 4h. Ten male volunteers participated in a randomized, double-blind, crossover, placebo-controlled trial. The four conditions were placebo plus placebo, placebo plus MDMA, MDMA plus placebo, and MDMA plus MDMA. Outcome variables included pharmacological effects and pharmacokinetic parameters. After a second dose of MDMA, most effects were similar to those after a single dose, despite a doubling of MDMA concentrations (except for systolic blood pressure and reaction time). After repeated MDMA administration, a 2-fold increase was observed in MDMA plasma concentrations. For a simple dose accumulation MDMA and MDA concentrations were higher (+23.1% Cmax and +17.1% AUC for MDMA and +14.2% Cmax and +10.3% AUC for MDA) and HMMA and HMA concentrations lower (-43.3% Cmax and -39.9% AUC for HMMA and -33.2% Cmax and -35.1% AUC for HMA) than expected, probably related to MDMA metabolic autoinhibition. Although MDMA concentrations doubled after the second dose, most pharmacological effects were similar or slightly higher in comparison to the single administration, except for systolic blood pressure and reaction time which were greater than predicted. The pharmacokinetic-effects relationship suggests that when MDMA is administered at a 4h interval there exists a phenomenon of acute tolerance to its effects.

  19. Repeated short climatic change affects the epidermal differentiation program and leads to matrix remodeling in a human organotypic skin model

    Science.gov (United States)

    Boutrand, Laetitia-Barbollat; Thépot, Amélie; Muther, Charlotte; Boher, Aurélie; Robic, Julie; Guéré, Christelle; Vié, Katell; Damour, Odile; Lamartine, Jérôme

    2017-01-01

    Human skin is subject to frequent changes in ambient temperature and humidity and needs to cope with these environmental modifications. To decipher the molecular response of human skin to repeated climatic change, a versatile model of skin equivalent subject to “hot–wet” (40°C, 80% relative humidity [RH]) or “cold–dry” (10°C, 40% RH) climatic stress repeated daily was used. To obtain an exhaustive view of the molecular mechanisms elicited by climatic change, large-scale gene expression DNA microarray analysis was performed and modulated function was determined by bioinformatic annotation. This analysis revealed several functions, including epidermal differentiation and extracellular matrix, impacted by repeated variations in climatic conditions. Some of these molecular changes were confirmed by histological examination and protein expression. Both treatments (hot–wet and cold–dry) reduced the expression of genes encoding collagens, laminin, and proteoglycans, suggesting a profound remodeling of the extracellular matrix. Strong induction of the entire family of late cornified envelope genes after cold–dry exposure, confirmed at protein level, was also observed. These changes correlated with an increase in epidermal differentiation markers such as corneodesmosin and a thickening of the stratum corneum, indicating possible implementation of defense mechanisms against dehydration. This study for the first time reveals the complex pattern of molecular response allowing adaption of human skin to repeated change in its climatic environment.

  20. Integrity of the human centromere DNA repeats is protected by CENP-A, CENP-C, and CENP-T.

    Science.gov (United States)

    Giunta, Simona; Funabiki, Hironori

    2017-02-21

    Centromeres are highly specialized chromatin domains that enable chromosome segregation and orchestrate faithful cell division. Human centromeres are composed of tandem arrays of α-satellite DNA, which spans up to several megabases. Little is known about the mechanisms that maintain integrity of the long arrays of α-satellite DNA repeats. Here, we monitored centromeric repeat stability in human cells using chromosome-orientation fluorescent in situ hybridization (CO-FISH). This assay detected aberrant centromeric CO-FISH patterns consistent with sister chromatid exchange at the frequency of 5% in primary tissue culture cells, whereas higher levels were seen in several cancer cell lines and during replicative senescence. To understand the mechanism(s) that maintains centromere integrity, we examined the contribution of the centromere-specific histone variant CENP-A and members of the constitutive centromere-associated network (CCAN), CENP-C, CENP-T, and CENP-W. Depletion of CENP-A and CCAN proteins led to an increase in centromere aberrations, whereas enhancing chromosome missegregation by alternative methods did not, suggesting that CENP-A and CCAN proteins help maintain centromere integrity independently of their role in chromosome segregation. Furthermore, superresolution imaging of centromeric CO-FISH using structured illumination microscopy implied that CENP-A protects α-satellite repeats from extensive rearrangements. Our study points toward the presence of a centromere-specific mechanism that actively maintains α-satellite repeat integrity during human cell proliferation.

  1. Transcellular activation of the human immunodeficiency virus type 1 long terminal repeat in cocultured lymphocytes.

    Science.gov (United States)

    Marcuzzi, A; Weinberger, J; Weinberger, O K

    1992-01-01

    One of the unexplained aspects of the progression of AIDS is that immunological abnormalities are detectable before CD4+ T-helper cell depletion occurs (A.R. Gruters, F.G. Terpstra, R. De Jong, C.J.M. Van Noesel, R.A.W. Van Lier, and F. Miedema, Eur. J. Immunol. 20:1039-1044, 1990; F. Miedema, A.J. Chantal-Petit, F.G. Terpstra, J.K.M.E. Schattenkerk, F. de Wolf, B.J.M. Al, M. Roos, J.M.A. Lang, S.A. Danner, J. Goudsmit, and P.T.A. Schellekens, J. Clin. Invest. 82:1908-1914, 1988; G.M. Shearer, D.C. Bernstein, K.S. Tung, C.S. Via, R. Redfield, S.Z. Salahuddin, and R.C. Gallo, J. Immunol. 137:2514-2521, 1986). In this report, we describe a mechanism by which human immunodeficiency virus type 1 (HIV-1)-infected cells can influence neighboring HIV-1-infected T lymphocytes and uninfected T cells as well. We have examined the interaction of T-cell and macrophage cell lines that are transfected with HIV-1 DNA by using cocultured lymphocytes. The HIV-1 constructs we used lack a functional pol gene and therefore do not produce infectious virus. Cocultivation results in the transcellular activation of the HIV long terminal repeat in the cocultured T cells. This transcellular activation is evident in as little as 3 h of cocultivation, at ratios of HIV-expressing cells to target cells as low as 1:1,000, and is dependent on the Tat-responsive element. The demonstration that a small number of HIV-expressing cells can affect a large number of uninfected bystander cells in a short period of time suggests a mechanism by which global immune dysfunction can precede the high prevalence of infected cells. Images PMID:1602543

  2. Computational study of the human dystrophin repeats: interaction properties and molecular dynamics.

    Science.gov (United States)

    Legrand, Baptiste; Giudice, Emmanuel; Nicolas, Aurélie; Delalande, Olivier; Le Rumeur, Elisabeth

    2011-01-01

    Dystrophin is a large protein involved in the rare genetic disease Duchenne muscular dystrophy (DMD). It functions as a mechanical linker between the cytoskeleton and the sarcolemma, and is able to resist shear stresses during muscle activity. In all, 75% of the dystrophin molecule consists of a large central rod domain made up of 24 repeat units that share high structural homology with spectrin-like repeats. However, in the absence of any high-resolution structure of these repeats, the molecular basis of dystrophin central domain's functions has not yet been deciphered. In this context, we have performed a computational study of the whole dystrophin central rod domain based on the rational homology modeling of successive and overlapping tandem repeats and the analysis of their surface properties. Each tandem repeat has very specific surface properties that make it unique. However, the repeats share enough electrostatic-surface similarities to be grouped into four separate clusters. Molecular dynamics simulations of four representative tandem repeats reveal specific flexibility or bending properties depending on the repeat sequence. We thus suggest that the dystrophin central rod domain is constituted of seven biologically relevant sub-domains. Our results provide evidence for the role of the dystrophin central rod domain as a scaffold platform with a wide range of surface features and biophysical properties allowing it to interact with its various known partners such as proteins and membrane lipids. This new integrative view is strongly supported by the previous experimental works that investigated the isolated domains and the observed heterogeneity of the severity of dystrophin related pathologies, especially Becker muscular dystrophy.

  3. Computational study of the human dystrophin repeats: interaction properties and molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Baptiste Legrand

    Full Text Available Dystrophin is a large protein involved in the rare genetic disease Duchenne muscular dystrophy (DMD. It functions as a mechanical linker between the cytoskeleton and the sarcolemma, and is able to resist shear stresses during muscle activity. In all, 75% of the dystrophin molecule consists of a large central rod domain made up of 24 repeat units that share high structural homology with spectrin-like repeats. However, in the absence of any high-resolution structure of these repeats, the molecular basis of dystrophin central domain's functions has not yet been deciphered. In this context, we have performed a computational study of the whole dystrophin central rod domain based on the rational homology modeling of successive and overlapping tandem repeats and the analysis of their surface properties. Each tandem repeat has very specific surface properties that make it unique. However, the repeats share enough electrostatic-surface similarities to be grouped into four separate clusters. Molecular dynamics simulations of four representative tandem repeats reveal specific flexibility or bending properties depending on the repeat sequence. We thus suggest that the dystrophin central rod domain is constituted of seven biologically relevant sub-domains. Our results provide evidence for the role of the dystrophin central rod domain as a scaffold platform with a wide range of surface features and biophysical properties allowing it to interact with its various known partners such as proteins and membrane lipids. This new integrative view is strongly supported by the previous experimental works that investigated the isolated domains and the observed heterogeneity of the severity of dystrophin related pathologies, especially Becker muscular dystrophy.

  4. Repeat remote ischaemic pre-conditioning for improved cardiovascular function in humans: A systematic review

    Directory of Open Access Journals (Sweden)

    J. Epps

    2016-06-01

    Conclusion: Repeated RIPC exposure has produced evidence of improvements in endothelial dependent vasodilation, ulcer healing and blood pressure but no benefit in non-endothelial dependent vasodilation, cutaneous vascular conductance or cardiorespiratory fitness. The optimal delivery of RIPC remains unclear, but at least 3 or preferably 4, 5 min exposures appears to be most beneficial, at least for reducing blood pressure. Aside from those undertaking cardiac surgery, other study populations with endothelial dysfunction may benefit from repeat exposure to RIPC.

  5. The use of protective barriers to deter inadvertent human intrusion into a mined geologic facility for the disposal of radioactive waste: A review of previous investigations and potential concepts

    Energy Technology Data Exchange (ETDEWEB)

    Tolan, T.L. [Tolan, Beeson and Associates, Kennewick, WA (United States)

    1993-06-01

    Sandia National Laboratories is evaluating the feasibility of developing protective barrier system for the Waste Isolation Pilot Plant (WIPP) to thwart inadvertent human intrusion into this radioactive-waste disposal system for a period of 9,900 years after assumed loss of active institutional controls. The protective barrier system would be part of a series of enduring passive institutional controls whose long-term function will be to reduce the likelihood of inadvertent human activities (e.g., exploratory drilling for resources) that could disrupt the WIPP disposal system.

  6. The origin and evolution of variable number tandem repeat of CLEC4M gene in the global human population.

    Directory of Open Access Journals (Sweden)

    Hui Li

    Full Text Available CLEC4M is a C-type lectin gene serving as cell adhesion receptor and pathogen recognition receptor. It recognizes several pathogens of important public health concern. In particular, a highly polymorphic variable number tandem repeat (VNTR at the neck-region of CLEC4M had been associated with genetic predisposition to some infectious diseases. To gain insight into the origin and evolution of this VNTR in CLEC4M, we studied 21 Africans, 20 Middle Easterns, 35 Europeans, 38 Asians, 13 Oceania, and 18 Americans (a total of 290 chromosomes from the (Human Genome Diversity Panel HGDP-CEPH panel; these samples covered most of alleles of this VNTR locus present in human populations. We identified a limited number of haplotypes among the basic repeat subunits that is 69 base pairs in length. Only 8 haplotypes were found. Their sequence identities were determined in the 290 chromosomes. VNTR alleles of different repeat length (from 4 to 9 repeats were analyzed for composition and orientation of these subunits. Our results showed that the subunit configuration of the same repeat number of VNTR locus from different populations were, in fact, virtually identical. It implies that most of the VNTR alleles existed before dispersion of modern humans outside Africa. Further analyses indicate that the present diversity profile of this locus in worldwide populations is generated from the effect of migration of different tribes and neutral evolution. Our findings do not support the hypothesis that the origin of the VNTR alleles were arisen by independent (separate mutation events and caused by differential allele advantage and natural selection as suggested by previous report based on SNP data.

  7. Wireless Intrusion Prevention Systems

    Directory of Open Access Journals (Sweden)

    Jack TIMOFTE

    2008-01-01

    Full Text Available The wireless networks have changed the way organizations work and offered a new range of possibilities, but at the same time they introduced new security threats. While an attacker needs physical access to a wired network in order to launch an attack, a wireless network allows anyone within its range to passively monitor the traffic or even start an attack. One of the countermeasures can be the use of Wireless Intrusion Prevention Systems.

  8. Effect of repeated forearm muscle cooling on the adaptation of skeletal muscle metabolism in humans

    Science.gov (United States)

    Wakabayashi, Hitoshi; Nishimura, Takayuki; Wijayanto, Titis; Watanuki, Shigeki; Tochihara, Yutaka

    2017-01-01

    This study aimed to investigate the effect of repeated cooling of forearm muscle on adaptation in skeletal muscle metabolism. It is hypothesized that repeated decreases of muscle temperature would increase the oxygen consumption in hypothermic skeletal muscle. Sixteen healthy males participated in this study. Their right forearm muscles were locally cooled to 25 °C by cooling pads attached to the skin. This local cooling was repeated eight times on separate days for eight participants (experimental group), whereas eight controls received no cold exposure. To evaluate adaptation in skeletal muscle metabolism, a local cooling test was conducted before and after the repeated cooling period. Change in oxy-hemoglobin content in the flexor digitorum at rest and during a 25-s isometric handgrip (10% maximal voluntary construction) was measured using near-infrared spectroscopy at every 2 °C reduction in forearm muscle temperature. The arterial blood flow was occluded for 15 s by upper arm cuff inflation at rest and during the isometric handgrip. The oxygen consumption in the flexor digitorum muscle was evaluated by a slope of the oxy-hemoglobin change during the arterial occlusion. In the experimental group, resting oxygen consumption in skeletal muscle did not show any difference between pre- and post-intervention, whereas muscle oxygen consumption during the isometric handgrip was significantly higher in post-intervention than in pre-test from thermoneutral baseline to 31 °C muscle temperature (P < 0.05). This result indicated that repeated local muscle cooling might facilitate oxidative metabolism in the skeletal muscle. In summary, skeletal muscle metabolism during submaximal isometric handgrip was facilitated after repeated local muscle cooling.

  9. Repeated static contractions increase mitochondrial vulnerability toward oxidative stress in human skeletal muscle

    DEFF Research Database (Denmark)

    Sahlin, Kent; Nielsen, Jens Steen; Mogensen, Martin

    2006-01-01

    Repeated static contractions (RSC) induce large fluctuations in tissue oxygen tension and increase the generation of reactive oxygen species (ROS). This study investigated the effect of RSC on muscle contractility, mitochondrial respiratory function, and in vitro sarcoplasmic reticulum (SR) Ca(2+...

  10. Tandem repeats and G-rich sequences are enriched at human CNV breakpoints.

    Directory of Open Access Journals (Sweden)

    Promita Bose

    Full Text Available Chromosome breakage in germline and somatic genomes gives rise to copy number variation (CNV responsible for genomic disorders and tumorigenesis. DNA sequence is known to play an important role in breakage at chromosome fragile sites; however, the sequences susceptible to double-strand breaks (DSBs underlying CNV formation are largely unknown. Here we analyze 140 germline CNV breakpoints from 116 individuals to identify DNA sequences enriched at breakpoint loci compared to 2800 simulated control regions. We find that, overall, CNV breakpoints are enriched in tandem repeats and sequences predicted to form G-quadruplexes. G-rich repeats are overrepresented at terminal deletion breakpoints, which may be important for the addition of a new telomere. Interstitial deletions and duplication breakpoints are enriched in Alu repeats that in some cases mediate non-allelic homologous recombination (NAHR between the two sides of the rearrangement. CNV breakpoints are enriched in certain classes of repeats that may play a role in DNA secondary structure, DSB susceptibility and/or DNA replication errors.

  11. Effect of repeated forearm muscle cooling on the adaptation of skeletal muscle metabolism in humans

    Science.gov (United States)

    Wakabayashi, Hitoshi; Nishimura, Takayuki; Wijayanto, Titis; Watanuki, Shigeki; Tochihara, Yutaka

    2017-07-01

    This study aimed to investigate the effect of repeated cooling of forearm muscle on adaptation in skeletal muscle metabolism. It is hypothesized that repeated decreases of muscle temperature would increase the oxygen consumption in hypothermic skeletal muscle. Sixteen healthy males participated in this study. Their right forearm muscles were locally cooled to 25 °C by cooling pads attached to the skin. This local cooling was repeated eight times on separate days for eight participants (experimental group), whereas eight controls received no cold exposure. To evaluate adaptation in skeletal muscle metabolism, a local cooling test was conducted before and after the repeated cooling period. Change in oxy-hemoglobin content in the flexor digitorum at rest and during a 25-s isometric handgrip (10% maximal voluntary construction) was measured using near-infrared spectroscopy at every 2 °C reduction in forearm muscle temperature. The arterial blood flow was occluded for 15 s by upper arm cuff inflation at rest and during the isometric handgrip. The oxygen consumption in the flexor digitorum muscle was evaluated by a slope of the oxy-hemoglobin change during the arterial occlusion. In the experimental group, resting oxygen consumption in skeletal muscle did not show any difference between pre- and post-intervention, whereas muscle oxygen consumption during the isometric handgrip was significantly higher in post-intervention than in pre-test from thermoneutral baseline to 31 °C muscle temperature ( P muscle cooling might facilitate oxidative metabolism in the skeletal muscle. In summary, skeletal muscle metabolism during submaximal isometric handgrip was facilitated after repeated local muscle cooling.

  12. Short- and long-term effects of unpredictable repeated negative stimuli on Japanese quail's fear of humans.

    Directory of Open Access Journals (Sweden)

    Agathe Laurence

    Full Text Available Numerous aversive events occur in poultry production, and if repeated and unpredictable, can result in an impaired welfare. Some events such as handling can be perceived negatively and it is of interest to understand how humans' behaviour could affect poultry's behaviours and especially its avoidance of humans. Our aim was to evaluate short- and long-lasting effects of a 3-week procedure involving unpredictable repeated negative stimuli (URNS applied during the post-juvenile period on quail's reactivity to humans. We compared the reactions of two sets of quail: URNS was applied to one set (treated quail and the other set was left undisturbed (control quail. When two weeks old, treated quail were exposed to a variety of negative stimuli, either applied automatically or involving human presence. One and seven weeks after the termination of the procedure, the reactivity of control and treated quail to a passive human being was evaluated. Furthermore, the experimenter with her hand on a trough containing a mealworm assessed the propensity of quail of both groups to habituate to feed close to a human being. In the presence of a seated observer, treated quail were more inhibited and more alert than control quail. Likewise, seven weeks after the end of the URNS procedure, more treated than control quail adopted a fear posture. Moreover, whereas control quail spent as much time in the different areas of their cages, treated quail spent more time in the rear part of their cages. Finally, whereas control quail habituated gradually to feed near the experimenter's hand, treated quail did not. All these tests evidence negative short- and long-term effects on treated quail's reactivity to a passive human being and on their habituation to a human being when her presence is positively reinforced. This highlights the importance of young poultry's experience with humans in production.

  13. Short- and long-term effects of unpredictable repeated negative stimuli on Japanese quail's fear of humans.

    Science.gov (United States)

    Laurence, Agathe; Lumineau, Sophie; Calandreau, Ludovic; Arnould, Cécile; Leterrier, Christine; Boissy, Alain; Houdelier, Cécilia

    2014-01-01

    Numerous aversive events occur in poultry production, and if repeated and unpredictable, can result in an impaired welfare. Some events such as handling can be perceived negatively and it is of interest to understand how humans' behaviour could affect poultry's behaviours and especially its avoidance of humans. Our aim was to evaluate short- and long-lasting effects of a 3-week procedure involving unpredictable repeated negative stimuli (URNS) applied during the post-juvenile period on quail's reactivity to humans. We compared the reactions of two sets of quail: URNS was applied to one set (treated quail) and the other set was left undisturbed (control quail). When two weeks old, treated quail were exposed to a variety of negative stimuli, either applied automatically or involving human presence. One and seven weeks after the termination of the procedure, the reactivity of control and treated quail to a passive human being was evaluated. Furthermore, the experimenter with her hand on a trough containing a mealworm assessed the propensity of quail of both groups to habituate to feed close to a human being. In the presence of a seated observer, treated quail were more inhibited and more alert than control quail. Likewise, seven weeks after the end of the URNS procedure, more treated than control quail adopted a fear posture. Moreover, whereas control quail spent as much time in the different areas of their cages, treated quail spent more time in the rear part of their cages. Finally, whereas control quail habituated gradually to feed near the experimenter's hand, treated quail did not. All these tests evidence negative short- and long-term effects on treated quail's reactivity to a passive human being and on their habituation to a human being when her presence is positively reinforced. This highlights the importance of young poultry's experience with humans in production.

  14. Short- and Long-Term Effects of Unpredictable Repeated Negative Stimuli on Japanese Quail's Fear of Humans

    Science.gov (United States)

    Laurence, Agathe; Lumineau, Sophie; Calandreau, Ludovic; Arnould, Cécile; Leterrier, Christine; Boissy, Alain; Houdelier, Cécilia

    2014-01-01

    Numerous aversive events occur in poultry production, and if repeated and unpredictable, can result in an impaired welfare. Some events such as handling can be perceived negatively and it is of interest to understand how humans' behaviour could affect poultry's behaviours and especially its avoidance of humans. Our aim was to evaluate short- and long-lasting effects of a 3-week procedure involving unpredictable repeated negative stimuli (URNS) applied during the post-juvenile period on quail's reactivity to humans. We compared the reactions of two sets of quail: URNS was applied to one set (treated quail) and the other set was left undisturbed (control quail). When two weeks old, treated quail were exposed to a variety of negative stimuli, either applied automatically or involving human presence. One and seven weeks after the termination of the procedure, the reactivity of control and treated quail to a passive human being was evaluated. Furthermore, the experimenter with her hand on a trough containing a mealworm assessed the propensity of quail of both groups to habituate to feed close to a human being. In the presence of a seated observer, treated quail were more inhibited and more alert than control quail. Likewise, seven weeks after the end of the URNS procedure, more treated than control quail adopted a fear posture. Moreover, whereas control quail spent as much time in the different areas of their cages, treated quail spent more time in the rear part of their cages. Finally, whereas control quail habituated gradually to feed near the experimenter's hand, treated quail did not. All these tests evidence negative short- and long-term effects on treated quail's reactivity to a passive human being and on their habituation to a human being when her presence is positively reinforced. This highlights the importance of young poultry's experience with humans in production. PMID:24668017

  15. Isolation of human minisatellite loci detected by synthetic tandem repeat probes: direct comparison with cloned DNA fingerprinting probes.

    Science.gov (United States)

    Armour, J A; Vergnaud, G; Crosier, M; Jeffreys, A J

    1992-08-01

    As a direct comparison with cloned 'DNA fingerprinting' probes, we present the results of screening an ordered array Charomid library for hypervariable human loci using synthetic tandem repeat (STR) probes. By recording the coordinates of positive hybridization signals, the subset of clones within the library detected by each STR probe can be defined, and directly compared with the set of clones detected by naturally occurring (cloned) DNA fingerprinting probes. The STR probes vary in the efficiency of detection of polymorphic minisatellite loci; among the more efficient probes, there is a strong overlap with the sets of clones detected by the DNA fingerprinting probes. Four new polymorphic loci were detected by one or more of the STR probes but not by any of the naturally occurring repeats. Sequence comparisons with the probe(s) used to detect the locus suggest that a relatively poor match, for example 10 out of 14 bases in a limited region of each repeat, is sufficient for the positive detection of tandem repeats in a clone in this type of library screening by hybridization. These results not only provide a detailed evaluation of the usefulness of STR probes in the isolation of highly variable loci, but also suggest strategies for the use of these multi-locus probes in screening libraries for clones from hypervariable loci.

  16. Determination of microsatellite repeats in the human thyroid peroxidase (TPOX) gene using an automated gene analysis system with nanoscale engineered biomagnetite.

    Science.gov (United States)

    Nakagawa, Takahito; Maruyama, Kohei; Takeyama, Haruko; Matsunaga, Tadashi

    2007-04-15

    The number of repeat in the microsatellite region (AATG)(5-14) of the human thyroid peroxidase gene (TOPX) was determined using an automated DNA analysis system with nano-scale engineered biomagnetite. Thermal melting curve analysis of DNA duplexes on biomagnetite indicated that shorter repeat sequences (less than 9 repeats) were easily discriminated. However, it was difficult to determine the number of repeats at more than nine. In order to improve the selectivity of this method for the longer repeats, a "double probe hybridization assay" was performed in which an intermediate probe was used to replace a target repeat sequence having more than 9 repeats with a shorter sequence possessing less than 9 repeats. Thermal probe melting curve analyses and Tm determination confirmed that the target with 10 repeats was converted to 5 repeats, 11 repeats converted to 4 and 12 to 3, respectively. Furthermore, rapid determination of repeat numbers was possible by measuring fluorescence intensities obtained by probe dissociation at 56 and 66 degrees C, and 40, 60 and 80 degrees C for signal normalization.

  17. Visualization and quantitative analysis of extrachromosomal telomere-repeat DNA in individual human cells by Halo-FISH.

    Science.gov (United States)

    Komosa, Martin; Root, Heather; Meyn, M Stephen

    2015-02-27

    Current methods for characterizing extrachromosomal nuclear DNA in mammalian cells do not permit single-cell analysis, are often semi-quantitative and frequently biased toward the detection of circular species. To overcome these limitations, we developed Halo-FISH to visualize and quantitatively analyze extrachromosomal DNA in single cells. We demonstrate Halo-FISH by using it to analyze extrachromosomal telomere-repeat (ECTR) in human cells that use the Alternative Lengthening of Telomeres (ALT) pathway(s) to maintain telomere lengths. We find that GM847 and VA13 ALT cells average ∼80 detectable G/C-strand ECTR DNA molecules/nucleus, while U2OS ALT cells average ∼18 molecules/nucleus. In comparison, human primary and telomerase-positive cells contain 300), range widely in length (200 kb) and are composed of primarily G- or C-strand telomere-repeat DNA. Halo-FISH enables, for the first time, the simultaneous analysis of ECTR DNA and chromosomal telomeres in a single cell. We find that ECTR DNA comprises ∼15% of telomere-repeat DNA in GM847 and VA13 cells, but FISH can facilitate the study of a wide variety of extrachromosomal DNA in mammalian cells.

  18. Consolidation effect of repeated processing of declarative knowledge in mental experiences during human sleep.

    Science.gov (United States)

    Cipolli, Carlo; Fagioli, Igino; Mazzetti, Michela; Tuozzi, Giovanni

    2006-05-15

    Sleep may positively influence declarative memory through the processing, which transforms items of declarative knowledge into contents of mental sleep experience (MSE). A prediction from this general hypothesis is that the consolidation level should be higher for the output of items repeatedly processed and transformed into identical or very similar (so-called interrelated) contents of distinct MSEs of the same night rather than for the output of items presumably processed once (that is, all other, non-interrelated contents). Two experiments examined whether and how far the frequency and long-term retention of interrelated contents depend on the repeated processing of given items rather than on the experimental procedure applied for detection of interrelated contents. This procedure entails both multiple awakenings and a verbal report of MSE after awakening. Multiple awakenings could facilitate the re-access and elaboration of some contents into the subsequent (i.e. contiguous) MSE rather than non-contiguous MSEs; verbal reports could enhance the delayed recall of interrelated contents in as much as repeatedly encoded. The first experiment showed that interrelated contents were more frequent and better retained than both non-interrelated and pseudo-interrelated (i.e. by-chance similar or identical) contents, and even more in pairs of contiguous than non-contiguous MSEs collected from the first four periods of REM sleep on each experimental night. The second experiment showed that the frequency and retention rate of interrelated contents, while higher than those of non-interrelated and pseudo-interrelated contents, were not significantly different in pairs of MSEs which were verbally or mentally recalled after awakening provoked during the first four periods of REM sleep in each experimental night. Taken together, these findings indicate that the advantage provided by repeated processing during REM sleep for the consolidation of the output of items of declarative

  19. Influence of repeated daily menthol exposure on human temperature regulation and perception.

    Science.gov (United States)

    Gillis, D Jason; Weston, Neil; House, James R; Tipton, Michael J

    2015-02-01

    A single exposure to menthol can, depending on concentration, enhance both cool sensations and encourage body heat storage. This study tested whether there is an habituation in either response after repeated-daily exposures. Twenty-two participants were assigned to one of three spray groups: Control (CON; n=6), 0.05% L-menthol (M(0.05%); n=8), and 0.2% L-menthol (M(0.2%); n=8). On Monday (20°C, 50% rh) participants were sprayed with 100 mL of solution and undertook 40 min of cycling at 45% of their peak power (Ex1), from Tuesday to Thursday (30°C, 50% rh) they were sprayed twice daily whilst resting (R1 to R6), Friday was a repeat of Monday (Ex2). Thermal sensation (TS), thermal comfort, perceived exertion, irritation, rectal and skin temperature (Tsk), skin blood flow (SkBF) and sweat rate were monitored. A two-way ANOVA (alpha=0.05) compared responses from the beginning (Ex1, R1) and end (Ex2, R5) of the testing week. M(0.2%) induced significantly (PMenthol caused a heat storage response, mediated by vasoconstriction, at the beginning and end of the week, suggesting the habituation of TS occurred in a pathway specific to sensation. In summary, the cooling influence of 0.2% menthol habituates after repeated-daily exposures, but with no habituation in heat storage.

  20. [Mutation in microsatellite repeats of DNA and embryonal death in humans].

    Science.gov (United States)

    Nikitina, T V; Nazarenko, S A

    2000-07-01

    In the analysis of tetranucleotide DNA repeats inheritance carried out in 55 families with a history of spontaneous miscarriages and normal karyotypes in respect to 21 loci located on seven autosomes, 8 embryos (14.5%) demonstrating 12 cases of the presence of alleles absent in both parents were described. The study of chromosome segregation using other DNA markers permitted highly probable exclusion of false paternity as well as uniparental disomy as the reasons for parent/child allele mismatches. The high probability of paternity together with the presence of a "new" allele at any offspring locus points to the mutation having occurred during game-togenesis in one of the parents. Examination of mutation in spontaneous abortuses revealed an increased number of tandem repeat units at microsatellite loci in three cases and an decreased number of these repeats in six cases. In two abortuses, a third allele absent in both parents, which resulted from a somatic mutation that occurred during embryonic development, was observed. The prevalence of the male germline mutations, revealed during investigation of the mutation origin, was probably associated with an increased number of DNA replication cycles in sperm compared to the oocytes. In spontaneous abortuses, the mean mutation rate of the tetranucleotide repeat complexes analyzed was 9.8 x 10(-3) per locus per gamete per generation. This was about five times higher than the spontaneous mutation rate of these STR loci. It can be suggested that genome instability detected at the level of repeated DNA sequences can involve not only genetically neutral loci but also active genomic regions crucial for embryonic viability. This results in cell death and termination of embryonic development. Our findings indicate that the death of embryos with normal karyotypes in most cases is associated with an increased frequency of germline and somatic microsatellite mutations. The data of the present study also provide a practical tool for

  1. Structural and Biochemical Consequences of Disease-Causing Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Channel

    Energy Technology Data Exchange (ETDEWEB)

    Inada, Hitoshi; Procko, Erik; Sotomayor, Marcos; Gaudet, Rachelle (Harvard-Med); (Harvard)

    2012-10-23

    The TRPV4 calcium-permeable cation channel plays important physiological roles in osmosensation, mechanosensation, cell barrier formation, and bone homeostasis. Recent studies reported that mutations in TRPV4, including some in its ankyrin repeat domain (ARD), are associated with human inherited diseases, including neuropathies and skeletal dysplasias, probably because of the increased constitutive activity of the channel. TRPV4 activity is regulated by the binding of calmodulin and small molecules such as ATP to the ARD at its cytoplasmic N-terminus. We determined structures of ATP-free and -bound forms of human TRPV4-ARD and compared them with available TRPV-ARD structures. The third inter-repeat loop region (Finger 3 loop) is flexible and may act as a switch to regulate channel activity. Comparisons of TRPV-ARD structures also suggest an evolutionary link between ARD structure and ATP binding ability. Thermal stability analyses and molecular dynamics simulations suggest that ATP increases stability in TRPV-ARDs that can bind ATP. Biochemical analyses of a large panel of TRPV4-ARD mutations associated with human inherited diseases showed that some impaired thermal stability while others weakened ATP binding ability, suggesting molecular mechanisms for the diseases.

  2. Molecular cloning and long terminal repeat sequences of human endogenous retrovirus genes related to types A and B retrovirus genes

    Energy Technology Data Exchange (ETDEWEB)

    Ono, M.

    1986-06-01

    By using a DNA fragment primarily encoding the reverse transcriptase (pol) region of the Syrian hamster intracisternal A particle (IAP; type A retrovirus) gene as a probe, human endogenous retrovirus genes, tentatively termed HERV-K genes, were cloned from a fetal human liver gene library. Typical HERV-K genes were 9.1 or 9.4 kilobases in length, having long terminal repeats (LTRs) of ca. 970 base pairs. Many structural features commonly observed on the retrovirus LTRs, such as the TATAA box, polyadenylation signal, and terminal inverted repeats, were present on each LTR, and a lysine (K) tRNA having a CUU anticodon was identified as a presumed primer tRNA. The HERV-K LTR, however, had little sequence homology to either the IAP LTR or other typical oncovirus LTRs. By filter hybridization, the number of HERV-K genes was estimated to be ca. 50 copies per haploid human genome. The cloned mouse mammary tumor virus (type B) gene was found to hybridize with both the HERV-K and IAP genes to essentially the same extent.

  3. Crystal structures of the human G3BP1 NTF2-like domain visualize FxFG Nup Repeat Specificity

    DEFF Research Database (Denmark)

    Vognsen, Tina Reinholdt; Möller, Ingvar Rúnar; Kristensen, Ole

    2013-01-01

    Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both alone and in complex with an FxFG Nup repeat...... crystal form might indicate a novel ligand binding site that, however, remains to be validated. The crystal structures give insight into the nuclear transportation mechanisms of G3BP and provide a basis for future structure based drug design....

  4. Rapid isolation of antibody from a synthetic human antibody library by repeated fluorescence-activated cell sorting (FACS.

    Directory of Open Access Journals (Sweden)

    Sung Sun Yim

    Full Text Available Antibodies and their derivatives are the most important agents in therapeutics and diagnostics. Even after the significant progress in the technology for antibody screening from huge libraries, it takes a long time to isolate an antibody, which prevents a prompt action against the spread of a disease. Here, we report a new strategy for isolating desired antibodies from a combinatorial library in one day by repeated fluorescence-activated cell sorting (FACS. First, we constructed a library of synthetic human antibody in which single-chain variable fragment (scFv was expressed in the periplasm of Escherichia coli. After labeling the cells with fluorescent antigen probes, the highly fluorescent cells were sorted by using a high-speed cell sorter, and these cells were reused without regeneration in the next round of sorting. After repeating this sorting, the positive clones were completely enriched in several hours. Thus, we screened the library against three viral antigens, including the H1N1 influenza virus, Hepatitis B virus, and Foot-and-mouth disease virus. Finally, the potential antibody candidates, which show K(D values between 10 and 100 nM against the target antigens, could be successfully isolated even though the library was relatively small (∼ 10(6. These results show that repeated FACS screening without regeneration of the sorted cells can be a powerful method when a rapid response to a spreading disease is required.

  5. Repeat-element driven activation of proto-oncogenes in human malignancies.

    Science.gov (United States)

    Lamprecht, Björn; Bonifer, Constanze; Mathas, Stephan

    2010-11-01

    Recent data demonstrated that the aberrant activity of endogenous repetitive elements of the DNA in humans can drive the expression of proto-oncogenes. This article summarizes these results and gives an outlook on the impact of these findings on the pathogenesis and therapy of human cancer.

  6. Intrusive growth of sclerenchyma fibers

    NARCIS (Netherlands)

    Snegireva, A.V.; Ageeva, M.V.; Amenitskii, S.I.; Chernova, T.E.; Ebskamp, M.; Gorshkova, T.A.

    2010-01-01

    Intrusive growth is a type of cell elongation when the rate of its longitudinal growth is higher than that of surrounding cells; therefore, these cells intrude between the neighboring cells penetrating the middle lamella. The review considers the classical example of intrusive growth, e.g., elongati

  7. Solvents and vapor intrusion pathways.

    Science.gov (United States)

    Phillips, Scott D; Krieger, Gary R; Palmer, Robert B; Waksman, Javier C

    2004-08-01

    Vapor intrusion must be recognized appropriately as a separate pathway of contamination. Although many issues resemble those of other forms of contamination (particularly its entryway, which is similar to that of radon seepage), vapor intrusion stands apart as a unique risk requiring case-specific action. This article addresses these issues and the current understanding of the most appropriate and successful remedial actions.

  8. High throughput multiple locus variable number of tandem repeat analysis (MLVA) of Staphylococcus aureus from human, animal and food sources.

    Science.gov (United States)

    Sobral, Daniel; Schwarz, Stefan; Bergonier, Dominique; Brisabois, Anne; Feßler, Andrea T; Gilbert, Florence B; Kadlec, Kristina; Lebeau, Benoit; Loisy-Hamon, Fabienne; Treilles, Michaël; Pourcel, Christine; Vergnaud, Gilles

    2012-01-01

    Staphylococcus aureus is a major human pathogen, a relevant pathogen in veterinary medicine, and a major cause of food poisoning. Epidemiological investigation tools are needed to establish surveillance of S. aureus strains in humans, animals and food. In this study, we investigated 145 S. aureus isolates recovered from various animal species, disease conditions, food products and food poisoning events. Multiple Locus Variable Number of Tandem Repeat (VNTR) analysis (MLVA), known to be highly efficient for the genotyping of human S. aureus isolates, was used and shown to be equally well suited for the typing of animal S. aureus isolates. MLVA was improved by using sixteen VNTR loci amplified in two multiplex PCRs and analyzed by capillary electrophoresis ensuring a high throughput and high discriminatory power. The isolates were assigned to twelve known clonal complexes (CCs) and--a few singletons. Half of the test collection belonged to four CCs (CC9, CC97, CC133, CC398) previously described as mostly associated with animals. The remaining eight CCs (CC1, CC5, CC8, CC15, CC25, CC30, CC45, CC51), representing 46% of the animal isolates, are common in humans. Interestingly, isolates responsible for food poisoning show a CC distribution signature typical of human isolates and strikingly different from animal isolates, suggesting a predominantly human origin.

  9. High throughput multiple locus variable number of tandem repeat analysis (MLVA of Staphylococcus aureus from human, animal and food sources.

    Directory of Open Access Journals (Sweden)

    Daniel Sobral

    Full Text Available Staphylococcus aureus is a major human pathogen, a relevant pathogen in veterinary medicine, and a major cause of food poisoning. Epidemiological investigation tools are needed to establish surveillance of S. aureus strains in humans, animals and food. In this study, we investigated 145 S. aureus isolates recovered from various animal species, disease conditions, food products and food poisoning events. Multiple Locus Variable Number of Tandem Repeat (VNTR analysis (MLVA, known to be highly efficient for the genotyping of human S. aureus isolates, was used and shown to be equally well suited for the typing of animal S. aureus isolates. MLVA was improved by using sixteen VNTR loci amplified in two multiplex PCRs and analyzed by capillary electrophoresis ensuring a high throughput and high discriminatory power. The isolates were assigned to twelve known clonal complexes (CCs and--a few singletons. Half of the test collection belonged to four CCs (CC9, CC97, CC133, CC398 previously described as mostly associated with animals. The remaining eight CCs (CC1, CC5, CC8, CC15, CC25, CC30, CC45, CC51, representing 46% of the animal isolates, are common in humans. Interestingly, isolates responsible for food poisoning show a CC distribution signature typical of human isolates and strikingly different from animal isolates, suggesting a predominantly human origin.

  10. Repeated short climatic change affects the epidermal differentiation program and leads to matrix remodeling in a human organotypic skin model

    Directory of Open Access Journals (Sweden)

    Boutrand LB

    2017-02-01

    Full Text Available Laetitia-Barbollat Boutrand,1 Amélie Thépot,2 Charlotte Muther,3 Aurélie Boher,2 Julie Robic,4 Christelle Guéré,4 Katell Vié,4 Odile Damour,5 Jérôme Lamartine1,3 1Departement de Biologie, Université Claude Bernard Lyon I, 2LabSkinCreations, 3CNRS UMR5305, Laboratoire de Biologie Tissulaire et d’Ingénierie Thérapeutique (LBTI, Lyon, 4Laboratoires Clarins, Cergy-Pontoise, 5Banque de Tissus et Cellules, Hospices Civiles de Lyon, Lyon, France Abstract: Human skin is subject to frequent changes in ambient temperature and humidity and needs to cope with these environmental modifications. To decipher the molecular response of human skin to repeated climatic change, a versatile model of skin equivalent subject to “hot–wet” (40°C, 80% relative humidity [RH] or “cold–dry” (10°C, 40% RH climatic stress repeated daily was used. To obtain an exhaustive view of the molecular mechanisms elicited by climatic change, large-scale gene expression DNA microarray analysis was performed and modulated function was determined by bioinformatic annotation. This analysis revealed several functions, including epidermal differentiation and extracellular matrix, impacted by repeated variations in climatic conditions. Some of these molecular changes were confirmed by histological examination and protein expression. Both treatments (hot–wet and cold–dry reduced the expression of genes encoding collagens, laminin, and proteoglycans, suggesting a profound remodeling of the extracellular matrix. Strong induction of the entire family of late cornified envelope genes after cold–dry exposure, confirmed at protein level, was also observed. These changes correlated with an increase in epidermal differentiation markers such as corneodesmosin and a thickening of the stratum corneum, indicating possible implementation of defense mechanisms against dehydration. This study for the first time reveals the complex pattern of molecular response allowing

  11. DRPLA transgenic mouse substrains carrying single copy of full-length mutant human DRPLA gene with variable sizes of expanded CAG repeats exhibit CAG repeat length- and age-dependent changes in behavioral abnormalities and gene expression profiles.

    Science.gov (United States)

    Suzuki, Kazushi; Zhou, Jiayi; Sato, Toshiya; Takao, Keizo; Miyagawa, Tsuyoshi; Oyake, Mutsuo; Yamada, Mitunori; Takahashi, Hitoshi; Takahashi, Yuji; Goto, Jun; Tsuji, Shoji

    2012-05-01

    Dentatorubral-pallidoluysian atrophy (DRPLA) is an autosomal dominant progressive neurodegenerative disorder with intellectual deterioration and various motor deficits including ataxia, choreoathetosis, and myoclonus, caused by an abnormal expansion of CAG repeats in the DRPLA gene. Longer expanded CAG repeats contribute to an earlier age of onset, faster progression, and more severe neurological symptoms in DRPLA patients. In this study, we have established DRPLA transgenic mouse lines (sublines) harboring a single copy of the full-length mutant human DRPLA gene carrying various lengths of expanded CAG repeats (Q76, Q96, Q113, and Q129), which have clearly shown motor deficits and memory disturbance whose severity increases with the length of expanded CAG repeats and age, and successfully replicated the CAG repeat length- and age-dependent features of DRPLA patients. Neuronal intranuclear accumulation of the mutant DRPLA protein has been suggested to cause transcriptional dysregulation, leading to alteration in gene expression and neuronal dysfunction. In this study, we have conducted a comprehensive analysis of gene expression profiles in the cerebrum and cerebellum of transgenic mouse lines at 4, 8, and 12 weeks using multiple microarray platforms, and demonstrated that both the number and expression levels of the altered genes are highly dependent on CAG repeat length and age in both brain regions. Specific groups of genes and their function categories were identified by further agglomerative cluster analysis and gene functional annotation analysis. Calcium signaling and neuropeptide signaling, among others, were implicated in the pathophysiology of DRPLA. Our study provides unprecedented CAG-repeat-length-dependent mouse models of DRPLA, which are highly valuable not only for elucidating the CAG-repeat-length-dependent pathophysiology of DRPLA but also for developing therapeutic strategies for DRPLA.

  12. Mitochondrial tolerance to single and repeat exposure to simulated sunlight in human epidermal and dermal skin cells.

    Science.gov (United States)

    Kelly, J; Murphy, J E J

    2016-12-01

    Sunlight represents the primary threat to mitochondrial integrity in skin given the unique nature of the mitochondrial genome and its proximity to the electron transport chain. The accumulation of mitochondrial DNA (mtDNA) mutations is a key factor in many human pathologies and this is linked to key roles of mitochondrial function in terms of energy production and cell regulation. The main objective of this study was to evaluate solar radiation induced changes in mitochondrial integrity, function and dynamics in human skin cells using a Q-Sun solar simulator to deliver a close match to the intensity of summer sunlight. Spontaneously immortalised human skin epidermal keratinocytes (HaCaT) and Human Dermal Fibroblasts (HDFn) were divided into two groups. Group A were irradiated once and Group B twice 7days apart and evaluated using cell survival, viability and mitochondrial membrane potential (MMP) and mass at 1, 4 and 7days post one exposure for Group A and 1, 4, 7 and 14days post second exposure for Group B. Viability and survival of HaCaT and HDFn cells decreased after repeat exposure to Simulated Sunlight Irradiation (SSI) with no recovery. HDFn cells showed no loss in MMP after one or two exposures to SSI compared to HaCaT cells which showed a periodic loss of MMP after one exposure with a repeat exposure causing a dramatic decrease from which cells did not recover. Mitochondrial Mass in exposed HDFn cells was consistent with control after one or two exposures to SSI; however mitochondrial mass was significantly decreased in HaCaT cells. Data presented here suggests that mitochondria in epidermal cells are more sensitive to sunlight damage compared to mitochondria in dermal cells, despite their origin, confirming a skin layer specific sensitivity to sunlight, but not as expected. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Exons I and VII of the gene (Ker10) encoding human keratin 10 undergo structural rearrangements within repeats.

    Science.gov (United States)

    Tkachenko, A V; Buchman, V L; Bliskovsky, V V; Shvets YuP; Kisselev, L L

    1992-07-15

    A genomic fragment containing the K51 gene previously isolated from a rat genomic library by hybridization with the v-mos probe in nonstringent conditions [Chumakov et al., Dokl. Akad. Nauk SSSR 290 (1986) 1252-1254], resembles a human keratin type-I-encoding gene [Shvets et al., Mol. Biol. 24 (1990) 663-677]. This genomic clone, K51, has been used as a probe to search for related human genes. A recombinant clone, HK51, with a 1.5-kb insert, was isolated from a human embryonic skin cDNA library, and its nucleotide (nt) sequence was determined. Analysis has shown that the cloned cDNA encodes human keratin 10 (Ker10). All presently known nt sequences of the human Ker10-encoding gene (Ker10) are not identical. Differences are concentrated in the 5'-end of the first exon and in the middle of the seventh exon within repeats. In spite of structural rearrangements in two of eight exons, the reading frame and position of the stop codon are preserved. The genetic rearrangements cause changes in hydrophobicity profiles of the N and C termini of Ker10. It was also noticed that insertion of one nt leads to the formation of an unusual 3'-end of the transcript.

  14. Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses.

    Science.gov (United States)

    Pride, David T; Salzman, Julia; Relman, David A

    2012-09-01

    Explorations of human microbiota have provided substantial insight into microbial community composition; however, little is known about interactions between various microbial components in human ecosystems. In response to the powerful impact of viral predation, bacteria have acquired potent defences, including an adaptive immune response based on the clustered regularly interspaced short palindromic repeats (CRISPRs)/Cas system. To improve our understanding of the interactions between bacteria and their viruses in humans, we analysed 13 977 streptococcal CRISPR sequences and compared them with 2 588 172 virome reads in the saliva of four human subjects over 17 months. We found a diverse array of viruses and CRISPR spacers, many of which were specific to each subject and time point. There were numerous viral sequences matching CRISPR spacers; these matches were highly specific for salivary viruses. We determined that spacers and viruses coexist at the same time, which suggests that streptococcal CRISPR/Cas systems are under constant pressure from salivary viruses. CRISPRs in some subjects were just as likely to match viral sequences from other subjects as they were to match viruses from the same subject. Because interactions between bacteria and viruses help to determine the structure of bacterial communities, CRISPR-virus analyses are likely to provide insight into the forces shaping the human microbiome.

  15. Molecular characterization of long terminal repeat sequences from Brazilian human immunodeficiency virus type 1 isolates.

    Science.gov (United States)

    Ferraro, Geraldo A; Monteiro-Cunha, Joana P; Fernandes, Flora M C; Mota-Miranda, Aline C A; Brites, Carlos; Alcantara, Luiz C J; Galvão-Castro, Bernardo; Morgado, Mariza G

    2013-05-01

    HIV-1 provirus activation is under control of the long terminal repeat (LTR)-5' viral promoter region, which presents remarkable genetic variation among HIV-1 subtypes. It is possible that molecular features of the LTR contribute to the unusual profile of the subtype C epidemic in the Brazilian Southern region. To characterize the LTR of Brazilian HIV isolates, we analyzed sequences from 21 infected individuals from Porto Alegre and Salvador cities. Sequences were compared with subtype B and C reference strains from different countries. Phylogenetic analysis showed that 17 (81%) samples were subtype B and four (19%) were subtype C. Common patterns of transcription factor binding sites (TFBS) in subtypes B and C sequences were confirmed and other potential TFBS specific for subtype C were found. Brazilian subtype C sequences contained an additional NF-κB biding site, as previously described for the majority of subtype C isolates. The high level of LTR polymorphisms identified in this study might be important for viral fitness.

  16. Gene expression in human skeletal muscle: alternative normalization method and effect of repeated biopsies

    DEFF Research Database (Denmark)

    Lundby, Carsten; Nordsborg, Nikolai; Kusuhara, K.

    2005-01-01

    The reverse transcriptase-polymerase chain reaction (RT-PCR) method has lately become widely used to determine transcription and mRNA content in rodent and human muscle samples. However, the common use of endogenous controls for correcting for variance in cDNA between samples is not optimal. Spec...

  17. Urinary excretion of phthalates and paraben after repeated whole-body topical application in humans

    DEFF Research Database (Denmark)

    Janjua, Nadeem Rezaq; Frederiksen, Hanne; Skakkebaek, Niels E

    2008-01-01

    Diethyl phthalate (DEP), dibutyl phthalate (DBP) and butyl paraben (BP) are man-made chemicals used in personal care products, such as lotions and creams. Exposure to these chemicals causes a variety of adverse reproductive outcomes in animal studies. Humans can be exposed to these chemicals...

  18. Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

    Science.gov (United States)

    Waye, J S; Willard, H F

    1986-09-01

    The centromeric regions of all human chromosomes are characterized by distinct subsets of a diverse tandemly repeated DNA family, alpha satellite. On human chromosome 17, the predominant form of alpha satellite is a 2.7-kilobase-pair higher-order repeat unit consisting of 16 alphoid monomers. We present the complete nucleotide sequence of the 16-monomer repeat, which is present in 500 to 1,000 copies per chromosome 17, as well as that of a less abundant 15-monomer repeat, also from chromosome 17. These repeat units were approximately 98% identical in sequence, differing by the exclusion of precisely 1 monomer from the 15-monomer repeat. Homologous unequal crossing-over is suggested as a probable mechanism by which the different repeat lengths on chromosome 17 were generated, and the putative site of such a recombination event is identified. The monomer organization of the chromosome 17 higher-order repeat unit is based, in part, on tandemly repeated pentamers. A similar pentameric suborganization has been previously demonstrated for alpha satellite of the human X chromosome. Despite the organizational similarities, substantial sequence divergence distinguishes these subsets. Hybridization experiments indicate that the chromosome 17 and X subsets are more similar to each other than to the subsets found on several other human chromosomes. We suggest that the chromosome 17 and X alpha satellite subsets may be related components of a larger alphoid subfamily which have evolved from a common ancestral repeat into the contemporary chromosome-specific subsets.

  19. Using Jquery with Snort to Visualize Intrusion

    Directory of Open Access Journals (Sweden)

    Alaa El - Din Riad

    2012-01-01

    Full Text Available The explosive growth of malicious activities on worldwide communication networks, such as the Internet, has highlighted the need for efficient intrusion detection systems. The efficiency of traditional intrusion detection systems is limited by their inability to effectively relay relevant information due to their lack of interactive / immersive technologies. Visualized information is a technique that can encode large amounts of complex interrelated data, being at the same time easily quantified, manipulated, and processed by a human user. Authors have found that the representations can be quite effective at conveying the needed information and resolving the relationships extremely rapidly. To facilitate the creation of novel visualizations this paper presents a new framework that is designed with using data visualization technique by using Jquery Php for analysis and visualizes snort result data for user.

  20. Serological analysis of human anti-human antibody responses in colon cancer patients treated with repeated doses of humanized monoclonal antibody A33.

    Science.gov (United States)

    Ritter, G; Cohen, L S; Williams, C; Richards, E C; Old, L J; Welt, S

    2001-09-15

    Mouse monoclonal antibody A33 (mAb A33) recognizes a M(r) 43,000 cell surface glycoprotein (designated A33) expressed in human colonic epithelium and colon cancer but absent from most other normal tissues. In patients, mAb A33 localizes with high specificity to colon cancer and is retained for up to 6 weeks in the cancer but cleared rapidly from normal colon (5-6 days). As a carrier of (125)I or (131)I, mAb A33 has shown antitumor activity. Induction of strong human anti-mouse antibody (immunoglobulin; HAMA) responses in patients, however, limits the use of the murine mAb A33 to very few injections. A humanized version of this antibody (huAb A33) has been prepared for Phase I and II clinical studies in patients with colon cancer. In those studies, immunogenicity of huAb A33 has been monitored using a novel, highly sensitive BIACORE method, which allows measurement of human anti-human antibodies (HAHAs) without the use of secondary reagents. We found that 63% (26 of 41) of the patients treated with repeated doses of huAb A33 developed HAHAs against a conformational antigenic determinant located in the V(L) and V(H) regions of huAb A33. Detailed serological analysis showed two distinct types of HAHAs. HAHA of type I (49% of patients) was characterized by an early onset with peak HAHA levels after 2 weeks of treatment, which declined with ongoing huAb A33 treatment. HAHA of type II (17% of patients) was characterized by a typically later onset of HAHA than in type I and by progressively increasing HAHA levels with each subsequent huAb A33 administration. Colon cancer patients with type I HAHAs did not develop infusion-related adverse events. In contrast, HAHA of type II was indicative of infusion-related adverse events. By using this new method, we were able to distinguish these two types of HAHAs in patients while on antibody treatment, allowing patients to be removed from study prior to the onset of severe infusion-related adverse events.

  1. Multiple-locus variable-number tandem-repeat analysis (MLVA) genotyping of human Brucella isolates in Malaysia.

    Science.gov (United States)

    Tay, Bee Yong; Ahmad, Norazah; Hashim, Rohaidah; Mohamed Zahidi, Jama'ayah; Thong, Kwai Lin; Koh, Xiu Pei; Mohd Noor, Azura

    2015-06-02

    Brucellosis is one of the most common zoonotic diseases worldwide. It can cause acute febrile illness in human and is a major health problem. Studies in human brucellosis in Malaysia is limited and so far no genotyping studies has been done on Brucella isolates. The aim of the study was to determine the genetic diversity among Brucella species isolated from human brucellosis, obtained over a 6-year period (2009-2014). In this study, the genotypic characteristics of 43 human Brucella melitensis isolates were analysed using multiple-locus variable-number tandem-repeat analysis (MLVA) which consisted of eight minisatellite loci (panel 1) and eight microsatellite loci; panels 2A (3 microsatellite loci) and panel 2B (5 microsatellite loci). Two human Brucella suis isolates were also investigated using the MLVA assay. Using panel 1 (MLVA8), two genotypes namely genotype 43 and 44 were obtained from the 43 B. melitensis isolates. Using the combination of panels 1 and 2A loci (MLVA11), two genotypes were obtained while using the complete panels 1, 2A and 2B, nine genotypes were obtained. The polymorphisms in using the complete panels (MLVA16) were observed in three loci from panel 2B, which showed a diversity index higher than 0.17. All B. melitensis isolates were closely related to the East Mediterranean group. For B. suis isolates, only genotype 6 and genotype 33 were obtained using panel 1 and MLVA11 respectively. In conclusion, the results of the present study showed a low genetic diversity among B. melitensis and B. suis isolates from human patients. Based on the MLVA16 assay, B. melitensis belonging to the East Mediterranean group is responsible for the vast majority of Brucella infections in our Malaysian patients. To our knowledge, this is the first genotyping study of human Brucella isolates in Malaysia.

  2. Granitoid intrusions and related deposits

    Institute of Scientific and Technical Information of China (English)

    孟良义; 李绪俊

    1996-01-01

    Taking the Bainaimiao copper and gold deposits, Inner Mongolia and the Wushan copper deposits, Jiangxi Province as examples, a discussion is devoted to the relationship between the granitoid intrusions and related deposits from different lines of evidence: the spatial distribution, country rocks and alteration of the deposits, trace element contents and vertical zoning of elements in deposits, the metallogenic preference of granitoid intrusions, the metallogenic models and stable isotopic geology. It is concluded that the ore-bearing fluids mainly come from granitoid magmas and granitoid intrusions are closely associated with the related deposits in space.

  3. Novel Model for Intrusion Detection

    Institute of Scientific and Technical Information of China (English)

    Li Jia-chun; Li Zhi-tang

    2003-01-01

    It's very difficult that the traditional intrusion detection methods based on accurate match adapt to the blur and uncertainty of user information and expert knowledge, it results in failing to report the variations of attack signature. In addition security itself includes fuzziness, the judgment standard of confidentiality, integrity and availability of system resource is uncertain. In this paper fuzzy intrusion detection based on partial match is presented to detect some types of attacks availably and alleviate some of the difficulties of above approaches, the architecture of fuzzy intrusion detection system(FIDS) is introduced and its performance is analyzed.

  4. Novel Model for Intrusion Detection

    Institute of Scientific and Technical Information of China (English)

    Li; Jia-chun; Li; Zhi-tang

    2003-01-01

    It's very difficult that the traditional intrusion detection methods based on accurate match adapt to the blur and uncertainty of user information and expert knowledge, it results in failing to report the variation of attack signature.In addition security itself includes fuzziness, the judgment standard of confidentiality, integrity and availability of system resource is uncertain. In this paper fuzzy intrusion detection based on partial match is presented to detect some types of attacks availably and alleviate some of the difficulties of above approaches, the architecture of fuzzy intrusion detection system(FIDS) is introduced and its performance is analyzed.

  5. A novel function of RNAs arising from the long terminal repeat of human endogenous retrovirus 9 in cell cycle arrest.

    Science.gov (United States)

    Xu, Lai; Elkahloun, Abdel G; Candotti, Fabio; Grajkowski, Andrzej; Beaucage, Serge L; Petricoin, Emanuel F; Calvert, Valerie; Juhl, Hartmut; Mills, Frederick; Mason, Karen; Shastri, Neal; Chik, Josh; Xu, Cynthia; Rosenberg, Amy S

    2013-01-01

    The human genome contains approximately 50 copies of the replication-defective human endogenous retrovirus 9 (ERV-9) and thousands of copies of its solitary long term repeat (sLTR) element. While some sLTRs are located upstream of critical genes and have enhancer activity, other sLTRs are located within introns and may be transcribed as RNAs. We found that intronic RNAs arising from U3 sLTRs of ERV-9 were expressed as both sense (S) and antisense (AS) transcripts in all human cells tested but that expression levels differed in malignant versus nonmalignant cells. In nonmalignant cells, AS was expressed at higher levels than S and at higher levels than in malignant cells; in malignant cells, AS was expressed at amounts equivalent to those of S RNA. Critically, U3 AS RNA was found to physically bind to key transcription factors for cellular proliferation, including NF-Y, p53, and sp1, indicating that such RNA transcripts may function as decoy targets or traps for NF-Y and thus inhibit the growth of human cancer cells. Indeed, short U3 oligodeoxynucleotides (ODNs) based on these RNA sequences ably inhibited proliferation of cancer cell lines driven by cyclins B1/B2, the gene targets of NF-Y.

  6. In vitro kinetics of amiodarone and its major metabolite in two human liver cell models after acute and repeated treatments.

    Science.gov (United States)

    Pomponio, Giuliana; Savary, Camille C; Parmentier, Céline; Bois, Frederic; Guillouzo, André; Romanelli, Luca; Richert, Lysiane; Di Consiglio, Emma; Testai, Emanuela

    2015-12-25

    The limited value of in vitro toxicity data for the in vivo extrapolation has been often attributed to the lack of kinetic data. Here the in vitro kinetics of amiodarone (AMI) and its mono-N-desethyl (MDEA) metabolite was determined and modelled in primary human hepatocytes (PHH) and HepaRG cells, after single and repeated administration of clinically relevant concentrations. AMI bioavailability was influenced by adsorption to the plastic and the presence of protein in the medium (e.g. 10% serum protein reduced the uptake by half in HepaRG cells). The cell uptake was quick (within 3h), AMI metabolism was efficient and a dynamic equilibrium was reached in about a week after multiple dosing. In HepaRG cells the metabolic clearance was higher than in PHH and increased over time, as well as CYP3A4. The interindividual variability in MDEA production in PHHs was not proportional to the differences in CYP3A4 activities, suggesting the involvement of other CYPs and/or AMI-related CYP inhibition. After repeated treatment AMI showed a slight potential for bioaccumulation, whereas much higher intracellular MDEA levels accumulated over time, especially in the HepaRG cells, associated with occurrence of phospholipidosis. The knowledge of in vitro biokinetics is important to transform an actual in vitro concentration-effect into an in vivo dose-effect relationship by using appropriate modelling, thus improving the in vitro-to-in vivo extrapolation.

  7. Human tandem-repeat-type galectins bind bacterial non-βGal polysaccharides

    DEFF Research Database (Denmark)

    Knirel, Yu A.; Gabius, H.-J.; Blixt, Klas Ola;

    2014-01-01

    ), prompted us to establish an array with bacterial polysaccharides. We addressed the question whether sugar determinants other than β-galactosides may be docking sites, using human galectins-4, -8, and -9. Positive controls with histo-blood group ABH-epitopes and the E. coli 086 polysaccharide ascertained...... the suitability of the set-up. Significant signal generation, depending on type of galectin and polysacchride, was obtained. Presence of cognate β-galactoside-related epitopes within a polysaccharide chain or its branch will not automatically establish binding properties, and structural constellations lacking...

  8. Repeated Structural Imaging Reveals Nonlinear Progression of Experience-Dependent Volume Changes in Human Motor Cortex.

    Science.gov (United States)

    Wenger, Elisabeth; Kühn, Simone; Verrel, Julius; Mårtensson, Johan; Bodammer, Nils Christian; Lindenberger, Ulman; Lövdén, Martin

    2017-05-01

    Evidence for experience-dependent structural brain change in adult humans is accumulating. However, its time course is not well understood, as intervention studies typically consist of only 2 imaging sessions (before vs. after training). We acquired up to 18 structural magnetic resonance images over a 7-week period while 15 right-handed participants practiced left-hand writing and drawing. After 4 weeks, we observed increases in gray matter of both left and right primary motor cortices relative to a control group; 3 weeks later, these differences were no longer reliable. Time-series analyses revealed that gray matter in the primary motor cortices expanded during the first 4 weeks and then partially renormalized, in particular in the right hemisphere, despite continued practice and increasing task proficiency. Similar patterns of expansion followed by partial renormalization are also found in synaptogenesis, cortical map plasticity, and maturation, and may qualify as a general principle of structural plasticity. Research on human brain plasticity needs to encompass more than 2 measurement occasions to capture expansion and potential renormalization processes over time. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. Multiple-locus variable-number tandem-repeat analysis genotyping of human Brucella isolates from Turkey.

    Science.gov (United States)

    Kiliç, Selçuk; Ivanov, Ivan N; Durmaz, Riza; Bayraktar, Mehmet Refik; Ayaslioglu, Ergin; Uyanik, M Hamidullah; Aliskan, Hikmet; Yasar, Ekrem; Bayramoglu, Gülçin; Arslantürk, Ahmet; Vergnaud, Gilles; Kantardjiev, Todor V

    2011-09-01

    A multiple-locus variable-number tandem-repeat analysis (MLVA) was applied to investigate the epidemiological relationship and genetic diversity among 162 human Brucella isolates collected from all geographic regions of Turkey in an 8-year period (2001 to 2008). The isolates were genotyped by using an MLVA assay developed in Orsay, France (MLVA-16(Orsay)) including eight minisatellite (panel 1) and eight microsatellite (panel 2, subdivided into 2A and 2B) markers. Panels 1 and 2A distinguish 14 genotypes; two of these represented 85% of the strains. Panel 2B displayed a very high discriminatory power. Three loci from panel 2B had diversity index values higher than 0.74. MLVA-16(Orsay) yielded 105 genotypes; 73 were represented by a unique isolate, and 32 included two to eight isolates. The isolates from different patients within the same outbreak or from the same patient before first-line therapy and after relapse showed identical genotypes. A number of MLVA genotypes appeared to be partially restricted to some geographic areas and displayed no annual variation, possibly reflecting persistence of genotypes in certain areas for a time span of at least a decade. This study, representing the first molecular typing results of human Brucella isolates from Turkey, indicated that Turkish human Brucella melitensis isolates were most closely related to the neighboring countries' isolates included in the East Mediterranean group.

  10. Multiple-Locus Variable-Number Tandem-Repeat Analysis Genotyping of Human Brucella Isolates from Turkey▿†

    Science.gov (United States)

    Kılıç, Selçuk; Ivanov, Ivan N.; Durmaz, Rıza; Bayraktar, Mehmet Refik; Ayaşlıoğlu, Ergin; Uyanık, M. Hamidullah; Alışkan, Hikmet; Yaşar, Ekrem; Bayramoğlu, Gülçin; Arslantürk, Ahmet; Vergnaud, Gilles; Kantardjiev, Todor V.

    2011-01-01

    A multiple-locus variable-number tandem-repeat analysis (MLVA) was applied to investigate the epidemiological relationship and genetic diversity among 162 human Brucella isolates collected from all geographic regions of Turkey in an 8-year period (2001 to 2008). The isolates were genotyped by using an MLVA assay developed in Orsay, France (MLVA-16Orsay) including eight minisatellite (panel 1) and eight microsatellite (panel 2, subdivided into 2A and 2B) markers. Panels 1 and 2A distinguish 14 genotypes; two of these represented 85% of the strains. Panel 2B displayed a very high discriminatory power. Three loci from panel 2B had diversity index values higher than 0.74. MLVA-16Orsay yielded 105 genotypes; 73 were represented by a unique isolate, and 32 included two to eight isolates. The isolates from different patients within the same outbreak or from the same patient before first-line therapy and after relapse showed identical genotypes. A number of MLVA genotypes appeared to be partially restricted to some geographic areas and displayed no annual variation, possibly reflecting persistence of genotypes in certain areas for a time span of at least a decade. This study, representing the first molecular typing results of human Brucella isolates from Turkey, indicated that Turkish human Brucella melitensis isolates were most closely related to the neighboring countries' isolates included in the East Mediterranean group. PMID:21795514

  11. Evolution of human alpha 1-acid glycoprotein genes and surrounding Alu repeats.

    Science.gov (United States)

    Merritt, C M; Easteal, S; Board, P G

    1990-04-01

    There is a mosaic pattern of variation between the two tandemly arranged human alpha 1-acid glycoprotein genes. Both the synonymous and the nonsynonymous sites of exons 3 and 4 are more divergent than the rest of the gene, suggesting that they have had a different evolutionary history. Comparisons of the two gene sequences with rat AGP indicate that exons 3 and 4 of AGP2 have been evolving without functional constraint since their divergence from AGP1. It is proposed that the conserved region of the gene has been homogenized recently by gene conversion with the homologous regions of AGP1. The Alu sequences surrounding the genes appear to have been involved in both the gene duplication and the gene conversion events.

  12. Repeatability of corticospinal and spinal measures during lengthening and shortening contractions in the human tibialis anterior muscle.

    Directory of Open Access Journals (Sweden)

    Jamie Tallent

    Full Text Available UNLABELLED: Elements of the human central nervous system (CNS constantly oscillate. In addition, there are also methodological factors and changes in muscle mechanics during dynamic muscle contractions that threaten the stability and consistency of transcranial magnetic stimulation (TMS and perpherial nerve stimulation (PNS measures. PURPOSE: To determine the repeatability of TMS and PNS measures during lengthening and shortening muscle actions in the intact human tibialis anterior. METHODS: On three consecutive days, 20 males performed lengthening and shortening muscle actions at 15, 25, 50 and 80% of maximal voluntary contraction (MVC. The amplitude of the Motor Evoked Potentials (MEPs produced by TMS was measured at rest and during muscle contraction at 90° of ankle joint position. MEPs were normalised to Mmax determined with PNS. The corticospinal silent period was recorded at 80% MVC. Hoffman reflex (H-reflex at 10% isometric and 25% shortening and lengthening MVCs, and V-waves during MVCs were also evoked on each of the three days. RESULTS: With the exception of MEPs evoked at 80% shortening MVC, all TMS-derived measures showed good reliability (ICC = 0.81-0.94 from days 2 to 3. Confidence intervals (CI, 95% were lower between days 2 and 3 when compared to days 1 and 2. MEPs significantly increased at rest from days 1 to 2 (P = 0.016 and days 1 to 3 (P = 0.046. The H-reflex during dynamic muscle contraction was reliable across the three days (ICC = 0.76-0.84. V-waves (shortening, ICC = 0.77, lengthening ICC = 0.54 and the H-reflex at 10% isometric MVC (ICC = 0.66 was generally less reliable over the three days. CONCLUSION: Although it is well known that measures of the intact human CNS exhibit moment-to-moment fluctuations, careful experimental arrangements make it possible to obtain consistent and repeatable measurements of corticospinal and spinal excitability in the actively lengthening and shortening human

  13. Recent advances in vapor intrusion site investigations.

    Science.gov (United States)

    McHugh, Thomas; Loll, Per; Eklund, Bart

    2017-02-22

    Our understanding of vapor intrusion has evolved rapidly since the discovery of the first high profile vapor intrusion sites in the late 1990s and early 2000s. Research efforts and field investigations have improved our understanding of vapor intrusion processes including the role of preferential pathways and natural barriers to vapor intrusion. This review paper addresses recent developments in the regulatory framework and conceptual model for vapor intrusion. In addition, a number of innovative investigation methods are discussed.

  14. Three Dimensional Vapor Intrusion Modeling: Model Validation and Uncertainty Analysis

    Science.gov (United States)

    Akbariyeh, S.; Patterson, B.; Rakoczy, A.; Li, Y.

    2013-12-01

    Volatile organic chemicals (VOCs), such as chlorinated solvents and petroleum hydrocarbons, are prevalent groundwater contaminants due to their improper disposal and accidental spillage. In addition to contaminating groundwater, VOCs may partition into the overlying vadose zone and enter buildings through gaps and cracks in foundation slabs or basement walls, a process termed vapor intrusion. Vapor intrusion of VOCs has been recognized as a detrimental source for human exposures to potential carcinogenic or toxic compounds. The simulation of vapor intrusion from a subsurface source has been the focus of many studies to better understand the process and guide field investigation. While multiple analytical and numerical models were developed to simulate the vapor intrusion process, detailed validation of these models against well controlled experiments is still lacking, due to the complexity and uncertainties associated with site characterization and soil gas flux and indoor air concentration measurement. In this work, we present an effort to validate a three-dimensional vapor intrusion model based on a well-controlled experimental quantification of the vapor intrusion pathways into a slab-on-ground building under varying environmental conditions. Finally, a probabilistic approach based on Monte Carlo simulations is implemented to determine the probability distribution of indoor air concentration based on the most uncertain input parameters.

  15. Activation of the Long Terminal Repeat of Human Endogenous Retrovirus K by Melanoma-Specific Transcription Factor MITF-M

    Directory of Open Access Journals (Sweden)

    Iyoko Katoh

    2011-11-01

    Full Text Available The human and Old World primate genomes possess conserved endogenous retrovirus sequences that have been implicated in evolution, reproduction, and carcinogenesis. Human endogenous retrovirus (HERV-K with 5′LTR-gag-pro-pol-env-rec/np9-3′LTR sequences represents the newest retrovirus family that integrated into the human genome 1 to 5 million years ago. Although a high-level expression of HERV-K in melanomas, breast cancers, and terato-carcinomas has been demonstrated, the mechanism of the lineage-specific activation of the long terminal repeat (LTR remains obscure. We studied chromosomal HERV-K expression in MeWo melanoma cells in comparison with the basal expression in human embryonic kidney 293 (HEK293 cells. Cloned LTR of HERV-K (HML-2.HOM was also characterized by mutation and transactivation experiments. We detected multiple transcriptional initiator (Inr sites in the LTR by rapid amplification of complementary DNA ends (5′ RACE. HEK293 and MeWo showed different Inr usage. The most potent Inr was associated with a TATA box and three binding motifs of microphthalmia-associated transcription factor (MITF. Both chromosomal HERV-K expression and the cloned LTR function were strongly activated in HEK293 by transfection with MITF-M, a melanocyte/melanoma–specific isoform of MITF. Coexpression of MITF and the HERV-K core antigen was detected in retinal pigmented epithelium by an immunofluorescence analysis. Although malignant melanoma lines MeWo, G361, and SK-MEL-28 showed enhanced HERV-K transcription compared with normal melanocytes, the level of MITF-M messenger RNA persisted from normal to transformed melanocytes. Thus, MITF-M may be a prerequisite for the pigmented cell lineage–specific function of HERV-K LTR, leading to the high-level expression in malignant melanomas.

  16. Dike intrusions during rifting episodes obey scaling relationships similar to earthquakes

    Science.gov (United States)

    L., Passarelli; E., Rivalta; A., Shuler

    2014-01-01

    As continental rifts evolve towards mid-ocean ridges, strain is accommodated by repeated episodes of faulting and magmatism. Discrete rifting episodes have been observed along two subaerial divergent plate boundaries, the Krafla segment of the Northern Volcanic Rift Zone in Iceland and the Manda-Hararo segment of the Red Sea Rift in Ethiopia. In both cases, the initial and largest dike intrusion was followed by a series of smaller intrusions. By performing a statistical analysis of these rifting episodes, we demonstrate that dike intrusions obey scaling relationships similar to earthquakes. We find that the dimensions of dike intrusions obey a power law analogous to the Gutenberg-Richter relation, and the long-term release of geodetic moment is governed by a relationship consistent with the Omori law. Due to the effects of magma supply, the timing of secondary dike intrusions differs from that of the aftershocks. This work provides evidence of self-similarity in the rifting process. PMID:24469260

  17. Telomerase repeat amplification protocol (TRAP) activity upon recombinant expression and purification of human telomerase in a bacterial system.

    Science.gov (United States)

    Hansen, Debra T; Thiyagarajan, Thirumagal; Larson, Amy C; Hansen, Jeffrey L

    2016-07-01

    Telomerase biogenesis is a highly regulated process that solves the DNA end-replication problem. Recombinant expression has so far been accomplished only within a eukaryotic background. Towards structural and functional analyses, we developed bacterial expression of human telomerase. Positive activity by the telomerase repeat amplification protocol (TRAP) was identified in cell extracts of Escherichia coli expressing a sequence-optimized hTERT gene, the full-length hTR RNA with a self-splicing hepatitis delta virus ribozyme, and the human heat shock complex of Hsp90, Hsp70, p60/Hop, Hsp40, and p23. The Hsp90 inhibitor geldanamycin did not affect post-assembly TRAP activity. By various purification methods, TRAP activity was also obtained upon expression of only hTERT and hTR. hTERT was confirmed by tandem mass spectrometry in a ∼120 kDa SDS-PAGE fragment from a TRAP-positive purification fraction. TRAP activity was also supported by hTR constructs lacking the box H/ACA small nucleolar RNA domain. End-point TRAP indicated expression levels within 3-fold of that from HeLa carcinoma cells, which is several orders of magnitude below detection by the direct assay. These results represent the first report of TRAP activity from a bacterium and provide a facile system for the investigation of assembly factors and anti-cancer therapeutics independently of a eukaryotic setting.

  18. The Telomeric Repeats of Human Herpesvirus 6A (HHV-6A) Are Required for Efficient Virus Integration.

    Science.gov (United States)

    Wallaschek, Nina; Sanyal, Anirban; Pirzer, Fabian; Gravel, Annie; Mori, Yasuko; Flamand, Louis; Kaufer, Benedikt B

    2016-05-01

    Human herpesvirus 6A (HHV-6A) and 6B (HHV-6B) are ubiquitous betaherpesviruses that infects humans within the first years of life and establishes latency in various cell types. Both viruses can integrate their genomes into telomeres of host chromosomes in latently infected cells. The molecular mechanism of viral integration remains elusive. Intriguingly, HHV-6A, HHV-6B and several other herpesviruses harbor arrays of telomeric repeats (TMR) identical to human telomere sequences at the ends of their genomes. The HHV-6A and HHV-6B genomes harbor two TMR arrays, the perfect TMR (pTMR) and the imperfect TMR (impTMR). To determine if the TMR are involved in virus integration, we deleted both pTMR and impTMR in the HHV-6A genome. Upon reconstitution, the TMR mutant virus replicated comparable to wild type (wt) virus, indicating that the TMR are not essential for HHV-6A replication. To assess the integration properties of the recombinant viruses, we established an in vitro integration system that allows assessment of integration efficiency and genome maintenance in latently infected cells. Integration of HHV-6A was severely impaired in the absence of the TMR and the virus genome was lost rapidly, suggesting that integration is crucial for the maintenance of the virus genome. Individual deletion of the pTMR and impTMR revealed that the pTMR play the major role in HHV-6A integration, whereas the impTMR only make a minor contribution, allowing us to establish a model for HHV-6A integration. Taken together, our data shows that the HHV-6A TMR are dispensable for virus replication, but are crucial for integration and maintenance of the virus genome in latently infected cells.

  19. The Telomeric Repeats of Human Herpesvirus 6A (HHV-6A Are Required for Efficient Virus Integration.

    Directory of Open Access Journals (Sweden)

    Nina Wallaschek

    2016-05-01

    Full Text Available Human herpesvirus 6A (HHV-6A and 6B (HHV-6B are ubiquitous betaherpesviruses that infects humans within the first years of life and establishes latency in various cell types. Both viruses can integrate their genomes into telomeres of host chromosomes in latently infected cells. The molecular mechanism of viral integration remains elusive. Intriguingly, HHV-6A, HHV-6B and several other herpesviruses harbor arrays of telomeric repeats (TMR identical to human telomere sequences at the ends of their genomes. The HHV-6A and HHV-6B genomes harbor two TMR arrays, the perfect TMR (pTMR and the imperfect TMR (impTMR. To determine if the TMR are involved in virus integration, we deleted both pTMR and impTMR in the HHV-6A genome. Upon reconstitution, the TMR mutant virus replicated comparable to wild type (wt virus, indicating that the TMR are not essential for HHV-6A replication. To assess the integration properties of the recombinant viruses, we established an in vitro integration system that allows assessment of integration efficiency and genome maintenance in latently infected cells. Integration of HHV-6A was severely impaired in the absence of the TMR and the virus genome was lost rapidly, suggesting that integration is crucial for the maintenance of the virus genome. Individual deletion of the pTMR and impTMR revealed that the pTMR play the major role in HHV-6A integration, whereas the impTMR only make a minor contribution, allowing us to establish a model for HHV-6A integration. Taken together, our data shows that the HHV-6A TMR are dispensable for virus replication, but are crucial for integration and maintenance of the virus genome in latently infected cells.

  20. Repeated assessment of exploration and novelty seeking in the human behavioral pattern monitor in bipolar disorder patients and healthy individuals.

    Directory of Open Access Journals (Sweden)

    Arpi Minassian

    Full Text Available BACKGROUND: Exploration and novelty seeking are cross-species adaptive behaviors that are dysregulated in bipolar disorder (BD and are critical features of the illness. While these behaviors have been extensively quantified in animals, multivariate human paradigms of exploration are lacking. The human Behavioral Pattern Monitor (hBPM, a human version of the animal open field, identified a signature pattern of hyper-exploration in manic BD patients, but whether exploratory behavior changes with treatment is unknown. The objective of this study was to assess the sensitivity of the hBPM to changes in manic symptoms, a necessary step towards elucidating the neurobiology underlying BD. METHODOLOGY AND PRINCIPAL FINDINGS: Twelve acutely hospitalized manic BD subjects and 21 healthy volunteers were tested in the hBPM over three sessions; all subjects were retested one week after their first session and two weeks after their second session. Motor activity, spatial and entropic (degree of unpredictability patterns of exploration, and interactions with novel objects were quantified. Manic BD patients demonstrated greater motor activity, extensive and more unpredictable patterns of exploration, and more object interactions than healthy volunteers during all three sessions. Exploration and novelty-seeking slightly decreased in manic BD subjects over the three sessions as their symptoms responded to treatment, but never to the level of healthy volunteers. Among healthy volunteers, exploration did not significantly decrease over time, and hBPM measures were highly correlated between sessions. CONCLUSIONS/SIGNIFICANCE: Manic BD patients showed a modest reduction in symptoms yet still demonstrated hyper-exploration and novelty seeking in the hBPM, suggesting that these illness features may be enduring characteristics of BD. Furthermore, behavior in the hBPM is not subject to marked habituation effects. The hBPM can be reliably used in a repeated-measures design

  1. Interrogation of the protein-protein interactions between human BRCA2 BRC repeats and RAD51 reveals atomistic determinants of affinity.

    Directory of Open Access Journals (Sweden)

    Daniel J Cole

    2011-07-01

    Full Text Available The breast cancer suppressor BRCA2 controls the recombinase RAD51 in the reactions that mediate homologous DNA recombination, an essential cellular process required for the error-free repair of DNA double-stranded breaks. The primary mode of interaction between BRCA2 and RAD51 is through the BRC repeats, which are ∼35 residue peptide motifs that interact directly with RAD51 in vitro. Human BRCA2, like its mammalian orthologues, contains 8 BRC repeats whose sequence and spacing are evolutionarily conserved. Despite their sequence conservation, there is evidence that the different human BRC repeats have distinct capacities to bind RAD51. A previously published crystal structure reports the structural basis of the interaction between human BRC4 and the catalytic core domain of RAD51. However, no structural information is available regarding the binding of the remaining seven BRC repeats to RAD51, nor is it known why the BRC repeats show marked variation in binding affinity to RAD51 despite only subtle sequence variation. To address these issues, we have performed fluorescence polarisation assays to indirectly measure relative binding affinity, and applied computational simulations to interrogate the behaviour of the eight human BRC-RAD51 complexes, as well as a suite of BRC cancer-associated mutations. Our computational approaches encompass a range of techniques designed to link sequence variation with binding free energy. They include MM-PBSA and thermodynamic integration, which are based on classical force fields, and a recently developed approach to computing binding free energies from large-scale quantum mechanical first principles calculations with the linear-scaling density functional code onetep. Our findings not only reveal how sequence variation in the BRC repeats directly affects affinity with RAD51 and provide significant new insights into the control of RAD51 by human BRCA2, but also exemplify a palette of computational and

  2. Intrusion Detection using unsupervised learning

    Directory of Open Access Journals (Sweden)

    Kusum bharti

    2010-08-01

    Full Text Available Clustering is the one of the efficient datamining techniques for intrusion detection. In clustering algorithm kmean clustering is widely used for intrusion detection. Because it gives efficient results incase of huge datasets. But sometime kmean clustering fails to give best result because of class dominance problem and no class problem. So for removing these problems we are proposing two new algorithms for cluster to class assignment. According to our experimental results the proposed algorithm are having high precision and recall for low class instances.

  3. Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.

    Science.gov (United States)

    Quilez, Javier; Guilmatre, Audrey; Garg, Paras; Highnam, Gareth; Gymrek, Melissa; Erlich, Yaniv; Joshi, Ricky S; Mittelman, David; Sharp, Andrew J

    2016-05-05

    Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) quantitative trait loci. To test this we analyzed the effect of variation at 4849 promoter-associated TRs, genotyped in 120 individuals, on neighboring gene expression and DNA methylation. Polymorphic promoter TRs were associated with increased variance in local gene expression and DNA methylation, suggesting functional consequences related to TR variation. We identified >100 TRs associated with expression/methylation levels of adjacent genes. These potential eQTL/mQTL TRs were enriched for overlaps with transcription factor binding and DNaseI hypersensitivity sites, providing a rationale for their effects. Moreover, we showed that most TR variants are poorly tagged by nearby single nucleotide polymorphisms (SNPs) markers, indicating that many functional TR variants are not effectively assayed by SNP-based approaches. Our study assigns biological significance to TR variations in the human genome, and suggests that a significant fraction of TR variations exert functional effects via alterations of local gene expression or epigenetics. We conclude that targeted studies that focus on genotyping TR variants are required to fully ascertain functional variation in the genome. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties.

    Science.gov (United States)

    Garces, Robert G; Gillon, Wanda; Pai, Emil F

    2007-02-01

    Rcd-1, a protein highly conserved across eukaryotes, was initially identified as a factor essential for nitrogen starvation-invoked differentiation in fission yeast, and its Saccharomyces cerevisiae homolog, CAF40, has been identified as part of the CCR4-NOT transcription complex, where it interacts with the NOT1 protein. Mammalian homologs are involved in various cellular differentiation processes including retinoic acid-induced differentiation and hematopoetic cell development. Here, we present the 2.2 A X-ray structure of the highly conserved region of human Rcd-1 and investigate possible functional abilities of this and the full-length protein. The monomer is made up of six armadillo repeats forming a solvent-accessible, positively-charged cleft 21-22 A wide that, in contrast to other armadillo proteins, stays fully exposed in the dimer. Prompted by this finding, we established that Rcd-1 can bind to single- and double-stranded oligonucleotides in vitro with the affinity of G/C/T > A. Mutation of an arginine residue within the cleft strongly reduced or abolished oligonucleotide binding. Rcd-1's ability to bind to nucleic acids, in addition to the previously reported protein-protein interaction with NOT1, suggests a new feature in Rcd-1's role in regulation of overall cellular differentiation processes.

  5. Structural model for the interaction of a designed Ankyrin Repeat Protein with the human epidermal growth factor receptor 2.

    Directory of Open Access Journals (Sweden)

    V Chandana Epa

    Full Text Available Designed Ankyrin Repeat Proteins are a class of novel binding proteins that can be selected and evolved to bind to targets with high affinity and specificity. We are interested in the DARPin H10-2-G3, which has been evolved to bind with very high affinity to the human epidermal growth factor receptor 2 (HER2. HER2 is found to be over-expressed in 30% of breast cancers, and is the target for the FDA-approved therapeutic monoclonal antibodies trastuzumab and pertuzumab and small molecule tyrosine kinase inhibitors. Here, we use computational macromolecular docking, coupled with several interface metrics such as shape complementarity, interaction energy, and electrostatic complementarity, to model the structure of the complex between the DARPin H10-2-G3 and HER2. We analyzed the interface between the two proteins and then validated the structural model by showing that selected HER2 point mutations at the putative interface with H10-2-G3 reduce the affinity of binding up to 100-fold without affecting the binding of trastuzumab. Comparisons made with a subsequently solved X-ray crystal structure of the complex yielded a backbone atom root mean square deviation of 0.84-1.14 Ångstroms. The study presented here demonstrates the capability of the computational techniques of structural bioinformatics in generating useful structural models of protein-protein interactions.

  6. Increasing the repeating units of ethylene glycol-based dimethacrylates directed toward reduced oxidative stress and co-stimulatory factors expression in human monocytic cells.

    Science.gov (United States)

    Tamura, Atsushi; Fukumoto, Izumi; Yui, Nobuhiko; Matsumura, Mitsuaki; Miura, Hiroyuki

    2015-03-01

    The ethylene glycol-based dimethacrylates are commonly used in biomaterials and dental restorative materials as a cross-linking agent. In this study, toxic effect of triethylene glycol dimethacrylate (TEGDMA) and poly(ethylene glycol) dimethacrylates (PEG-DMAs) with various ethylene glycol repeating units was investigated in terms of cytotoxicity, oxidative stress, and the expression of co-stimulatory factors in human leukemia cell line (THP-1 cells) to verify the effect of ethylene glycol repeating units. Note that the 1-octanol/water partition coefficient of PEG-based dimethacrylates decreased with increasing the ethylene glycol repeating units, indicating that the hydrophilicity of PEG-DMAs increased with ethylene glycol repeating units. The toxic effect of PEG-DMAs such as cytotoxicity, oxidative stress, and the expression of CD86 in treated THP-1 cells are reduced with increasing the ethylene glycol repeating units in PEG-DMAs. However, the expression of CD54 in treated THP-1 cells was not influenced with the ethylene glycol repeating units and the maximal expression level of CD54 was observed at the concentration range of 2-4 mM for all samples. Accordingly, hydrophilic character of PEG-DMAs with long ethylene glycol chains definitely alleviates the some toxic aspect of PEG-based DMAs. This finding would provide important insight into the design of new biomaterials and dental materials with superior biocompatibility. © 2014 Wiley Periodicals, Inc.

  7. A software tool for network intrusion detection

    CSIR Research Space (South Africa)

    Van der Walt, C

    2012-10-01

    Full Text Available This presentation illustrates how a recently developed software tool enables operators to easily monitor a network and detect intrusions without requiring expert knowledge of network intrusion detections....

  8. Non-Intrusive Appliance Recognition

    NARCIS (Netherlands)

    Hoogsteen, G; Hoogsteen, Gerwin; Krist, J.O.; Bakker, Vincent; Smit, Gerardus Johannes Maria

    2012-01-01

    Energy conservation becomes more important nowadays. The use of smart meters and, in the near future, smart appliances, are the key to achieve reduction in energy consumption. This research proposes a non-intrusive appliance monitor and recognition system for implementation on an embedded system. Th

  9. Occurrence of seawater intrusion overshoot

    NARCIS (Netherlands)

    Morgan, L.K.; Bakker, M.; Werner, A.D.

    2015-01-01

    A number of numerical modeling studies of transient sea level rise (SLR) and seawater intrusion (SI) in flux-controlled aquifer systems have reported an overshoot phenomenon, whereby the freshwater-saltwater interface temporarily extends further inland than the eventual steady state position. Recent

  10. Final OSWER Vapor Intrusion Guidance

    Science.gov (United States)

    EPA is preparing to finalize its guidance on assessing and addressing vapor intrusion, which is defined as migration of volatile constituents from contaminated media in the subsurface (soil or groundwater) into the indoor environment. In November 2002, EPA issued draft guidance o...

  11. Experiences with network intrusion detection

    NARCIS (Netherlands)

    Coolen, R.; Luiijf, H.A.M.; Geloven, W.J.F. van; Bakker, E.A.

    2002-01-01

    This paper describes our experience with several commercial Network Intrusion Detection Systems (NIDSs)deployed in a network connected to the Internet. Specific problems in the operation of NIDS are highlighted, and a number of solutions to identified problems will be presented. Finally, we shall pr

  12. Intrusive luxation of 60 permanent incisors

    DEFF Research Database (Denmark)

    Tsilingaridis, Georgios; Malmgren, Barbro; Andreasen, Jens O;

    2012-01-01

    Intrusive luxation in the permanent dentition is an uncommon injury but it is considered one of the most severe types of dental trauma because of the risk for damage to the periodontal ligament, pulp and alveolar bone. Management of intrusive luxation in the permanent dentition is controversial....... The purpose of this study was to evaluate pulp survival and periodontal healing in intrusive luxated permanent teeth in relation to treatment alternatives, degree of intrusion and root development....

  13. Distributed intrusion detection system based on fuzzy rules

    Science.gov (United States)

    Qiao, Peili; Su, Jie; Liu, Yahui

    2006-04-01

    Computational Intelligence is the theory and method solving problems by simulating the intelligence of human using computer and it is the development of Artificial Intelligence. Fuzzy Technique is one of the most important theories of computational Intelligence. Genetic Fuzzy Technique and Neuro-Fuzzy Technique are the combination of Fuzzy Technique and novel techniques. This paper gives a distributed intrusion detection system based on fuzzy rules that has the characters of distributed parallel processing, self-organization, self-learning and self-adaptation by the using of Neuro-Fuzzy Technique and Genetic Fuzzy Technique. Specially, fuzzy decision technique can be used to reduce false detection. The results of the simulation experiment show that this intrusion detection system model has the characteristics of distributed, error tolerance, dynamic learning, and adaptation. It solves the problem of low identifying rate to new attacks and hidden attacks. The false detection rate is low. This approach is efficient to the distributed intrusion detection.

  14. Disruption of human papillomavirus 16 E6 gene by clustered regularly interspaced short palindromic repeat/Cas system in human cervical cancer cells

    Directory of Open Access Journals (Sweden)

    Yu L

    2014-12-01

    Full Text Available Lan Yu, Xiaoli Wang, Da Zhu, Wencheng Ding, Liming Wang, Changlin Zhang, Xiaohui Jiang, Hui Shen, Shujie Liao, Ding Ma, Zheng Hu, Hui Wang Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China Abstract: High-risk human papillomavirus (HPV, especially HPV16, is considered a main causative agent of cervical cancer. Upon HPV infection, the viral oncoprotein E6 disrupts the host tumor-suppressor protein p53, thus promoting malignant transformation of normal cervical cells. Here, we used the newly developed programmable ribonucleic acid-guided clustered regularly interspaced short palindromic repeat (CRISPR/Cas system to disrupt the HPV16 E6 gene. We showed that HPV16 E6 deoxyribonucleic acid was cleaved at specific sites, leading to apoptosis and growth inhibition of HPV16-positive SiHa and CaSki cells, but not HPV-negative C33A or human embryonic kidney 293 cells. We also observed downregulation of the E6 protein and restoration of the p53 protein. These data proved that the HPV16 E6 ribonucleic acid-guided CRISPR/Cas system might be an effective therapeutic agent in treating HPV infection-related cervical malignancy. Keywords: CRISPR/Cas system, E6, p53, SiHa, CaSki, cervical cancer

  15. Epstein-Barr virus nuclear antigen 2 transactivates the long terminal repeat of human immunodeficiency virus type 1.

    Science.gov (United States)

    Scala, G; Quinto, I; Ruocco, M R; Mallardo, M; Ambrosino, C; Squitieri, B; Tassone, P; Venuta, S

    1993-05-01

    Human immunodeficiency virus type 1 (HIV-1)-infected subjects show a high incidence of Epstein-Barr virus (EBV) infection. This suggests that EBV may function as a cofactor that affects HIV-1 activation and may play a major role in the progression of AIDS. To test this hypothesis, we generated two EBV-negative human B-cell lines that stably express the EBNA2 gene of EBV. These EBNA2-positive cell lines were transiently transfected with plasmids that carry either the wild type or deletion mutants of the HIV-1 long terminal repeat (LTR) fused to the chloramphenicol acetyltransferase (CAT) gene. There was a consistently higher HIV-1 LTR activation in EBNA2-expressing cells than in control cells, which suggested that EBNA2 proteins could activate the HIV-1 promoter, possibly by inducing nuclear factors binding to HIV-1 cis-regulatory sequences. To test this possibility, we used CAT-based plasmids carrying deletions of the NF-kappa B (pNFA-CAT), Sp1 (pSpA-CAT), or TAR (pTAR-CAT) region of the HIV-1 LTR and retardation assays in which nuclear proteins from EBNA2-expressing cells were challenged with oligonucleotides encompassing the NF-kappa B or Sp1 region of the HIV-1 LTR. We found that both the NF-kappa B and the Sp1 sites of the HIV-1 LTR are necessary for EBNA2 transactivation and that increased expression resulted from the induction of NF-kappa B-like factors. Moreover, experiments with the TAR-deleted pTAR-CAT and with the tat-expressing pAR-TAT plasmids indicated that endogenous Tat-like proteins could participate in EBNA2-mediated activation of the HIV-1 LTR and that EBNA2 proteins can synergize with the viral tat transactivator. Transfection experiments with plasmids expressing the EBNA1, EBNA3, and EBNALP genes did not cause a significant HIV-1 LTR activation. Thus, it appears that among the latent EBV genes tested, EBNA2 was the only EBV gene active on the HIV-1 LTR. The transactivation function of EBNA2 was also observed in the HeLa epithelial cell line

  16. Authentication of newly established human esophageal squamous cell carcinoma cell line (YM-1) using short tandem repeat (STR) profiling method.

    Science.gov (United States)

    Ayyoob, Khosravi; Masoud, Khoshnia; Vahideh, Kazeminejad; Jahanbakhsh, Asadi

    2016-03-01

    Cross-contamination during or early after establishment of a new cell line could result in the worldwide spread of a misidentified cell line. Therefore, newly established cell lines need to be authenticated by a reference standard method. This study was conducted to investigate the authenticity of a newly established epithelial cell line of human esophageal squamous cell carcinoma (ESCC) called YM-1 using short tandem repeat (STR) DNA profiling method. Primary human ESCC epithelial cells were cultured from the fresh tumor tissue of an adult female patient. Growth characteristics and epithelial originality of YM-1 cells were studied. Genomic DNA was isolated from YM-1 cells harvested at passage 22 and ESCC donor tumor sample on two different days to prevent probable DNA contamination. STR profiling was performed using AmpFℓSTR® Identifiler® Plus PCR Amplification Kit. To address whether YM-1 cells undergo genetic alteration as the passage number increases, STR profiling was performed again on harvested cells at passage 51. YM-1 cells grew as a monolayer with a population doubling time of 40.66 h. Epithelial originality of YM-1 cells was confirmed using ICC/IF staining of cytokeratins AE1/AE3. The STR profile of the ESCC donor tumor sample was the same with YM-1 cells at passage 22. However, STR profile of the donor tumor sample showed an off-ladder (OL) allele in their D7S820 locus. Also, re-profiling of YM-1 cells at passage 51 showed a loss of heterozygosity (LOH) at D18S51 locus. This suggests that long-term culture of cell lines may alter their DNA profile. Comparison of the DNA fingerprinting results in DSMZ, and ATCC STR profiling databases confirmed unique identity of YM-1 cell line. This study provides an easy, fast, and reliable procedure for authentication of newly established cell lines, which helps in preventing the spread of misidentified cells and improving the reproducibility and validity of experiments, consequently.

  17. How Saccade Intrusions Affect Subsequent Motor and Oculomotor Actions

    Science.gov (United States)

    Terao, Yasuo; Fukuda, Hideki; Tokushige, Shin-ichi; Inomata-Terada, Satomi; Ugawa, Yoshikazu

    2017-01-01

    In daily activities, there is a close spatial and temporal coupling between eye and hand movements that enables human beings to perform actions smoothly and accurately. If this coupling is disrupted by inadvertent saccade intrusions, subsequent motor actions suffer from delays, and lack of coordination. To examine how saccade intrusions affect subsequent voluntary actions, we used two tasks that require subjects to make motor/oculomotor actions in response to a visual cue. One was the memory guided saccade (MGS) task, and the other the hand reaction time (RT) task. The MGS task required subjects to initiate a voluntary saccade to a memorized target location, which is indicated shortly before by a briefly presented cue. The RT task required subjects to release a button on detection of a visual target, while foveating on a central fixation point. In normal subjects of various ages, inadvertent saccade intrusions delayed subsequent voluntary motor, and oculomotor actions. We also studied patients with Parkinson's disease (PD), who are impaired not only in initiating voluntary saccades but also in suppressing unwanted reflexive saccades. Saccade intrusions also delayed hand RT in PD patients. However, MGS was affected by the saccade intrusion differently. Saccade intrusion did not delay MGS latency in PD patients who could perform MGS with a relatively normal latency. In contrast, in PD patients who were unable to initiate MGS within the normal time range, we observed slightly decreased MGS latency after saccade intrusions. What explains this paradoxical phenomenon? It is known that motor actions slow down when switching between controlled and automatic behavior. We discuss how the effect of saccade intrusions on subsequent voluntary motor/oculomotor actions may reflect a similar switching cost between automatic and controlled behavior and a cost for switching between different motor effectors. In contrast, PD patients were unable to initiate internally guided MGS in

  18. Magmatic sill intrusions beneath El Hierro Island following the 2011-2012 submarine eruption

    Science.gov (United States)

    Benito-Saz, María Á.; Sigmundsson, Freysteinn; Parks, Michelle M.; García-Cañada, Laura; Domínguez Cerdeña, Itahiza

    2016-04-01

    El Hierro, the most southwestern island of Canary Islands, Spain, is a volcano rising from around 3600 m above the ocean floor and up to of 1500 m above sea level. A submarine eruption occurred off the coast of El Hierro in 2011-2012, which was the only confirmed eruption in the last ~ 600 years. Activity continued after the end of the eruption with six magmatic intrusions occurring between 2012-2014. Each of these intrusions was characterized by hundreds of earthquakes and 3-19 centimeters of observed ground deformation. Ground displacements at ten continuous GPS sites were initially inverted to determine the optimal source parameters (location, geometry, volume/pressure change) that best define these intrusions from a geodetic point of view. Each intrusive period appears to be associated with the formation of a separate sill, with inferred volumes between 0.02 - 0.3 km3. SAR images from the Canadian RADARSAT-2 satellite and the Italian Space Agency COSMO-SkyMed constellation have been used to produce high-resolution detailed maps of line-of-sight displacements for each of these intrusions. These data have been combined with the continuous GPS observations and a joint inversion undertaken to gain further constraints on the optimal source parameters for each of these separate intrusive events. The recorded activity helps to understand how an oceanic intraplate volcanic island grows through repeated sill intrusions; well documented by seismic, GPS and InSAR observations in the case of the El Hierro activity.

  19. Chip-based human liver-intestine and liver-skin co-cultures--A first step toward systemic repeated dose substance testing in vitro.

    Science.gov (United States)

    Maschmeyer, Ilka; Hasenberg, Tobias; Jaenicke, Annika; Lindner, Marcus; Lorenz, Alexandra Katharina; Zech, Julie; Garbe, Leif-Alexander; Sonntag, Frank; Hayden, Patrick; Ayehunie, Seyoum; Lauster, Roland; Marx, Uwe; Materne, Eva-Maria

    2015-09-01

    Systemic repeated dose safety assessment and systemic efficacy evaluation of substances are currently carried out on laboratory animals and in humans due to the lack of predictive alternatives. Relevant international regulations, such as OECD and ICH guidelines, demand long-term testing and oral, dermal, inhalation, and systemic exposure routes for such evaluations. So-called "human-on-a-chip" concepts are aiming to replace respective animals and humans in substance evaluation with miniaturized functional human organisms. The major technical hurdle toward success in this field is the life-like combination of human barrier organ models, such as intestine, lung or skin, with parenchymal organ equivalents, such as liver, at the smallest biologically acceptable scale. Here, we report on a reproducible homeostatic long-term co-culture of human liver equivalents with either a reconstructed human intestinal barrier model or a human skin biopsy applying a microphysiological system. We used a multi-organ chip (MOC) platform, which provides pulsatile fluid flow within physiological ranges at low media-to-tissue ratios. The MOC supports submerse cultivation of an intact intestinal barrier model and an air-liquid interface for the skin model during their co-culture with the liver equivalents respectively at (1)/100.000 the scale of their human counterparts in vivo. To increase the degree of organismal emulation, microfluidic channels of the liver-skin co-culture could be successfully covered with human endothelial cells, thus mimicking human vasculature, for the first time. Finally, exposure routes emulating oral and systemic administration in humans have been qualified by applying a repeated dose administration of a model substance - troglitazone - to the chip-based co-cultures.

  20. Glutamine repeat variants in human RUNX2 associated with decreased femoral neck BMD, broadband ultrasound attenuation and target gene transactivation.

    Directory of Open Access Journals (Sweden)

    Nigel A Morrison

    Full Text Available RUNX2 is an essential transcription factor required for skeletal development and cartilage formation. Haploinsufficiency of RUNX2 leads to cleidocranial displaysia (CCD a skeletal disorder characterised by gross dysgenesis of bones particularly those derived from intramembranous bone formation. A notable feature of the RUNX2 protein is the polyglutamine and polyalanine (23Q/17A domain coded by a repeat sequence. Since none of the known mutations causing CCD characterised to date map in the glutamine repeat region, we hypothesised that Q-repeat mutations may be related to a more subtle bone phenotype. We screened subjects derived from four normal populations for Q-repeat variants. A total of 22 subjects were identified who were heterozygous for a wild type allele and a Q-repeat variant allele: (15Q, 16Q, 18Q and 30Q. Although not every subject had data for all measures, Q-repeat variants had a significant deficit in BMD with an average decrease of 0.7SD measured over 12 BMD-related parameters (p = 0.005. Femoral neck BMD was measured in all subjects (-0.6SD, p = 0.0007. The transactivation function of RUNX2 was determined for 16Q and 30Q alleles using a reporter gene assay. 16Q and 30Q alleles displayed significantly lower transactivation function compared to wild type (23Q. Our analysis has identified novel Q-repeat mutations that occur at a collective frequency of about 0.4%. These mutations significantly alter BMD and display impaired transactivation function, introducing a new class of functionally relevant RUNX2 mutants.

  1. Zircon Recycling in Arc Intrusions

    Science.gov (United States)

    Miller, J.; Barth, A.; Matzel, J.; Wooden, J.; Burgess, S.

    2008-12-01

    Recycling of zircon has been well established in arc intrusions and arc volcanoes, but a better understanding of where and how zircons are recycled can help illuminate how arc magma systems are constructed. To that end, we are conducting age, trace element (including Ti-in-zircon temperatures; TzrnTi) and isotopic studies of zircons from the Late Cretaceous (95-85 Ma) Tuolumne Intrusive Suite (TIS) in the Sierra Nevada Batholith (CA). Within the TIS zircons inherited from ancient basement sources and/or distinctly older host rocks are uncommon, but recycled zircon antecrysts from earlier periods of TIS-related magmatism are common and conspicuous in the inner and two most voluminous units of the TIS, the Half Dome and Cathedral Peak Granodiorites. All TIS units have low bulk Zr ([Zr]825°C), [Zr] in the TIS is a factor of 2 to 3 lower than saturation values. Low [Zr] in TIS rocks might be attributed to a very limited supply of zircon in the source, by disequilibrium melting and rapid melt extraction [1], by melting reactions involving formation of other phases that can incorporate appreciable Zr [2], or by removal of zircon at an earlier stage of magma evolution. Based on a preliminary compilation of literature data, low [Zr] is common to Late Cretaceous N.A. Cordilleran granodioritic/tonalitic intrusions (typically Tzrnsat [3]. A corollary is that slightly older zircon antecrysts that are common in the inner units of the TIS could be considered inherited if they are derived from remelting of slightly older intrusions. Remelting at such low temperatures in the arc would require a source of external water. Refs: [1] Sawyer, J.Pet 32:701-738; [2] Fraser et al, Geology 25:607-610; [3] Harrison et al, Geology 35:635- 638

  2. Human State Computing – Employing different feature sources of non-intrusive biosignals for pattern recognition based automatic state recognition within occupational fields of application

    OpenAIRE

    Schoss, Tom

    2016-01-01

    The aim of the present thesis is to outline, how psychology in general and occupational psychology in particular can benefit from automatic biosignal analysis. Progress in this field within the last decade bears chances to widen the horizon of commonly employed statistics and use an interdisciplinary approach to gain new insights of typical occupational issues with the help of human state computing. Advances within psychological methodology are necessary, because recent approaches are neit...

  3. Flexible Training's Intrusion on Work/Life Balance

    OpenAIRE

    Zane BERGE; TAKIYA, Seema

    2005-01-01

    Flexible Training's Intrusion on Work/Life Balance Seema TAKIYAJennifer ARCHBOLDZane BERGEBaltimore, USA Learning interventions should be aligned with the human learning system. To be effective, they have to support human learning, not work against it. Thalheimer, 2004 ABSTRACT With more companies allowing flextime, more access to elearning, and telecomuting, the line between workplace flexibility and work-life balance begins to blur. Companies sell to employees the flexibility of being ab...

  4. A Hybrid Approach Towards Intrusion Detection Based on Artificial Immune System and Soft Computing

    CERN Document Server

    Sanyal, Sugata

    2012-01-01

    A number of works in the field of intrusion detection have been based on Artificial Immune System and Soft Computing. Artificial Immune System based approaches attempt to leverage the adaptability, error tolerance, self- monitoring and distributed nature of Human Immune Systems. Whereas Soft Computing based approaches are instrumental in developing fuzzy rule based systems for detecting intrusions. They are computationally intensive and apply machine learning (both supervised and unsupervised) techniques to detect intrusions in a given system. A combination of these two approaches could provide significant advantages for intrusion detection. In this paper we attempt to leverage the adaptability of Artificial Immune System and the computation intensive nature of Soft Computing to develop a system that can effectively detect intrusions in a given network.

  5. Association analysis of a highly polymorphic CAG Repeat in the human potassium channel gene KCNN3 and migraine susceptibility

    Directory of Open Access Journals (Sweden)

    Ovcaric Mick

    2005-09-01

    Full Text Available Abstract Background Migraine is a polygenic multifactorial disease, possessing environmental and genetic causative factors with multiple involved genes. Mutations in various ion channel genes are responsible for a number of neurological disorders. KCNN3 is a neuronal small conductance calcium-activated potassium channel gene that contains two polyglutamine tracts, encoded by polymorphic CAG repeats in the gene. This gene plays a critical role in determining the firing pattern of neurons and acts to regulate intracellular calcium channels. Methods The present association study tested whether length variations in the second (more 3' polymorphic CAG repeat in exon 1 of the KCNN3 gene, are involved in susceptibility to migraine with and without aura (MA and MO. In total 423 DNA samples from unrelated individuals, of which 202 consisted of migraine patients and 221 non-migraine controls, were genotyped and analysed using a fluorescence labelled primer set on an ABI310 Genetic Analyzer. Allele frequencies were calculated from observed genotype counts for the KCNN3 polymorphism. Analysis was performed using standard contingency table analysis, incorporating the chi-squared test of independence and CLUMP analysis. Results Overall, there was no convincing evidence that KCNN3 CAG lengths differ between Caucasian migraineurs and controls, with no significant difference in the allelic length distribution of CAG repeats between the population groups (P = 0.090. Also the MA and MO subtypes did not differ significantly between control allelic distributions (P > 0.05. The prevalence of the long CAG repeat (>19 repeats did not reach statistical significance in migraineurs (P = 0.15, nor was there a significant difference between the MA and MO subgroups observed compared to controls (P = 0.46 and P = 0.09, respectively, or between MA vs MO (P = 0.40. Conclusion This association study provides no evidence that length variations of the second polyglutamine array in

  6. Deployment Repeatability

    Science.gov (United States)

    2016-04-01

    controlled to great precision, but in a Cubesat , there may be no attitude determination at all. Such a Cubesat might treat sun angle and tumbling rates as...could be sensitive to small differences in motor controller timing. In these cases, the analyst might choose to model the entire deployment path, with...knowledge of the material damage model or motor controller timing precision. On the other hand, if many repeated and environmentally representative

  7. Molecular, physiological, and motor performance defects in DMSXL mice carrying >1,000 CTG repeats from the human DM1 locus.

    Directory of Open Access Journals (Sweden)

    Aline Huguet

    Full Text Available Myotonic dystrophy type 1 (DM1 is caused by an unstable CTG repeat expansion in the 3'UTR of the DM protein kinase (DMPK gene. DMPK transcripts carrying CUG expansions form nuclear foci and affect splicing regulation of various RNA transcripts. Furthermore, bidirectional transcription over the DMPK gene and non-conventional RNA translation of repeated transcripts have been described in DM1. It is clear now that this disease may involve multiple pathogenic pathways including changes in gene expression, RNA stability and splicing regulation, protein translation, and micro-RNA metabolism. We previously generated transgenic mice with 45-kb of the DM1 locus and >300 CTG repeats (DM300 mice. After successive breeding and a high level of CTG repeat instability, we obtained transgenic mice carrying >1,000 CTG (DMSXL mice. Here we described for the first time the expression pattern of the DMPK sense transcripts in DMSXL and human tissues. Interestingly, we also demonstrate that DMPK antisense transcripts are expressed in various DMSXL and human tissues, and that both sense and antisense transcripts accumulate in independent nuclear foci that do not co-localize together. Molecular features of DM1-associated RNA toxicity in DMSXL mice (such as foci accumulation and mild missplicing, were associated with high mortality, growth retardation, and muscle defects (abnormal histopathology, reduced muscle strength, and lower motor performances. We have found that lower levels of IGFBP-3 may contribute to DMSXL growth retardation, while increased proteasome activity may affect muscle function. These data demonstrate that the human DM1 locus carrying very large expansions induced a variety of molecular and physiological defects in transgenic mice, reflecting DM1 to a certain extent. As a result, DMSXL mice provide an animal tool to decipher various aspects of the disease mechanisms. In addition, these mice can be used to test the preclinical impact of systemic

  8. Molecular, physiological, and motor performance defects in DMSXL mice carrying >1,000 CTG repeats from the human DM1 locus.

    Science.gov (United States)

    Huguet, Aline; Medja, Fadia; Nicole, Annie; Vignaud, Alban; Guiraud-Dogan, Céline; Ferry, Arnaud; Decostre, Valérie; Hogrel, Jean-Yves; Metzger, Friedrich; Hoeflich, Andreas; Baraibar, Martin; Gomes-Pereira, Mário; Puymirat, Jack; Bassez, Guillaume; Furling, Denis; Munnich, Arnold; Gourdon, Geneviève

    2012-01-01

    Myotonic dystrophy type 1 (DM1) is caused by an unstable CTG repeat expansion in the 3'UTR of the DM protein kinase (DMPK) gene. DMPK transcripts carrying CUG expansions form nuclear foci and affect splicing regulation of various RNA transcripts. Furthermore, bidirectional transcription over the DMPK gene and non-conventional RNA translation of repeated transcripts have been described in DM1. It is clear now that this disease may involve multiple pathogenic pathways including changes in gene expression, RNA stability and splicing regulation, protein translation, and micro-RNA metabolism. We previously generated transgenic mice with 45-kb of the DM1 locus and >300 CTG repeats (DM300 mice). After successive breeding and a high level of CTG repeat instability, we obtained transgenic mice carrying >1,000 CTG (DMSXL mice). Here we described for the first time the expression pattern of the DMPK sense transcripts in DMSXL and human tissues. Interestingly, we also demonstrate that DMPK antisense transcripts are expressed in various DMSXL and human tissues, and that both sense and antisense transcripts accumulate in independent nuclear foci that do not co-localize together. Molecular features of DM1-associated RNA toxicity in DMSXL mice (such as foci accumulation and mild missplicing), were associated with high mortality, growth retardation, and muscle defects (abnormal histopathology, reduced muscle strength, and lower motor performances). We have found that lower levels of IGFBP-3 may contribute to DMSXL growth retardation, while increased proteasome activity may affect muscle function. These data demonstrate that the human DM1 locus carrying very large expansions induced a variety of molecular and physiological defects in transgenic mice, reflecting DM1 to a certain extent. As a result, DMSXL mice provide an animal tool to decipher various aspects of the disease mechanisms. In addition, these mice can be used to test the preclinical impact of systemic therapeutic

  9. Classification and Importance of Intrusion Detection System

    Directory of Open Access Journals (Sweden)

    Rajasekaran K

    2012-08-01

    Full Text Available An intrusion detection system (IDS is a device or software application that monitors network or system activities for malicious activities or policy violations and produces reports to a Management Station. Some systems may attempt to stop an intrusion attempt but this is neither required nor expected of a monitoring system. Due to a growing number of intrusion events and also because the Internet and local networks have become so ubiquitous, organizations are increasingly implementing various systems that monitor IT security breaches. This includes an overview of the classification of intrusion detection systems and introduces the reader to some fundamental concepts of IDS methodology: audit trail analysis and on-the-fly processing as well as anomaly detection and signature detection approaches. This research paper discusses the primary intrusion detection techniques and the classification of intrusion Detection system.

  10. Association Rules Applied to Intrusion Detection

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    We discuss the basic intrusion detection techniques, and focus on how to apply association rules to intrusion detection. Begin with analyzing some close relations between user's behaviors, we discuss the mining algorithm of association rules and apply to detect anomaly in IDS. Moreover, according to the characteristic of intrusion detection, we optimize the mining algorithm of association rules, and use fuzzy logic to improve the system performance.

  11. Non-intrusive refractometer sensor

    Indian Academy of Sciences (India)

    Pabitra Nath

    2010-04-01

    An experimental realization of a simple non-intrusive refractometer sensor is demonstrated in this communication. The working principle of the sensor is based on intensity modulation of the back-reflected light when output light from an optical fibre end focusses onto air–medium interface. The change in the refractive index of the medium affects the reflectance of the incident light signal and thus modulates the back-reflected signal. Refractive index variation as small as 0.002 RIU can be measured using the present technique. The advantages of the technique are its simplicity, cost efficiency and usefulness in monitoring refractive indices of acidic solutions.

  12. Sulfide intrusion and detoxification in Zostera marina

    DEFF Research Database (Denmark)

    Hasler-Sheetal, Harald; Holmer, Marianne

    2014-01-01

    nutrition in general. By a global review of sulfide intrusion, coupled with a series of field studies and in situ experiments we elucidate sulfide intrusion and different strategies of seagrasses to sustain sulfide intrusion. Using stable isotope tracing, scanning electron microscopy with x-ray analysis...... indicating a possible role of sulfide in the sulfur nutrition beside the detoxification function. Our results suggest different adaptations of Z. marina to reduced sediments and sulfide intrusion ranging from bacterial and chemical reoxidation of sulfide to sulfate to incorporation of sulfide into organic...

  13. An international perspective on Facebook intrusion.

    Science.gov (United States)

    Błachnio, Agata; Przepiorka, Aneta; Benvenuti, Martina; Cannata, Davide; Ciobanu, Adela Magdalena; Senol-Durak, Emre; Durak, Mithat; Giannakos, Michail N; Mazzoni, Elvis; Pappas, Ilias O; Popa, Camelia; Seidman, Gwendolyn; Yu, Shu; Wu, Anise M S; Ben-Ezra, Menachem

    2016-08-30

    Facebook has become one of the most popular social networking websites in the world. The main aim of the study was to present an international comparison of Facebook intrusion and Internet penetration while examining possible gender differences. The study consisted of 2589 participants from eight countries: China, Greece, Israel, Italy, Poland, Romania, Turkey, USA. Facebook intrusion and Internet penetration were taken into consideration. In this study the relationship between Facebook intrusion and Internet penetration was demonstrated. Facebook intrusion was slightly negatively related to Internet penetration in each country.

  14. Temporal associations and prior-list intrusions in free recall.

    Science.gov (United States)

    Zaromb, Franklin M; Howard, Marc W; Dolan, Emily D; Sirotin, Yevgeniy B; Tully, Michele; Wingfield, Arthur; Kahana, Michael J

    2006-07-01

    When asked to recall the words from a just-presented target list, subjects occasionally recall words that were not on the list. These intrusions either appeared on earlier lists (prior-list intrusions, or PLIs) or had not appeared over the course of the experiment (extra-list intrusions). The authors examined the factors that elicit PLIs in free recall. A reanalysis of earlier studies revealed that PLIs tend to come from semantic associates as well as from recently studied lists, with the rate of PLIs decreasing sharply with list recency. The authors report 3 new experiments in which some items in a given list also appeared on earlier lists. Although repetition enhanced recall of list items, subjects were significantly more likely to make PLIs following the recall of repeated items, suggesting that temporal associations formed in earlier lists can induce recall errors. The authors interpret this finding as evidence for the interacting roles of associative and contextual retrieval processes in recall. Although contextual information helps to focus recall on words in the target list, it does not form an impermeable boundary between current- and prior-list experiences. Copyright 2006 APA, all rights reserved.

  15. Differential responses of healthy and chronic obstructive pulmonary diseased human bronchial epithelial cells repeatedly exposed to air pollution-derived PM4.

    Science.gov (United States)

    Leclercq, B; Happillon, M; Antherieu, S; Hardy, E M; Alleman, L Y; Grova, N; Perdrix, E; Appenzeller, B M; Lo Guidice, J-M; Coddeville, P; Garçon, G

    2016-11-01

    While the knowledge of the underlying mechanisms by which air pollution-derived particulate matter (PM) exerts its harmful health effects is still incomplete, detailed in vitro studies are highly needed. With the aim of getting closer to the human in vivo conditions and better integrating a number of factors related to pre-existing chronic pulmonary inflammatory, we sought to develop primary cultures of normal human bronchial epithelial (NHBE) cells and chronic obstructive pulmonary disease (COPD)-diseased human bronchial epithelial (DHBE) cells, grown at the air-liquid interface. Pan-cytokeratin and MUC5AC immunostaining confirmed the specific cell-types of both these healthy and diseased cell models and showed they are closed to human bronchial epithelia. Thereafter, healthy and diseased cells were repeatedly exposed to air pollution-derived PM4 at the non-cytotoxic concentration of 5 μg/cm(2). The differences between the oxidative and inflammatory states in non-exposed NHBE and COPD-DHBE cells indicated that diseased cells conserved their specific physiopathological characteristics. Increases in both oxidative damage and cytokine secretion were reported in repeatedly exposed NHBE cells and particularly in COPD-DHBE cells. Diseased cells repeatedly exposed had lower capacities to metabolize the organic chemicals-coated onto the air-pollution-derived PM4, such as benzo[a]pyrene (B[a]P), but showed higher sensibility to the formation of OH-B[a]P DNA adducts, because their diseased state possibly affected their defenses. Differential profiles of epigenetic hallmarks (i.e., global DNA hypomethylation, P16 promoter hypermethylation, telomere length shortening, telomerase activation, and histone H3 modifications) occurred in repeatedly exposed NHBE and particularly in COPD-DHBE cells. Taken together, these results closely supported the highest responsiveness of COPD-DHBE cells to a repeated exposure to air pollution-derived PM4. The use of these innovative in

  16. Economic analysis of human papillomavirus triage, repeat cytology, and immediate colposcopy in management of women with minor cytological abnormalities in Sweden.

    Science.gov (United States)

    Ostensson, Ellinor; Fröberg, Maria; Hjerpe, Anders; Zethraeus, Niklas; Andersson, Sonia

    2010-10-01

    To assess the cost-effectiveness of using human papillomavirus testing (HPV triage) in the management of women with minor cytological abnormalities in Sweden. An economic analysis based on a clinical trial, complemented with data from published meta-analyses on accuracy of HPV triage. The study takes perspective of the Swedish healthcare system. The Swedish population-based cervical cancer screening program. A decision analytic model was constructed to evaluate cost-effectiveness of HPV triage compared to repeat cytology and immediate colposcopy with biopsy, stratifying by index cytology (ASCUS = atypical squamous cells of undetermined significance, and LSIL = low-grade squamous intraepithelial lesion) and age (23-60 years, cytological abnormalities. Today, immediate colposcopy with biopsy is a cost-effective alternative compared to HPV triage and repeat cytology.

  17. TU-C-12A-05: Repeatability Study of Reduced Field-Of-View Diffusion-Weighted MRI On Human Thyroid Gland

    Energy Technology Data Exchange (ETDEWEB)

    Shukla-Dave, A; Lu, Y; Hatzoglou, V; Stambuk, H; Mazaheri, Y [Memorial Sloan-Kettering Cancer Center, New York, New York (United States); Banerjee, S; Shankaranarayanan, A [GE Healthcare, Menlo Park, California (United States); Deasy, J [Memorial Sloan Kettering Cancer Center, New York, NY (United States)

    2014-06-15

    Purpose: To investigate the repeatability of reduced field-of-view diffusion-weighted imaging (rFOV DWI) in quantifying apparent diffusion coefficients (ADCs) for human thyroid glands in a clinical setting. Methods: Nine healthy human volunteers were enrolled and underwent 3T MRI exams. For each volunteer, 3 longitudinal exams (2 weeks apart) with 2 repetitive sessions within each exam, including rFOV and conventional full field-of-view (fFOV) DWI scans, were performed. In the acquired DWI images, a fixed-size region of interest (ROI; diameter=8mm) was placed on thyroid glands to calculate ADC. ADC was calculated using a monoexponential function with a noise correction scheme. The repeatability of ADC was assessed by using coefficient variation (CV) across sessions or exams, which was defined to be: r = 1-CV, 0 < r < 1, where CV=STD/m, STD is the standard deviation of ADC, and m is the average of ADC across sessions or exams. An experienced radiologist assessed and scored rFOV and fFOV DW images based on image characteristics (1, nondiagnostic; 2, poor; 3, satisfactory; 4, good; and 5, excellent).Analysis of variance (ANOVA) was performed to compare ADC values, CV of ADC, repeatability of ADC across sessions and exams, and radiologic scores between rFOV and fFOV DWI techniques. Results: There was no significant difference in ADC values across sessions and exams either in rFOV or fFOV DWI. The average CVs of both rFOV and fFOV DWI were less than 13%. The repeatability of ADC measurement between rFOV and fFOV DWI was not significantly different. The overall image quality was significantly higher with rFOV DWI than with fFOV DWI. Conclusion: This study suggested that ADCs from both rFOV and fFOV DWI were repeatable, but rFOV DWI had superior imaging quality for human thyroid glands in a clinical setting.

  18. Intrusive and Non-Intrusive Load Monitoring (A Survey

    Directory of Open Access Journals (Sweden)

    Marco Danilo Burbano Acuña

    2015-05-01

    Full Text Available There is not discussion about the need of energyconservation, it is well known that energy resources are limitedmoreover the global energy demands will double by the end of2030, which certainly will bring implications on theenvironment and hence to all of us.Non-Intrusive load monitoring (NILM is the process ofrecognize electrical devices and its energy consumption basedon whole home electric signals, where this aggregated load datais acquired from a single point of measurement outside thehousehold. The aim of this approach is to get optimal energyconsumption and avoid energy wastage. Intrusive loadmonitoring (ILM is the process of identify and locate singledevices through the use of sensing systems to support control,monitor and intervention of such devices. The aim of thisapproach is to offer a base for the development of importantapplications for remote and automatic intervention of energyconsumption inside buildings and homes as well. For generalpurposes this paper states a general framework of NILM andILM approaches.Appliance discerns can be tackled using approaches fromdata mining and machine learning, finding out the techniquesthat fit the best this requirements, is a key factor for achievingfeasible and suitable appliance load monitoring solutions. Thispaper presents common and interesting methods used.Privacy concerns have been one of the bigger obstacles forimplementing a widespread adoption of these solutions; despitethis fact, developed countries like those inside the EU and theUK have established a deadline for the implementation ofsmart meters in the whole country, whereas USA governmentstill struggles with the acceptance of this solution by itscitizens.The implementation of security over these approachesalong with fine-grained energy monitoring would lead to abetter public agreement of these solutions and hence a fasteradoption of such approaches. This paper reveals a lack ofsecurity over these approaches with a real scenario.

  19. Expression and sub-cellular localization of leucine-rich repeats and immunoglobulin-like domains are related to antioxidant enzymes in human ependymoma and oligodendroglioma

    Institute of Scientific and Technical Information of China (English)

    Wei Yi; Lin Liu; Okechi Humphrey; Qianxue Chen; Shulan Huang

    2011-01-01

    The current study investigated correlations between the expression of leucine-rich repeats and immunoglobulin-like domain 1 (LRIG1) and antioxidant enzymes and related proteins, including manganese superoxide dismutase, glutamate cysteine ligase catalytic or regulatory subunit, thioredoxin and thioredoxin reductase, in both human ependymoma and oligodendroglioma. Results revealed that the cytoplasmic expression of LRIG1 was associated with expression of glutamate cysteine ligase catalytic subunit in the human ependymoma, while the nuclear expression of LRIG1 was associated with expression of thioredoxin reductase. In human oligodendroglioma, the cytoplasmic expression of LRIG1 was associated with expression of the glutamate cysteine ligase catalytic subunit. Both the nuclear and perinuclear expressions of LRIG1 were associated with expression of glutamate cysteine ligase regulatory subunit. These results indicated that several antioxidant enzymes and related proteins contributed to LRIG1 expression, and that these may participate in the antioxidation of the cells.

  20. Tyms double (2R) and triple repeat (3R) confers risk for human oral squamous cell carcinoma.

    Science.gov (United States)

    Bezerra, Alexandre Medeiros; Sant'Ana, Thalita Araújo; Gomes, Adriana Vieira; de Lacerda Vidal, Aurora Karla; Muniz, Maria Tereza Cartaxo

    2014-12-01

    The oral cancer is responsible for approximately 3 % of cases of cancer in Brazil. Epidemiological studies have associated low folate intake with an increased risk of epithelial cancers, including oral cancer. Folic acid has a key role in DNA synthesis, repair, methylation and this is the basis of explanations for a putative role for folic acid in cancer prevention. The role of folic acid in carcinogenesis may be modulated by polymorphism C677T in MTHFR and tandem repeats 2R/3R in the promoter site of TYMS gene that are related to decreased enzymatic activity and quantity and availability of the enzyme, respectively. These events cause a decrease in the synthesis, repair and DNA methylation, which can lead to a disruption in the expression of tumor suppressor genes as TP53. The objective of this study was investigate the distribution of polymorphisms C677T and tandem repeats 2R/3R associated with the development of oral squamous cell carcinoma (OSCC). 53 paraffin-embedded samples from patients who underwent surgery but are no longer at the institution and 43 samples collected by method of oral exfoliation by cytobrush were selected. 132 healthy subjects were selected by specialists at the dental clinics of the Faculdade de Odontologia de Pernambuco-FOP. The MTHFR genotyping was performed by PCR-RFLP, and the TYMS genotyping was performed by conventional PCR. Fisher's Exact test at significant level of 5 %. Odds ratios (ORs) and 95 % confidence intervals (CIs) were used to measure the strength of association between genotype frequency and OSCC development. The results were statistically significant for the tandem repeats of the TYMS gene (p = 0.015). The TYMS 2R3R genotype was significantly associated with the development of OSCC (OR = 3.582; 95 % CI 1.240-10.348; p = 0.0262) and also the genotype 3R3R (OR = 3.553; 95 % CI 1.293-9.760; p = 0.0345). When analyzed together, the TYMS 2R3R + 3R3R genotypes also showed association (OR = 3.518; 95 % CI 11.188-10.348; p

  1. Effects of concentric and repeated eccentric exercise on muscle damage and calpain-calpastatin gene expression in human skeletal muscle

    DEFF Research Database (Denmark)

    Vissing, K.; Overgaard, K.; Nedergaard, A.

    2008-01-01

    The purpose of this study was to compare the responsiveness of changes in Ca2+-content and calpain-calpastatin gene expression to concentric and eccentric single-bout and repeated exercise. An exercise group (n = 14) performed two bouts of bench-stepping exercise with 8 weeks between exercise bouts...... for muscle Ca2+-content and mRNA levels for calpain isoforms and calpastatin. Exercise reduced muscle strength and increased muscle soreness predominantly in the eccentric leg (P ... eccentric exercise bout (P eccentric exercise 24 h post-exercise (P

  2. Vapour Intrusion into Buildings - A Literature Review

    Science.gov (United States)

    This chapter provides a review of recent research on vapour intrusion of volatile organic compounds (VOCs) into buildings. The chapter builds on a report from Tillman and Weaver (2005) which reviewed the literature on vapour intrusion through 2005. Firstly, the term ‘vapour intru...

  3. Methylation of HpaII and HhaI sites near the polymorphic CAG repeat in the human androgen-receptor gene correlates with X chromosome inactivation

    Energy Technology Data Exchange (ETDEWEB)

    Allen, R.C.; Zoghbi, H.Y.; Moseley, A.B.; Rosenblatt, H.M.; Belmont, J.W. (Baylor College of Medicine, Houston (United States))

    1992-12-01

    The human androgen-receptor gene (HUMARA; GenBank) contains a highly polymorphic trinucleotide repeat in the first exon. The authors have found that the methylation of HpaII and HhaI sites less than 100 pb away from this polymorphic short tandem repeat (STR) correlates with X inactivation. The close proximity of the restriction-enzyme sites to the STR allows the development of a PCR assay that distinguishes between the maternal and paternal alleles and identifies their methylation status. The accuracy of this assay was tested on (a) DNA from hamster/human hybrid cell lines containing either an active or inactive human X chromosome; (b) DNA from normal males and females; and (c) DNA from females showing nonrandom patterns of X inactivation. Data obtained using this assay correlated substantially with those obtained using the PGK, HPRT, and M27[beta] probes, which detect X inactivation patterns by Southern blot analysis. In order to demonstrate one application of this assay, the authors examined X inactivation patterns in the B lymphocytes of potential and obligate carriers of X-linked agammaglobulinemia. 42 refs., 5 figs., 1 tab.

  4. The protein network surrounding the human telomere repeat binding factors TRF1, TRF2, and POT1.

    Directory of Open Access Journals (Sweden)

    Richard J Giannone

    Full Text Available Telomere integrity (including telomere length and capping is critical in overall genomic stability. Telomere repeat binding factors and their associated proteins play vital roles in telomere length regulation and end protection. In this study, we explore the protein network surrounding telomere repeat binding factors, TRF1, TRF2, and POT1 using dual-tag affinity purification in combination with multidimensional protein identification technology liquid chromatography--tandem mass spectrometry (MudPIT LC-MS/MS. After control subtraction and data filtering, we found that TRF2 and POT1 co-purified all six members of the telomere protein complex, while TRF1 identified five of six components at frequencies that lend evidence towards the currently accepted telomere architecture. Many of the known TRF1 or TRF2 interacting proteins were also identified. Moreover, putative associating partners identified for each of the three core components fell into functional categories such as DNA damage repair, ubiquitination, chromosome cohesion, chromatin modification/remodeling, DNA replication, cell cycle and transcription regulation, nucleotide metabolism, RNA processing, and nuclear transport. These putative protein-protein associations may participate in different biological processes at telomeres or, intriguingly, outside telomeres.

  5. The protein network surrounding the human telomere repeat binding factors TRF1, TRF2, and POT1

    Energy Technology Data Exchange (ETDEWEB)

    Giannone, Richard J [ORNL; McDonald, W Hayes [ORNL; Hurst, Gregory {Greg} B [ORNL; Shen, Rong-Fong [National Institute on Aging, National Institutes of Health; Wang, Yisong [ORNL; Liu, Yie [National Institute on Aging, Baltimore

    2010-01-01

    Telomere integrity (including telomere length and capping) is critical in overall genomic stability. Telomere repeat binding factors and their associated proteins play vital roles in telomere length regulation and end protection. In this study, we explore the protein network surrounding telomere repeat binding factors, TRF1, TRF2, and POT1 using dual-tag affinity purification in combination with multidimensional protein identification technology liquid chromatography - tandem mass spectrometry (MudPIT LC-MS/MS). After control subtraction and data filtering, we found that TRF2 and POT1 co-purified all six members of the telomere protein complex, while TRF1 identified five of six components at frequencies that lend evidence towards the currently accepted telomere architecture. Many of the known TRF1 or TRF2 interacting proteins were also identified. Moreover, putative associating partners identified for each of the three core components fell into functional categories such as DNA damage repair, ubiquitination, chromosome cohesion, chromatin modification/remodeling, DNA replication, cell cycle and transcription regulation, nucleotide metabolism, RNA processing, and nuclear transport. These putative protein-protein associations may participate in different biological processes at telomeres or, intriguingly, outside telomeres.

  6. Three Huntington's Disease Specific Mutation-Carrying Human Embryonic Stem Cell Lines Have Stable Number of CAG Repeats upon In Vitro Differentiation into Cardiomyocytes.

    Science.gov (United States)

    Jacquet, Laureen; Neueder, Andreas; Földes, Gabor; Karagiannis, Panagiotis; Hobbs, Carl; Jolinon, Nelly; Mioulane, Maxime; Sakai, Takao; Harding, Sian E; Ilic, Dusko

    2015-01-01

    Huntington disease (HD; OMIM 143100), a progressive neurodegenerative disorder, is caused by an expanded trinucleotide CAG (polyQ) motif in the HTT gene. Cardiovascular symptoms, often present in early stage HD patients, are, in general, ascribed to dysautonomia. However, cardio-specific expression of polyQ peptides caused pathological response in murine models, suggesting the presence of a nervous system-independent heart phenotype in HD patients. A positive correlation between the CAG repeat size and severity of symptoms observed in HD patients has also been observed in in vitro HD cellular models. Here, we test the suitability of human embryonic stem cell (hESC) lines carrying HD-specific mutation as in vitro models for understanding molecular mechanisms of cardiac pathology seen in HD patients. We have differentiated three HD-hESC lines into cardiomyocytes and investigated CAG stability up to 60 days after starting differentiation. To assess CAG stability in other tissues, the lines were also subjected to in vivo differentiation into teratomas for 10 weeks. Neither directed differentiation into cardiomyocytes in vitro nor in vivo differentiation into teratomas, rich in immature neuronal tissue, led to an increase in the number of CAG repeats. Although the CAG stability might be cell line-dependent, induced pluripotent stem cells generated from patients with larger numbers of CAG repeats could have an advantage as a research tool for understanding cardiac symptoms of HD patients.

  7. Three Huntington's Disease Specific Mutation-Carrying Human Embryonic Stem Cell Lines Have Stable Number of CAG Repeats upon In Vitro Differentiation into Cardiomyocytes.

    Directory of Open Access Journals (Sweden)

    Laureen Jacquet

    Full Text Available Huntington disease (HD; OMIM 143100, a progressive neurodegenerative disorder, is caused by an expanded trinucleotide CAG (polyQ motif in the HTT gene. Cardiovascular symptoms, often present in early stage HD patients, are, in general, ascribed to dysautonomia. However, cardio-specific expression of polyQ peptides caused pathological response in murine models, suggesting the presence of a nervous system-independent heart phenotype in HD patients. A positive correlation between the CAG repeat size and severity of symptoms observed in HD patients has also been observed in in vitro HD cellular models. Here, we test the suitability of human embryonic stem cell (hESC lines carrying HD-specific mutation as in vitro models for understanding molecular mechanisms of cardiac pathology seen in HD patients. We have differentiated three HD-hESC lines into cardiomyocytes and investigated CAG stability up to 60 days after starting differentiation. To assess CAG stability in other tissues, the lines were also subjected to in vivo differentiation into teratomas for 10 weeks. Neither directed differentiation into cardiomyocytes in vitro nor in vivo differentiation into teratomas, rich in immature neuronal tissue, led to an increase in the number of CAG repeats. Although the CAG stability might be cell line-dependent, induced pluripotent stem cells generated from patients with larger numbers of CAG repeats could have an advantage as a research tool for understanding cardiac symptoms of HD patients.

  8. Intrusion Preventing System using Intrusion Detection System Decision Tree Data Mining

    Directory of Open Access Journals (Sweden)

    Syurahbil

    2009-01-01

    Full Text Available Problem statement: To distinguish the activities of the network traffic that the intrusion and normal is very difficult and to need much time consuming. An analyst must review all the data that large and wide to find the sequence of intrusion on the network connection. Therefore, it needs a way that can detect network intrusion to reflect the current network traffics. Approach: In this study, a novel method to find intrusion characteristic for IDS using decision tree machine learning of data mining technique was proposed. Method used to generate of rules is classification by ID3 algorithm of decision tree. Results: These rules can determine of intrusion characteristics then to implement in the firewall policy rules as prevention. Conclusion: Combination of IDS and firewall so-called the IPS, so that besides detecting the existence of intrusion also can execute by doing deny of intrusion as prevention.

  9. Vapor intrusion in urban settings: effect of foundation features and source location

    OpenAIRE

    Yao, Yijun; Pennell, Kelly G.; Suuberg, Eric

    2011-01-01

    In many urban settings, groundwater contains volatile organic compounds, such as tricholoroethene, tetrachloroethene, benzene, etc., at concentrations that are at or slightly below non-potable groundwater standards. Some non-potable groundwater standards do not protect against human health risks that might result from vapor intrusion. Vapor intrusion is a process by which vapor phase contaminants present in the subsurface migrate through the soil and ultimately enter a building through founda...

  10. In Vitro Study on Lethal Effect of Human Choroidal Melanoma OCM-1 Cell Line by Repeating-70℃Freeze Thawing%In Vitro Study on Lethal Effect of Human Choroidal Melanoma OCM-1 Cell Line by Repeating-70℃ Freeze Thawing

    Institute of Scientific and Technical Information of China (English)

    Bin Liu; Yongping Li; Bo Zhang; Wenxin Zhang

    2007-01-01

    Objective: To investigate the effects of repeating -70℃ freeze thawing on human choroidal melanoma cell line OCM-1.Methods: OCM-1 cells were frozen by repeating -70℃ freeze thawing with various durations and frequencies. Then the inhibit rate of cells was examined by MTT essay.The cell viability was measured by monoclonal formation assay. We also used the HE staining, immunohistochemistry staining and the laser-scanning confocal microscopy (LSCM) to investigate the morphological changes of the cells.Results: The growth of OCM-1 cells was inhibited by repeating -70℃ freeze thawing in time-dependent and frequency-dependent manners (P < 0.01). Different morphous including necrosis and apoptosis of the cells could be observed after -70℃ freeze thawing by the LSCM.Conclusion: Repeating -70℃ freeze thawing can not only kill cells directly and induce considerable cells to apoptosis, but also inhibit the growth of the survivals. The kill and wound ratio of the cells disposal with different times and frequencies present variance. And the distinction when treated with different frequencies during the same time is much more significant than different times with the same frequency, which guide clinical workers to choose repeating cryotherapy with short term method instead of single cryotherapy with long term in choroidal melanoma treatment.

  11. Rotating waves during human sleep spindles organize global patterns of activity that repeat precisely through the night

    Science.gov (United States)

    Muller, Lyle; Piantoni, Giovanni; Koller, Dominik; Cash, Sydney S; Halgren, Eric; Sejnowski, Terrence J

    2016-01-01

    During sleep, the thalamus generates a characteristic pattern of transient, 11-15 Hz sleep spindle oscillations, which synchronize the cortex through large-scale thalamocortical loops. Spindles have been increasingly demonstrated to be critical for sleep-dependent consolidation of memory, but the specific neural mechanism for this process remains unclear. We show here that cortical spindles are spatiotemporally organized into circular wave-like patterns, organizing neuronal activity over tens of milliseconds, within the timescale for storing memories in large-scale networks across the cortex via spike-time dependent plasticity. These circular patterns repeat over hours of sleep with millisecond temporal precision, allowing reinforcement of the activity patterns through hundreds of reverberations. These results provide a novel mechanistic account for how global sleep oscillations and synaptic plasticity could strengthen networks distributed across the cortex to store coherent and integrated memories. DOI: http://dx.doi.org/10.7554/eLife.17267.001 PMID:27855061

  12. Repeatability and interobserver reproducibility of Artemis-2 high-frequency ultrasound in determination of human corneal thickness

    Directory of Open Access Journals (Sweden)

    Ogbuehi KC

    2012-05-01

    Full Text Available Kelechi C Ogbuehi, Uchechukwu L OsuagwuOutpatient Clinic, Department of Optometry, King Saud University, Riyadh, Kingdom of Saudi ArabiaBackground: The purpose of this study was to assess the repeatability and limits of agreement of corneal thickness values measured by a high-frequency ultrasound (Artemis-2, hand-held ultrasound pachymeter (DGH-500 and a specular microscope (SP-3000P.Methods: Central corneal thickness (CCT was analyzed in this prospective randomized study that included 32 patients (18 men and 14 women aged 21–24 years. Measurements were obtained in two sessions, one week apart, by two examiners with three devices in a randomized order. Nine measurements were taken (three with each device on one randomly selected eye of each patient in each measurement session. The coefficient of repeatability and interobserver reproducibility for the values of each method were calculated. The limits of agreement between techniques were also evaluated.Results: There were no significant differences in CCT values between sessions for each of the three devices (P > 0.05. The repeatability coefficients for the Artemis-2 (±8 µm/±9 µm were superior to those of the SP-3000P (±9 µm/±11 µm and DGH 500 (±12 µm/±12 µm in session 1/session 2 respectively, while the interobserver reproducibility index (differences between session 1 and session 2 was superior for the SP-3000P (±17 µm with respect to DHG-500 (±29 µm and the Artemis-2 (±31 µm. In session 1 and session 2, the limits of agreement between the techniques were 35 µm to -31 µm and 34 to -20 µm, respectively, for DGH-500 versus Artemis-2, 73 µm to 3 µm and 60 µm to 9 µm for Artemis-2 versus SP-3000P, and 58 µm to 22 µm and 72 µm to 10 µm for DGH-500 versus SP-3000P comparisons. The DGH-500 and Artemis-2 gave similar values (P > 0.05 in both sessions, but both (Artemis-2 and DGH-500 values were significantly greater than that of the SP-3000P (P < 0.05 in both sessions

  13. The role of estrogen in intrusive memories.

    Science.gov (United States)

    Cheung, Jessica; Chervonsky, Liza; Felmingham, Kim L; Bryant, Richard A

    2013-11-01

    Intrusive memories are highly vivid, emotional and involuntary recollections which cause significant distress across psychological disorders including posttraumatic disorder (PTSD). Recent evidence has potentially extended our understanding of the development of intrusive memories by identifying biological factors which significantly impact on memories for emotionally arousing stimuli. This study investigated the role of stress on the development of intrusions for negative and neutral images, and indexed the potential contributions of sex (estrogen and progesterone) and stress (noradrenaline and cortisol) hormones. Whilst viewing the images, half the participants underwent a cold pressor stress (CPS) procedure to induce stress while the control participants immersed their hands in warm water. Saliva samples were collected to index estrogen, progesterone and noradrenergic and cortisol response. Participants (55 university students, 26 men, 29 women) viewed a series of negatively arousing and neutral images. Participants completed recall and intrusions measures 2 days later. Negative images resulted in greater recall and more intrusions than neutral images. In the cold water condition females recalled fewer neutral memories than males. Cortisol increase predicted decreased recall of negative memories in males, and estrogen predicted increased intrusions of negative images in women. These findings are consistent with evidence that circulating levels of ovarian hormones influence memory for emotionally arousing events, and provides the first evidence of the influence of sex hormones on intrusive memories. These results provide one possible explanation for the higher incidence of anxiety disorders in women.

  14. A base-modified PNA-graphene oxide platform as a turn-on fluorescence sensor for the detection of human telomeric repeats

    Science.gov (United States)

    Sabale, Pramod M.; George, Jerrin Thomas; Srivatsan, Seergazhi G.

    2014-08-01

    Given the biological and therapeutic significance of telomeres and other G-quadruplex forming sequences in human genome, it is highly desirable to develop simple methods to study these structures, which can also be implemented in screening formats for the discovery of G-quadruplex binders. The majority of telomere detection methods developed so far are laborious and use elaborate assay and instrumental setups, and hence, are not amenable to discovery platforms. Here, we describe the development of a simple homogeneous fluorescence turn-on method, which uses a unique combination of an environment-sensitive fluorescent nucleobase analogue, the superior base pairing property of PNA, and DNA-binding and fluorescence quenching properties of graphene oxide, to detect human telomeric DNA repeats of varying lengths. Our results demonstrate that this method, which does not involve a rigorous assay setup, would provide new opportunities to study G-quadruplex structures.Given the biological and therapeutic significance of telomeres and other G-quadruplex forming sequences in human genome, it is highly desirable to develop simple methods to study these structures, which can also be implemented in screening formats for the discovery of G-quadruplex binders. The majority of telomere detection methods developed so far are laborious and use elaborate assay and instrumental setups, and hence, are not amenable to discovery platforms. Here, we describe the development of a simple homogeneous fluorescence turn-on method, which uses a unique combination of an environment-sensitive fluorescent nucleobase analogue, the superior base pairing property of PNA, and DNA-binding and fluorescence quenching properties of graphene oxide, to detect human telomeric DNA repeats of varying lengths. Our results demonstrate that this method, which does not involve a rigorous assay setup, would provide new opportunities to study G-quadruplex structures. Electronic supplementary information (ESI

  15. Intrusion Protection against SQL Injection Attacks Using a Reverse Proxy

    Directory of Open Access Journals (Sweden)

    S. Fouzul Hidhaya

    2012-07-01

    Full Text Available In this era where Internet has captured the world, level of security that this Internet provides has not grown as fast as the Internet application. Internet has eased the life of human in numerous ways, but the drawbacks like the intrusions that are attached with the Internet applications sustains the growth of these applications. One such intrusion is the SQL Injection attacks (SQLIA. Since SQLIA contributes 25% of the total Internet attacks, much research is being carried out in this area. In this paper we propose a method to detect the SQL injection. We use a Reverse proxy and MD5 algorithm to check out SQL injection in user input. Using grammar expressions rules we check for SQL injection in URL’s. This system has been tested on standard test bed applications and our work has shown significant improvement detecting and curbing the SQLIA.

  16. Integrating Innate and Adaptive Immunity for Intrusion Detection

    CERN Document Server

    Tedesco, Gianni; Aickelin, Uwe

    2010-01-01

    Network Intrusion Detection Systems (NDIS) monitor a network with the aim of discerning malicious from benign activity on that network. While a wide range of approaches have met varying levels of success, most IDS's rely on having access to a database of known attack signatures which are written by security experts. Nowadays, in order to solve problems with false positive alters, correlation algorithms are used to add additional structure to sequences of IDS alerts. However, such techniques are of no help in discovering novel attacks or variations of known attacks, something the human immune system (HIS) is capable of doing in its own specialised domain. This paper presents a novel immune algorithm for application to an intrusion detection problem. The goal is to discover packets containing novel variations of attacks covered by an existing signature base.

  17. Signature Based Intrusion Detection System Using SNORT

    Directory of Open Access Journals (Sweden)

    Vinod Kumar

    2012-11-01

    Full Text Available Now a day’s Intrusion Detection systems plays very important role in Network security. As the use of internet is growing rapidly the possibility of attack is also increasing in that ratio. People are using signature based IDS’s. Snort is mostly used signature based IDS because of it is open source software. World widely it is used in intrusion detection and prevention domain. Basic analysis and security engine (BASE is also used to see the alerts generated by Snort. In the paper we have implementation the signature based intrusion detection using Snort. Our work will help to novel user to understand the concept of Snort based IDS.

  18. Transfer of genetic therapy across human populations: molecular targets for increasing patient coverage in repeat expansion diseases.

    Science.gov (United States)

    Varela, Miguel A; Curtis, Helen J; Douglas, Andrew G L; Hammond, Suzan M; O'Loughlin, Aisling J; Sobrido, Maria J; Scholefield, Janine; Wood, Matthew J A

    2016-02-01

    Allele-specific gene therapy aims to silence expression of mutant alleles through targeting of disease-linked single-nucleotide polymorphisms (SNPs). However, SNP linkage to disease varies between populations, making such molecular therapies applicable only to a subset of patients. Moreover, not all SNPs have the molecular features necessary for potent gene silencing. Here we provide knowledge to allow the maximisation of patient coverage by building a comprehensive understanding of SNPs ranked according to their predicted suitability toward allele-specific silencing in 14 repeat expansion diseases: amyotrophic lateral sclerosis and frontotemporal dementia, dentatorubral-pallidoluysian atrophy, myotonic dystrophy 1, myotonic dystrophy 2, Huntington's disease and several spinocerebellar ataxias. Our systematic analysis of DNA sequence variation shows that most annotated SNPs are not suitable for potent allele-specific silencing across populations because of suboptimal sequence features and low variability (>97% in HD). We suggest maximising patient coverage by selecting SNPs with high heterozygosity across populations, and preferentially targeting SNPs that lead to purine:purine mismatches in wild-type alleles to obtain potent allele-specific silencing. We therefore provide fundamental knowledge on strategies for optimising patient coverage of therapeutics for microsatellite expansion disorders by linking analysis of population genetic variation to the selection of molecular targets.

  19. New Repeat Polymorphism in the AKT1 Gene Predicts Striatal Dopamine D2/D3 Receptor Availability and Stimulant-Induced Dopamine Release in the Healthy Human Brain.

    Science.gov (United States)

    Shumay, Elena; Wiers, Corinde E; Shokri-Kojori, Ehsan; Kim, Sung Won; Hodgkinson, Colin A; Sun, Hui; Tomasi, Dardo; Wong, Christopher T; Weinberger, Daniel R; Wang, Gene-Jack; Fowler, Joanna S; Volkow, Nora D

    2017-05-10

    The role of the protein kinase Akt1 in dopamine neurotransmission is well recognized and has been implicated in schizophrenia and psychosis. However, the extent to which variants in the AKT1 gene influence dopamine neurotransmission is not well understood. Here we investigated the effect of a newly characterized variant number tandem repeat (VNTR) polymorphism in AKT1 [major alleles: L- (eight repeats) and H- (nine repeats)] on striatal dopamine D2/D3 receptor (DRD2) availability and on dopamine release in healthy volunteers. We used PET and [(11)C]raclopride to assess baseline DRD2 availability in 91 participants. In 54 of these participants, we also measured intravenous methylphenidate-induced dopamine release to measure dopamine release. Dopamine release was quantified as the difference in specific binding of [(11)C]raclopride (nondisplaceable binding potential) between baseline values and values following methylphenidate injection. There was an effect of AKT1 genotype on DRD2 availability at baseline for the caudate (F(2,90) = 8.2, p = 0.001) and putamen (F(2,90) = 6.6, p = 0.002), but not the ventral striatum (p = 0.3). For the caudate and putamen, LL showed higher DRD2 availability than HH; HL were in between. There was also a significant effect of AKT1 genotype on dopamine increases in the ventral striatum (F(2,53) = 5.3, p = 0.009), with increases being stronger in HH > HL > LL. However, no dopamine increases were observed in the caudate (p = 0.1) or putamen (p = 0.8) following methylphenidate injection. Our results provide evidence that the AKT1 gene modulates both striatal DRD2 availability and dopamine release in the human brain, which could account for its association with schizophrenia and psychosis. The clinical relevance of the newly characterized AKT1 VNTR merits investigation.SIGNIFICANCE STATEMENT The AKT1 gene has been implicated in schizophrenia and psychosis. This association is likely to reflect modulation of dopamine signaling by Akt1 kinase

  20. Repeatability of Corticospinal and Spinal Measures during Lengthening and Shortening Contractions in the Human Tibialis Anterior Muscle

    NARCIS (Netherlands)

    Tallent, Jamie; Goodall, Stuart; Hortobagyi, Tibor; Gibson, Alan St Clair; French, Duncan N.; Howatson, Glyn

    2012-01-01

    Elements of the human central nervous system (CNS) constantly oscillate. In addition, there are also methodological factors and changes in muscle mechanics during dynamic muscle contractions that threaten the stability and consistency of transcranial magnetic stimulation (TMS) and perpherial nerve s

  1. A novel tRNA variable number tandem repeat at human chromosome 1q23.3 is implicated as a boundary element based on conservation of a CTCF motif in mouse.

    Science.gov (United States)

    Darrow, Emily M; Chadwick, Brian P

    2014-06-01

    The human genome contains numerous large tandem repeats, many of which remain poorly characterized. Here we report a novel transfer RNA (tRNA) tandem repeat on human chromosome 1q23.3 that shows extensive copy number variation with 9-43 repeat units per allele and displays evidence of meiotic and mitotic instability. Each repeat unit consists of a 7.3 kb GC-rich sequence that binds the insulator protein CTCF and bears the chromatin hallmarks of a bivalent domain in human embryonic stem cells. A tRNA containing tandem repeat composed of at least three 7.6-kb GC-rich repeat units reside within a syntenic region of mouse chromosome 1. However, DNA sequence analysis reveals that, with the exception of the tRNA genes that account for less than 6% of a repeat unit, the remaining 7.2 kb is not conserved with the notable exception of a 24 base pair sequence corresponding to the CTCF binding site, suggesting an important role for this protein at the locus.

  2. The effect of repeated freeze-thaw cycles on human muscle tissue visualized by postmortem computed tomography (PMCT).

    Science.gov (United States)

    Klop, Anthony C; Vester, Marloes E M; Colman, Kerri L; Ruijter, Jan M; Van Rijn, Rick R; Oostra, Roelof-Jan

    2017-09-01

    The aim of this study was to determine whether effects of repetitive freeze-thaw cycles, with various thawing temperatures, on human muscle tissue can be quantified using postmortem computed tomography (PMCT) technology. An additional objective was to determine the preferred thawing temperature for muscle tissue in this study. Human cadaver upper extremities were divided into two different thawing temperature groups and underwent a series of four freeze-thaw cycles in total. Axial CT scans were performed after each cycle. CT attenuation (in Hounsfield units, HU) was measured in four muscles of the upper extremities. HU values changed significantly with the introduction of each subsequent freeze-thaw cycle. Moreover, the changes in HU values were different for each thawing group. There was a significant increase of HU values in both groups between t0 and t1 . Unfrozen tissue showed large variation of HU values in all samples. It was possible to distinguish between samples thawed at different thawing temperatures based on their respective HU values. It is advisable to keep the number of freeze-thaw cycles to just one, if the human cadaveric tissue is to be used for educational purposes. The preferred thawing temperature in this study is 2°C. Clin. Anat. 30:799-804, 2017. © 2017Wiley Periodicals, Inc. © 2017 The Authors Clinical Anatomy published by Wiley Periodicals, Inc. on behalf of American Association of Clinical Anatomists.

  3. Intrusion Detection Architecture Utilizing Graphics Processors

    Directory of Open Access Journals (Sweden)

    Branislav Madoš

    2012-12-01

    Full Text Available With the thriving technology and the great increase in the usage of computer networks, the risk of having these network to be under attacks have been increased. Number of techniques have been created and designed to help in detecting and/or preventing such attacks. One common technique is the use of Intrusion Detection Systems (IDS. Today, number of open sources and commercial IDS are available to match enterprises requirements. However, the performance of these systems is still the main concern. This paper examines perceptions of intrusion detection architecture implementation, resulting from the use of graphics processor. It discusses recent research activities, developments and problems of operating systems security. Some exploratory evidence is presented that shows capabilities of using graphical processors and intrusion detection systems. The focus is on how knowledge experienced throughout the graphics processor inclusion has played out in the design of intrusion detection architecture that is seen as an opportunity to strengthen research expertise.

  4. Periodontal changes following molar intrusion with miniscrews

    Directory of Open Access Journals (Sweden)

    Shahin Bayani

    2015-01-01

    Conclusion: Within the limitations of this study, these results suggest that not only periodontal status was not negatively affected by intrusion, but also there were signs of periodontal improvement including attachment gain and shortening of clinical crown height.

  5. A phased approach to network intrusion detection

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, K.A.; DuBois, D.H.; Stallings, C.A.

    1991-01-01

    This paper describes the design and development of a prototype intrusion detection system for the Los Alamos National Laboratory's Integrated Computing Network (ICN). The development of this system is based on three basic assumptions: (1) that statistical analysis of computer system and user activates may be used to characterize normal system and user behavior, and that given the resulting statistical profiles, behavior which deviates beyond certain bounds can be detected, (2) that expert system techniques can be applied to security auditing and intrusion detection, and (3) that successful intrusion detection may take place while monitoring a limited set of network activities. The Network Anomaly Detection and Intrusion Reporter (NADIR) design intent was to duplicate and improve the audit record review activities which had previously been undertaken by security personnel, to replace the manual review of audit logs with a near realtime expert system.

  6. Immune Based Intrusion Detector Generating Algorithm

    Institute of Scientific and Technical Information of China (English)

    DONG Xiao-mei; YU Ge; XIANG Guang

    2005-01-01

    Immune-based intrusion detection approaches are studied. The methods of constructing self set and generating mature detectors are researched and improved. A binary encoding based self set construction method is applied. First,the traditional mature detector generating algorithm is improved to generate mature detectors and detect intrusions faster. Then, a novel mature detector generating algorithm is proposed based on the negative selection mechanism. Accord ing to the algorithm, less mature detectors are needed to detect the abnormal activities in the network. Therefore, the speed of generating mature detectors and intrusion detection is improved. By comparing with those based on existing algo rithms, the intrusion detection system based on the algorithm has higher speed and accuracy.

  7. A Citizen's Guide to Vapor Intrusion Mitigation

    Science.gov (United States)

    This guide describes how vapor intrusion is the movement of chemical vapors from contaminated soil and groundwater into nearby buildings.Vapors primarily enter through openings in the building foundation or basement walls.

  8. Intrusion Detection System Using Advanced Honeypots

    CERN Document Server

    Singh, Ram Kumar

    2009-01-01

    The exponential growth of Internet traffic has made public servers increasingly vulnerable to unauthorized accesses and intrusions. In addition to maintaining low latency for the client, filtering unauthorized accesses has become one of the major concerns of a server maintainer. This implementation of an Intrusion Detection System distinguishes between the traffic coming from clients and the traffic originated from the attackers, in an attempt to simultaneously mitigate the problems of both latency and security. We then present the results of a series of stress and scalability tests, and suggest a number of potential uses for such a system. As computer attacks are becoming more and more difficult to identify the need for better and more efficient intrusion detection systems increases. The main problem with current intrusion detection systems is high rate of false alarms. Using honeypots provides effective solution to increase the security.

  9. Intrusion-Tolerant Architectures: Concepts and Design

    OpenAIRE

    Paulo Veríssimo; Nuno Ferreira Neves; Miguel Correia

    2003-01-01

    There is a significant body of research on distributed computing architectures, methodologies and algorithms, both in the fields of fault tolerance and security. Whilst they have taken separate paths until recently, the problems to be solved are of similar nature. In classical dependability, fault tolerance has been the workhorse of many solutions. Classical security-related work has on the other hand privileged, with few exceptions, intrusion prevention. Intrusion tolerance (IT) is a new app...

  10. Comparison of Variable-Number Tandem-Repeat Markers typing and IS1245 Restriction Fragment Length Polymorphism fingerprinting of Mycobacterium avium subsp. hominissuis from human and porcine origins

    Directory of Open Access Journals (Sweden)

    Marttila Harri

    2010-03-01

    Full Text Available Abstract Background Animal mycobacterioses are regarded as a potential zoonotic risk and cause economical losses world wide. M. avium subsp. hominissuis is a slow-growing subspecies found in mycobacterial infected humans and pigs and therefore rapid and discriminatory typing methods are needed for epidemiological studies. The genetic similarity of M. avium subsp. hominissuis from human and porcine origins using two different typing methods have not been studied earlier. The objective of this study was to compare the IS1245 RFLP pattern and MIRU-VNTR typing to study the genetic relatedness of M. avium strains isolated from slaughter pigs and humans in Finland with regard to public health aspects. Methods A novel PCR-based genotyping method, variable number tandem repeat (VNTR typing of eight mycobacterial interspersed repetitive units (MIRUs, was evaluated for its ability to characterize Finnish Mycobacterium avium subsp. hominissuis strains isolated from pigs (n = 16 and humans (n = 13 and the results were compared with those obtained by the conventional IS1245 RFLP method. Results The MIRU-VNTR results showed a discriminatory index (DI of 0,92 and the IS1245 RFLP resulted in DI 0,98. The combined DI for both methods was 0,98. The MIRU-VNTR test has the advantages of being simple, reproducible, non-subjective, which makes it suitable for large-scale screening of M. avium strains. Conclusions Both typing methods demonstrated a high degree of similarity between the strains of human and porcine origin. The parallel application of the methods adds epidemiological value to the comparison of the strains and their origins. The present approach and results support the hypothesis that there is a common source of M. avium subsp. hominissuis infection for pigs and humans or alternatively one species may be the infective source to the other.

  11. Analysis of polyglutamine-coding repeats in the TATA-binding protein in different human populations and in patients with schizophrenia an bipolar affective disorder

    Energy Technology Data Exchange (ETDEWEB)

    Rubinsztein, D.C.; Leggo, J. [Addenbrooke`s National Health Service Trust, Cambridge (United Kingdom); Crow, T.J. [Cambridge Univ. (United Kingdom)] [and others

    1996-09-20

    A new class of disease (including Huntington disease, Kennedy disease, and spinocerebellar ataxias types 1 and 3) results from abnormal expansions of CAG trinucleotides in the coding regions of genes. In all of these diseases the CAG repeats are thought to be translated into polyglutamine tracts. There is accumulating evidence arguing for CAG trinucleotide expansions as one of the causative disease mutations in schizophrenia and bipolar affective disorder. We and others believe that the TATA-binding protein (TBP) is an important candidate to investigate in these diseases as it contains a highly polymorphic stretch of glutamine codons, which are close to the threshold length where the polyglutamine tracts start to be associated with disease. Thus, we examined the lengths of this polyglutamine repeat in normal unrelated East Anglians, South African Blacks, sub-Saharan Africans mainly from Nigeria, and Asian Indians. We also examined 43 bipolar affective disorder patients and 65 schizophrenic patients. The range of polyglutamine tract-lengths that we found in humans was from 26-42 codons. No patients with bipolar affective disorder and schizophrenia had abnormal expansions at this locus. 22 refs., 1 tab.

  12. Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats

    Directory of Open Access Journals (Sweden)

    Eisenberg Eli

    2010-07-01

    Full Text Available Abstract Background Alu repeats in the human transcriptome undergo massive adenosine to inosine RNA editing. This process is selective, as editing efficiency varies greatly among different adenosines. Several studies have identified weak sequence motifs characterizing the editing sites, but these alone do not account for the large diversity observed. Results Here we build a dataset of 29,971 editing sites and use it to characterize editing preferences. We focus on structural aspects, studying the double-stranded RNA structure of the Alu repeats, and show the editing frequency of a given site to depend strongly on the micro-structure it resides in. Surprisingly, we find that interior loops, and especially the nucleotides at their edges, are more likely to be edited than helices. In addition, the sequence motifs characterizing editing sites vary with the micro-structure. Finally, we show that thermodynamic stability of the site is important for its editing. Conclusions Analysis of a large dataset of editing events reveals more information on sequence and structural motifs characterizing the A-to-I editing process

  13. Effect of variable number of tandem repeats polymorphism in the human dopamine transporter gene on conflict information processing according to event-related potential

    Institute of Scientific and Technical Information of China (English)

    Chunyu Han; Yuping Wang; Xin Wang; Ying Liu

    2010-01-01

    The dopamine transporter(DAT)is responsible for dopamine reuptake from the synaptic cleft.A variable number of tandem repeats polymorphism in the DAT gene is related to DAT availability and has been associated with cognition.With the advantage of high-time resolution,event-related potential is an important method to study the time course of human information processing.Previous results have suggested that dopamine exhibits a close relationship with conflicting information processing.Therefore,the present study assumed that conflicting information processing could be influenced by DAT variable number of tandem repeats polymorphism.To confirm this,the present study analyzed the influence of DAT genotypes on N270,which is presumed to reflect neural activity of conflict information processing in young healthy adults.A S1-S2 matching task was performed in healthy adults with 10/10 genotype(n = 14)and 10/9genotypes(n = 14),respectively,when event-related potentials were recorded.Results demonstrated that subjects with the 10/10 genotype exhibited shorter N270 latency and quicker reaction times compared with subjects with the 10/9 genotype.There were no differences in N270amplitude between the two genotypes.These results suggested that 10/10 genotype subjects more efficiently processed conflict information.

  14. Two novel DXZ4-associated long noncoding RNAs show developmental changes in expression coincident with heterochromatin formation at the human (Homo sapiens) macrosatellite repeat.

    Science.gov (United States)

    Figueroa, Debbie M; Darrow, Emily M; Chadwick, Brian P

    2015-12-01

    On the male X and female active X chromosome (Xa), the macrosatellite repeat (MSR) DXZ4 is packaged into constitutive heterochromatin characterized by CpG methylation and histone H3 tri-methylated at lysine-9 (H3K9me3). In contrast, DXZ4 on the female inactive X chromosome (Xi), is packaged into euchromatin, is bound by the architectural protein CCCTC-binding factor, and mediates Xi-specific long-range cis contact with similarly packaged tandem repeats on the Xi. In cancer, male DXZ4 can inappropriately revert to a Xi-like state and other MSRs have been reported to adopt alternate chromatin configurations in response to disease. Given this plasticity, we sought to identify factors that might control heterochromatin at DXZ4. In human embryonic stem cells, we found low levels of 5-hydroxymethylcytosine at DXZ4 and that this mark is lost upon differentiation as H3K9me3 is acquired. We identified two previously undescribed DXZ4 associated noncoding transcripts (DANT1 and DANT2) that are transcribed toward DXZ4 from promoters flanking the array. Each generates transcript isoforms that traverse the MSR. However, upon differentiation, enhancer of Zeste-2 silences DANT1, and DANT2 transcription terminates prior to entering DXZ4. These data support a model wherein DANT1 and/or DANT2 may function to regulate constitutive heterochromatin formation at this MSR.

  15. Two novel DXZ4-associated long noncoding RNAs show developmental changes in expression coincident with heterochromatin formation at the human (Homo sapiens) macrosatellite repeat

    Science.gov (United States)

    Figueroa, Debbie M.; Darrow, Emily M.; Chadwick, Brian P.

    2015-01-01

    On the male X and female active X chromosome (Xa), the macrosatellite repeat (MSR) DXZ4 is packaged into constitutive heterochromatin characterized by CpG methylation and histone H3 tri-methylated at lysine-9 (H3K9me3). In contrast, DXZ4 on the female inactive X chromosome (Xi), is packaged into euchromatin, is bound by the architectural protein CCCTC-binding factor, and mediates Xi-specific long-range cis contact with similarly packaged tandem repeats on the Xi. In cancer, male DXZ4 can inappropriately revert to a Xi-like state and other MSRs have been reported to adopt alternate chromatin configurations in response to disease. Given this plasticity, we sought to identify factors that might control heterochromatin at DXZ4. In human embryonic stem cells, we found low levels of 5-hydroxymethylcytosine at DXZ4, and that this mark is lost upon differentiation as H3K9me3 is acquired. We identified two previously undescribed DXZ4 associated non-coding transcripts (DANT1 and DANT2) that are transcribed towards DXZ4 from promoters flanking the array. Each generates transcript isoforms that traverse the MSR. However, upon differentiation, Enhancer of Zeste-2 silences DANT1, and DANT2 transcription terminates prior to entering DXZ4. These data support a model wherein DANT1 and/or DANT2 may function to regulate constitutive heterochromatin formation at this MSR. PMID:26188586

  16. Cluster based Intrusion Detection System for Manets

    Directory of Open Access Journals (Sweden)

    Nisha Dang

    2012-07-01

    Full Text Available Manets are the ad hoc networks that are build on demand or instantly when some mobile nodes come in the mobility range of each other and decide to cooperate for data transfer and communication. Therefore there is no defined topology for Manets. They communicate in dynamic topology which continuously changes as nodes are not stable. Due to this lack of infrastructure and distributed nature they are more vulnerable for attacks and provide a good scope to malicious users to become part of the network. To prevent the security of mobile ad hoc networks many security measures are designed such as encryption algorithms, firewalls etc. But still there is some scope of malicious actions. So, Intrusion detection systems are proposed to detect any intruder in the network and its malicious activities. Cluster based intrusion detection system is also designed to restrict the intruders activities in clusters of mobile nodes. In clusters each node run some intrusion detection code to detect local as well as global intrusion. In this paper we have taken insight of intrusion detection systems and different attacks on Manet security. Then we proposed how overhead involved in cluster based intrusion detection system can be reduced.

  17. A system for distributed intrusion detection

    Energy Technology Data Exchange (ETDEWEB)

    Snapp, S.R.; Brentano, J.; Dias, G.V.; Goan, T.L.; Heberlein, L.T.; Ho, Che-Lin; Levitt, K.N.; Mukherjee, B. (California Univ., Davis, CA (USA). Div. of Computer Science); Grance, T. (Air Force Cryptologic Support Center, San Antonio, TX (USA)); Mansur, D.L.; Pon, K.L. (Lawrence Livermore National Lab., CA (USA)); Smaha, S.E. (Haystack Labs., Inc., Austin, TX (USA))

    1991-01-01

    The study of providing security in computer networks is a rapidly growing area of interest because the network is the medium over which most attacks or intrusions on computer systems are launched. One approach to solving this problem is the intrusion-detection concept, whose basic premise is that not only abandoning the existing and huge infrastructure of possibly-insecure computer and network systems is impossible, but also replacing them by totally-secure systems may not be feasible or cost effective. Previous work on intrusion-detection systems were performed on stand-alone hosts and on a broadcast local area network (LAN) environment. The focus of our present research is to extend our network intrusion-detection concept from the LAN environment to arbitarily wider areas with the network topology being arbitrary as well. The generalized distributed environment is heterogeneous, i.e., the network nodes can be hosts or servers from different vendors, or some of them could be LAN managers, like our previous work, a network security monitor (NSM), as well. The proposed architecture for this distributed intrusion-detection system consists of the following components: a host manager in each host; a LAN manager for monitoring each LAN in the system; and a central manager which is placed at a single secure location and which receives reports from various host and LAN managers to process these reports, correlate them, and detect intrusions. 11 refs., 2 figs.

  18. Monoclonal antibodies recognizing the non-tandem repeat regions of the human mucin MUC4 in pancreatic cancer.

    Directory of Open Access Journals (Sweden)

    Maneesh Jain

    Full Text Available The MUC4 mucin is a high molecular weight, membrane-bound, and highly glycosylated protein. It is a multi-domain protein that is putatively cleaved into a large mucin-like subunit (MUC4α and a C-terminal growth-factor like subunit (MUC4β. MUC4 plays critical roles in physiological and pathological conditions and is aberrantly overexpressed in several cancers, including those of the pancreas, cervix, breast and lung. It is also a potential biomarker for the diagnosis, prognosis and progression of several malignancies. Further, MUC4 plays diverse functional roles in cancer initiation and progression as evident from its involvement in oncogenic transformation, proliferation, inhibition of apoptosis, motility and invasion, and resistance to chemotherapy in human cancer cells. We have previously generated a monoclonal antibody 8G7, which is directed against the TR region of MUC4, and has been extensively used to study the expression of MUC4 in several malignancies. Here, we describe the generation of anti-MUC4 antibodies directed against the non-TR regions of MUC4. Recombinant glutathione-S-transferase (GST-fused MUC4α fragments, both upstream (MUC4α-N-Ter and downstream (MUC4α-C-Ter of the TR domain, were used as immunogens to immunize BALB/c mice. Following cell fusion, hybridomas were screened using the aforementioned recombinant proteins ad lysates from human pancreatic cell lines. Three anti MUC4α-N-Ter and one anti-MUC4α-C-Ter antibodies were characterized by several inmmunoassays including enzyme-linked immunosorbent assay (ELISA, immunoblotting, immunofluorescene, flow cytometry and immunoprecipitation using MUC4 expressing human pancreatic cancer cell lines. The antibodies also reacted with the MUC4 in human pancreatic tumor sections in immunohistochemical analysis. The new domain-specific anti-MUC4 antibodies will serve as important reagents to study the structure-function relationship of MUC4 domains and for the development of MUC4

  19. Saltwater Intrusion: Climate change mitigation or just water resources management?

    Science.gov (United States)

    Ferguson, G. A.; Gleeson, T.

    2011-12-01

    Climate change and population growth are expected to substantially increase the vulnerability of global water resources throughout the 21st century. Coastal groundwater systems are a nexus of the world's changing oceanic and hydrologic systems and a critical resource for the over one billion people living in coastal areas as well as for terrestrial and offshore ecosystems. Synthesis studies and detailed simulations predict that rising sea levels could negatively impact coastal aquifers by causing saltwater to intrude landward within coastal aquifers or by saltwater inundation of coastal regions. Saltwater intrusion caused by excessive extraction is already impacting entire island nations and globally in diverse regions such as Nile River delta in Egypt, Queensland, Australia and Long Island, USA. However, the vulnerability of coastal aquifers to sea level rise and excessive extraction has not been systematically compared. Here we show that coastal aquifers are much more vulnerable to groundwater extraction than predicted sea level rise in wide-ranging hydrogeologic conditions and population densities. Low lying areas with small hydraulic gradients are more sensitive to climate change but a review of existing coastal aquifer indicates that saltwater intrusion problems are more likely to arise where water demand is high. No cases studies were found linking saltwater intrusion to sea level rise during the past century. Humans are a key driver in the hydrology of coastal aquifers and that adapting to sea level rise at the expense of better water management is misguided.

  20. Transcellular activation of the human immunodeficiency virus type 1 long terminal repeat in T lymphocytes requires CD4-gp120 binding.

    Science.gov (United States)

    Marcuzzi, A; Lowy, I; Weinberger, O K

    1992-01-01

    Cells expressing human immunodeficiency virus type 1 (HIV-1) tat can transactivate the HIV-1 long terminal repeat (LTR) in cocultured T lymphocytes. In this report, we describe the molecular requirements for transcellular activation of the LTR in Jurkat cells. An analysis with deletion mutants and blocking antibodies demonstrated a requirement for env expression in addition to tat expression for transcellular activation to occur. The results suggest that the transient association of CD4 and gp120 in cocultured cells is required for tat-mediated transcellular activation. The events that follow CD4-gp120 binding in transactivation, however, do not require the gp120-neutralizing domain, in contrast to HIV-mediated fusion and infection. The consequences of this interaction on cellular function are currently under investigation. Images PMID:1351104

  1. Time course of the induction of homeostatic plasticity generated by repeated transcranial direct current stimulation of the human motor cortex.

    Science.gov (United States)

    Fricke, K; Seeber, A A; Thirugnanasambandam, N; Paulus, W; Nitsche, M A; Rothwell, J C

    2011-03-01

    Several mechanisms have been proposed that control the amount of plasticity in neuronal circuits and guarantee dynamic stability of neuronal networks. Homeostatic plasticity suggests that the ease with which a synaptic connection is facilitated/suppressed depends on the previous amount of network activity. We describe how such homeostatic-like interactions depend on the time interval between two conditioning protocols and on the duration of the preconditioning protocol. We used transcranial direct current stimulation (tDCS) to produce short-lasting plasticity in the motor cortex of healthy humans. In the main experiment, we compared the aftereffect of a single 5-min session of anodal or cathodal tDCS with the effect of a 5-min tDCS session preceded by an identical 5-min conditioning session administered 30, 3, or 0 min beforehand. Five-minute anodal tDCS increases excitability for about 5 min. The same duration of cathodal tDCS reduces excitability. Increasing the duration of tDCS to 10 min prolongs the duration of the effects. If two 5-min periods of tDCS are applied with a 30-min break between them, the effect of the second period of tDCS is identical to that of 5-min stimulation alone. If the break is only 3 min, then the second session has the opposite effect to 5-min tDCS given alone. Control experiments show that these shifts in the direction of plasticity evolve during the 10 min after the first tDCS session and depend on the duration of the first tDCS but not on intracortical inhibition and facilitation. The results are compatible with a time-dependent "homeostatic-like" rule governing the response of the human motor cortex to plasticity probing protocols.

  2. Sewer Gas: An Indoor Air Source of PCE to Consider During Vapor Intrusion Investigations.

    Science.gov (United States)

    Pennell, Kelly G; Scammell, Madeleine Kangsen; McClean, Michael D; Ames, Jennifer; Weldon, Brittany; Friguglietti, Leigh; Suuberg, Eric M; Shen, Rui; Indeglia, Paul A; Heiger-Bernays, Wendy J

    2013-01-01

    The United States Environmental Protection Agency (USEPA) is finalizing its vapor intrusion guidelines. One of the important issues related to vapor intrusion is background concentrations of volatile organic chemicals (VOCs) in indoor air, typically attributed to consumer products and building materials. Background concentrations can exist even in the absence of vapor intrusion and are an important consideration when conducting site assessments. In addition, the development of accurate conceptual models that depict pathways for vapor entry into buildings is important during vapor intrusion site assessments. Sewer gas, either as a contributor to background concentrations or as part of the site conceptual model, is not routinely evaluated during vapor intrusion site assessments. The research described herein identifies an instance where vapors emanating directly from a sanitary sewer pipe within a residence were determined to be a source of tetrachloroethylene (PCE) detected in indoor air. Concentrations of PCE in the bathroom range from 2.1 to 190 ug/m(3) and exceed typical indoor air concentrations by orders of magnitude resulting in human health risk classified as an "Imminent Hazard" condition. The results suggest that infiltration of sewer gas resulted in PCE concentrations in indoor air that were nearly two-orders of magnitude higher as compared to when infiltration of sewer gas was not known to be occurring. This previously understudied pathway whereby sewers serve as sources of PCE (and potentially other VOC) vapors is highlighted. Implications for vapor intrusion investigations are also discussed.

  3. The specificity of stimulus-specific adaptation in human auditory cortex increases with repeated exposure to the adapting stimulus.

    Science.gov (United States)

    Briley, Paul M; Krumbholz, Katrin

    2013-12-01

    The neural response to a sensory stimulus tends to be more strongly reduced when the stimulus is preceded by the same, rather than a different, stimulus. This stimulus-specific adaptation (SSA) is ubiquitous across the senses. In hearing, SSA has been suggested to play a role in change detection as indexed by the mismatch negativity. This study sought to test whether SSA, measured in human auditory cortex, is caused by neural fatigue (reduction in neural responsiveness) or by sharpening of neural tuning to the adapting stimulus. For that, we measured event-related cortical potentials to pairs of pure tones with varying frequency separation and stimulus onset asynchrony (SOA). This enabled us to examine the relationship between the degree of specificity of adaptation as a function of frequency separation and the rate of decay of adaptation with increasing SOA. Using simulations of tonotopic neuron populations, we demonstrate that the fatigue model predicts independence of adaptation specificity and decay rate, whereas the sharpening model predicts interdependence. The data showed independence and thus supported the fatigue model. In a second experiment, we measured adaptation specificity after multiple presentations of the adapting stimulus. The multiple adapters produced more adaptation overall, but the effect was more specific to the adapting frequency. Within the context of the fatigue model, the observed increase in adaptation specificity could be explained by assuming a 2.5-fold increase in neural frequency selectivity. We discuss possible bottom-up and top-down mechanisms of this effect.

  4. A melodic contour repeatedly experienced by human near-term fetuses elicits a profound cardiac reaction one month after birth.

    Directory of Open Access Journals (Sweden)

    Carolyn Granier-Deferre

    Full Text Available BACKGROUND: Human hearing develops progressively during the last trimester of gestation. Near-term fetuses can discriminate acoustic features, such as frequencies and spectra, and process complex auditory streams. Fetal and neonatal studies show that they can remember frequently recurring sounds. However, existing data can only show retention intervals up to several days after birth. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that auditory memories can last at least six weeks. Experimental fetuses were given precisely controlled exposure to a descending piano melody twice daily during the 35(th, 36(th, and 37(th weeks of gestation. Six weeks later we assessed the cardiac responses of 25 exposed infants and 25 naive control infants, while in quiet sleep, to the descending melody and to an ascending control piano melody. The melodies had precisely inverse contours, but similar spectra, identical duration, tempo and rhythm, thus, almost identical amplitude envelopes. All infants displayed a significant heart rate change. In exposed infants, the descending melody evoked a cardiac deceleration that was twice larger than the decelerations elicited by the ascending melody and by both melodies in control infants. CONCLUSIONS/SIGNIFICANCE: Thus, 3-weeks of prenatal exposure to a specific melodic contour affects infants 'auditory processing' or perception, i.e., impacts the autonomic nervous system at least six weeks later, when infants are 1-month old. Our results extend the retention interval over which a prenatally acquired memory of a specific sound stream can be observed from 3-4 days to six weeks. The long-term memory for the descending melody is interpreted in terms of enduring neurophysiological tuning and its significance for the developmental psychobiology of attention and perception, including early speech perception, is discussed.

  5. Comparative systems toxicology analysis of cigarette smoke and aerosol from a candidate modified risk tobacco product in organotypic human gingival epithelial cultures: A 3-day repeated exposure study.

    Science.gov (United States)

    Zanetti, Filippo; Titz, Bjoern; Sewer, Alain; Lo Sasso, Giuseppe; Scotti, Elena; Schlage, Walter K; Mathis, Carole; Leroy, Patrice; Majeed, Shoaib; Torres, Laura Ortega; Keppler, Brian R; Elamin, Ashraf; Trivedi, Keyur; Guedj, Emmanuel; Martin, Florian; Frentzel, Stefan; Ivanov, Nikolai V; Peitsch, Manuel C; Hoeng, Julia

    2017-03-01

    Smoking is one of the major lifestyle-related risk factors for periodontal diseases. Modified risk tobacco products (MRTP) offer a promising alternative in the harm reduction strategy for adult smokers unable to quit. Using a systems toxicology approach, we investigated and compared the exposure effects of a reference cigarette (3R4F) and a heat-not-burn technology-based candidate MRTP, the Tobacco Heating System (THS) 2.2. Human gingival epithelial organotypic cultures were repeatedly exposed (3 days) for 28 min at two matching concentrations of cigarette smoke (CS) or THS2.2 aerosol. Results showed only minor histopathological alterations and minimal cytotoxicity upon THS2.2 aerosol exposure compared to CS (1% for THS2.2 aerosol vs. 30% for CS, at the high concentration). Among the 14 proinflammatory mediators analyzed, only 5 exhibited significant alterations with THS2.2 exposure compared with 11 upon CS exposure. Transcriptomic and metabolomic analysis indicated a general reduction of the impact in THS2.2 aerosol-exposed samples with respect to CS (∼79% lower biological impact for the high THS2.2 aerosol concentration compared to CS, and 13 metabolites significantly perturbed for THS2.2 vs. 181 for CS). This study indicates that exposure to THS2.2 aerosol had a lower impact on the pathophysiology of human gingival organotypic cultures than CS. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. A New Method for Intrusion Detection using Manifold Learning Algorithm

    Directory of Open Access Journals (Sweden)

    Guoping Hou

    2013-07-01

    Full Text Available Computer and network security has received and will still receive much attention. Any unexpected intrusion will damage the network. It is therefore imperative to detect the network intrusion to ensure the normal operation of the internet. There are many studies in the intrusion detection and intrusion patter recognition. The artificial neural network (ANN has proven to be powerful for the intrusion detection. However, very little work has discussed the optimization of the input intrusion features for the ANN. Generally, the intrusion features contain a certain number of useless features, which is useless for the intrusion detection. Large dimensions of the feature data will also affect the intrusion detection performance of the ANN. In order to improve the ANN performance, a new approach for network intrusion detection based on nonlinear feature dimension reduction and ANN is proposed in this work. The manifold learning algorithm was used to reduce the intrusion feature vector. Then an ANN classifier was employed to identify the intrusion. The efficiency of the proposed method was evaluated with the real intrusion data. The test result shows that the proposed approach has good intrusion detection performance.

  7. Long-Term Safety of Repeated Blood-Brain Barrier Opening via Focused Ultrasound with Microbubbles in Non-Human Primates Performing a Cognitive Task.

    Directory of Open Access Journals (Sweden)

    Matthew E Downs

    Full Text Available Focused Ultrasound (FUS coupled with intravenous administration of microbubbles (MB is a non-invasive technique that has been shown to reliably open (increase the permeability of the blood-brain barrier (BBB in multiple in vivo models including non-human primates (NHP. This procedure has shown promise for clinical and basic science applications, yet the safety and potential neurological effects of long term application in NHP requires further investigation under parameters shown to be efficacious in that species (500 kHz, 200-400 kPa, 4-5 μm MB, 2 minute sonication. In this study, we repeatedly opened the BBB in the caudate and putamen regions of the basal ganglia of 4 NHP using FUS with systemically-administered MB over 4-20 months. We assessed the safety of the FUS with MB procedure using MRI to detect edema or hemorrhaging in the brain. Contrast enhanced T1-weighted MRI sequences showed a 98% success rate for openings in the targeted regions. T2-weighted and SWI sequences indicated a lack edema in the majority of the cases. We investigated potential neurological effects of the FUS with MB procedure through quantitative cognitive testing of' visual, cognitive, motivational, and motor function using a random dot motion task with reward magnitude bias presented on a touchpanel display. Reaction times during the task significantly increased on the day of the FUS with MB procedure. This increase returned to baseline within 4-5 days after the procedure. Visual motion discrimination thresholds were unaffected. Our results indicate FUS with MB can be a safe method for repeated opening of the BBB at the basal ganglia in NHP for up to 20 months without any long-term negative physiological or neurological effects with the parameters used.

  8. Expanded complexity of unstable repeat diseases

    OpenAIRE

    Polak, Urszula; McIvor, Elizabeth; Dent, Sharon Y.R.; Wells, Robert D.; Napierala, Marek.

    2012-01-01

    Unstable Repeat Diseases (URDs) share a common mutational phenomenon of changes in the copy number of short, tandemly repeated DNA sequences. More than 20 human neurological diseases are caused by instability, predominantly expansion, of microsatellite sequences. Changes in the repeat size initiate a cascade of pathological processes, frequently characteristic of a unique disease or a small subgroup of the URDs. Understanding of both the mechanism of repeat instability and molecular consequen...

  9. Data Mining and Intrusion Detection Systems

    Directory of Open Access Journals (Sweden)

    Zibusiso Dewa

    2016-01-01

    Full Text Available The rapid evolution of technology and the increased connectivity among its components, imposes new cyber-security challenges. To tackle this growing trend in computer attacks and respond threats, industry professionals and academics are joining forces in order to build Intrusion Detection Systems (IDS that combine high accuracy with low complexity and time efficiency. The present article gives an overview of existing Intrusion Detection Systems (IDS along with their main principles. Also this article argues whether data mining and its core feature which is knowledge discovery can help in creating Data mining based IDSs that can achieve higher accuracy to novel types of intrusion and demonstrate more robust behaviour compared to traditional IDSs.

  10. Intrusion Detection System: Security Monitoring System

    Directory of Open Access Journals (Sweden)

    ShabnamNoorani,

    2015-10-01

    Full Text Available An intrusion detection system (IDS is an ad hoc security solution to protect flawed computer systems. It works like a burglar alarm that goes off if someone tampers with or manages to get past other security mechanisms such as authentication mechanisms and firewalls. An Intrusion Detection System (IDS is a device or a software application that monitors network or system activities for malicious activities or policy violations and produces reports to a management station.Intrusion Detection System (IDS has been used as a vital instrument in defending the network from this malicious or abnormal activity..In this paper we are comparing host based and network based IDS and various types of attacks possible on IDS.

  11. An Adaptive Clustering Algorithm for Intrusion Detection

    Institute of Scientific and Technical Information of China (English)

    QIU Juli

    2007-01-01

    In this paper,we introduce an adaptive clustering algorithm for intrusion detection based on wavecluster which was introduced by Gholamhosein in 1999 and used with success in image processing.Because of the non-stationary characteristic of network traffic,we extend and develop an adaptive wavecluster algorithm for intrusion detection.Using the multiresolution property of wavelet transforms,we can effectively identify arbitrarily shaped clusters at different scales and degrees of detail,moreover,applying wavelet transform removes the noise from the original feature space and make more accurate cluster found.Experimental results on KDD-99 intrusion detection dataset show the efficiency and accuracy of this algorithm.A detection rate above 96% and a false alarm rate below 3% are achieved.

  12. An Overview on Intrusion Detection in Manet

    Directory of Open Access Journals (Sweden)

    Rajesh D. Wagh

    2015-05-01

    Full Text Available A mobile ad hoc network (MANET is a self-configuring of mobile devices network connected without wires and hence MANET has become a very popular technology now days. A MANETS are the networks that are building, when some mobile nodes come in the mobility range of each other for data transfer and communication. In MANET, nodes are not stable hence the communication topology is not stable due to this vulnerable for attacks. MANET devices are connected via wireless links without using an existing network infrastructure or centralized administration due to which MANETs are not able to diverse types of attacks and intrusions. Hence intrusion detection has attracted many researchers. This paper gives an overview and different methods to detect intrusion in MANET.

  13. An overview to Software Architecture in Intrusion Detection System

    CERN Document Server

    Bahrami, Mehdi

    2012-01-01

    Network intrusion detection systems provide proactive defense against security threats by detecting and blocking attack-related traffic. This task can be highly complex, and therefore, software based network intrusion detection systems have difficulty in handling high speed links. This paper reviews of many type of software architecture in intrusion detection systems and describes the design and implementation of a high-performance network intrusion detection system that combines the use of software-based network intrusion detection sensors and a network processor board. The network processor acts as a customized load balancing splitter that cooperates with a set of modified content-based network intrusion detection sensors in processing network traffic.

  14. Effective analysis of cloud based intrusion detection system

    Directory of Open Access Journals (Sweden)

    Sanjay Ram

    2012-08-01

    Full Text Available The goal of IDS is to analyze events on the network and identify attacks. The increasing number of network security related incidents makes it necessary for organizations to actively protect their sensitive data with the installation of intrusion detection systems (IDS. People are paid more attention on intrusion detection which as an important computer network security technology. According to the development trend of intrusion detection, detecting all kinds of intrusions effectively requires a global view of the monitored network, Here, discuss about new intrusion detection mechanism based on cloud computing, which can make up for the deficiency of traditional intrusion detection, and proved to be great scalable.

  15. Perceived illness intrusion among patients on hemodialysis

    Directory of Open Access Journals (Sweden)

    Bapat Usha

    2009-01-01

    Full Text Available Dialysis therapy is extremely stressful as it interferes with all spheres of daily acti-vities of the patients. This study is aimed at understanding the perceived illness intrusion among pa-tients on hemodialysis (HD and to find the association between illness intrusion and patient demo-graphics as well as duration of dialysis. A cross sectional study involving 90 patients with chronic kidney disease (CKD stage V, on HD was performed during the period from 2005 to 2006. The subjects included were above 18 years of age, willing, stable and on dialysis for at least two months. Patients with psychiatric co-morbidity were excluded. A semi-structured interview schedule covering socio-demographics and a 13 item illness intrusion checklist covering the various aspects of life was ca-rried out. The study patients were asked to rate the illness intrusion and the extent. The data were ana-lyzed statistically. The mean age of the subjects was 50.28 ± 13.69 years, males were predominant (85%, 73% were married, 50% belonged to Hindu religion, 25% had pre-degree education, 25% were employed and 22% were housewives. About 40% and 38% of the study patients belonged to middle and upper socio-economic strata respectively; 86% had urban background and lived in nuclear fami-lies. The mean duration on dialysis was 24 ± 29.6 months. All the subjects reported illness intrusion to a lesser or greater extent in various areas including: health (44%, work (70% finance (55%, diet (50% sexual life (38% and psychological status (25%. Illness had not intruded in areas of rela-tionship with spouse (67%, friends (76%, family (79%, social (40% and religious functions (72%. Statistically significant association was noted between illness intrusion and occupation (P= 0.02.

  16. Computationally Efficient Neural Network Intrusion Security Awareness

    Energy Technology Data Exchange (ETDEWEB)

    Todd Vollmer; Milos Manic

    2009-08-01

    An enhanced version of an algorithm to provide anomaly based intrusion detection alerts for cyber security state awareness is detailed. A unique aspect is the training of an error back-propagation neural network with intrusion detection rule features to provide a recognition basis. Network packet details are subsequently provided to the trained network to produce a classification. This leverages rule knowledge sets to produce classifications for anomaly based systems. Several test cases executed on ICMP protocol revealed a 60% identification rate of true positives. This rate matched the previous work, but 70% less memory was used and the run time was reduced to less than 1 second from 37 seconds.

  17. Adaptive Genetic Algorithm Model for Intrusion Detection

    Directory of Open Access Journals (Sweden)

    K. S. Anil Kumar

    2012-09-01

    Full Text Available Intrusion detection systems are intelligent systems designed to identify and prevent the misuse of computer networks and systems. Various approaches to Intrusion Detection are currently being used, but they are relatively ineffective. Thus the emerging network security systems need be part of the life system and this ispossible only by embedding knowledge into the network. The Adaptive Genetic Algorithm Model - IDS comprising of K-Means clustering Algorithm, Genetic Algorithm and Neural Network techniques. Thetechnique is tested using multitude of background knowledge sets in DARPA network traffic datasets.

  18. Intrusion Detection Using Cost-Sensitive Classification

    CERN Document Server

    Mitrokotsa, Aikaterini; Douligeris, Christos

    2008-01-01

    Intrusion Detection is an invaluable part of computer networks defense. An important consideration is the fact that raising false alarms carries a significantly lower cost than not detecting at- tacks. For this reason, we examine how cost-sensitive classification methods can be used in Intrusion Detection systems. The performance of the approach is evaluated under different experimental conditions, cost matrices and different classification models, in terms of expected cost, as well as detection and false alarm rates. We find that even under unfavourable conditions, cost-sensitive classification can improve performance significantly, if only slightly.

  19. Design of Secure Distributed Intrusion Detection Systems

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Intrusion Detection System (IDS) have received a great deal of attention because of their excellent ability of preventing network incidents. Recently, many efficient approaches have been proposed to improve detection ability of IDS. While the self-protection ability of IDS is relatively worse and easy to be exploited by attackers, this paper gives a scheme of Securely Distributed Intrusion Detection System (SDIDS). This system adopts special measurements to enforce the security of IDS components. A new secure mechanism combining role-based access control and attribute certificate is used to resist attack to communication.

  20. Intrusion Detection Approach Using Connectionist Expert System

    Institute of Scientific and Technical Information of China (English)

    MA Rui; LIU Yu-shu; DU Yan-hui

    2005-01-01

    In order to improve the detection efficiency of rule-based expert systems, an intrusion detection approach using connectionist expert system is proposed. The approach converts the AND/OR nodes into the corresponding neurons, adopts the three-layered feed forward network with full interconnection between layers,translates the feature values into the continuous values belong to the interval [0, 1 ], shows the confidence degree about intrusion detection rules using the weight values of the neural networks and makes uncertain inference with sigmoid function. Compared with the rule-based expert system, the neural network expert system improves the inference efficiency.

  1. Intrusion Detection amp Prevention Systems - Sourcefire Snort

    Directory of Open Access Journals (Sweden)

    Rajesh Vuppala

    2015-08-01

    Full Text Available Information security is a challenging issue for all business organizations today amidst increasing cyber threats. While there are many alternative intrusion detection amp prevention systems available to choose from selecting the best solution to implement to detect amp prevent cyber-attacks is a difficult task. The best solution is of the one that gets the best reviews and suits the organizations needs amp budget. In this review paper we summarize various classes of intrusion detection and prevention systems compare features of alternative solutions and make recommendation for implementation of one as the best solution for business organization in Fiji.

  2. Computationally Efficient Neural Network Intrusion Security Awareness

    Energy Technology Data Exchange (ETDEWEB)

    Todd Vollmer; Milos Manic

    2009-08-01

    An enhanced version of an algorithm to provide anomaly based intrusion detection alerts for cyber security state awareness is detailed. A unique aspect is the training of an error back-propagation neural network with intrusion detection rule features to provide a recognition basis. Network packet details are subsequently provided to the trained network to produce a classification. This leverages rule knowledge sets to produce classifications for anomaly based systems. Several test cases executed on ICMP protocol revealed a 60% identification rate of true positives. This rate matched the previous work, but 70% less memory was used and the run time was reduced to less than 1 second from 37 seconds.

  3. Intrusive and Non-Intrusive Instruction in Dynamic Skill Training.

    Science.gov (United States)

    1981-10-01

    Bachrach Environmental Stress Program Center I Dr. Lloyd Hitchcock Naval Medical Research Institute Human Factors Engineering Bethesda, MD 20014 Division...22217 Washington, DC 20350 5 Personnel & Training Research Programs 1 Dr. Alfred F. Smode (Code 458) Training Analysis & Evaluation Group Office of... Alfred R. Fregly Arlington, VA 22217 AFOSR/NL, Bldg. 410] Bolling AFB 1 DR. A.L. SLAFKOSKY Washington, DC 20332 SCIENTIFIC ADVISOR (CODE RD-i) HO

  4. Repeat-until-success quantum repeaters

    Science.gov (United States)

    Bruschi, David Edward; Barlow, Thomas M.; Razavi, Mohsen; Beige, Almut

    2014-09-01

    We propose a repeat-until-success protocol to improve the performance of probabilistic quantum repeaters. Conventionally, these rely on passive static linear-optics elements and photodetectors to perform Bell-state measurements (BSMs) with a maximum success rate of 50%. This is a strong impediment for entanglement swapping between distant quantum memories. Every time a BSM fails, entanglement needs to be redistributed between the corresponding memories in the repeater link. The key ingredients of our scheme are repeatable BSMs. Under ideal conditions, these turn probabilistic quantum repeaters into deterministic ones. Under realistic conditions, our protocol too might fail. However, using additional threshold detectors now allows us to improve the entanglement generation rate by almost orders of magnitude, at a nominal distance of 1000 km, compared to schemes that rely on conventional BSMs. This improvement is sufficient to make the performance of our scheme comparable to the expected performance of some deterministic quantum repeaters.

  5. Repression of Human T-lymphotropic virus type 1 Long Terminal Repeat sense transcription by Sp1 recruitment to novel Sp1 binding sites

    Science.gov (United States)

    Fauquenoy, Sylvain; Robette, Gwenaëlle; Kula, Anna; Vanhulle, Caroline; Bouchat, Sophie; Delacourt, Nadège; Rodari, Anthony; Marban, Céline; Schwartz, Christian; Burny, Arsène; Rohr, Olivier; Van Driessche, Benoit; Van Lint, Carine

    2017-01-01

    Human T-lymphotropic Virus type 1 (HTLV-1) infection is characterized by viral latency in the majority of infected cells and by the absence of viremia. These features are thought to be due to the repression of viral sense transcription in vivo. Here, our in silico analysis of the HTLV-1 Long Terminal Repeat (LTR) promoter nucleotide sequence revealed, in addition to the four Sp1 binding sites previously identified, the presence of two additional potential Sp1 sites within the R region. We demonstrated that the Sp1 and Sp3 transcription factors bound in vitro to these two sites and compared the binding affinity for Sp1 of all six different HTLV-1 Sp1 sites. By chromatin immunoprecipitation experiments, we showed Sp1 recruitment in vivo to the newly identified Sp1 sites. We demonstrated in the nucleosomal context of an episomal reporter vector that the Sp1 sites interfered with both the sense and antisense LTR promoter activities. Interestingly, the Sp1 sites exhibited together a repressor effect on the LTR sense transcriptional activity but had no effect on the LTR antisense activity. Thus, our results demonstrate the presence of two new functional Sp1 binding sites in the HTLV-1 LTR, which act as negative cis-regulatory elements of sense viral transcription. PMID:28256531

  6. UafB is a serine-rich repeat adhesin of Staphylococcus saprophyticus that mediates binding to fibronectin, fibrinogen and human uroepithelial cells.

    Science.gov (United States)

    King, Nathan P; Beatson, Scott A; Totsika, Makrina; Ulett, Glen C; Alm, Richard A; Manning, Paul A; Schembri, Mark A

    2011-04-01

    Staphylococcus saprophyticus is an important cause of urinary tract infection (UTI), particularly among young women, and is second only to uropathogenic Escherichia coli as the most frequent cause of UTI. The molecular mechanisms of urinary tract colonization by S. saprophyticus remain poorly understood. We have identified a novel 6.84 kb plasmid-located adhesin-encoding gene in S. saprophyticus strain MS1146 which we have termed uro-adherence factor B (uafB). UafB is a glycosylated serine-rich repeat protein that is expressed on the surface of S. saprophyticus MS1146. UafB also functions as a major cell surface hydrophobicity factor. To characterize the role of UafB we generated an isogenic uafB mutant in S. saprophyticus MS1146 by interruption with a group II intron. The uafB mutant had a significantly reduced ability to bind to fibronectin and fibrinogen. Furthermore, we show that a recombinant protein containing the putative binding domain of UafB binds specifically to fibronectin and fibrinogen. UafB was not involved in adhesion in a mouse model of UTI; however, we observed a striking UafB-mediated adhesion phenotype to human uroepithelial cells. We have also identified genes homologous to uafB in other staphylococci which, like uafB, appear to be located on transposable elements. Thus, our data indicate that UafB is a novel adhesin of S. saprophyticus that contributes to cell surface hydrophobicity, mediates adhesion to fibronectin and fibrinogen, and exhibits tropism for human uroepithelial cells.

  7. Experimental saltwater intrusion in coastal aquifers using automated image analysis: Applications to homogeneous aquifers

    Science.gov (United States)

    Robinson, G.; Ahmed, Ashraf A.; Hamill, G. A.

    2016-07-01

    This paper presents the applications of a novel methodology to quantify saltwater intrusion parameters in laboratory-scale experiments. The methodology uses an automated image analysis procedure, minimising manual inputs and the subsequent systematic errors that can be introduced. This allowed the quantification of the width of the mixing zone which is difficult to measure in experimental methods that are based on visual observations. Glass beads of different grain sizes were tested for both steady-state and transient conditions. The transient results showed good correlation between experimental and numerical intrusion rates. The experimental intrusion rates revealed that the saltwater wedge reached a steady state condition sooner while receding than advancing. The hydrodynamics of the experimental mixing zone exhibited similar traits; a greater increase in the width of the mixing zone was observed in the receding saltwater wedge, which indicates faster fluid velocities and higher dispersion. The angle of intrusion analysis revealed the formation of a volume of diluted saltwater at the toe position when the saltwater wedge is prompted to recede. In addition, results of different physical repeats of the experiment produced an average coefficient of variation less than 0.18 of the measured toe length and width of the mixing zone.

  8. Data Mining Approaches for Intrusion Detection

    Science.gov (United States)

    2007-11-02

    In this paper we discuss our research in developing general and systematic methods for intrusion detection. The key ideas are to use data mining techniques...two general data mining algorithms that we have implemented: the association rules algorithm and the frequent episodes algorithm. These algorithms can

  9. Intrusion Detection System Visualization of Network Alerts

    Science.gov (United States)

    2010-07-01

    Intrusion Detection System Visualization of Network Alerts Dolores M. Zage and Wayne M. Zage Ball State University Final Report July 2010...contracts. Staff Wayne Zage, Director of the S2ERC and Professor, Department of Computer Science, Ball State University Dolores Zage, Research

  10. Chemical Observations of a Polar Vortex Intrusion

    Science.gov (United States)

    Schoeberl, M. R.; Kawa, S. R.; Douglass, A. R.; McGee, T. J.; Browell, E.; Waters, J.; Livesey, N.; Read, W.; Froidevaux, L.

    2006-01-01

    An intrusion of vortex edge air in D the interior of the Arctic polar vortex was observed on the January 31,2005 flight of the NASA DC-8 aircraft. This intrusion was identified as anomalously high values of ozone by the AROTAL and DIAL lidars. Our analysis shows that this intrusion formed when a blocking feature near Iceland collapsed, allowing edge air to sweep into the vortex interior. along the DC-8 flight track also shows the intrusion in both ozone and HNO3. Polar Stratospheric Clouds (PSCs) were observed by the DIAL lidar on the DC-8. The spatial variability of the PSCs can be explained using MLS HNO3 and H2O observations and meteorological analysis temperatures. We also estimate vortex denitrification using the relationship between N2O and HNO3. Reverse domain fill back trajectory calculations are used to focus on the features in the MLS data. The trajectory results improve the agreement between lidar measured ozone and MLS ozone and also improve the agreement between the HNO3 measurements PSC locations. The back trajectory calculations allow us to compute the local denitrification rate and reduction of HCl within the filament. We estimate a denitrification rate of about lO%/day after exposure to below PSC formation temperature. Analysis of Aura MLS observations made

  11. Root resorption after orthodontic intrusion and extrusion:.

    NARCIS (Netherlands)

    Han, G.; Huang, S.; Hoff, J.W. Von den; Zeng, X.; Kuijpers-Jagtman, A.M.

    2005-01-01

    The aim of this investigation was to compare root resorption in the same individual after application of continuous intrusive and extrusive forces. In nine patients (mean age 15.3 years), the maxillary first premolars were randomly intruded or extruded with a continuous force of 100 cN for eight wee

  12. Access Control from an Intrusion Detection Perspective

    NARCIS (Netherlands)

    Nunes Leal Franqueira, V.

    Access control and intrusion detection are essential components for securing an organization's information assets. In practice, these components are used in isolation, while their fusion would contribute to increase the range and accuracy of both. One approach to accomplish this fusion is the

  13. How stratospheric are deep stratospheric intrusions?

    Science.gov (United States)

    Trickl, T.; Vogelmann, H.; Giehl, H.; Scheel, H.-E.; Sprenger, M.; Stohl, A.

    2014-09-01

    Preliminary attempts of quantifying the stratospheric ozone contribution in the observations at the Zugspitze summit (2962 m a.s.l.) next to Garmisch-Partenkirchen in the German Alps had yielded an approximate doubling of the stratospheric fraction of the Zugspitze ozone during the time period 1978 to 2004. These investigations had been based on data filtering by using low relative humidity (RH) and elevated 7Be as the criteria for selecting half-hour intervals of ozone data representative of stratospheric intrusion air. To quantify the residual stratospheric component in stratospherically influenced air masses, however, the mixing of tropospheric air into the stratospheric intrusion layers must be taken into account. In fact, the dewpoint mirror instrument at the Zugspitze summit station rarely registers RH values lower than 10% in stratospheric air intrusions. Since 2007 a programme of routine lidar sounding of ozone, water vapour and aerosol has been conducted in the Garmisch-Partenkirchen area. The lidar results demonstrate that the intrusion layers are drier by roughly one order of magnitude than indicated in the in situ measurements. Even in thin layers RH values clearly below 1% have frequently been observed. These thin, undiluted layers present an important challenge for atmospheric modelling. Although the ozone values never reach values typical of the lower-stratosphere it becomes, thus, obvious that, without strong wind shear or convective processes, mixing of stratospheric and tropospheric air must be very slow in most of the free troposphere. As a consequence, the analysis the Zugspitze data can be assumed to be more reliable than anticipated. Finally, the concentrations of Zugspitze carbon monoxide rarely drop inside intrusion layers and normally stay clearly above full stratospheric values. This indicates that most of the CO, and thus the intrusion air mass, originates in the shallow "mixing layer" around the thermal tropopause. The CO mixing ratio in

  14. How stratospheric are deep stratospheric intrusions?

    Directory of Open Access Journals (Sweden)

    T. Trickl

    2014-06-01

    Full Text Available Preliminary attempts of quantifying the stratospheric ozone contribution in the observations at the Zugspitze summit (2962 m a.s.l. next to Garmisch-Partenkirchen in the German Alps had yielded an approximate doubling of the stratospheric fraction of the Zugspitze ozone during the time period 1978 and 2004. These investigations had been based on data filtering by using low relative humidity and elevated 7Be as the criteria for selecting half-hour intervals of ozone data representative of stratospheric intrusion air. For quantifying the residual stratospheric component in stratospherically influenced air masses, however, the mixing of tropospheric air into the stratospheric intrusion layers must be taken into account. In fact, the dew-point-mirror instrument at the Zugspitze summit station rarely registers relative humidity (RH values lower than 10% in stratospheric air intrusions. Since 2007 a programme of routine lidar sounding of ozone, water vapour and aerosol has been conducted in the Garmisch-Partenkirchen area. The lidar results demonstrate that the intrusion layers are dryer by roughly one order of magnitude than indicated in the in-situ measurements. Even in thin layers frequently RH values clearly below 1% have been observed. These thin, undiluted layers present an important challenge for atmospheric modelling. Although the ozone values never reach values typical of the lower-stratosphere it becomes, thus, obvious that, without strong wind shear or convective processes, mixing of stratospheric and tropospheric air must be very slow in most of the free troposphere. As a consequence, the analysis the Zugspitze data can be assumed to be more reliable than anticipated. Finally, the concentrations of Zugspitze carbon monoxide rarely drop inside intrusion layers and normally stay clearly above full stratospheric values. This indicates that most of the CO and, thus, the intrusion air mass originate in the shallow "mixing layer" around the

  15. How stratospheric are deep stratospheric intrusions?

    Directory of Open Access Journals (Sweden)

    T. Trickl

    2014-09-01

    Full Text Available Preliminary attempts of quantifying the stratospheric ozone contribution in the observations at the Zugspitze summit (2962 m a.s.l. next to Garmisch-Partenkirchen in the German Alps had yielded an approximate doubling of the stratospheric fraction of the Zugspitze ozone during the time period 1978 to 2004. These investigations had been based on data filtering by using low relative humidity (RH and elevated 7Be as the criteria for selecting half-hour intervals of ozone data representative of stratospheric intrusion air. To quantify the residual stratospheric component in stratospherically influenced air masses, however, the mixing of tropospheric air into the stratospheric intrusion layers must be taken into account. In fact, the dewpoint mirror instrument at the Zugspitze summit station rarely registers RH values lower than 10% in stratospheric air intrusions. Since 2007 a programme of routine lidar sounding of ozone, water vapour and aerosol has been conducted in the Garmisch-Partenkirchen area. The lidar results demonstrate that the intrusion layers are drier by roughly one order of magnitude than indicated in the in situ measurements. Even in thin layers RH values clearly below 1% have frequently been observed. These thin, undiluted layers present an important challenge for atmospheric modelling. Although the ozone values never reach values typical of the lower-stratosphere it becomes, thus, obvious that, without strong wind shear or convective processes, mixing of stratospheric and tropospheric air must be very slow in most of the free troposphere. As a consequence, the analysis the Zugspitze data can be assumed to be more reliable than anticipated. Finally, the concentrations of Zugspitze carbon monoxide rarely drop inside intrusion layers and normally stay clearly above full stratospheric values. This indicates that most of the CO, and thus the intrusion air mass, originates in the shallow "mixing layer" around the thermal tropopause. The

  16. NADIR (Network Anomaly Detection and Intrusion Reporter): A prototype network intrusion detection system

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, K.A.; DuBois, D.H.; Stallings, C.A.

    1990-01-01

    The Network Anomaly Detection and Intrusion Reporter (NADIR) is an expert system which is intended to provide real-time security auditing for intrusion and misuse detection at Los Alamos National Laboratory's Integrated Computing Network (ICN). It is based on three basic assumptions: that statistical analysis of computer system and user activities may be used to characterize normal system and user behavior, and that given the resulting statistical profiles, behavior which deviates beyond certain bounds can be detected, that expert system techniques can be applied to security auditing and intrusion detection, and that successful intrusion detection may take place while monitoring a limited set of network activities such as user authentication and access control, file movement and storage, and job scheduling. NADIR has been developed to employ these basic concepts while monitoring the audited activities of more than 8000 ICN users.

  17. Simulation of network intrusion detection system with GPenSim

    OpenAIRE

    2011-01-01

    In recent years, network has penetrated into every aspect of our life with its rapid growth and popularization. More and more serious network security problems have occurred together with this process, especially network intrusion problem. It has seriously affected the normal use of network, so research of network intrusion detection has become one of the hottest research areas. This thesis simulated a network intrusion detection system based on particle filter to solve the network intrusion ...

  18. Towards Multi-Stage Intrusion Detection using IP Flow Records

    OpenAIRE

    Muhammad Fahad Umer; Muhammad Sher; Imran Khan

    2016-01-01

    Traditional network-based intrusion detection sys-tems using deep packet inspection are not feasible for modern high-speed networks due to slow processing and inability to read encrypted packet content. As an alternative to packet-based intrusion detection, researchers have focused on flow-based intrusion detection techniques. Flow-based intrusion detection systems analyze IP flow records for attack detection. IP flow records contain summarized traffic information. However, flow data is very ...

  19. Efficiency of Svm and Pca to Enhance Intrusion Detection System

    OpenAIRE

    Soukaena Hassan Hashem

    2013-01-01

    Intrusion detection system (IDS) is a system that gathers and analyzes information from various areas within a computer or a network to identify attacks made against these components. This research proposed an Intrusion Detection Model (IDM) for detection intrusion attempts, the proposal is a hybrid IDM because it considers both features of network packets and host features that are sensitive to most intrusions. The dataset used to build the hybrid IDM is the proposed HybD (Hybrid Dataset) da...

  20. Transport and biodegradation of volatile organic compounds : influence on vapor intrusion into buildings

    NARCIS (Netherlands)

    Picone, S.

    2012-01-01

    Vapor intrusion occurs when volatile subsurface contaminants, migrating from the saturated zone through the unsaturated zone, accumulate in buildings. It is often the most relevant pathway for human health risks at contaminated sites, especially in urban areas; yet its assessment is controversial. F

  1. Anomaly based intrusion detection for a biometric identification system using neural networks

    CSIR Research Space (South Africa)

    Mgabile, T

    2012-10-01

    Full Text Available detection technique that analyses the fingerprint biometric network traffic for evidence of intrusion. The neural network algorithm that imitates the way a human brain works is used in this study to classify normal traffic and learn the correct traffic...

  2. Simulated Conversations With Virtual Humans to Improve Patient-Provider Communication and Reduce Unnecessary Prescriptions for Antibiotics: A Repeated Measure Pilot Study

    Science.gov (United States)

    2017-01-01

    Background Despite clear evidence that antibiotics do not cure viral infections, the problem of unnecessary prescribing of antibiotics in ambulatory care persists, and in some cases, prescribing patterns have increased. The overuse of antibiotics for treating viral infections has created numerous economic and clinical consequences including increased medical costs due to unnecessary hospitalizations, antibiotic resistance, disruption of gut bacteria, and obesity. Recent research has underscored the importance of collaborative patient-provider communication as a means to reduce the high rates of unnecessary prescriptions for antibiotics. However, most patients and providers do not feel prepared to engage in such challenging conversations. Objectives The aim of this pilot study was to assess the ability of a brief 15-min simulated role-play conversation with virtual humans to serve as a preliminary step to help health care providers and patients practice, and learn how to engage in effective conversations about antibiotics overuse. Methods A total of 69 participants (35 providers and 34 patients) completed the simulation once in one sitting. A pre-post repeated measures design was used to assess changes in patients’ and providers’ self-reported communication behaviors, activation, and preparedness, intention, and confidence to effectively communicate in the patient-provider encounter. Changes in patients’ knowledge and beliefs regarding antibiotic use were also evaluated. Results Patients experienced a short-term positive improvement in beliefs about appropriate antibiotic use for infection (F1,30=14.10, P=.001). Knowledge scores regarding the correct uses of antibiotics improved immediately postsimulation, but decreased at the 1-month follow-up (F1,30=31.16, P.10) Patients with lower levels of activation exhibited positive, short-term benefits in increased intent and confidence to discuss their needs and ask questions in the clinic visit, positive attitudes

  3. Vapor intrusion in urban settings: effect of foundation features and source location.

    Science.gov (United States)

    Yao, Yijun; Pennell, Kelly G; Suuberg, Eric

    2011-01-01

    In many urban settings, groundwater contains volatile organic compounds, such as tricholoroethene, tetrachloroethene, benzene, etc., at concentrations that are at or slightly below non-potable groundwater standards. Some non-potable groundwater standards do not protect against human health risks that might result from vapor intrusion. Vapor intrusion is a process by which vapor phase contaminants present in the subsurface migrate through the soil and ultimately enter a building through foundation cracks. The end result is a decrease in air quality within the building. Predicting whether or not vapor intrusion will occur at rates sufficient to cause health risks is extremely difficult and depends on many factors. In many cities, a wide-range of property uses take place over a relatively small area. For instance, schools, commercial buildings and residential buildings may all reside within a few city blocks. Most conceptual site models assume the ground surface is open to the atmosphere (i.e. green space); however the effect that an impervious surface (e.g. paving) may have on vapor transport rates is not routinely considered. Using a 3-D computational fluid dynamics model, we are investigating how the presence of impervious surfaces affects vapor intrusion rates. To complement our modeling efforts, we are in the initial stages of conducting a field study in a neighborhood where vapor intrusion is occurring.

  4. Immune System Approaches to Intrusion Detection - A Review

    CERN Document Server

    Kim, Jungwon; Aickelin, Uwe; Greensmith, Julie; Tedesco, Gianni; Twycross, Jamie

    2008-01-01

    The use of artificial immune systems in intrusion detection is an appealing concept for two reasons. Firstly, the human immune system provides the human body with a high level of protection from invading pathogens, in a robust, self-organised and distributed manner. Secondly, current techniques used in computer security are not able to cope with the dynamic and increasingly complex nature of computer systems and their security. It is hoped that biologically inspired approaches in this area, including the use of immune-based systems will be able to meet this challenge. Here we review the algorithms used, the development of the systems and the outcome of their implementation. We provide an introduction and analysis of the key developments within this field, in addition to making suggestions for future research.

  5. The state of the art in intrusion prevention and detection

    CERN Document Server

    Pathan, Al-Sakib Khan

    2013-01-01

    The State of the Art in Intrusion Prevention and Detection analyzes the latest trends and issues surrounding intrusion detection systems in computer networks, especially in communications networks. Its broad scope of coverage includes wired, wireless, and mobile networks; next-generation converged networks; and intrusion in social networks.Presenting cutting-edge research, the book presents novel schemes for intrusion detection and prevention. It discusses tracing back mobile attackers, secure routing with intrusion prevention, anomaly detection, and AI-based techniques. It also includes infor

  6. Research on IPv6 intrusion detection system Snort-based

    Science.gov (United States)

    Shen, Zihao; Wang, Hui

    2010-07-01

    This paper introduces the common intrusion detection technologies, discusses the work flow of Snort intrusion detection system, and analyzes IPv6 data packet encapsulation and protocol decoding technology. We propose the expanding Snort architecture to support IPv6 intrusion detection in accordance with CIDF standard combined with protocol analysis technology and pattern matching technology, and present its composition. The research indicates that the expanding Snort system can effectively detect various intrusion attacks; it is high in detection efficiency and detection accuracy and reduces false alarm and omission report, which effectively solves the problem of IPv6 intrusion detection.

  7. Crystal structure and size-dependent neutralization properties of HK20, a human monoclonal antibody binding to the highly conserved heptad repeat 1 of gp41.

    Directory of Open Access Journals (Sweden)

    Charles Sabin

    Full Text Available The human monoclonal antibody (mAb HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1 of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2.3 Å resolution. HK20 employs its heavy chain CDR H2 and H3 loops to bind into a conserved hydrophobic HR1 pocket that is occupied by HR2 residues in the gp41 post fusion conformation. Compared to the previously described HR1-specific mAb D5, HK20 approaches its epitope with a different angle which might favor epitope access and thus contribute to its higher neutralization breadth and potency. Comparison of the neutralization activities of HK20 IgG, Fab and scFv employing both single cycle and multiple cycle neutralization assays revealed much higher potencies for the smaller Fab and scFv over IgG, implying that the target site is difficult to access for complete antibodies. Nevertheless, two thirds of sera from HIV-1 infected individuals contain significant titers of HK20-inhibiting antibodies. The breadth of neutralization of primary isolates across all clades, the higher potencies for C-clade viruses and the targeting of a distinct site as compared to the fusion inhibitor T-20 demonstrate the potential of HK20 scFv as a therapeutic tool.

  8. Overexpression of collagen triple helix repeat containing 1 (CTHRC1) is associated with tumour aggressiveness and poor prognosis in human non-small cell lung cancer.

    Science.gov (United States)

    Ke, Zunfu; He, Weiling; Lai, Yuanhui; Guo, Xuefeng; Chen, Sharon; Li, Shuhua; Wang, Yuefeng; Wang, Liantang

    2014-10-15

    Collagen triple helix repeat-containing 1 (CTHRC1), a novel oncogene, was identified to be aberrantly overexpressed in several malignant tumors. However, the expression profile of CTHRC1 and its clinical significance in non-small cell lung cancer (NSCLC) remain unknown. In this study, we showed that CTHRC1 was evidently overexpressed in human NSCLC tissues and NSCLC cell lines at the protein and mRNA level. Ectopic up-regulation of CTHRC1 in cancer cells resulted in elevated invasive and proliferative abilities, which were attenuated by the specific CTHRC1 siRNA. The biological effect of CTHRC1 on metastasis and proliferation was mediated by the activation of the Wnt/β-catenin pathway. Furthermore, CTHRC1 immunoreactivity was evidently overexpressed in paraffin-embedded NSCLC tissues (212/292, 72.60%) in comparison to corresponding adjacent non-cancerous tissues (6/66, 9.09%) (p<0.001). Clinicopathologic analysis showed that CTHRC1 expression was significantly correlated with differentiation degree (p<0.001), clinical stage (p<0.001), T classification (p<0.001), lymph node metastasis (p=0.013) and distant metastasis (p<0.001). Kaplan-Meier analysis revealed that patients with high CTHRC1 expression had poorer overall survival rates than those with low CTHRC1 expression. Multivariate analysis indicated that CTHRC1 expression was an independent prognostic factor for the overall survival of NSCLC patients. Collectively, CTHRC1 plays important roles in NSCLC progression, and the evaluation of CTHRC1 expression could serve as a potential marker for metastasis progression and prognosis in NSCLC patients.

  9. ISDTM:An Intrusion Signatures Description Temporal Model

    Institute of Scientific and Technical Information of China (English)

    OuYangMing-guang; ZhouYang-bo

    2003-01-01

    ISDTM, based on an augmented Allen's interval temporal logic (ITL) and first-order predicate calculus, is a formal temporal model for representing intrusion signatures.It is augmented with some real time extensions which enhance the expressivity. Intrusion scenarios usually are the set of events and system states, wherethe temporal sequence is their basic relation. Intrusion signatures description, therefore, is to represent such temporal relations in a sense. While representing these signatures, ISDTM decomposes the intrusion process into the sequence of events according to their relevant intervals, and then specifies network states in these Intervals. The uncertain intrusion signatures as well as basic temporal modes of events, which consist of the parallel mode,the sequential mode and the hybrid mode, can be succinctly and naturally represented in ISDTM. Mode chart is the visualization of intrusion signatures in ISDTM, which makes the formulas more readable. The intrusion signatures descriptions in ISDTM have advantages of compact construct, concise syntax, scalability and easy implementation.

  10. A Comprehensive Study in Data Mining Frameworks for Intrusion Detection

    Directory of Open Access Journals (Sweden)

    R.Venkatesan

    2012-12-01

    Full Text Available Intrusions are the activities that violate the security policy of system. Intrusion Detection is the process used to identify intrusions. Network security is to be considered as a major issue in recent years, since the computer network keeps on expanding every day. An Intrusion Detection System (IDS is a system for detecting intrusions and reporting to the authority or to the network administration. Data mining techniques have been successfully applied in many fields like Network Management, Education, Science, Business, Manufacturing, Process control, and Fraud Detection. Data Mining for IDS is the technique which can be used mainly to identify unknown attacks and to raise alarms when security violations are detected. The purpose of this survey paper is to describe the methods/ techniques which are being used for Intrusion Detection based on Data mining concepts and the designed frame works for the same. We are also going to review the related works for intrusion detection.

  11. Iron isotope systematics of the Skaergaard intrusion

    DEFF Research Database (Denmark)

    Lesher, Charles; Lundstrom, C.C.; Barfod, Gry

    report the results of a broad study of the iron isotope compositions of gabbros within the layered and upper border series of the Skaergaard intrusion, pegmatite and granophyre associated with these gabbroic rocks, and the sandwich horizon thought to represent the product of extreme differentiation and/or...... crystallization on non-traditional stable isotope systems, particularly iron. FeTi oxide minerals (titanomagnetite and ilmenite) appear after ~60% of the magma had solidified. This was a significant event affecting the liquid line of descent and potentially accompanied by iron isotope fractionation. Here we...... liquid immiscibility. Forty-eight whole rock samples from well-constrained stratigraphic levels in the intrusion were crushed, powdered and dissolved, followed by iron separation by ion chromatography. Purified solutions were analyzed by MC- ICPMS in high-resolution mode using the sample-std bracket...

  12. In-situ trainable intrusion detection system

    Energy Technology Data Exchange (ETDEWEB)

    Symons, Christopher T.; Beaver, Justin M.; Gillen, Rob; Potok, Thomas E.

    2016-11-15

    A computer implemented method detects intrusions using a computer by analyzing network traffic. The method includes a semi-supervised learning module connected to a network node. The learning module uses labeled and unlabeled data to train a semi-supervised machine learning sensor. The method records events that include a feature set made up of unauthorized intrusions and benign computer requests. The method identifies at least some of the benign computer requests that occur during the recording of the events while treating the remainder of the data as unlabeled. The method trains the semi-supervised learning module at the network node in-situ, such that the semi-supervised learning modules may identify malicious traffic without relying on specific rules, signatures, or anomaly detection.

  13. An immune based dynamic intrusion detection model

    Institute of Scientific and Technical Information of China (English)

    LI Tao

    2005-01-01

    With the dynamic description method for self and antigen, and the concept of dynamic immune tolerance for lymphocytes in network-security domain presented in this paper, a new immune based dynamic intrusion detection model (Idid) is proposed. In Idid, the dynamic models and the corresponding recursive equations of the lifecycle of mature lymphocytes, and the immune memory are built. Therefore, the problem of the dynamic description of self and nonself in computer immune systems is solved, and the defect of the low efficiency of mature lymphocyte generating in traditional computer immune systems is overcome. Simulations of this model are performed, and the comparison experiment results show that the proposed dynamic intrusion detection model has a better adaptability than the traditional methods.

  14. Iron isotope systematics of the Skaergaard intrusion

    DEFF Research Database (Denmark)

    Lesher, Charles; Lundstrom, C.C.; Barfod, Gry

    crystallization on non-traditional stable isotope systems, particularly iron. FeTi oxide minerals (titanomagnetite and ilmenite) appear after ~60% of the magma had solidified. This was a significant event affecting the liquid line of descent and potentially accompanied by iron isotope fractionation. Here we...... report the results of a broad study of the iron isotope compositions of gabbros within the layered and upper border series of the Skaergaard intrusion, pegmatite and granophyre associated with these gabbroic rocks, and the sandwich horizon thought to represent the product of extreme differentiation and....../or liquid immiscibility. Forty-eight whole rock samples from well-constrained stratigraphic levels in the intrusion were crushed, powdered and dissolved, followed by iron separation by ion chromatography. Purified solutions were analyzed by MC- ICPMS in high-resolution mode using the sample-std bracket...

  15. A Survey on Intrusion Detection in MANETs.

    Science.gov (United States)

    BakeyaLakshmi, P.; Santhi, K.

    2012-10-01

    A mobile ad hoc network is an infrastructureless network that changes its links dynamically, which makes routing in MANET a difficult process. As Mobile Ad-Hoc Network (MANET) has become a very important technology, research concerning its security problem, especially, in intrusion detection has attracted many researchers. Feature selection methodology plays a vital role in the data analysis process. PCA is used to analyze the selected features. This is because, redundant and irrelevant features often reduce performance of the intrusion detection system. It performs better in increasing speed and predictive accuracy. This survey aims to select and analyze the network features using principal component analysis. While performing various experiments, normal and attack states are simulated and the results for the selected features are analyzed.

  16. Intrusion Detection in Wireless Body Sensor Networks

    Directory of Open Access Journals (Sweden)

    Nadya El MOUSSAID

    2017-01-01

    Full Text Available The recent advances in electronic and robotics industry have enabled the manufacturing of sensors capable of measuring a set of application-oriented parameters and transmit them back to the base station for analysis purposes. These sensors are widely used in many applications including the healthcare systems forming though a Wireless Body Sensor Networks. The medical data must be highly secured and possible intrusion has to be fully detected to proceed with the prevention phase. In this paper, we propose a new intrusion superframe schema for 802.15.6 standard to detect the cloning attack. The results proved the efficiency of our technique in detecting this type of attack based on 802.15.6 parameters performances coupled with frequency switching at the radio model.

  17. Sensing Danger: Innate Immunology for Intrusion Detection

    CERN Document Server

    Uwe, Aickelin

    2008-01-01

    The immune system provides an ideal metaphor for anomaly detection in general and computer security in particular. Based on this idea, artificial immune systems have been used for a number of years for intrusion detection, unfortunately so far with little success. However, these previous systems were largely based on immunological theory from the 1970s and 1980s and over the last decade our understanding of immunological processes has vastly improved. In this paper we present two new immune inspired algorithms based on the latest immunological discoveries, such as the behaviour of Dendritic Cells. The resultant algorithms are applied to real world intrusion problems and show encouraging results. Overall, we believe there is a bright future for these next generation artificial immune algorithms.

  18. A Survey on VANET Intrusion Detection Systems

    Directory of Open Access Journals (Sweden)

    Mohammed ERRITALI

    2013-04-01

    Full Text Available In recent years, the security issues on Vehicular ad hoc networks (VANETs have become one of the primary concerns. The VANET is inherently very vulnerable to attacks than wired network because it is characterized by high mobility, shared wireless medium and the absence of centralized security services offered by dedicated equipment such as firewalls and authentication servers. Attackcountermeasures such as digital signature and encryption, can be used as the first line of defense for reducing the possibilities of attacks. However, these techniques have limited prevention in general, and they are designed for a set of known attacks. They are unlikely to avoid most recent attacks that are designed to circumvent existing security measures. For this reason, there is a need of second technique to “detect and notify” these newer attacks, i.e. “intrusion detection”. This article aims to present and classifycurrent techniques of Intrusion Detection System (IDS aware VANETs.

  19. Multilayer Statistical Intrusion Detection in Wireless Networks

    Directory of Open Access Journals (Sweden)

    Noureddine Boudriga

    2008-12-01

    Full Text Available The rapid proliferation of mobile applications and services has introduced new vulnerabilities that do not exist in fixed wired networks. Traditional security mechanisms, such as access control and encryption, turn out to be inefficient in modern wireless networks. Given the shortcomings of the protection mechanisms, an important research focuses in intrusion detection systems (IDSs. This paper proposes a multilayer statistical intrusion detection framework for wireless networks. The architecture is adequate to wireless networks because the underlying detection models rely on radio parameters and traffic models. Accurate correlation between radio and traffic anomalies allows enhancing the efficiency of the IDS. A radio signal fingerprinting technique based on the maximal overlap discrete wavelet transform (MODWT is developed. Moreover, a geometric clustering algorithm is presented. Depending on the characteristics of the fingerprinting technique, the clustering algorithm permits to control the false positive and false negative rates. Finally, simulation experiments have been carried out to validate the proposed IDS.

  20. Test-retest repeatability of the pupil light response to blue and red light stimuli in normal human eyes using a novel pupillometer

    DEFF Research Database (Denmark)

    Herbst, Kristina; Sander, Birgit; Milea, Dan

    2011-01-01

    In this study, we evaluated the repeatability of pupil responses to colored light stimuli in healthy subjects using a prototype chromatic pupillometer. One eye of 10 healthy subjects was tested twice in the same day using monochromatic light exposure at two selected wavelengths (660 and 470¿nm......, we have developed a novel prototype of color pupillometer which demonstrates good repeatability in evoking and recording the pupillary response to a bright blue and red light stimulus....

  1. Molecular, Physiological, and Motor Performance Defects in DMSXL Mice Carrying >1,000 CTG Repeats from the Human DM1 Locus

    OpenAIRE

    Aline Huguet; Fadia Medja; Annie Nicole; Alban Vignaud; Céline Guiraud-Dogan; Arnaud Ferry; Valérie Decostre; Jean-Yves Hogrel; Friedrich Metzger; Andreas Hoeflich; Martin Baraibar; Mário Gomes-Pereira; Jack Puymirat; Guillaume Bassez; Denis Furling

    2012-01-01

    Myotonic dystrophy type 1 (DM1) is caused by an unstable CTG repeat expansion in the 3'UTR of the DM protein kinase (DMPK) gene. DMPK transcripts carrying CUG expansions form nuclear foci and affect splicing regulation of various RNA transcripts. Furthermore, bidirectional transcription over the DMPK gene and non-conventional RNA translation of repeated transcripts have been described in DM1. It is clear now that this disease may involve multiple pathogenic pathways including changes in gene ...

  2. A Review of Vapor Intrusion Models

    OpenAIRE

    Yao, Yijun; Suuberg, Eric M.

    2013-01-01

    A complete vapor intrusion (VI) model, describing vapor entry of volatile organic chemicals (VOCs) into buildings located on contaminated sites, generally consists of two main parts-one describing vapor transport in the soil and the other its entry into the building. Modeling the soil vapor transport part involves either analytically or numerically solving the equations of vapor advection and diffusion in the subsurface. Contaminant biodegradation must often also be included in this simulatio...

  3. Artificial Intrusion Detection Techniques: A Survey

    Directory of Open Access Journals (Sweden)

    Ashutosh Gupta

    2014-08-01

    Full Text Available Networking has become the most integral part of our cyber society. Everyone wants to connect themselves with each other. With the advancement of network technology, we find this most vulnerable to breach and take information and once information reaches to the wrong hands it can do terrible things. During recent years, number of attacks on networks have been increased which drew the attention of many researchers on this field. There have been many researches on intrusion detection lately. Many methods have been devised which are really very useful but they can only detect the attacks which already took place. These methods will always fail whenever there is a foreign attack which is not famous or which is new to the networking world. In order to detect new intrusions in the network, researchers have devised artificial intelligence technique for Intrusion detection prevention system. In this paper we are going to cover what types evolutionary techniques have been devised and their significance and modification.

  4. A BOOSTING APPROACH FOR INTRUSION DETECTION

    Institute of Scientific and Technical Information of China (English)

    Zan Xin; Han Jiuqiang; Zhang Junjie; Zheng Qinghua; Han Chongzhao

    2007-01-01

    Intrusion detection can be essentially regarded as a classification problem,namely,distinguishing normal profiles from intrusive behaviors.This paper introduces boosting classification algorithm into the area of intrusion detection to learn attack signatures.Decision tree algorithm is used as simple base learner of boosting algorithm.Furthermore,this paper employs the Principle Component Analysis(PCA)approach,an effective data reduction approach,to extract the key attribute set from the original high-dimensional network traffic data.KDD CUP 99 data set is used in these exDeriments to demonstrate that boosting algorithm can greatly improve the clas.sification accuracy of weak learners by combining a number of simple"weak learners".In our experiments,the error rate of training phase of boosting algorithm is reduced from 30.2%to 8%after 10 iterations.Besides,this Daper also compares boosting algorithm with Support Vector Machine(SVM)algorithm and shows that the classification accuracy of boosting algorithm is little better than SVM algorithm's.However,the generalization ability of SVM algorithm is better than boosting algorithm.

  5. Intrusion Detection with Multi-Connected Representation

    Directory of Open Access Journals (Sweden)

    Abdelkader Khobzaoui

    2016-01-01

    Full Text Available Recently, considerable attention has been given to data mining techniques to improve the performance of intrusion detection systems (IDS. This has led to the application of various classification and clustering techniques for the purpose of intrusion detection. Most of them assume that behaviors, both normal and intrusions, are represented implicitly by connected classes. We state that such assumption isn't evident and is a source of the low detection rate and false alarm. This paper proposes a suitable method able to reach high detection rate and overcomes the disadvantages of conventional approaches which consider that behaviors must be closed to connected representation only. The main strategy of the proposed method is to segment sufficiently each behavior representation by connected subsets called natural classes which are used, with a suitable metric, as tools to build the expected classifier. The results show that the proposed model has many qualities compared to conventional models; especially regarding those have used DARPA data set for testing the effectiveness of their methods. The proposed model provides decreased rates both for false negative rates and for false positives.

  6. Intrusion detection using rough set classification

    Institute of Scientific and Technical Information of China (English)

    张连华; 张冠华; 郁郎; 张洁; 白英彩

    2004-01-01

    Recently machine learning-based intrusion detection approaches have been subjected to extensive researches because they can detect both misuse and anomaly. In this paper, rough set classification (RSC), a modern learning algorithm, is used to rank the features extracted for detecting intrusions and generate intrusion detection models. Feature ranking is a very critical step when building the model. RSC performs feature ranking before generating rules, and converts the feature ranking to minimal hitting set problem addressed by using genetic algorithm (GA). This is done in classical approaches using Support Vector Machine (SVM) by executing many iterations, each of which removes one useless feature. Compared with those methods, our method can avoid many iterations. In addition, a hybrid genetic algorithm is proposed to increase the convergence speed and decrease the training time of RSC. The models generated by RSC take the form of"IF-THEN" rules, which have the advantage of explication. Tests and comparison of RSC with SVM on DARPA benchmark data showed that for Probe and DoS attacks both RSC and SVM yielded highly accurate results (greater than 99% accuracy on testing set).

  7. Intrusion detection using rough set classification

    Institute of Scientific and Technical Information of China (English)

    张连华; 张冠华; 郁郎; 张洁; 白英彩

    2004-01-01

    Recently machine learning-based intrusion detection approaches have been subjected to extensive researches because they can detect both misuse and anomaly. In this paper, rough set classification (RSC), a modem learning algorithm,is used to rank the features extracted for detecting intrusions and generate intrusion detection models. Feature ranking is a very critical step when building the model. RSC performs feature ranking before generating rules, and converts the feature ranking to minimal hitting set problem addressed by using genetic algorithm (GA). This is done in classical approaches using Support Vector Machine (SVM) by executing many iterations, each of which removes one useless feature. Compared with those methods, our method can avoid many iterations. In addition, a hybrid genetic algorithm is proposed to increase the convergence speed and decrease the training time of RSC. The models generated by RSC take the form of"IF-THEN" rules,which have the advantage of explication. Tests and comparison of RSC with SVM on DARPA benchmark data showed that for Probe and DoS attacks both RSC and SVM yielded highly accurate results (greater than 99% accuracy on testing set).

  8. Intrusion detection using pattern recognition methods

    Science.gov (United States)

    Jiang, Nan; Yu, Li

    2007-09-01

    Today, cyber attacks such as worms, scanning, active attackers are pervasive in Internet. A number of security approaches are proposed to address this problem, among which the intrusion detection system (IDS) appears to be one of the major and most effective solutions for defending against malicious users. Essentially, intrusion detection problem can be generalized as a classification problem, whose goal is to distinguish normal behaviors and anomalies. There are many well-known pattern recognition algorithms for classification purpose. In this paper we describe the details of applying pattern recognition methods to the intrusion detection research field. Experimenting on the KDDCUP 99 data set, we first use information gain metric to reduce the dimensionality of the original feature space. Two supervised methods, the support vector machine as well as the multi-layer neural network have been tested and the results display high detection rate and low false alarm rate, which is promising for real world applications. In addition, three unsupervised methods, Single-Linkage, K-Means, and CLIQUE, are also implemented and evaluated in the paper. The low computational complexity reveals their application in initial data reduction process.

  9. Count out your intrusions: effects of verbal encoding on intrusive memories.

    Science.gov (United States)

    Krans, Julie; Naring, Gerard; Becker, Eni S

    2009-11-01

    Peri-traumatic information processing is thought to affect the development of intrusive trauma memories. This study aimed to replicate and improve the study by Holmes, Brewin, and Hennessy (2004, Exp. 3) on the role of peri-traumatic verbal processing in analogue traumatic intrusion development. Participants viewed an aversive film under one of three conditions: counting backwards in 3s ("verbal interference"), verbalising emotions and thoughts ("verbal enhancement"), or without an extra task. A dual-process account of PTSD would predict that verbal interference would increase intrusion frequency compared to no task, whereas verbal enhancement would lead to a decrease. In contrast, mainstream memory theory predicts a decrease in intrusion frequency from any concurrent task that diverts attention away from the trauma film. The main finding was that the verbal interference task led to a decrease in intrusive memories of the film compared to the other two conditions. This finding does not support a dual-process account of PTSD, but is in line with general theories of memory and attention.

  10. Short Tandem Repeat DNA Internet Database

    Science.gov (United States)

    SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

  11. Random rapid amplification of cDNA ends (RRACE) allows for cloning of multiple novel human cDNA fragments containing (CAG)n repeats.

    Science.gov (United States)

    Carney, J P; McKnight, C; VanEpps, S; Kelley, M R

    1995-04-03

    We describe a new technique for isolating cDNA fragments in which (i) either a partial sequence of the cDNA is known or (ii) a repeat sequence is utilized. We have used this technique, termed random rapid amplification of cDNA ends (random RACE), to isolate a number of trinucleotide repeat (CAG)n-containing genes. Using the random RACE (RRACE) technique, we have isolated over a hundred (CAG)n-containing genes. The results of our initial analysis of ten clones indicate that three are identical to previously cloned (CAG)n-containing genes. Three of our clones matched with expressed sequence tags, one of which contained a CA repeat. The remaining four clones did not match with any sequence in GenBank. These results indicate that this approach provides a rapid and efficient method for isolating trinucleotide repeat-containing cDNA fragments. Finally, this technique may be used for purposes other than cloning repeat-containing cDNA fragments. If only a partial sequence of a gene is known, our system, described here, provides a rapid and efficient method for isolating a fragment of the gene of interest.

  12. Frequency of intrusive luxation in deciduous teeth and its effects.

    Science.gov (United States)

    Carvalho, Vivian; Jacomo, Diana Ribeiro; Campos, Vera

    2010-08-01

    The aims of this study were three-fold: First, to determine the prevalence of partial and total intrusion of the primary anterior teeth. Second, to investigate the sequelae of total and partial intrusive luxation in the primary anterior teeth and in their successors and finally, to establish whether the sequelae on both deciduous and permanent teeth were related to the child's age at the time of the intrusion. Data collected from records of 169 boys and 138 girls, all between the ages of zero and 10 years, who were undergoing treatment during the period of March 1996 to December 2004. The sample was composed of 753 traumatized deciduous teeth, of which 221 presented intrusive luxation injury. Children with ages ranging from one to 4 years were the most affected with falls being the main cause of intrusion. Of all intruded teeth 128 (57.9%) were totally intruded and 93 (42.1%) partially. Pulp necrosis/premature loss and color change were the most frequent sequelae in both total and partial intrusions. Concerning permanent dentition, the most common disturbances were color change and/or enamel hypoplasia. Both types of intrusion caused eruption disturbance. Total intrusion was the most frequent type of intrusive luxation. There was no significant correlation between the child's age at the time of intrusion and the frequency of subsequent sequela on primary injured teeth (P = 0.035), between the age at the time of injury and the developmental disturbances on permanent teeth (P = 0.140).

  13. Test-retest repeatability of the pupil light response to blue and red light stimuli in normal human eyes using a novel pupillometer

    DEFF Research Database (Denmark)

    Herbst, Kristina; Sander, Birgit; Milea, Dan;

    2011-01-01

    In this study, we evaluated the repeatability of pupil responses to colored light stimuli in healthy subjects using a prototype chromatic pupillometer. One eye of 10 healthy subjects was tested twice in the same day using monochromatic light exposure at two selected wavelengths (660 and 470 nm...... stimulation as the total area between a reference line representing baseline pupil size and the line representing actual pupil size over 20 s (area under the curve). There was no significant difference in the repeated measure compared to the first test for any of the pupil response parameters. In conclusion......, we have developed a novel prototype of color pupillometer which demonstrates good repeatability in evoking and recording the pupillary response to a bright blue and red light stimulus....

  14. An Immune Inspired Network Intrusion Detection System Utilising Correlation Context

    CERN Document Server

    Tedesco, Gianni

    2009-01-01

    Network Intrusion Detection Systems (NIDS) are computer systems which monitor a network with the aim of discerning malicious from benign activity on that network. While a wide range of approaches have met varying levels of success, most IDSs rely on having access to a database of known attack signatures which are written by security experts. Nowadays, in order to solve problems with false positive alerts, correlation algorithms are used to add additional structure to sequences of IDS alerts. However, such techniques are of no help in discovering novel attacks or variations of known attacks, something the human immune system (HIS) is capable of doing in its own specialised domain. This paper presents a novel immune algorithm for application to the IDS problem. The goal is to discover packets containing novel variations of attacks covered by an existing signature base.

  15. An Intrusion Detection System for Kaminsky DNS Cache poisoning

    Directory of Open Access Journals (Sweden)

    Dhrubajyoti Pathak, Kaushik Baruah

    2013-09-01

    Full Text Available Domain Name System (DNS is the largest and most actively distributed, hierarchical and scalable database system which plays an incredibly inevitable role behind the functioning of the Internet as we know it today. A DNS translates human readable and meaningful domain names such as www.iitg.ernet.in into an Internet Protocol (IP address such as 202.141.80.6. It is used for locating a resource on the World Wide Web. Without a DNS, the Internet services as we know it, would come to a halt. In our thesis, we proposed an Intrusion Detection System(IDS for Kaminsky cache poisoning attacks. Our system relies on the existing properties of the DNS protocol.

  16. Quantification of Vapor Intrusion Pathways into a Slab-on-Ground Building: an Integration of Mathematical Modeling and Field Experiments

    Science.gov (United States)

    Li, Y.; Akbariyeh, S.; Patterson, B.

    2014-12-01

    Vapor intrusion of volatile organic compounds into buildings can be a significant source of human exposure to hazardous materials. Field assessment is essential to evaluate the vapor intrusion pathways, which has been recognized to be challenging due to the heterogeneity of sites and uncontrolled site environments. Modeling of vapor intrusion processes can predict subsurface vapor and oxygen concentrations and indoor air concentration under various environmental site conditions. However, detailed experimental quantification for model validation is typically unavailable. In this work, we report our efforts to quantifying vapor intrusion pathways into a slab-on-ground building by integrating mathematical modeling with well-controlled field measurements under three different pressure and ventilation site conditions. Comparisons between modeling and field measurements include indoor air concentration, contaminant and oxygen distribution profile beneath and inside the building, diffusive and advective flux under different pressure and air vitalization conditions. In addition to typically identified key factors influencing vapor intrusion (e.g. the building construction, the properties of compounds, and depth to the source), we found several additional parameters, such as anisotropic property of surface soil, locations of crack, and dependency of reaction rates on oxygen concentration, are critical to evaluate vapor intrusion pathways.

  17. Detecting Danger: Applying a Novel Immunological Concept to Intrusion Detection Systems

    CERN Document Server

    Greensmith, Julie; Twycross, Jamie

    2010-01-01

    In recent years computer systems have become increasingly complex and consequently the challenge of protecting these systems has become increasingly difficult. Various techniques have been implemented to counteract the misuse of computer systems in the form of firewalls, anti-virus software and intrusion detection systems. The complexity of networks and dynamic nature of computer systems leaves current methods with significant room for improvement. Computer scientists have recently drawn inspiration from mechanisms found in biological systems and, in the context of computer security, have focused on the human immune system (HIS). The human immune system provides a high level of protection from constant attacks. By examining the precise mechanisms of the human immune system, it is hoped the paradigm will improve the performance of real intrusion detection systems. This paper presents an introduction to recent developments in the field of immunology. It discusses the incorporation of a novel immunological parad...

  18. Rapid laccolith intrusion driven by explosive volcanic eruption

    Science.gov (United States)

    Castro, Jonathan M.; Cordonnier, Benoit; Schipper, C. Ian; Tuffen, Hugh; Baumann, Tobias S.; Feisel, Yves

    2016-11-01

    Magmatic intrusions and volcanic eruptions are intimately related phenomena. Shallow magma intrusion builds subsurface reservoirs that are drained by volcanic eruptions. Thus, the long-held view is that intrusions must precede and feed eruptions. Here we show that explosive eruptions can also cause magma intrusion. We provide an account of a rapidly emplaced laccolith during the 2011 rhyolite eruption of Cordón Caulle, Chile. Remote sensing indicates that an intrusion began after eruption onset and caused severe (>200 m) uplift over 1 month. Digital terrain models resolve a laccolith-shaped body ~0.8 km3. Deformation and conduit flow models indicate laccolith depths of only ~20-200 m and overpressures (~1-10 MPa) that likely stemmed from conduit blockage. Our results show that explosive eruptions may rapidly force significant quantities of magma in the crust to build laccoliths. These iconic intrusions can thus be interpreted as eruptive features that pose unique and previously unrecognized volcanic hazards.

  19. Corticostriatal circuitry in regulating diseases characterized by intrusive thinking.

    Science.gov (United States)

    Kalivas, Benjamin C; Kalivas, Peter W

    2016-03-01

    Intrusive thinking triggers clinical symptoms in many neuropsychiatric disorders. Using drug addiction as an exemplar disorder sustained in part by intrusive thinking, we explore studies demonstrating that impairments in corticostriatal circuitry strongly contribute to intrusive thinking. Neuroimaging studies have long implicated this projection in cue-induced craving to use drugs, and preclinical models show that marked changes are produced at corticostriatal synapses in the nucleus accumbens during a relapse episode. We delineate an accumbens microcircuit that mediates cue-induced drug seeking becoming an intrusive event. This microcircuit harbors many potential therapeutic targets. We focus on preclinical and clinical studies, showing that administering N-acetylcysteine restores uptake of synaptic glutamate by astroglial glutamate transporters and thereby inhibits intrusive thinking. We posit that because intrusive thinking is a shared endophenotype in many disorders, N-acetylcysteine has positive effects in clinical trials for a variety of neuropsychiatric disorders, including drug addiction, gambling, trichotillomania, and depression.

  20. Multi-agent cooperative intrusion response in mobile adhoc networks

    Institute of Scientific and Technical Information of China (English)

    Yi Ping; Zou Futai; Jiang Xinghao; Li Jianhua

    2007-01-01

    The nature of adhoc networks makes them vulnerable to security attacks. Many security technologies such as intrusion prevention and intrusion detection are passive in response to intrusions in that their countermeasures are only to protect the networks, and there is no automated network-wide counteraction against detected intrusions. the architecture of cooperation intrusion response based multi-agent is propose. The architecture is composed of mobile agents. Monitor agent resides on every node and monitors its neighbor nodes. Decision agent collects information from monitor nodes and detects an intrusion by security policies. When an intruder is found in the architecture, the block agents will get to the neighbor nodes of the intruder and form the mobile firewall to isolate the intruder. In the end, we evaluate it by simulation.

  1. Network Intrusion Detection based on GMKL Algorithm

    Directory of Open Access Journals (Sweden)

    Li Yuxiang

    2013-06-01

    Full Text Available According to the 31th statistical reports of China Internet network information center (CNNIC, by the end of December 2012, the number of Chinese netizens has reached 564 million, and the scale of mobile Internet users also reached 420 million. But when the network brings great convenience to people's life, it also brings huge threat in the life of people. So through collecting and analyzing the information in the computer system or network we can detect any possible behaviors that can damage the availability, integrity and confidentiality of the computer resource, and make timely treatment to these behaviors which have important research significance to improve the operation environment of network and network service. At present, the Neural Network, Support Vector machine (SVM and Hidden Markov Model, Fuzzy inference and Genetic Algorithms are introduced into the research of network intrusion detection, trying to build a healthy and secure network operation environment. But most of these algorithms are based on the total sample and it also hypothesizes that the number of the sample is infinity. But in the field of network intrusion the collected data often cannot meet the above requirements. It often shows high latitudes, variability and small sample characteristics. For these data using traditional machine learning methods are hard to get ideal results. In view of this, this paper proposed a Generalized Multi-Kernel Learning method to applied to network intrusion detection. The Generalized Multi-Kernel Learning method can be well applied to large scale sample data, dimension complex, containing a large number of heterogeneous information and so on. The experimental results show that applying GMKL to network attack detection has high classification precision and low abnormal practical precision.

  2. Intelligent Intrusion Detection System Model Using Rough Neural Network

    Institute of Scientific and Technical Information of China (English)

    YAN Huai-zhi; HU Chang-zhen; TAN Hui-min

    2005-01-01

    A model of intelligent intrusion detection based on rough neural network (RNN), which combines the neural network and rough set, is presented. It works by capturing network packets to identify network intrusions or malicious attacks using RNN with sub-nets. The sub-net is constructed by detection-oriented signatures extracted using rough set theory to detect different intrusions. It is proved that RNN detection method has the merits of adaptive, high universality,high convergence speed, easy upgrading and management.

  3. Performance Assessment of Network Intrusion-Alert Prediction

    Science.gov (United States)

    2012-09-01

    personnel information, credit card information theft, etc. The focus has shifted to attacks that can cause significant damage. Intrusion detection...Maintaining access Miscellanous Reverse engineering RFID tools Table 3. BackTrack Intrusion-detection System/Intrusion-prevention System Penetration...high processing power. 22 Machine 1’s network interface card connected to the mirroring port on the first port of the Ethernet switch. Machine 2’s

  4. Use of multiple-locus variable-number of tandem repeats analysis (MLVA) to investigate genetic diversity of Salmonella enterica subsp. enterica serovar Typhimurium isolates from human, food, and veterinary sources

    DEFF Research Database (Denmark)

    Mateva, Gergana; Pedersen, Karl; Sørensen, Gitte

    2017-01-01

    -locus variable-number of tandem repeats analysis (MLVA) and compared results with antimicrobial resistance (AMR) determinations for 100 S. Typhimurium strains isolated in Bulgaria during 2008-2012 (50 veterinary/food and 50 human isolates). Results showed that isolates were divided into 80 and 34 groups using......). No clustering of isolates related to susceptibility/resistance to antimicrobials, source of isolation, or year of isolation was observed. Some MLVA types were found in both human and veterinary/food isolates, indicating a possible route of transmission. A majority (83%) of the isolates were found...

  5. Introduction to gravity currents and intrusions

    CERN Document Server

    Ungarish, Marius

    2009-01-01

    The whole book is well written in a clear and pedagogical general style. … the author has, in my opinion, produced the first comprehensive book entirely devoted to the modeling of gravity currents and intrusions. This book will be particularly useful to graduate and PhD students, as well as to academics and research engineers working in this field. It may be used as a self-consistent document to get a detailed idea of the state of knowledge about a given problem or a guide toward more specialized papers. It is rich with ideas regarding the direction in which further research is warranted. This

  6. Forensic Analysis of Windows Registry Against Intrusion

    Directory of Open Access Journals (Sweden)

    Haoyang Xie

    2012-03-01

    Full Text Available Windows Registry forensics is an important branch of computer and network forensics. Windows Registry is often considered as the heart of Windows Operating Systems because it contains allof the configuration setting of specific users, groups, hardware, software, and networks. Therefore, Windows Registry can be viewed as a gold mine of forensic evidences which could be used in courts. This paper introduces the basics of Windows Registry, describes its structure and its keys and subkeys thathave forensic values. This paper also discusses how the Windows Registry forensic keys can be applied in intrusion detection.

  7. Sulfide intrusion and detoxification in seagrasses ecosystems

    DEFF Research Database (Denmark)

    Hasler-Sheetal, Harald; Holmer, Marianne

    strategies of seagrasses to sustain sulfide intrusion. Using stable isotope tracing, scanning electron microscopy with x-ray analysis, tracing sulfur compounds combined with ecosystem parameters we found different spatial, intraspecific and interspecific strategies to cope with sulfidic sediments. 1......) Tolerance, by elimination (eg. Zostera marina); where we found precipitation of sulfide as non-toxic elemental sulfur on the inner wall of the root lacunae. 2) Utilization (eg. Z. marina), where seagrasses detoxify and incorporate sulfides by active uptake and metabolize to sulfate, representing a non...

  8. Quantum repeated games revisited

    CERN Document Server

    Frackiewicz, Piotr

    2011-01-01

    We present a scheme for playing quantum repeated 2x2 games based on the Marinatto and Weber's approach to quantum games. As a potential application, we study twice repeated Prisoner's Dilemma game. We show that results not available in classical game can be obtained when the game is played in the quantum way. Before we present our idea, we comment on the previous scheme of playing quantum repeated games.

  9. Types of saltwater intrusion of the Changjiang Estuary

    Institute of Scientific and Technical Information of China (English)

    茅志昌; 沈焕庭; JamesT.Liu; D.Eisma

    2001-01-01

    The Changjiang Estuary is characterized by multi-order bifurcations, unsteady submerged sandbars, mid-channel sandbars, creeks and riffles. The following four types of saltwater intrusion are found: (1) direct intrusion from the sea; (2) intrusion during tidal flooding; (3) intrusion from tidal flats overflow; and (4) salt water coming upstream through other waterways. These result in a complicated temporal and spatial salinity distribution. A high chlorinity concentration zone exists from the Liuhekou to the Sidongkou along the South Branch. The salinity during neap tide or ordinary tide is higher than during spring tide.

  10. Quantal Response Equilibrium-Based Strategies for Intrusion Detection in WSNs

    Directory of Open Access Journals (Sweden)

    Shigen Shen

    2015-01-01

    Full Text Available This paper is to solve the problem stating that applying Intrusion Detection System (IDS to guarantee security of Wireless Sensor Networks (WSNs is computationally costly for sensor nodes due to their limited resources. For this aim, we obtain optimal strategies to save IDS agents’ power, through Quantal Response Equilibrium (QRE that is more realistic than Nash Equilibrium. A stage Intrusion Detection Game (IDG is formulated to describe interactions between the Attacker and IDS agents. The preference structures of different strategy profiles are analyzed. Upon these structures, the payoff matrix is obtained. As the Attacker and IDS agents interact continually, the stage IDG is extended to a repeated IDG and its payoffs are correspondingly defined. The optimal strategies based on QRE are then obtained. These optimal strategies considering bounded rationality make IDS agents not always be in Defend. Sensor nodes’ power consumed in performing intrusion analyses can thus be saved. Experiment results show that the probabilities of the actions adopted by the Attacker can be predicted and thus the IDS can respond correspondingly to protect WSNs.

  11. Advanced Trace Pattern For Computer Intrusion Discovery

    CERN Document Server

    Rahayu, S Siti; Shahrin, S; Zaki, M Mohd; Faizal, M A; Zaheera, Z A

    2010-01-01

    The number of crime committed based on the malware intrusion is never ending as the number of malware variants is growing tremendously and the usage of internet is expanding globally. Malicious codes easily obtained and use as one of weapon to gain their objective illegally. Hence, in this research, diverse logs from different OSI layer are explored to identify the traces left on the attacker and victim logs in order to establish worm trace pattern to defending against the attack and help revealing true attacker or victim. For the purpose of this paper, it focused on malware intrusion and traditional worm namely sasser worm variants. The concept of trace pattern is created by fusing the attacker's and victim's perspective. Therefore, the objective of this paper is to propose a general worm trace pattern for attacker's, victim's and multi-step (attacker/victim)'s by combining both perspectives. These three proposed worm trace patterns can be extended into research areas in alert correlation and computer forens...

  12. Characterizing and Improving Distributed Intrusion Detection Systems.

    Energy Technology Data Exchange (ETDEWEB)

    Hurd, Steven A; Proebstel, Elliot P.

    2007-11-01

    Due to ever-increasing quantities of information traversing networks, network administrators are developing greater reliance upon statistically sampled packet information as the source for their intrusion detection systems (IDS). Our research is aimed at understanding IDS performance when statistical packet sampling is used. Using the Snort IDS and a variety of data sets, we compared IDS results when an entire data set is used to the results when a statistically sampled subset of the data set is used. Generally speaking, IDS performance with statistically sampled information was shown to drop considerably even under fairly high sampling rates (such as 1:5). Characterizing and Improving Distributed Intrusion Detection Systems4AcknowledgementsThe authors wish to extend our gratitude to Matt Bishop and Chen-Nee Chuah of UC Davis for their guidance and support on this work. Our thanks are also extended to Jianning Mai of UC Davis and Tao Ye of Sprint Advanced Technology Labs for their generous assistance.We would also like to acknowledge our dataset sources, CRAWDAD and CAIDA, without which this work would not have been possible. Support for OC48 data collection is provided by DARPA, NSF, DHS, Cisco and CAIDA members.

  13. A Bayesian Networks in Intrusion Detection Systems

    Directory of Open Access Journals (Sweden)

    M. Mehdi

    2007-01-01

    Full Text Available Intrusion detection systems (IDSs have been widely used to overcome security threats in computer networks. Anomaly-based approaches have the advantage of being able to detect previously unknown attacks, but they suffer from the difficulty of building robust models of acceptable behaviour which may result in a large number of false alarms caused by incorrect classification of events in current systems. We propose a new approach of an anomaly Intrusion detection system (IDS. It consists of building a reference behaviour model and the use of a Bayesian classification procedure associated to unsupervised learning algorithm to evaluate the deviation between current and reference behaviour. Continuous re-estimation of model parameters allows for real time operation. The use of recursive Log-likelihood and entropy estimation as a measure for monitoring model degradation related with behavior changes and the associated model update show that the accuracy of the event classification process is significantly improved using our proposed approach for reducing the missing-alarm.

  14. INTRODUCING A NEW REMOVABLE APPLIANCE FOR INTRUSION OF POSTERIOR TEETH

    Directory of Open Access Journals (Sweden)

    A.M KALANTAR MOTAMEDI Karimi

    2000-09-01

    Full Text Available Introduction. In patients with anterior open bite, wether with skeletal factors, or with dental factors, the excessive eruption of posterior teeth, is one of the specific findings, and this excessive eruption causes the backward and downward rotation of mandible, which results in an increase in lower facial height and steep mandibular plane. In these patients, depressing of posterior teeth is the ideal treatment and to achieve this goal is one of the most difficult tooth movements for orthodontist. Methods. For this purpose, a removable appliance was designed and to evaluate its eficacy, six patients were selected, four of them were in permanent dentition and two in mixed dentition period. They were under treatment with this appliance, full time for three to three and a half months. Before starting treatment, lateral cephalometric radiograph and study casts were prepared and the above mentioned period were repeated. The amount of bite closure was measured by comparing study casts before and after treatment. Also cephalometric changes were evaluated by comparing pre-and-post treatment records. Results. As a result average of maxillary first molar intrusion was 1.1 mm and average of mandibular first molar intrusion was 1.3 mm , which had resulted in upward and forward rotation of the mandible. The average changes due to mandibular rotation were: The amount of bite closure 3.7mm; Decrease in lower facial height 3mm; Prominence of chin 3.2 mm; Decrease in mandibular plane angle 2.3; Decrease in y-axis angle 2; Increase in facial angle 2.3. Discussion. Therefore it is obvious that clinically the suggested appliance is capable of, intruding posterior teeth in both of maxilla and mandible and then due to upward and forward rotation of the mandible, the steep mandibular plane and lower facial height are decreased. Now according to the results of this investigation can be highly hopefull that, the number of patients who need orthographic surgery, for

  15. Research on the dry intrusion accompanying the low vortex precipitation

    Institute of Scientific and Technical Information of China (English)

    YAO; XiuPing; WU; GuoXiong; ZHAO; BingKe; YU; YuBin; YANG; GuiMing

    2007-01-01

    By employing the 6.7μm satellite vapor cloud images and NCEP/NCAR 1°×1° reanalysis datasets, the characteristics and mechanism of the dry intrusion, as well as its impacts on the low vortex precipitation at the Meiyu front are explored in this paper. It is found that the formation,development and maintenance of the low vortex precipitation at the Meiyu front are closely related to the evolution of the dry intrusion. The dry intrusion is characterized by high potential vorticity (PV), low humidity and cold air. The dry intrusion exhibits as an obvious dark zone on vapor cloud images, an area in which atmospheric relative humidity is lower than 60%. However, the features of the dry intrusion on the vapor images are clearer than that of the humidity field, for the former is the digital vapor cloud images with high temporal and spatial resolution, and it can be used to explore the finer characteristics of the development, evolution and supplement of the intrusion during the development of the low vortex. The dry intrusion impacts accompanying the low vortex precipitation at the Meiyu front come from all levels of the troposphere, with the strongest intrusion located at the upper troposphere. The dry and cold air intrudes the vicinity of the low vortex from the upper isentropic surface to the lower one, slanting east-ward from lower to higher level. The low vortex precipitation region is usually situated in front of the dry intrusion where the relative humidity gradient is higher. The research also reveals that the mechanism of the dry intrusion is that the high potential vorticity descends from the upper troposphere to the lower level, therefore, the dry intrusion can be used as an important index of the high PV forcing. To the west of the low vortex precipitation, the upper level northerlies descend across the isentropic surface, then the dry cold advection can trigger the instable development in the midlow troposphere. The dry intru-sion enhances the low vortex

  16. Test-retest repeatability of the pupil light response to blue and red light stimuli in normal human eyes using a novel pupillometer

    Directory of Open Access Journals (Sweden)

    Kristina eHerbst

    2011-02-01

    Full Text Available In this study, we evaluated the repeatability of pupil responses to colored light stimuli in healthy subjects using a prototype chromatic pupillometer. One eye of 10 healthy subjects was tested twice in the same day using monochromatic light exposure at 2 selected wavelengths (660 nm and 470 nm, intensity 300 cd/m2 presented continuously for 20 seconds. Pupil responses were recorded in real time before, during and after light exposure. Maximal contraction amplitude and sustained contraction amplitude were calculated. In addition, we quantified the summed pupil response during continuous light stimulation as the total area between a reference line representing baseline pupil size and the line representing actual pupil size over 20 seconds (area under the curve. There was no significant difference in the repeated measure compared to the first test for any of the pupil response parameters. In conclusion, we have developed a novel prototype of color pupillometer which demonstrates good repeatability in evoking and recording the pupillary response to a bright blue and red light stimulus.

  17. Young women's experiences of intrusive behavior in 12 countries.

    Science.gov (United States)

    Sheridan, Lorraine; Scott, Adrian J; Roberts, Karl

    2016-01-01

    The present study provides international comparisons of young women's (N = 1,734) self-reported experiences of intrusive activities enacted by men. Undergraduate psychology students from 12 countries (Armenia, Australia, England, Egypt, Finland, India, Indonesia, Italy, Japan, Portugal, Scotland, and Trinidad) indicated which of 47 intrusive activities they had personally experienced. Intrusive behavior was not uncommon overall, although large differences were apparent between countries when women's personal experiences of specific intrusive activities were compared. Correlations were carried out between self-reported intrusive experiences, the Gender Empowerment Measure (GEM), and Hofstede's dimensions of national cultures. The primary associations were between women's experiences of intrusive behavior and the level of power they are afforded within the 12 countries. Women from countries with higher GEM scores reported experiencing more intrusive activities relating to courtship and requests for sex, while the experiences of women from countries with lower GEM scores related more to monitoring and ownership. Intrusive activities, many of them constituent of harassment and stalking, would appear to be widespread and universal, and their incidence and particular form reflect national level gender inequalities.

  18. Salt intrusion study in Cochin estuary - Using empirical models

    Digital Repository Service at National Institute of Oceanography (India)

    Jacob, B.; Revichandran, C.; NaveenKumar, K.R.

    Intensive measurements of salt intrusion are taken at high and low waters during spring and neap tide for each month respectively from June 2007 to May 2008. Salt intrusion length at high water varied from 10 km in monsoon 2008 to more than 40 km...

  19. An improved unsupervised clustering-based intrusion detection method

    Science.gov (United States)

    Hai, Yong J.; Wu, Yu; Wang, Guo Y.

    2005-03-01

    Practical Intrusion Detection Systems (IDSs) based on data mining are facing two key problems, discovering intrusion knowledge from real-time network data, and automatically updating them when new intrusions appear. Most data mining algorithms work on labeled data. In order to set up basic data set for mining, huge volumes of network data need to be collected and labeled manually. In fact, it is rather difficult and impractical to label intrusions, which has been a big restrict for current IDSs and has led to limited ability of identifying all kinds of intrusion types. An improved unsupervised clustering-based intrusion model working on unlabeled training data is introduced. In this model, center of a cluster is defined and used as substitution of this cluster. Then all cluster centers are adopted to detect intrusions. Testing on data sets of KDDCUP"99, experimental results demonstrate that our method has good performance in detection rate. Furthermore, the incremental-learning method is adopted to detect those unknown-type intrusions and it decreases false positive rate.

  20. Soft-sensing, non-intrusive multiphase flow meter

    NARCIS (Netherlands)

    Wrobel, K.; Schiferli, W.

    2009-01-01

    For single phase flow meters more and better non-intrusive or even clamp-on meters become available. This allows for a wider use of meters and for easier flow control. As the demand for multiphase meters is increasing, the current aim is to develop a non-intrusive multiphase flow meter. The non-intr

  1. Reinforced Intrusion Detection Using Pursuit Reinforcement Competitive Learning

    Directory of Open Access Journals (Sweden)

    Indah Yulia Prafitaning Tiyas

    2014-06-01

    Full Text Available Today, information technology is growing rapidly,all information can be obtainedmuch easier. It raises some new problems; one of them is unauthorized access to the system. We need a reliable network security system that is resistant to a variety of attacks against the system. Therefore, Intrusion Detection System (IDS required to overcome the problems of intrusions. Many researches have been done on intrusion detection using classification methods. Classification methodshave high precision, but it takes efforts to determine an appropriate classification model to the classification problem. In this paper, we propose a new reinforced approach to detect intrusion with On-line Clustering using Reinforcement Learning. Reinforcement Learning is a new paradigm in machine learning which involves interaction with the environment.It works with reward and punishment mechanism to achieve solution. We apply the Reinforcement Learning to the intrusion detection problem with considering competitive learning using Pursuit Reinforcement Competitive Learning (PRCL. Based on the experimental result, PRCL can detect intrusions in real time with high accuracy (99.816% for DoS, 95.015% for Probe, 94.731% for R2L and 99.373% for U2R and high speed (44 ms.The proposed approach can help network administrators to detect intrusion, so the computer network security systembecome reliable. Keywords: Intrusion Detection System, On-Line Clustering, Reinforcement Learning, Unsupervised Learning.

  2. Seawater intrusion mapping using electrical resistivity tomography and hydrochemical data. An application in the coastal area of eastern Thermaikos Gulf, Greece

    Energy Technology Data Exchange (ETDEWEB)

    Kazakis, N., E-mail: kazanera@yahoo.com [Aristotle University of Thessaloniki, Department of Geology, Lab. of Engineering Geology & Hydrogeology, 54124 Thessaloniki (Greece); Pavlou, A. [Aristotle University of Thessaloniki, Department of Geology, Lab. of Engineering Geology & Hydrogeology, 54124 Thessaloniki (Greece); Vargemezis, G. [Aristotle University of Thessaloniki, Department of Geology, Lab. of Applied Geophysics, 54124 Thessaloniki (Greece); Voudouris, K.S.; Soulios, G. [Aristotle University of Thessaloniki, Department of Geology, Lab. of Engineering Geology & Hydrogeology, 54124 Thessaloniki (Greece); Pliakas, F. [Democritus University of Thrace, Department of Civil Engineering, Xanthi 67100 (Greece); Tsokas, G. [Aristotle University of Thessaloniki, Department of Geology, Lab. of Applied Geophysics, 54124 Thessaloniki (Greece)

    2016-02-01

    The aim of this study was to determine the extent and geometrical characteristics of seawater intrusion in the coastal aquifer of the eastern Thermaikos Gulf, Greece. Hydrochemical data and geoelectrical measurements were combined and supplemented to determine the hydrochemical regime of the study site in regard to seawater phenomena. Chemical analysis of groundwater was performed in 126 boreholes and fifteen electrical resistivity tomographies (ERT) were measured, whereas in two sites the ERT measurements were repeated following the wet season. The Cl{sup −} concentrations recorded reached 2240 mg/L indicating seawater intrusion which was also verified by ionic ratios. The ionic ratios were overlapped and a seawater intrusion map (SWIM) was produced. A significant part of the coastal aquifer (up to 150 km{sup 2}) is influenced by seawater intrusion. The areas with the most intensive salinization are located between Nea Kallikratia–Epanomi and Aggelochori–Peraia. According to the ERTs, in the influenced areas the salinization of the aquifer exceeds 1 km toward the mainland and its depth reaches 200 m. In the area surrounding Thessaloniki airport, the ERTs revealed salinization of the upper aquifer to depths of up to 40 m, whereas the lower aquifer is uninfluenced. This abnormal distribution of seawater intrusion demonstrates the value of geoelectrical methods in the study of seawater intrusion especially in areas with limited available hydrochemical data. - Highlights: • ERTs determined the geometrical characteristics of the saline aquifer. • An abnormal distribution of seawater intrusion was recorded. • Four ionic ratios overlapped and a seawater intrusion map was produced. • Cl{sup −} concentrations increased significantly from 2005 to 2010 by up to 1800 mg/L.

  3. Reconfigurable multiport EPON repeater

    Science.gov (United States)

    Oishi, Masayuki; Inohara, Ryo; Agata, Akira; Horiuchi, Yukio

    2009-11-01

    An extended reach EPON repeater is one of the solutions to effectively expand FTTH service areas. In this paper, we propose a reconfigurable multi-port EPON repeater for effective accommodation of multiple ODNs with a single OLT line card. The proposed repeater, which has multi-ports in both OLT and ODN sides, consists of TRs, BTRs with the CDR function and a reconfigurable electrical matrix switch, can accommodate multiple ODNs to a single OLT line card by controlling the connection of the matrix switch. Although conventional EPON repeaters require full OLT line cards to accommodate subscribers from the initial installation stage, the proposed repeater can dramatically reduce the number of required line cards especially when the number of subscribers is less than a half of the maximum registerable users per OLT. Numerical calculation results show that the extended reach EPON system with the proposed EPON repeater can save 17.5% of the initial installation cost compared with a conventional repeater, and can be less expensive than conventional systems up to the maximum subscribers especially when the percentage of ODNs in lightly-populated areas is higher.

  4. Revisiting the TALE repeat.

    Science.gov (United States)

    Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

    2014-04-01

    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

  5. Boron isotope method for study of seawater intrusion

    Institute of Scientific and Technical Information of China (English)

    肖应凯; 尹德忠; 刘卫国; 王庆忠; 魏海珍

    2001-01-01

    A distinct difference in boron isotopes between seawater and terrestrial water is emphasized by δ11B values reported for seawater and groundwater, with an average of 38.8‰ and in the range of -8.9‰ to 9.8‰, respectively. The isotopic composition of boron in groundwater can be used to quantify seawater intrusion and identify intrusion types, e.g. seawater or brine intrusions with different chemical and isotopic characteristics, by using the relation of δ11B and chloride concentration. The feasibility of utilizing boron isotope in groundwater for studying seawater intrusion in Laizhou Bay Region, China, is reported in this study, which shows that boron isotope is a useful and excellent tool for the study of seawater intrusion.

  6. Network Security using Linux Intrusion Detection System / IJORCS

    Directory of Open Access Journals (Sweden)

    Arul Anitha

    2011-12-01

    Full Text Available Attacks on the nation’s computer infrastructures are becoming an increasingly serious problem. Firewalls provide a certain amount of security, but can be fooled at times by attacks like IP spoofing and the so called authorized users. So an intelligent system that can detect attacks and intrusions is required. The tool GRANT (Global Real-time Analysis of Network Traffic being a Linux based Intrusion Detection System(LIDs, takes the advantage of the security of a Linux box and secures the other nodes in the perimeter of the network. It is capable of detecting intrusions and probes as and when they occur and capable of responding to “already” successful attacks, thus causing minimal or no damage to the entire network. For better performance, this Linux Intrusion Detection System should be part of a defense in depth strategy such as Firewall and Intrusion Prevention.

  7. Intrusive Thoughts Mediate the Association between Neuroticism and Cognitive Function.

    Science.gov (United States)

    Munoz, Elizabeth; Sliwinski, Martin J; Smyth, Joshua M; Almeida, David M; King, Heather A

    2013-11-01

    Although research has established a negative association between trait neuroticism and cognition, little is known about the mechanisms that underlie this relationship. We examined the tendency to experience intrusive thoughts and negative affect as potential mediators of the relationship between neuroticism and cognitive performance. We hypothesized that the tendency to experience intrusive thoughts reflects ineffective attentional control and would account for the relationship between neuroticism and cognitive performance over and above the mediating effect of negative affect. Three hundred seventeen adults (Mage =49.43) completed a series of attention-demanding cognitive tasks as well as self-report measures of intrusive thoughts, negative affect, and neuroticism. Intrusive thoughts mediated the association between trait neuroticism and cognitive performance beyond negative affect. These findings are consistent with the hypothesis that the tendency to experience intrusive thoughts is a mechanism through which trait neuroticism influences cognitive performance.

  8. Intrusion-Tolerant Based Survivable Model of Database System

    Institute of Scientific and Technical Information of China (English)

    ZHUJianming; WANGChao; MAJianfeng

    2005-01-01

    Survivability has become increasingly important with society's increased dependence of critical infrastructures on computers. Intrusiontolerant systems extend traditional secure systems to be able to survive or operate through attacks, thus it is an approach for achieving survivability. This paper proposes survivable model of database system based on intrusion-tolerant mechanisms. The model is built on three layers security architecture, to defense intrusion at the outer layer, to detect intrusion at the middle layer, and to tolerate intrusion at the inner layer. We utilize the techniques of both redundancy and diversity and threshold secret sharing schemes to implement the survivability of database and to protect confidential data from compromised servers in the presence of intrusions. Comparing with the existing schemes, our approach has realized the security and robustness for the key functions of a database system by using the integration security strategy and multiple security measures.

  9. Multi-core Processors based Network Intrusion Detection Method

    Directory of Open Access Journals (Sweden)

    Ziqian Wan

    2012-09-01

    Full Text Available It is becoming increasingly hard to build an intrusion detection system (IDS, because of the higher traffic throughput and the rising sophistication of attacking. Scale will be an important issue to address in the intrusion detection area. For hardware, tomorrow’s performance gains will come from multi-core architectures in which a number of CPU executes concurrently. We take the advantage of multi-core processors’ full power for intrusion detection in this work. We present an intrusion detection system based on the Snort open-source IDS that exploits the computational power of MIPS multi-core architecture to offload the costly pattern matching operations from the CPU, and thus increase the system’s processing throughput. A preliminary experiment demonstrates the potential of this system. The experiment results indicate that this method can be used effectively to speed up intrusion detection systems.

  10. Coastal Marsh Monitoring for Persistent Saltwater Intrusion

    Science.gov (United States)

    Hall, Callie M.

    2008-01-01

    This viewgraph presentation reviews NASA's work on the project that supports the Gulf of Mexico Alliance (GOMA) Governors Action Plan to monitor the coastal wetlands for saltwater intrusion. The action items that relate to the task are: (1) Obtain information on projected relative sea level rise, subsidence, and storm vulnerability to help prioritize conservation projects, including restoration, enhancement, and acquisition, and (2) Develop and apply ecosystem models to forecast the habitat structure and succession following hurricane disturbance and changes in ecological functions and services that impact vital socio-economic aspects of coastal systems. The objectives of the program are to provide resource managers with remote sensing products that support ecosystem forecasting models requiring salinity and inundation data. Specifically, the proposed work supports the habitat-switching modules in the Coastal Louisiana Ecosystem Assessment and Restoration (CLEAR) model, which provides scientific evaluation for restoration management.

  11. Multimodal Evolution Approach to Multidimensional Intrusion Detection

    Institute of Scientific and Technical Information of China (English)

    Weng Guang'an; Yu Shengsheng; Zhou Jingli

    2006-01-01

    An artificial immunity based multimodal evolution algorithm is developed to generate detectors with variable coverage for multidimensional intrusion detection. In this algorithm, a proper fitness function is used to drive the detectors to fill in those detection holes close to self set or among self spheres, and genetic algorithm is adopted to reduce the negative effects that different distribution of self imposes on the detector generating process. The validity of the algorithm is tested with spherical and rectangular detectors,respectively, and experiments performed on two real data sets ( machine learning database and DAPRA99) indicate that the proposed algorithm can obtain good results on spherical detectors, and that its performances in detection rate, false alarm rate, stability, time cost, and adaptability to incomplete training set on spherical detectors are all better than on rectangular ones.

  12. Introduction To Intrusion Detection System Review

    Directory of Open Access Journals (Sweden)

    Rajni Tewatia

    2015-05-01

    Full Text Available Abstract Security of a network is always an important issue. With the continuously growing network the basic security such as firewall virus scanner is easily deceived by modern attackers who are experts in using software vulnerabilities to achieve their goals. For preventing such attacks we need even smarter security mechanism which act proactively and intelligently. Intrusion Detection System is the solution of such requirement. Many techniques have been used to implement IDS. These technique basically used in the detector part of IDS such as Neural Network Clustering Pattern Matching Rule Based Fuzzy Logic Genetic Algorithms and many more. To improve the performance of an IDS these approaches may be used in combination to build a hybrid IDS so that benefits of two o more approaches may be combined.

  13. Recursive quantum repeater networks

    CERN Document Server

    Van Meter, Rodney; Horsman, Clare

    2011-01-01

    Internet-scale quantum repeater networks will be heterogeneous in physical technology, repeater functionality, and management. The classical control necessary to use the network will therefore face similar issues as Internet data transmission. Many scalability and management problems that arose during the development of the Internet might have been solved in a more uniform fashion, improving flexibility and reducing redundant engineering effort. Quantum repeater network development is currently at the stage where we risk similar duplication when separate systems are combined. We propose a unifying framework that can be used with all existing repeater designs. We introduce the notion of a Quantum Recursive Network Architecture, developed from the emerging classical concept of 'recursive networks', extending recursive mechanisms from a focus on data forwarding to a more general distributed computing request framework. Recursion abstracts independent transit networks as single relay nodes, unifies software layer...

  14. Flexible Training's Intrusion on Work/Life Balance

    Directory of Open Access Journals (Sweden)

    Zane BERGE

    2005-04-01

    Full Text Available Flexible Training's Intrusion on Work/Life Balance Seema TAKIYAJennifer ARCHBOLDZane BERGEBaltimore, USA Learning interventions should be aligned with the human learning system. To be effective, they have to support human learning, not work against it. Thalheimer, 2004 ABSTRACT With more companies allowing “flextime”, more access to elearning, and telecomuting, the line between workplace flexibility and work-life balance begins to blur. Companies “sell” to employees the flexibility of being able to complete training programs from the comfort of the participant's home, allowing them to learn at their own speed. In many ways, this solution is of great value to many employees. What also must be considered with the flexibility such training offers, is the unintentional consequences. This article explores questions such as does this flexibility create a 24-hour work day where the employee is continually accessible to work? Does it result in less family, personal and leisure time to the detriment of the worker?

  15. In vitro nucleosome positioning features of DNA repeats sequence associated with human genetic disease%与人遗传病相关的DNA重复序列的体外核小体定位特性

    Institute of Scientific and Technical Information of China (English)

    柴荣; 赵宏宇; 蔡禄

    2013-01-01

    Objective To investigate the nucleosome positioning of DNA repeats sequence ire vitro which can cause human genetic disease. Methods The recombinant plasmids containing (GAA)42, (ATTCT)43, (GCCT)18 and 601 sequence were cloned. The histone and plasmids were used to assemble chromatin structure ire vitro,and then analyzed by agarose gel electrophoresis after micrococcal nuclease digestion. Results The plasmid containing ATTCT repeats sequence was easier to form nucleosome than GAA containing repeats sequence ire vitro. Conclusions The recombinant plasmids' ability to form chromatin structure was changed because of the insert of the different repeats sequence fragment.%目的 研究与人遗传病相关的DNA重复序列的体外核小体定位.方法 构建含有(GAA)42、(ATTCT)43、(GCCT)18和601序列的重组质粒,体外利用盐透析将质粒与组蛋白八聚体组装形成染色质结构,微球菌核酸酶消化后,用琼脂糖凝胶电泳分析染色质的结构.结果 含有ATTCT重复序列的质粒较含GAA重复序列质粒在体外易于形成核小体.结论 在重组质粒中,由于引入的重复序列片段形成核小体能力的不同会影响其局部染色质结构.

  16. Exposure assessment modeling for volatiles--towards an Australian indoor vapor intrusion model.

    Science.gov (United States)

    Turczynowicz, Leonid; Robinson, Neville I

    2007-10-01

    Human health risk assessment of sites contaminated by volatile hydrocarbons involves site-specific evaluations of soil or groundwater contaminants and development of Australian soil health-based investigation levels (HILs). Exposure assessment of vapors arising from subsurface sources includes the use of overseas-derived commercial models to predict indoor air concentrations. These indoor vapor intrusion models commonly consider steady-state assumptions, infinite sources, limited soil biodegradation, negligible free phase, and equilibrium partitioning into air and water phases to represent advective and diffusive processes. Regional model construct influences and input parameters affect model predictions while steady-state assumptions introduce conservatism and jointly highlight the need for Australian-specific indoor vapor intrusion assessment. An Australian non-steady-state indoor vapor intrusion model has been developed to determine cumulative indoor human doses (CIHDs) and to address these concerns by incorporating Australian experimental field data to consider mixing, dilution, ventilation, sink effects and first-order soil and air degradation. It was used to develop provisional HILs for benzene, toluene, ethylbenzene, and xylene (BTEX), naphthalene, and volatile aliphatic and aromatic total petroleum hydrocarbons (TPH) < or = EC16 fractions for crawl space dwellings. This article summarizes current state of knowledge and discusses proposed research for differing exposure scenarios based on Australian dwelling and subsurface influences, concurrent with sensitivity analyses of input parameters and in-field model validation.

  17. The role of stress during memory reactivation on intrusive memories.

    Science.gov (United States)

    Cheung, Jessica; Garber, Benjamin; Bryant, Richard A

    2015-09-01

    Intrusive memories are unwanted recollections that maintain distress in psychological disorders. Increasing evidence suggests that memories that are reactivated through retrieval become temporarily vulnerable to environmental or pharmacological manipulation, including changes in levels of circulating stress hormones. This study investigated the influence of stress during memory reactivation of an emotionally arousing trauma film on subsequent intrusive memories. Three groups of participants (N=63) viewed a trauma film depicting a serious car accident at baseline. Two days later (Time 2), one group received a reactivation induction following a socially evaluated cold pressor test (SECPT; Stress/Reactivation condition), whilst the second group reactivated the memory after a control procedure (Reactivation condition). A third group underwent the SECPT but was not asked to reactivate memory of the trauma film (Stress condition). Two days later (Time 3), all participants received a surprise cued memory recall test and intrusions questionnaire which they completed online. Results showed that those in the Stress/Reactivation group had higher intrusions scores than the other two groups, suggesting that acute stress promotes intrusive memories only when the memory trace is reactivated shortly afterwards. Increased cortisol predicted enhanced intrusive experiences in the Stress/Reactivation condition but not in the other conditions. This pattern of results suggests that acute stress during the reactivation of emotional material impacts on involuntary emotional memories. These findings suggest a possible explanation for the mechanism underlying the maintenance of intrusive memories in clinical disorders. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. A Frequency-Based Approach to Intrusion Detection

    Directory of Open Access Journals (Sweden)

    Mian Zhou

    2004-06-01

    Full Text Available Research on network security and intrusion detection strategies presents many challenging issues to both theoreticians and practitioners. Hackers apply an array of intrusion and exploit techniques to cause disruption of normal system operations, but on the defense, firewalls and intrusion detection systems (IDS are typically only effective in defending known intrusion types using their signatures, and are far less than mature when faced with novel attacks. In this paper, we adapt the frequency analysis techniques such as the Discrete Fourier Transform (DFT used in signal processing to the design of intrusion detection algorithms. We demonstrate the effectiveness of the frequency-based detection strategy by running synthetic network intrusion data in simulated networks using the OPNET software. The simulation results indicate that the proposed intrusion detection strategy is effective in detecting anomalous traffic data that exhibit patterns over time, which include several types of DOS and probe attacks. The significance of this new strategy is that it does not depend on the prior knowledge of attack signatures, thus it has the potential to be a useful supplement to existing signature-based IDS and firewalls.

  19. Accurate Modeling of The Siemens S7 SCADA Protocol For Intrusion Detection And Digital Forensic

    Directory of Open Access Journals (Sweden)

    Amit Kleinmann

    2014-09-01

    Full Text Available The Siemens S7 protocol is commonly used in SCADA systems for communications between a Human Machine Interface (HMI and the Programmable Logic Controllers (PLCs. This paper presents a model-based Intrusion Detection Systems (IDS designed for S7 networks. The approach is based on the key observation that S7 traffic to and from a specific PLC is highly periodic; as a result, each HMI-PLC channel can be modeled using its own unique Deterministic Finite Automaton (DFA. The resulting DFA-based IDS is very sensitive and is able to flag anomalies such as a message appearing out of its position in the normal sequence or a message referring to a single unexpected bit. The intrusion detection approach was evaluated on traffic from two production systems. Despite its high sensitivity, the system had a very low false positive rate - over 99.82% of the traffic was identified as normal.

  20. Experimental modelling of ground deformation associated with shallow magma intrusions

    Science.gov (United States)

    Galland, O.

    2012-04-01

    Active volcanoes experience ground deformation as a response to the dynamics of underground magmatic systems. The analysis of ground deformation patterns may provide important constraints on the dynamics and shape of the underlying volcanic plumbing systems. Nevertheless, these analyses usually take into account simplistic shapes (sphere, dykes, sills) and the results cannot be verified as the modelled systems are buried. In this contribution, I will present new results from experimental models of magma intrusion, in which both the evolution of ground deformation during intrusion and the shape of the underlying intrusion are monitored in 3D. The models consisted of a molten vegetable oil, simulating low viscosity magma, injected into cohesive fine-grained silica flour, simulating the brittle upper crust; oil injection resulted is sheet intrusions (dykes, sills and cone sheets). The initial topography in the models was flat. While the oil was intruding, the surface of the models slightly lifted up to form a smooth relief, which was mapped through time. After an initial symmetrical development, the uplifted area developed asymmetrically; at the end of the experiments, the oil always erupted at the steepest edge of the uplifted area. After the experiment, the oil solidified, the intrusion was excavated and the shape of its top surface mapped. The comparison between the uplifted zone and the underlying intrusions showed that (1) the complex shapes of the uplifted areas reflected the complex shapes of the underlying intrusions, (2) the time evolution of the uplifted zone was correlated with the evolution of the underlying intrusion, and (3) the early asymmetrical evolution of the uplifted areas can be used to predict the location of the eruption of the oil. The experimental results also suggest that complex intrusion shapes (inclined sheet, cone sheet, complex sill) may have to be considered more systematically in analyses of ground deformation patterns on volcanoes.

  1. Remarkable selective constraints on exonic dinucleotide repeats.

    Science.gov (United States)

    Haasl, Ryan J; Payseur, Bret A

    2014-09-01

    Long dinucleotide repeats found in exons present a substantial mutational hazard: mutations at these loci occur often and generate frameshifts. Here, we provide clear and compelling evidence that exonic dinucleotides experience strong selective constraint. In humans, only 18 exonic dinucleotides have repeat lengths greater than six, which contrasts sharply with the genome-wide distribution of dinucleotides. We genotyped each of these dinucleotides in 200 humans from eight 1000 Genomes Project populations and found a near-absence of polymorphism. More remarkably, divergence data demonstrate that repeat lengths have been conserved across the primate phylogeny in spite of what is likely considerable mutational pressure. Coalescent simulations show that even a very low mutation rate at these loci fails to explain the anomalous patterns of polymorphism and divergence. Our data support two related selective constraints on the evolution of exonic dinucleotides: a short-term intolerance for any change to repeat length and a long-term prevention of increases to repeat length. In general, our results implicate purifying selection as the force that eliminates new, deleterious mutants at exonic dinucleotides. We briefly discuss the evolution of the longest exonic dinucleotide in the human genome--a 10 x CA repeat in fibroblast growth factor receptor-like 1 (FGFRL1)--that should possess a considerably greater mutation rate than any other exonic dinucleotide and therefore generate a large number of deleterious variants. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  2. Intrusion detection in wireless ad-hoc networks

    CERN Document Server

    Chaki, Nabendu

    2014-01-01

    Presenting cutting-edge research, Intrusion Detection in Wireless Ad-Hoc Networks explores the security aspects of the basic categories of wireless ad-hoc networks and related application areas. Focusing on intrusion detection systems (IDSs), it explains how to establish security solutions for the range of wireless networks, including mobile ad-hoc networks, hybrid wireless networks, and sensor networks.This edited volume reviews and analyzes state-of-the-art IDSs for various wireless ad-hoc networks. It includes case studies on honesty-based intrusion detection systems, cluster oriented-based

  3. Novel Hybrid Intrusion Detection System For Clustered Wireless Sensor Network

    Directory of Open Access Journals (Sweden)

    Hichem Sedjelmaci

    2011-08-01

    Full Text Available Wireless sensor network (WSN is regularly deployed in unattended and hostile environments. The WSN isvulnerable to security threats and susceptible to physical capture. Thus, it is necessary to use effective mechanisms to protect the network. It is widely known, that the intrusion detection is one of the mostefficient security mechanisms to protect the network against malicious attacks or unauthorized access. In this paper, we propose a hybrid intrusion detection system for clustered WSN. Our intrusion framework uses a combination between the Anomaly Detection based on support vector machine (SVM and the Misuse Detection. Experiments results show that most of routing attacks can be detected with low falsealarm.

  4. Assessing the pollution risk of a groundwater source field at western Laizhou Bay under seawater intrusion.

    Science.gov (United States)

    Zeng, Xiankui; Wu, Jichun; Wang, Dong; Zhu, Xiaobin

    2016-07-01

    Coastal areas have great significance for human living, economy and society development in the world. With the rapid increase of pressures from human activities and climate change, the safety of groundwater resource is under the threat of seawater intrusion in coastal areas. The area of Laizhou Bay is one of the most serious seawater intruded areas in China, since seawater intrusion phenomenon was firstly recognized in the middle of 1970s. This study assessed the pollution risk of a groundwater source filed of western Laizhou Bay area by inferring the probability distribution of groundwater Cl(-) concentration. The numerical model of seawater intrusion process is built by using SEAWAT4. The parameter uncertainty of this model is evaluated by Markov Chain Monte Carlo (MCMC) simulation, and DREAM(ZS) is used as sampling algorithm. Then, the predictive distribution of Cl(-) concentration at groundwater source field is inferred by using the samples of model parameters obtained from MCMC. After that, the pollution risk of groundwater source filed is assessed by the predictive quantiles of Cl(-) concentration. The results of model calibration and verification demonstrate that the DREAM(ZS) based MCMC is efficient and reliable to estimate model parameters under current observation. Under the condition of 95% confidence level, the groundwater source point will not be polluted by seawater intrusion in future five years (2015-2019). In addition, the 2.5% and 97.5% predictive quantiles show that the Cl(-) concentration of groundwater source field always vary between 175mg/l and 200mg/l. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. The Pentapeptide Repeat Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Vetting,M.; Hegde, S.; Fajardo, J.; Fiser, A.; Roderick, S.; Takiff, H.; Blanchard, J.

    2006-01-01

    The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S, T,A, V][D, N][L, F]-[S, T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Mycobacterium tuberculosis. The structure revealed that the pentapeptide repeats encode the folding of a novel right-handed quadrilateral {beta}-helix. MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable size, shape and electrostatic similarity to DNA.

  6. Repeating the Past

    Science.gov (United States)

    Moore, John W.

    1998-05-01

    As part of the celebration of the Journal 's 75th year, we are scanning each Journal issue from 25, 50, and 74 years ago. Many of the ideas and practices described are so similar to present-day "innovations" that George Santayana's adage (1) "Those who cannot remember the past are condemned to repeat it" comes to mind. But perhaps "condemned" is too strong - sometimes it may be valuable to repeat something that was done long ago. One example comes from the earliest days of the Division of Chemical Education and of the Journal.

  7. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes.

    Science.gov (United States)

    Richard, Guy-Franck; Kerrest, Alix; Dujon, Bernard

    2008-12-01

    Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.

  8. Abstracting audit data for lightweight intrusion detection

    KAUST Repository

    Wang, Wei

    2010-01-01

    High speed of processing massive audit data is crucial for an anomaly Intrusion Detection System (IDS) to achieve real-time performance during the detection. Abstracting audit data is a potential solution to improve the efficiency of data processing. In this work, we propose two strategies of data abstraction in order to build a lightweight detection model. The first strategy is exemplar extraction and the second is attribute abstraction. Two clustering algorithms, Affinity Propagation (AP) as well as traditional k-means, are employed to extract the exemplars, and Principal Component Analysis (PCA) is employed to abstract important attributes (a.k.a. features) from the audit data. Real HTTP traffic data collected in our institute as well as KDD 1999 data are used to validate the two strategies of data abstraction. The extensive test results show that the process of exemplar extraction significantly improves the detection efficiency and has a better detection performance than PCA in data abstraction. © 2010 Springer-Verlag.

  9. KUROSHIO INTRUSION INTO THE SOUTH CHINA SEA

    Institute of Scientific and Technical Information of China (English)

    ZHANG Qing-hua; FAN Hai-mei; QU Yuan-yuan

    2006-01-01

    In this article, the circulation of the South China Sea (SCS), which is idealized as the rectangular basin with constant depth, is studied under Kuroshio boundary forces. Starting from the linearly quasi-geostrophic vorticity equation, the solution of the SCS circulation is given in the form of corrected Fourier series under proper boundary conditions. The results show that the intruded current flows westward and separates into the northward branch and the southward branch before arriving at the western boundary. The southward branch flows out of the SCS through the southwestern passage, at the same time, the induced cyclonic (anti-clockwise) ring almost occupies the middle and southern parts, and concomitant anti-cyclonic (clockwise) vortex appears between the cyclone and the western boundary. While the northward branch outflows through the northeastern passage, the anti-cyclonic (clockwise) ring is triggered at the northern part of the SCS. The above two vortexes are both intensified if the south-entering and the north-leaving current loop intrusion are superposed. The outer flow of the northern vortex flows westward, then northward, and then eastward, and it is very similar to the configuration of the SCS Warm Current (SCSWC) at the northern part of the SCS, thus, a kind of generating mechanism of the SCSWC is presented.

  10. Expansion of CAG triplet repeats by human DNA polymerases λ and β in vitro, is regulated by flap endonuclease 1 and DNA ligase 1.

    Science.gov (United States)

    Crespan, Emmanuele; Hübscher, Ulrich; Maga, Giovanni

    2015-05-01

    Huntington's disease (HD) is a neurological genetic disorder caused by the expansion of the CAG trinucleotide repeats (TNR) in the N-terminal region of coding sequence of the Huntingtin's (HTT) gene. This results in the addition of a poly-glutamine tract within the Huntingtin protein, resulting in its pathological form. The mechanism by which TRN expansion takes place is not yet fully understood. We have recently shown that DNA polymerase (Pol) β can promote the microhomology-mediated end joining and triplet expansion of a substrate mimicking a double strand break in the TNR region of the HTT gene. Here we show that TNR expansion is dependent on the structure of the DNA substrate, as well as on the two essential Pol β co-factors: flap endonuclease 1 (Fen1) and DNA ligase 1 (Lig1). We found that Fen1 significantly stimulated TNR expansion by Pol β, but not by the related enzyme Pol λ, and subsequent ligation of the DNA products by Lig1. Interestingly, the deletion of N-terminal domains of Pol λ, resulted in an enzyme which displayed properties more similar to Pol β, suggesting a possible evolutionary mechanism. These results may suggest a novel mechanism for somatic TNR expansion in HD.

  11. Repeated ketamine administration alters N-methyl-d-aspartic acid receptor subunit gene expression: Implication of genetic vulnerability for ketamine abuse and ketamine psychosis in humans

    Science.gov (United States)

    Lipsky, Robert H

    2015-01-01

    For more than 40 years following its approval by the Food and Drug Administration (FDA) as an anesthetic, ketamine, a non-competitive N-methyl-d-aspartic acid (NMDA) receptor antagonist, has been used as a tool of psychiatric research. As a psychedelic drug, ketamine induces psychotic symptoms, cognitive impairment, and mood elevation, which resemble some symptoms of schizophrenia. Recreational use of ketamine has been increasing in recent years. However, little is known of the underlying molecular mechanisms responsible for ketamine-associated psychosis. Recent animal studies have shown that repeated ketamine administration significantly increases NMDA receptor subunit gene expression, in particular subunit 1 (NR1 or GluN1) levels. This results in neurodegeneration, supporting a potential mechanism where up-regulation of NMDA receptors could produce cognitive deficits in chronic ketamine abuse patients. In other studies, NMDA receptor gene variants are associated with addictive behavior. Here, we focus on the roles of NMDA receptor gene subunits in ketamine abuse and ketamine psychosis and propose that full sequencing of NMDA receptor genes may help explain individual vulnerability to ketamine abuse and ketamine-associated psychosis. PMID:25245072

  12. Non-intrusive practitioner pupil detection for unmodified microscope oculars.

    Science.gov (United States)

    Fuhl, Wolfgang; Santini, Thiago; Reichert, Carsten; Claus, Daniel; Herkommer, Alois; Bahmani, Hamed; Rifai, Katharina; Wahl, Siegfried; Kasneci, Enkelejda

    2016-12-01

    Modern microsurgery is a long and complex task requiring the surgeon to handle multiple microscope controls while performing the surgery. Eye tracking provides an additional means of interaction for the surgeon that could be used to alleviate this situation, diminishing surgeon fatigue and surgery time, thus decreasing risks of infection and human error. In this paper, we introduce a novel algorithm for pupil detection tailored for eye images acquired through an unmodified microscope ocular. The proposed approach, the Hough transform, and six state-of-the-art pupil detection algorithms were evaluated on over 4000 hand-labeled images acquired from a digital operating microscope with a non-intrusive monitoring system for the surgeon eyes integrated. Our results show that the proposed method reaches detection rates up to 71% for an error of ≈3% w.r.t the input image diagonal; none of the state-of-the-art pupil detection algorithms performed satisfactorily. The algorithm and hand-labeled data set can be downloaded at:: www.ti.uni-tuebingen.de/perception. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Intrusion Prevention/Intrusion Detection System (IPS/IDS for Wifi Networks

    Directory of Open Access Journals (Sweden)

    Michal Korcak

    2014-07-01

    Full Text Available The nature of wireless networks itself created new vulnerabilities that in the classical wired network s do not exist. This results in an evolutional requireme nt to implement new sophisticated security mechanis m in form of Intrusion Detection and Prevention Systems. This paper deals with security issues of small off ice and home office wireless networks. The goal of our work is to design and evaluate wireless IDPS with u se of packet injection method. Decrease of attacker’s traffic by 95% was observed when compared to attacker’s traffic without deployment of proposed I DPS system.

  14. Effectiveness of Intrusion Prevention Systems (IPS) in Fast Networks

    CERN Document Server

    Shafi, Muhammad Imran; Hayat, Sikandar; Sohail, Imran

    2010-01-01

    Computer systems are facing biggest threat in the form of malicious data which causing denial of service, information theft, financial and credibility loss etc. No defense technique has been proved successful in handling these threats. Intrusion Detection and Prevention Systems (IDPSs) being best of available solutions. These techniques are getting more and more attention. Although Intrusion Prevention Systems (IPSs) show a good level of success in detecting and preventing intrusion attempts to networks, they show a visible deficiency in their performance when they are employed on fast networks. In this paper we have presented a design including quantitative and qualitative methods to identify improvement areas in IPSs. Focus group is used for qualitative analysis and experiment is used for quantitative analysis. This paper also describes how to reduce the responding time for IPS when an intrusion occurs on network, and how can IPS be made to perform its tasks successfully without effecting network speed nega...

  15. Security Enrichment in Intrusion Detection System Using Classifier Ensemble

    Directory of Open Access Journals (Sweden)

    Uma R. Salunkhe

    2017-01-01

    Full Text Available In the era of Internet and with increasing number of people as its end users, a large number of attack categories are introduced daily. Hence, effective detection of various attacks with the help of Intrusion Detection Systems is an emerging trend in research these days. Existing studies show effectiveness of machine learning approaches in handling Intrusion Detection Systems. In this work, we aim to enhance detection rate of Intrusion Detection System by using machine learning technique. We propose a novel classifier ensemble based IDS that is constructed using hybrid approach which combines data level and feature level approach. Classifier ensembles combine the opinions of different experts and improve the intrusion detection rate. Experimental results show the improved detection rates of our system compared to reference technique.

  16. Probabilistic risk assessment for six vapour intrusion algorithms

    NARCIS (Netherlands)

    Provoost, J.; Reijnders, L.; Bronders, J.; Van Keer, I.; Govaerts, S.

    2014-01-01

    A probabilistic assessment with sensitivity analysis using Monte Carlo simulation for six vapour intrusion algorithms, used in various regulatory frameworks for contaminated land management, is presented here. In addition a deterministic approach with default parameter sets is evaluated against obse

  17. Probabilistic risk assessment for six vapour intrusion algorithms

    NARCIS (Netherlands)

    Provoost, J.; Reijnders, L.; Bronders, J.; Van Keer, I.; Govaerts, S.

    2014-01-01

    A probabilistic assessment with sensitivity analysis using Monte Carlo simulation for six vapour intrusion algorithms, used in various regulatory frameworks for contaminated land management, is presented here. In addition a deterministic approach with default parameter sets is evaluated against

  18. SVM Intrusion Detection Model Based on Compressed Sampling

    Directory of Open Access Journals (Sweden)

    Shanxiong Chen

    2016-01-01

    Full Text Available Intrusion detection needs to deal with a large amount of data; particularly, the technology of network intrusion detection has to detect all of network data. Massive data processing is the bottleneck of network software and hardware equipment in intrusion detection. If we can reduce the data dimension in the stage of data sampling and directly obtain the feature information of network data, efficiency of detection can be improved greatly. In the paper, we present a SVM intrusion detection model based on compressive sampling. We use compressed sampling method in the compressed sensing theory to implement feature compression for network data flow so that we can gain refined sparse representation. After that SVM is used to classify the compression results. This method can realize detection of network anomaly behavior quickly without reducing the classification accuracy.

  19. Vapor Intrusion Facility Boundaries - Approximate Extent of Contamination

    Data.gov (United States)

    U.S. Environmental Protection Agency — Theses polygons represent the approximate extent of contamination for Vapor Intrusion facilities. Polygons for non-Federal Facility sites were updated in January,...

  20. An expert system application for network intrusion detection

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, K.A.; Dubois, D.H.; Stallings, C.A.

    1991-01-01

    The paper describes the design of a prototype intrusion detection system for the Los Alamos National Laboratory's Integrated Computing Network (ICN). The Network Anomaly Detection and Intrusion Reporter (NADIR) differs in one respect from most intrusion detection systems. It tries to address the intrusion detection problem on a network, as opposed to a single operating system. NADIR design intent was to copy and improve the audit record review activities normally done by security auditors. We wished to replace the manual review of audit logs with a near realtime expert system. NADIR compares network activity, as summarized in user profiles, against expert rules that define network security policy, improper or suspicious network activities, and normal network and user activity. When it detects deviant (anomalous) behavior, NADIR alerts operators in near realtime, and provides tools to aid in the investigation of the anomalous event. 15 refs., 2 figs.

  1. Tropical upper tropospheric humidity variations due to potential vorticity intrusions

    Science.gov (United States)

    Sandhya, M.; Sridharan, S.; Indira Devi, M.

    2015-09-01

    Four cases (March 2009, May 2009, April 2010 and February 2012) are presented in which the ERA-interim relative humidity (RH) shows consistent increase by more than 50 % in the upper troposphere (200-250 hPa) over tropics at the eastward side of the potential vorticity (PV) intrusion region. The increase in RH is confirmed with the spaceborne microwave limb sounder observations and radiosonde observations over Gadanki (13.5° N, 79.2° E) and is observed irrespective of whether the PV intrusions are accompanied by deep convection or not. It is demonstrated that the increase in RH is due to poleward advection induced by the PV intrusions in their eastward side at the upper tropospheric heights. It is suggested that the low-latitude convection, which is not necessarily triggered by the PV intrusion, might have transported water vapour to the upper tropospheric heights.

  2. Probabilistic risk assessment for six vapour intrusion algorithms

    NARCIS (Netherlands)

    Provoost, J.; Reijnders, L.; Bronders, J.; Van Keer, I.; Govaerts, S.

    2014-01-01

    A probabilistic assessment with sensitivity analysis using Monte Carlo simulation for six vapour intrusion algorithms, used in various regulatory frameworks for contaminated land management, is presented here. In addition a deterministic approach with default parameter sets is evaluated against obse

  3. Novel Non-Intrusive Vibration Monitoring System for Turbopumps Project

    Data.gov (United States)

    National Aeronautics and Space Administration — AI Signal Research, Inc. proposes to develop a Non-Intrusive Vibration Measurement System (NI-VMS) for turbopumps which will provide effective on-board/off-board...

  4. Novel Non-Intrusive Vibration Monitoring System for Turbopumps Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ASRI proposes to develop an advanced and commercially viable Non-Intrusive Vibration Monitoring System (NI-VMS) which can provide effective on-line/off-line engine...

  5. Combining Naive Bayes and Decision Tree for Adaptive Intrusion Detection

    CERN Document Server

    Farid, Dewan Md; Rahman, Mohammad Zahidur; 10.5121/ijnsa.2010.2202

    2010-01-01

    In this paper, a new learning algorithm for adaptive network intrusion detection using naive Bayesian classifier and decision tree is presented, which performs balance detections and keeps false positives at acceptable level for different types of network attacks, and eliminates redundant attributes as well as contradictory examples from training data that make the detection model complex. The proposed algorithm also addresses some difficulties of data mining such as handling continuous attribute, dealing with missing attribute values, and reducing noise in training data. Due to the large volumes of security audit data as well as the complex and dynamic properties of intrusion behaviours, several data miningbased intrusion detection techniques have been applied to network-based traffic data and host-based data in the last decades. However, there remain various issues needed to be examined towards current intrusion detection systems (IDS). We tested the performance of our proposed algorithm with existing learn...

  6. Vapor intrusion from entrapped NAPL sources and groundwater plumes

    Science.gov (United States)

    Illangasekare, Tissa H.; Sakaki, Toshihiro; Christ, John; Petri, Bejamin; Sauck, Carolyn; Cihan, Abdullah

    2010-05-01

    Volatile organic compounds (VOC) are commonly found entrapped as non-aqueous phase liquids (NAPLs) in the soil pores or dissolved in groundwater at industrial waste sites and refineries. Vapors emitted from these contaminant sources readily disperse into the atmosphere, into air-filled void spaces within the soil, and migrate below surface structures, leading to the intrusion of contaminant vapors into indoor air through basements and other underground structures. This process referred to as vapor intrusion (VI) represents a potential threat to human health, and is a possible exposure pathway of concern to regulatory agencies. To assess whether this exposure pathway is present, remediation project managers often rely in part on highly simplified screening level models that do not take into consideration the complex flow dynamics controlled by subsurface heterogeneities and soil moisture conditions affected by the mass and heat flux boundary conditions at the land/atmospheric interface. A research study is under way to obtain an improved understanding of the processes and mechanisms controlling vapor generation from entrapped NAPL sources and groundwater plumes, their subsequent migration through the subsurface, and their attenuation in naturally heterogeneous vadose zones under various natural physical, climatic, and geochemical conditions. Experiments conducted at multiple scales will be integrated with analytical and numerical modeling and field data to test and validate existing VI theories and models. A set of preliminary experiments where the fundamental process of vapor generation from entrapped NAPL sources and dissolved plumes under fluctuating water were investigated in small cells and two-dimensional test tanks. In another task, intermediate scale experiments were conducted to generate quantitative data on how the heat and mass flux boundary conditions control the development of dynamic VI pathways. The data from the small cell and tank experiments were

  7. Numerical and physical modeling of cutoff walls against saltwater intrusion

    Science.gov (United States)

    Crestani, Elena; Camporese, Matteo; Salandin, Paolo

    2017-04-01

    Seawater intrusion is a relevant problem for many communities living in small islands, where the amount of fresh water available for human consumption depends on the delicate equilibrium between the natural groundwater recharge from rainfall and the surrounding sea. However, it can represent a significant issue also for coastal regions where groundwater is extracted for water supply: an excessive extraction to meet growing demands for drinking water and irrigation purposes leads to a decrease of seaward flows of fresh water and consequently to an increase of seawater intrusion into coastal aquifers. Cutoff walls represent one of the possible strategies that can be adopted to reduce seawater intrusion into coastal aquifers and to limit the inland progression of the saltwater wedge. In this study, on the basis of several preliminary simulations developed by the SUTRA code, a cutoff wall occluding 70% of the aquifer depth is designed for a physical experiment, whose setup details are reported as follows. The physical model represents the terminal part of a coastal aquifer and consists of a flume 500 cm long, 30 cm wide and 60 cm high, filled for an height of 49 cm with glass beads with a d50 of 0.6 mm and a uniformity coefficient d60/d10 1.5. The resulting porous medium is homogeneous, with porosity of about 0.37 and hydraulic conductivity of about 1.3 10-3 m/s. Upstream from the sandbox, a tank filled by freshwater provides recharge for the aquifer. The downstream tank simulates the sea and red food dye is added to the saltwater to easily visualize the salt wedge. The volume of the downstream tank is about five times the upstream one, and, due to the small filtration discharge, minimizing salt concentration variations due to the incoming freshwater flow. The hydraulic gradient during the tests is constant, due to the fixed water level in the tanks. Water levels and discharged flow rate are continuously monitored. The cutoff wall was realized with sodium bentonite

  8. All-optical repeater.

    Science.gov (United States)

    Silberberg, Y

    1986-06-01

    An all-optical device containing saturable gain, saturable loss, and unsaturable loss is shown to transform weak, distorted optical pulses into uniform standard-shape pulses. The proposed device performs thresholding, amplification, and pulse shaping as required from an optical repeater. It is shown that such a device could be realized by existing semiconductor technology.

  9. Bidirectional Manchester repeater

    Science.gov (United States)

    Ferguson, J.

    1980-01-01

    Bidirectional Manchester repeater is inserted at periodic intervals along single bidirectional twisted pair transmission line to detect, amplify, and transmit bidirectional Manchester 11 code signals. Requiring only 18 TTL 7400 series IC's, some line receivers and drivers, and handful of passive components, circuit is simple and relatively inexpensive to build.

  10. Environmental data processor of the adaptive intrusion data system

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, M.S.

    1977-06-01

    A data acquisition system oriented specifically toward collection and processing of various meteorological and environmental parameters has been designed around a National Semiconductor IMP-16 microprocessor, This system, called the Environmental Data Processor (EDP), was developed specifically for use with the Adaptive Intrusion Data System (AIDS) in a perimeter intrusion alarm evaluation, although its design is sufficiently general to permit use elsewhere. This report describes in general detail the design of the EDP and its interaction with other AIDS components.

  11. A Subset Feature Elimination Mechanism for Intrusion Detection System

    OpenAIRE

    Herve Nkiama; Syed Zainudeen Mohd Said; Muhammad Saidu

    2016-01-01

    several studies have suggested that by selecting relevant features for intrusion detection system, it is possible to considerably improve the detection accuracy and performance of the detection engine. Nowadays with the emergence of new technologies such as Cloud Computing or Big Data, large amount of network traffic are generated and the intrusion detection system must dynamically collected and analyzed the data produce by the incoming traffic. However in a large dataset not all features con...

  12. Enhancing BATTLEMIND: Preventing PTSD by Coping with Intrusive Thoughts

    Science.gov (United States)

    2013-05-01

    replace it right away. This thought replacing skill is especially good to use late at night if you are having trouble sleeping . But, you will need to...then this is a good skill for you to practice with at home so that you can learn to be decent toward yourself. When you spend your time and energy...about intrusive thoughts ◦ CONTROL: traditional CBT skills for coping ◦ RESET: Mindfulness-based skills for coping Thoughts on intrusive thoughts

  13. Managing Temporal and Spatial Variability in Vapor Intrusion Data

    Science.gov (United States)

    2012-03-28

    Managing Temporal and Spatial Variability in Vapor Intrusion Data Todd McAlary, M.Sc., P.Eng., P.G. Geosyntec Consultants, Inc...TITLE AND SUBTITLE Managing Temporal and Spatial Variability in Vapor Intrusion Data 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER...Koc (mL/g) OSWER indoor conc. at 10-6 risk (ppb) Vapour pressure (atm) Water solubility (g/l) 1,1,1-Trichloroethane 110 400

  14. Intrusion and extrusion of water in hydrophobic mesopores

    OpenAIRE

    Barrat, Jean-Louis; Lefevre, Benoit; Bocquet, Lyderic; Saugey, Anthony; Vigier, Gérard; Gobin, Pierre-François; Charlaix, Elisabeth

    2003-01-01

    We present experimental and theoretical results on intrusion-extrusion cycles of water in hydrophobic mesoporous materials, characterized by independent cylindrical pores. The intrusion, which takes place above the bulk saturation pressure, can be well described using a macroscopic capillary model. Once the material is saturated with water, extrusion takes place upon reduction of the externally applied pressure; Our results for the extrusion pressure can only be understood by assuming that th...

  15. Biochemical and Clinical Assessments of Segmental Maxillary Posterior Tooth Intrusion

    Science.gov (United States)

    Tasanapanont, Jintana; Wattanachai, Tanapan; Apisariyakul, Janya; Pothacharoen, Peraphan; Kongtawelert, Prachya; Midtbø, Marit

    2017-01-01

    Objective. To compare chondroitin sulphate (CS) levels around maxillary second premolars, first molars, and second molars between the unloaded and the loaded periods and to measure the rates of intrusion of maxillary posterior teeth during segmental posterior tooth intrusion. Materials and Methods. In this prospective clinical study, 105 teeth (from 15 patients exhibiting anterior open bite and requiring maxillary posterior tooth intrusion) were studied. Competitive ELISA was used to detect CS levels. Dental casts (during the unloaded and loaded periods) were scanned, and posterior tooth intrusion distances were measured. Results. During the unloaded period, the median CS levels around maxillary second premolars, first molars, second molars (experimental teeth), and mandibular first molars (negative control) were 0.006, 0.055, 0.056, and 0.012 and during the loaded period were 2.592, 5.738, 4.727, and 0.163 ng/μg of total protein, respectively. The median CS levels around experimental teeth were significantly elevated during the loaded period. The mean rates of maxillary second premolar and first and second molar intrusion were 0.72, 0.58, and 0.40 mm/12 weeks, respectively. Conclusions. Biochemical and clinical assessments suggested that the segmental posterior tooth intrusion treatment modality with 50 g of vertical force per side was sufficient. Trial Registration. The study is registered as TCTR20170206006. PMID:28321256

  16. Combining Naive Bayes and Decision Tree for Adaptive Intrusion Detection

    Directory of Open Access Journals (Sweden)

    Dewan Md. Farid

    2010-04-01

    Full Text Available In this paper, a new learning algorithm for adaptive network intrusion detection using naive Bayesian classifier and decision tree is presented, which performs balance detections and keeps false positives at acceptable level for different types of network attacks, and eliminates redundant attributes as well as contradictory examples from training data that make the detection model complex. The proposedalgorithm also addresses some difficulties of data mining such as handling continuous attribute, dealing with missing attribute values, and reducing noise in training data. Due to the large volumes of security audit data as well as the complex and dynamic properties of intrusion behaviours, several data miningbased intrusion detection techniques have been applied to network-based traffic data and host-based data in the last decades. However, there remain various issues needed to be examined towards current intrusion detection systems (IDS. We tested the performance of our proposed algorithm with existing learning algorithms by employing on the KDD99 benchmark intrusion detection dataset. The experimental results prove that the proposed algorithm achieved high detection rates (DR andsignificant reduce false positives (FP for different types of network intrusions using limited computational resources

  17. The effects of nicotine on intrusive memories in nonsmokers.

    Science.gov (United States)

    Hawkins, Kirsten A; Cougle, Jesse R

    2013-12-01

    Correlational research suggests that smoking increases risk of posttraumatic stress disorder (PTSD), though such research by nature cannot rule out third variable explanations for this relationship. The present study used an analogue trauma film design to experimentally test the effects of nicotine on the occurrence of intrusive memories. Fifty-four healthy nonsmokers were randomly assigned to ingest either a nicotine or placebo lozenge before viewing a film depicting motor vehicle accidents. Participants recorded intrusive memories immediately after the film and for a week via diary. Participants in the nicotine condition reported significantly more intrusive memories immediately after watching the film, yet no group differences emerged on intrusions or intrusion-related distress reported during the following week. Among participants low in dispositional rumination, those who had ingested a nicotine lozenge reported more intrusions in the subsequent week than those in the placebo condition. These findings provide novel experimental evidence for the role of nicotine in increasing risk of PTSD and suggest that nicotine may contribute to trauma-related rumination but not heightened reactivity to trauma cues.

  18. Saltwater intrusion in coastal regions of North America

    Science.gov (United States)

    Barlow, Paul M.; Reichard, Eric G.

    2010-01-01

    Saltwater has intruded into many of the coastal aquifers of the United States, Mexico, and Canada, but the extent of saltwater intrusion varies widely among localities and hydrogeologic settings. In many instances, the area contaminated by saltwater is limited to small parts of an aquifer and to specific wells and has had little or no effect on overall groundwater supplies; in other instances, saltwater contamination is of regional extent and has resulted in the closure of many groundwater supply wells. The variability of hydrogeologic settings, three-dimensional distribution of saline water, and history of groundwater withdrawals and freshwater drainage has resulted in a variety of modes of saltwater intrusion into coastal aquifers. These include lateral intrusion from the ocean; upward intrusion from deeper, more saline zones of a groundwater system; and downward intrusion from coastal waters. Saltwater contamination also has occurred along open boreholes and within abandoned, improperly constructed, or corroded wells that provide pathways for vertical migration across interconnected aquifers. Communities within the coastal regions of North America are taking actions to manage and prevent saltwater intrusion to ensure a sustainable source of groundwater for the future. These actions can be grouped broadly into scientific monitoring and assessment, engineering techniques, and regulatory approaches.

  19. Towards Multi-Stage Intrusion Detection using IP Flow Records

    Directory of Open Access Journals (Sweden)

    Muhammad Fahad Umer

    2016-10-01

    Full Text Available Traditional network-based intrusion detection sys-tems using deep packet inspection are not feasible for modern high-speed networks due to slow processing and inability to read encrypted packet content. As an alternative to packet-based intrusion detection, researchers have focused on flow-based intrusion detection techniques. Flow-based intrusion detection systems analyze IP flow records for attack detection. IP flow records contain summarized traffic information. However, flow data is very large in high-speed networks and cannot be processed in real-time by the intrusion detection system. In this paper, an efficient multi-stage model for intrusion detection using IP flows records is proposed. The first stage in the model classifies the traffic as normal or malicious. The malicious flows are further analyzed by a second stage. The second stage associates an attack type with malicious IP flows. The proposed multi-stage model is efficient because the majority of IP flows are discarded in the first stage and only malicious flows are examined in detail. We also describe the implementation of our model using machine learning techniques.

  20. Dissociation between the time courses of femoral artery blood flow and pulmonary VO2 during repeated bouts of heavy knee extension exercise in humans.

    Science.gov (United States)

    Fukuba, Yoshiyuki; Ohe, Yukie; Miura, Akira; Kitano, Asami; Endo, Masako; Sato, Hironori; Miyachi, Motohiko; Koga, Shunsaku; Fukuda, Osamu

    2004-05-01

    It has frequently been demonstrated that prior heavy cycling exercise facilitates pulmonary O(2) kinetics at the onset of subsequent heavy exercise. This might be due to improved muscle perfusion via acidosis-induced vasodilating effects. However, it is difficult to measure the blood flow (BF) to the working muscles (via the femoral artery) during cycling exercise. We therefore selected supine knee extension (KE) exercise as an alternative, and investigated whether the faster O(2) kinetics in the 2nd bout was matched by proportionally faster BF kinetics to the exercising muscle. Nine healthy subjects (aged 21-44 years) volunteered to participate in this study. The protocol consisted of two consecutive 6-min KE exercise bouts in a supine position (work rate: 70-75% of peak power) separated by a 6-min baseline rest (EX1 to EX2). During the protocol, a pulsed Doppler ultrasound technique was utilized to continuously measure the BF in the right femoral artery. The protocol was repeated at least 6 times to characterize the precise kinetics. In agreement with previous studies using cycling exercise, the O(2) kinetics in the 2nd bout were facilitated compared with that in the 1st bout [mean +/-s.d. of the 'effective' time constant (tau): EX1, 68.6 +/- 15.9, versus EX2, 58.0 +/- 14.4 s. Phase II-tau: EX1, 48.7 +/- 9.0, versus EX2, 41.2 +/- 13.3 s. Empirical index of the slow component (Delta O(2(6-3))): EX1, 78 +/- 44, versus EX2, 57 +/- 36 ml min(-1) (P 0.05)]. It was concluded that the faster pulmonary O(2) kinetics during heavy KE exercise following prior heavy exercise was not associated with a similar modulation in the BF to the working muscles.

  1. Kissing Bug (Triatoma spp.) Intrusion into Homes: Troublesome Bites and Domiciliation.

    Science.gov (United States)

    Klotz, Stephen A; Shirazi, F Mazda; Boesen, Keith; Beatty, Norman L; Dorn, Patricia L; Smith, Shannon; Schmidt, Justin O

    2016-01-01

    Kissing bugs (Triatoma spp.) frequently enter homes and bite human and pet occupants. Bites may lead to severe allergic reactions and, in some cases, death. Kissing bugs are also vectors of Trypanosoma cruzi, the cause of Chagas disease. In general, modern houses in the United States are not conducive to domiciliation of kissing bugs (bugs living out their entire life within the home with the presence of eggs, nymphs, adults, and exuviae). Construction features such as concrete foundations, solid walls and ceilings, window screens, tight thresholds for doors and windows, and other measures impede bug entry into homes, and air conditioning reduces the need for open doors and windows. Where Chagas disease is endemic in Mexico and Central and South America, homes often have thatch roofs, adobe walls, and open doors and windows. We investigated numerous instances of kissing bug intrusions into homes in Southern Arizona, California, and Louisiana and documented the reactions to kissing bug bites. Our work confirms the importance of modern home construction in limiting kissing bug intrusions. Older homes, especially those lacking modern screening, caulking, and weather stripping to reduce air leakage, may be subject to kissing bug intrusions and domiciliation. We describe a community in Southern Arizona where domiciliation of homes by Triatoma recurva is common. We also provide recent data regarding kissing bug bites and allergic reactions to the bites.

  2. Biosynthesis of highly enriched 13C-lycopene for human metabolic studies using repeated batch tomato cell culturing with 13C-glucose

    OpenAIRE

    Moran, Nancy E.; Rogers, Randy B.; Lu, Chi-Hua; Conlon, Lauren E.; Lila, Mary Ann; Clinton, Steven K.; Erdman, John W

    2013-01-01

    While putative disease-preventing lycopene metabolites are found in both tomato (Solanum lycopersicum) products and in their consumers, mammalian lycopene metabolism is poorly understood. Advances in tomato cell culturing techniques offer an economical tool for generation of highly-enriched 13C-lycopene for human bioavailability and metabolism studies. To enhance the 13C-enrichment and yields of labeled lycopene from the hp-1 tomato cell line, cultures were first grown in 13C-glucose media fo...

  3. Non-Intrusive Battery Health Monitoring

    Directory of Open Access Journals (Sweden)

    Gajewski Laurent

    2017-01-01

    Full Text Available The “Non-intrusive battery health monitoring”, developed by Airbus Defence and Space (ADS in cooperation with the CIRIMAT-CNRS laboratory and supported by CNES, aims at providing a diagnosis of the battery ageing in flight, called State of Health (SOH, using only the post-treatment of the battery telemetries. The battery current and voltage telemetries are used by a signal processing tool on ground to characterize and to model the battery at low frequencies which allows monitoring the evolution of its degradation with great accuracy. The frequential behaviour estimation is based on inherent disturbances on the current during the nominal functioning of the battery. For instance, on-board thermal control or equipment consumption generates random disturbances on battery current around an average current. The battery voltage response to these current random disturbances enables to model the low frequency impedance of the battery by a signal processing tool. The re-created impedance is then compared with the evolution model of the low frequencies impedance as a function of the battery ageing to estimate accurately battery degradation. Hence, this method could be applied to satellites which are already in orbit and whose battery telemetries acquisition system fulfils the constraints determined in the study. This innovative method is an improvement of present state-of-the-art and is important to have a more accurate in-flight knowledge of battery ageing which is crucial for mission and operation planning and also for possible satellite mission extension or deorbitation. This method is patented by Airbus Defence and Space and CNES.

  4. A Fiber-Optical Intrusion Alarm System Based on Quasi-Distributed Fiber Bragg Grating Sensors

    Institute of Scientific and Technical Information of China (English)

    Qi Jiang; Yun-Jiang Rao; De-Hong Zeng

    2008-01-01

    A fiber-optical intrusion alarm system based on quasi-distributed fiber Bragg grating (FBG) sensors is demonstrated in this paper. The algorithms of empirical mode decomposition (EMD) and wavelet packet characteristic entropy are adopted to determine the intrusion location. The intrusion alarm software based on the Labview is developed, and it is also proved by the experiments. The results show that such a fiber-optical intrusion alarm system can offer the automatic intrusion alarm in real-time.

  5. The human [gamma]-aminobutyric acid receptor subunit [beta]3 and [alpha]5 gene cluster in chromosome 15q11-q13 is rich in highly polymorphic (CA)[sub n] repeats

    Energy Technology Data Exchange (ETDEWEB)

    Glatt, K.; Lalande, M. (Howard Hughes Medical Institute, Boston, MA (United States)); Sinnett, D. (Harvard Medical School, Boston, MA (United States))

    1994-01-01

    The [gamma]-aminobutyric acid (GABA[sub A]) receptor [beta]33 (GABRB3) and [alpha]5 (GABRA5) subunit genes have been localized to the Angelman and Prader-Willi syndrome region of chromosome 15q11-q13. GABRB3, which encompasses 250 kb, is located 100 kb proximal of GABRA5, with the two genes arranged in head-to-head transcriptional orientation. In screening 135 kb of cloned DNA within a 260-kb interval extending from within GABRB3 to the 5[prime] end of GABRA5, 10 new (CA), repeats have been identified. Five of these have been analyzed in detail and found to be highly polymorphic, with the polymorphism information content (PIC) ranging from 0.7 to 0.85 and with heterozygosities of 67 to 94%. In the clones from GABRB3/GABRA5 region, therefore, the frequency of (CA)[sub n] with PICs [ge] 0.7 is 1 per 27 kb. Previous estimates of the density of (CA)[sub n] with PICs [ge] 0.7 in the human genome have been approximately 10-fold lower. The GABRB3/GABRA5 region appears, therefore, to be enriched for highly informative (CA)[sub n]. This set of closely spaced, short tandem repeat polymorphisms will be useful in the molecular analyses of Prader-Willi and Angelman syndromes and in high-resolution studies of genetic recombination within this region. 21 refs., 2 figs., 1 tab.

  6. Developments toward a low-cost approach for long-term, unattended vapor intrusion monitoring.

    Science.gov (United States)

    Patel, Sanjay V; Tolley, William K

    2014-08-07

    There are over 450 000 sites contaminated by chemicals in the US. This large number of contaminated sites and the speed of subsurface migration of chemicals pose considerable risk to nearby residences and commercial buildings. The high costs for monitoring around these sites stem from the labor involved in placing and replacing the passive sorbent vapor samplers and the resultant laboratory analysis. This monitoring produces sparse data sets that do not track temporal changes well. To substantially reduce costs and better track exposures, less costly, unattended systems for monitoring soil gases and vapor intrusion into homes and businesses are desirable to aid in the remediation of contaminated sites. This paper describes progress toward the development of an inexpensive system specifically for monitoring vapor intrusion; the system can operate repeatedly without user intervention with low detection limits (1 × 10(-9), or 1 part-per-billion). Targeted analytes include chlorinated hydrocarbons (dichloroethylene, trichloroethane, trichloroethylene, and perchloroethylene) and benzene. The system consists of a trap-and-purge preconcentrator for vapor collection in conjunction with a compact gas chromatography instrument to separate individual compounds. Chemical detection is accomplished with an array of chemicapacitors and a metal-oxide semiconductor combustibles sensor. Both the preconcentrator and the chromatography column are resistively heated. All components are compatible with ambient air, which serves as the carrier gas for the gas chromatography and detectors.

  7. Duct Leakage Repeatability Testing

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Iain [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sherman, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-01-01

    Duct leakage often needs to be measured to demonstrate compliance with requirements or to determine energy or Indoor Air Quality (IAQ) impacts. Testing is often done using standards such as ASTM E1554 (ASTM 2013) or California Title 24 (California Energy Commission 2013 & 2013b), but there are several choices of methods available within the accepted standards. Determining which method to use or not use requires an evaluation of those methods in the context of the particular needs. Three factors that are important considerations are the cost of the measurement, the accuracy of the measurement and the repeatability of the measurement. The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards.

  8. Intrusion of incisors in adult patients with marginal bone loss.

    Science.gov (United States)

    Melsen, B; Agerbaek, N; Markenstam, G

    1989-09-01

    Elongated and spaced incisors are common problems in patients suffering from severe periodontal disease. Thirty patients characterized by marginal bone loss and deep overbite were treated by intrusion of incisors. Three different methods for intrusion were applied: (1) J hooks and extraoral high-pull headgear, (2) utility arches, (3) intrusion bent into a loop in a 0.17 x 0.25-inch wire, and (4) base arch as described by Burstone. The intrusion was evaluated from the displacement of the apex, incision, and the center of resistance of the most prominent or elongated central incisor. Change in the marginal bone level and the amount of root resorption were evaluated on standardized intraoral radiographs. The pockets were assessed by standardized probing and the clinical crown length was measured on study casts. The results showed that the true intrusion of the center of resistance varied from 0 to 3.5 mm and was most pronounced when intrusion was performed with a base arch. The clinical crown length was generally reduced by 0.5 to 1.0 mm. The marginal bone level approached the cementoenamel junction in all but six cases. All cases demonstrated root resorption varying from 1 to 3 mm. The total amount of alveolar support--that is, the calculated area of the alveolar wall--was unaltered or increased in 19 of the 30 cases. The dependency of the results on the oral hygiene, the force distribution, and the perioral function was evaluated in relation to the individual cases. It was obvious that intrusion was best performed when (1) forces were low (5 to 15 gm per tooth) with the line of action of the force passing through or close to the center of resistance, (2) the gingiva status was healthy, and (3) no interference with perioral function was present.

  9. Single chain fragment variable antibodies developed by using as target the 3rd fibronectin type III homologous repeat fragment of human neural cell adhesion molecule L1 promote cell migration and neuritogenesis.

    Science.gov (United States)

    Tang, Dan-Yang; Yu, Yang; Zhao, Xuan-Jun; Schachner, Melitta; Zhao, Wei-Jiang

    2015-01-15

    L1CAM plays important roles during ontogeny, including promotion of neuronal cell migration and neuritogenesis, and stimulation of axonal outgrowth, fasciculation and myelination. These functions are at least partially exerted through a 16-mer amino acid sequence in the third fibronectin type III-like repeat of L1, which associates with several interaction partners, including integrins, other adhesion molecules and growth factor receptors. Here, using the Tomlinson I library for phage display, we obtained two single-chain variable fragment antibodies (scFvs) against this peptide sequence of human L1, hereafter called H3 peptide. Both scFvs recognize the H3 peptide and the extracellular domain of L1, as tested by enzyme-linked immunosorbent assay (ELISA), Western blot analysis and immunofluorescence staining of L1 expresssing cells. Furthermore, both scFvs reduce U-87 MG cell adhesion to fibronectin, while stimulating cell migration. Application of scFvs to human neuroblastoma SK-N-SH cells promote process outgrowth. Similar to triggering of endogenous L1 functions at the cell surface, both scFvs activate the signal transducers Erk and Src in these cells. Our results indicate that scFvs against a functionally pivotal domain in L1 trigger its regeneration-beneficial functions in vitro, encouraging thoughts on therapy of neurodegenerative diseases in the hope to ameliorate human nervous system diseases.

  10. Epstein-Barr virus immediate-early gene product trans-activates gene expression from the human immunodeficiency virus long terminal repeat

    Energy Technology Data Exchange (ETDEWEB)

    Kenney, S.; Kamine, J.; Markovitz, D.; Fenrick, R.; Pagano, J.

    1988-03-01

    Acquired immunodeficiency syndrome patients are frequently coinfected with Epstein-Barr virus (EBV). In this report, the authors demonstrate that an EBV immediate-early gene product, BamHI MLF1, stimulates expression of the bacterial chloramphenicol acetyltransferase (CAT) gene linked to the human immunodeficiency virus (HIV) promoter. The HIV promoter sequences necessary for trans-activation by EBV do not include the tat-responsive sequences. In addition, in contrast to the other herpesvirus trans-activators previously studied, the EBV BamHI MLF1 gene product appears to function in part by a posttranscriptional mechanism, since it increases pHIV-CAT protein activity more than it increases HIV-CAT mRNA. This ability of an EBV gene product to activate HIV gene expression may have biologic consequences in persons coinfected with both viruses.

  11. In vitro systems toxicology approach to investigate the effects of repeated cigarette smoke exposure on human buccal and gingival organotypic epithelial tissue cultures

    Science.gov (United States)

    Schlage, Walter K.; Kostadinova, Radina; Xiang, Yang; Sewer, Alain; Majeed, Shoaib; Kuehn, Diana; Frentzel, Stefan; Talikka, Marja; Geertz, Marcel; Mathis, Carole; Ivanov, Nikolai; Hoeng, Julia; Peitsch, Manuel C.

    2014-01-01

    Smoking has been associated with diseases of the lung, pulmonary airways and oral cavity. Cytologic, genomic and transcriptomic changes in oral mucosa correlate with oral pre-neoplasia, cancer and inflammation (e.g. periodontitis). Alteration of smoking-related gene expression changes in oral epithelial cells is similar to that in bronchial and nasal epithelial cells. Using a systems toxicology approach, we have previously assessed the impact of cigarette smoke (CS) seen as perturbations of biological processes in human nasal and bronchial organotypic epithelial culture models. Here, we report our further assessment using in vitro human oral organotypic epithelium models. We exposed the buccal and gingival organotypic epithelial tissue cultures to CS at the air–liquid interface. CS exposure was associated with increased secretion of inflammatory mediators, induction of cytochrome P450s activity and overall weak toxicity in both tissues. Using microarray technology, gene-set analysis and a novel computational modeling approach leveraging causal biological network models, we identified CS impact on xenobiotic metabolism-related pathways accompanied by a more subtle alteration in inflammatory processes. Gene-set analysis further indicated that the CS-induced pathways in the in vitro buccal tissue models resembled those in the in vivo buccal biopsies of smokers from a published dataset. These findings support the translatability of systems responses from in vitro to in vivo and demonstrate the applicability of oral organotypical tissue models for an impact assessment of CS on various tissues exposed during smoking, as well as for impact assessment of reduced-risk products. PMID:25046638

  12. In vitro systems toxicology approach to investigate the effects of repeated cigarette smoke exposure on human buccal and gingival organotypic epithelial tissue cultures.

    Science.gov (United States)

    Schlage, Walter K; Iskandar, Anita R; Kostadinova, Radina; Xiang, Yang; Sewer, Alain; Majeed, Shoaib; Kuehn, Diana; Frentzel, Stefan; Talikka, Marja; Geertz, Marcel; Mathis, Carole; Ivanov, Nikolai; Hoeng, Julia; Peitsch, Manuel C

    2014-10-01

    Smoking has been associated with diseases of the lung, pulmonary airways and oral cavity. Cytologic, genomic and transcriptomic changes in oral mucosa correlate with oral pre-neoplasia, cancer and inflammation (e.g. periodontitis). Alteration of smoking-related gene expression changes in oral epithelial cells is similar to that in bronchial and nasal epithelial cells. Using a systems toxicology approach, we have previously assessed the impact of cigarette smoke (CS) seen as perturbations of biological processes in human nasal and bronchial organotypic epithelial culture models. Here, we report our further assessment using in vitro human oral organotypic epithelium models. We exposed the buccal and gingival organotypic epithelial tissue cultures to CS at the air-liquid interface. CS exposure was associated with increased secretion of inflammatory mediators, induction of cytochrome P450s activity and overall weak toxicity in both tissues. Using microarray technology, gene-set analysis and a novel computational modeling approach leveraging causal biological network models, we identified CS impact on xenobiotic metabolism-related pathways accompanied by a more subtle alteration in inflammatory processes. Gene-set analysis further indicated that the CS-induced pathways in the in vitro buccal tissue models resembled those in the in vivo buccal biopsies of smokers from a published dataset. These findings support the translatability of systems responses from in vitro to in vivo and demonstrate the applicability of oral organotypical tissue models for an impact assessment of CS on various tissues exposed during smoking, as well as for impact assessment of reduced-risk products.

  13. Time-resolved seismic tomography detects magma intrusions at Mount Etna.

    Science.gov (United States)

    Patanè, D; Barberi, G; Cocina, O; De Gori, P; Chiarabba, C

    2006-08-11

    The continuous volcanic and seismic activity at Mount Etna makes this volcano an important laboratory for seismological and geophysical studies. We used repeated three-dimensional tomography to detect variations in elastic parameters during different volcanic cycles, before and during the October 2002-January 2003 flank eruption. Well-defined anomalous low P- to S-wave velocity ratio volumes were revealed. Absent during the pre-eruptive period, the anomalies trace the intrusion of volatile-rich (>/=4 weight percent) basaltic magma, most of which rose up only a few months before the onset of eruption. The observed time changes of velocity anomalies suggest that four-dimensional tomography provides a basis for more efficient volcano monitoring and short- and midterm eruption forecasting of explosive activity.

  14. Simulating spatial adaption of groundwater pumping on seawater intrusion in coastal regions

    Science.gov (United States)

    Grundmann, Jens; Ladwig, Robert; Schütze, Niels; Walther, Marc

    2016-04-01

    Coastal aquifer systems are used intensively to meet the growing demands for water in those regions. They are especially at risk for the intrusion of seawater due to aquifer overpumping, limited groundwater replenishment and unsustainable groundwater management which in turn also impacts the social and economical development of coastal regions. One example is the Al-Batinah coastal plain in northern Oman where irrigated agriculture is practiced by lots of small scaled farms in different distances from the sea, each of them pumping their water from coastal aquifer. Due to continuous overpumping and progressing saltwater intrusion farms near the coast had to close since water for irrigation got too saline. For investigating appropriate management options numerical density dependent groundwater modelling is required which should also portray the adaption of groundwater abstraction schemes on the water quality. For addressing this challenge a moving inner boundary condition is implemented in the numerical density dependent groundwater model which adjusts the locations for groundwater abstraction according to the position of the seawater intrusion front controlled by thresholds of relative chloride concentration. The adaption process is repeated for each management cycle within transient model simulations and allows for considering feedbacks with the consumers e.g. the agriculture by moving agricultural farms more inland or towards the sea if more fertile soils at the coast could be recovered. For finding optimal water management strategies efficiently, the behaviour of the numerical groundwater model for different extraction and replenishment scenarios is approximated by an artificial neural network using a novel approach for state space surrogate model development. Afterwards the derived surrogate is coupled with an agriculture module within a simulation based water management optimisation framework to achieve optimal cropping pattern and water abstraction schemes

  15. Cre/loxP-mediated excision of a neomycin resistance expression unit from an integrated retroviral vector increases long terminal repeat-driven transcription in human hematopoietic cells.

    Science.gov (United States)

    Fernex, C; Dubreuil, P; Mannoni, P; Bagnis, C

    1997-01-01

    Recombinant retroviruses are currently the most attractive vehicles for gene transfer into hematopoietic cells. Retroviral vectors often contain an easily selectable marker gene in addition to the gene of interest. However, the presence and selection for expression of the selectable gene often result in a significant reduction of the expression of the gene of interest in the transduced cells. In order to circumvent this problem, we have developed a Cre/loxP recombination system for specific excision of the selectable expression unit from integrated retroviruses. A retroviral vector, containing both a neomycin resistance expression unit flanked by loxP sites and granulocyte-macrophage colony-stimulating factor cDNA, was used to transduce the human hematopoietic K-562 cell line. Four transduced cell clones were then superinfected with a retrovirus containing a Cre recombinase expression unit. Molecular analyses of 30 doubly transduced subclones showed a strict correlation between cre expression and loxP-flanked selectable cassette excision, thus implying that Cre recombinase activity is very efficient in a retroviral context. Moreover, the excision of the selectable cassette results in a significant increase of granulocyte-macrophage colony-stimulating factor transcription driven by the retroviral promoter. PMID:9311833

  16. Biosynthesis of highly enriched 13C-lycopene for human metabolic studies using repeated batch tomato cell culturing with 13C-glucose.

    Science.gov (United States)

    Moran, Nancy Engelmann; Rogers, Randy B; Lu, Chi-Hua; Conlon, Lauren E; Lila, Mary Ann; Clinton, Steven K; Erdman, John W

    2013-08-15

    While putative disease-preventing lycopene metabolites are found in both tomato (Solanum lycopersicum) products and in their consumers, mammalian lycopene metabolism is poorly understood. Advances in tomato cell culturing techniques offer an economical tool for generation of highly-enriched (13)C-lycopene for human bioavailability and metabolism studies. To enhance the (13)C-enrichment and yields of labelled lycopene from the hp-1 tomato cell line, cultures were first grown in (13)C-glucose media for three serial batches and produced increasing proportions of uniformly labelled lycopene (14.3±1.2%, 39.6±0.5%, and 48.9±1.5%) with consistent yields (from 5.8 to 9 mg/L). An optimised 9-day-long (13)C-loading and 18-day-long labelling strategy developed based on glucose utilisation and lycopene yields, yielded (13)C-lycopene with 93% (13)C isotopic purity, and 55% of isotopomers were uniformly labelled. Furthermore, an optimised acetone and hexane extraction led to a fourfold increase in lycopene recovery from cultures compared to a standard extraction.

  17. Repeated exposure of human fibroblasts to ionizing radiation reveals an adaptive response that is not mediated by interleukin-6 or TGF-{beta}

    Energy Technology Data Exchange (ETDEWEB)

    Dieriks, Birger, E-mail: birger.dieriks@ugent.be [Bio-imaging and Cytometry Unit, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Gent (Belgium); De Vos, Winnok [Bio-imaging and Cytometry Unit, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Gent (Belgium); Baatout, Sarah [Bio-imaging and Cytometry Unit, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Gent (Belgium); Radiobiology Unit, Laboratory Molecular and Cellular Biology, Radiobiology Unit, Belgian Nuclear Research Center, SCK.CEN, Boeretang 200, 2400 Mol (Belgium); Van Oostveldt, Patrick, E-mail: Patrick.VanOostveldt@UGent.be [Bio-imaging and Cytometry Unit, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Gent (Belgium)

    2011-10-01

    Exposing cells to a low dose can protect them against a subsequent higher exposure. This phenomenon is known as adaptive response and is frequently observed in a variety of cells. Even though similarities are suspected with other non-targeted effects, such as bystander effects, the exact mechanism behind adaptive response is not fully clarified. In this study human primary fibroblasts were tested for their response to ionizing radiation (IR) after administrating a low priming dose (0.1-0.5 Gy). Both the abundance of {gamma}H2AX as a marker for double-stranded breaks and the levels of cytokines, secreted in the medium, were monitored in time. Upon challenge, IR-primed cells showed modified {gamma}H2AX spot size distributions and altered repair kinetics, consistent with an adaptive response. In addition, 24 h after priming with IR, four cytokines were significantly upregulated in the medium - GM-CSF (1.33x); IL6 (4.24x); IL8 (1.33x); TGF-{beta} (1.46x). In order to mimick the protective effect of IR priming, we primed the cells with either IL6 or TGF-{beta}. This did not elicit an altered {gamma}H2AX response as observed in IR-primed cells, indicating that the adaptive response in these primary fibroblasts is regulated in an IL-6 and TGF-{beta} independent manner.

  18. Methylation at global LINE-1 repeats in human blood are affected by gender but not by age or natural hormone cycles.

    Directory of Open Access Journals (Sweden)

    Osman El-Maarri

    Full Text Available Previously, we reported on inter-individual and gender specific variations of LINE-1 methylation in healthy individuals. In this study, we investigated whether this variability could be influenced by age or sex hormones in humans. To this end, we studied LINE-1 methylation in vivo in blood-derived DNA from individuals aged 18 to 64 years and from young healthy females at various hormone levels during the menstrual cycle. Our results show that no significant association with age was observed. However, the previously reported increase of LINE-1 methylation in males was reconfirmed. In females, although no correlation between LINE-1 or Alu methylation and hormone levels was observed, a significant stable individual specific level of methylation was noted. In vitro results largely confirmed these findings, as neither estrogen nor dihydrotestosterone affected LINE-1 or Alu methylation in Hek293T, HUVEC, or MDA-kb2 cell lines. In contrast, a decrease in methylation was observed in estrogen-treated T47-Kbluc cell lines strongly expressing estrogen receptor. The very low expression of estrogen receptor in blood cells could explain the observed insensitivity of methylation at LINE-1 to natural hormonal variations in females. In conclusion, neither natural cycle of hormones nor age has a detectable effect on the LINE-1 methylation in peripheral blood cells, while gender remains an important factor.

  19. Preference of the recombination sites involved in the formation of extrachromosomal copies of the human alphoid Sau3A repeat family.

    Science.gov (United States)

    Ohki, R; Oishi, M; Kiyama, R

    1995-01-01

    The human alphoid Sau3A repetitive family DNA is one of the DNA species that are actively amplified to form extrachromosomal circular DNA in several cell lines. The circularization takes place between two of the five approximately 170 bp subunits with an average of 73.1% homology as well as between identical subunits. To investigate the nature of the recombination reaction, we cloned and analyzed the subunits containing recombination junctions. Analysis of a total of 68 junctions revealed that recombination had occurred preferentially at four positions 10-25 (A), 40-50 (B), 85-90 (C) and 135-160 (D) in the 170bp subunit structure. Two regions (B and C) were overlapped with the regions with higher homology between subunits, while other two regions (A and D) cannot be explained solely by the regional homology between the subunits. These regions were located at both junctions of the nucleosomal and the linker region, and overlapped with the binding motifs for alpha protein and CENP-B. Approximately 90% of the recombination occurred between the subunits located next but one (+/- 2 shift), although the frequency of recombination between the adjoining subunits (+/- 1 shift) was approximately 10%. Images PMID:8559653

  20. Intrusão dentária utilizando mini-implantes Orthodontic intrusion with mini-implant anchorage

    Directory of Open Access Journals (Sweden)

    Telma Martins de Araújo

    2008-10-01

    Full Text Available INTRODUÇÃO: dentre os diversos tipos de movimentos dentários induzidos ortodonticamente, o de intrusão é, sem dúvida, um dos mais difíceis de serem conseguidos. A mecânica intrusiva convencional, apesar de viável, é complexa, no que diz respeito ao controle de seus efeitos colaterais. Isso, em grande parte, refere-se à dificuldade em se obter uma ancoragem satisfatória. Neste contexto, os mini-implantes, por oferecerem efetiva ancoragem esquelética, têm se mostrado de extrema valia para os ortodontistas, tornando a intrusão, tanto de dentes anteriores quanto posteriores, um procedimento cada vez mais simples, do ponto de vista mecânico. OBJETIVO: pretende-se, então, neste artigo, descrever e demonstrar, clinicamente, as diversas possibilidades de utilização dos mini-implantes como recurso de ancoragem para o movimento de intrusão.INTRODUCTION: Among all different varieties of orthodontically induced tooth movement, intrusion is, without doubt, one of the most difficult movements to be reached. Conventional intrusive biomechanics, although possible, may lead to undesirable side-effects. These events, in most cases, are related to the difficulty in obtaining an efficient anchorage unit. Then, mini-implants, because of their high success rates of effective skeletal anchorage, are valuable devices to orthodontists, transforming the intrusion movement, both at the anterior and the posterior regions, a more and more uncomplicated biomechanical procedure. AIM: to describe and show, clinically, different ways of using mini-implants as an anchorage system to intrusion movement.

  1. Fuzzy Aided Application Layer Semantic Intrusion Detection System - FASIDS

    CERN Document Server

    Sangeetha, S; 10.5121/ijnsa.2010.2204

    2010-01-01

    The objective of this is to develop a Fuzzy aided Application layer Semantic Intrusion Detection System (FASIDS) which works in the application layer of the network stack. FASIDS consist of semantic IDS and Fuzzy based IDS. Rule based IDS looks for the specific pattern which is defined as malicious. A non-intrusive regular pattern can be malicious if it occurs several times with a short time interval. For detecting such malicious activities, FASIDS is proposed in this paper. At application layer, HTTP traffic's header and payload are analyzed for possible intrusion. In the proposed misuse detection module, the semantic intrusion detection system works on the basis of rules that define various application layer misuses that are found in the network. An attack identified by the IDS is based on a corresponding rule in the rule-base. An event that doesn't make a 'hit' on the rule-base is given to a Fuzzy Intrusion Detection System (FIDS) for further analysis.

  2. Intrusion problematic during water supply systems' operation

    Energy Technology Data Exchange (ETDEWEB)

    Mora-Rodriguez, Jesus; Lopez-Jimenez, P. Amparo [Departamento de Ingenieria Hidraulica y Medio Ambiente, Universidad Politecnica de Valencia, Camino de Vera, s/n, 46022, Valencia (Spain); Ramos, Helena M. [Civil Engineering Department and CEHIDRO, Instituto Superior Tecnico, Technical University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon (Portugal)

    2011-07-01

    Intrusion through leaks occurrence is a phenomenon when external fluid comes into water pipe systems. This phenomenon can cause contamination problems in drinking pipe systems. Hence, this paper focuses on the entry of external fluids across small leaks during normal operation conditions. This situation is especially important in elevated points of the pipe profile. Pressure variations can origin water volume losses and intrusion of contaminants into the drinking water pipes. This work focuses in obtaining up the physical representation on a specific case intrusion in a pipe water system. The combination of two factors is required to generate this kind of intrusion in a water supply system: on one hand the existence of at least a leak in the system; on the other hand, a pressure variation could occur during the operation of the system due to consumption variation, pump start-up or shutdown. The potential of intrusion during a dynamic or transient event is here analyzed. To obtain this objective an experimental case study of pressure transient scenario is analyzed with a small leak located nearby the transient source.

  3. A HIERARCHICAL INTRUSION DETECTION ARCHITECTURE FOR WIRELESS SENSOR NETWORKS

    Directory of Open Access Journals (Sweden)

    Hossein Jadidoleslamy

    2011-10-01

    Full Text Available Networks protection against different types of attacks is one of most important posed issue into the network andinformation security application domains. This problem on Wireless Sensor Networks (WSNs, in attention to theirspecial properties, has more importance. Now, there are some of proposed architectures and guide lines to protectWireless Sensor Networks (WSNs against different types of intrusions; but any one of them do not has acomprehensive view to this problem and they are usually designed and implemented in single-purpose; but, theproposed design in this paper tries to has been a comprehensive view to this issue by presenting a complete andcomprehensive Intrusion Detection Architecture (IDA. The main contribution of this architecture is its hierarchicalstructure; i.e., it is designed and applicable, in one or two levels, consistent to the application domain and itsrequired security level. Focus of this paper is on the clustering WSNs, designing and deploying Cluster-basedIntrusion Detection System (CIDS on cluster-heads and Wireless Sensor Network wide level Intrusion DetectionSystem (WSNIDS on the central server. Suppositions of the WSN and Intrusion Detection Architecture (IDA are:static and heterogeneous network, hierarchical and clustering structure, clusters' overlapping and using hierarchicalrouting protocol such as LEACH, but along with minor changes. Finally, the proposed idea has been verified bydesigning a questionnaire, representing it to some (about 50 people experts and then, analyzing and evaluating itsacquired results.

  4. Sensitive Data Protection Based on Intrusion Tolerance in Cloud Computing

    Directory of Open Access Journals (Sweden)

    Jingyu Wang

    2011-02-01

    Full Text Available Service integration and supply on-demand coming from cloud computing can significantly improve the utilization of computing resources and reduce power consumption of per service, and effectively avoid the error of computing resources. However, cloud computing is still facing the problem of intrusion tolerance of the cloud computing platform and sensitive data of new enterprise data center. In order to address the problem of intrusion tolerance of cloud computing platform and sensitive data in new enterprise data center, this paper constructs a virtualization intrusion tolerance system based on cloud computing by researching on the existing virtualization technology, and then presents a method of intrusion tolerance to protect sensitive data in cloud data center based on virtual adversary structure by utilizing secret sharing. This system adopts the method of hybrid fault model, active and passive replicas, state update and transfer, proactive recovery and diversity, and initially implements to tolerate F faulty replicas in N=2F+1 replicas and ensure that only F+1 active replicas to execute during the intrusion-free stage. The remaining replicas are all put into passive mode, which significantly reduces the resource consuming in cloud platform. At last we prove the reconstruction and confidentiality property of sensitive data by utilizing secret sharing.

  5. Perception of the English intrusive stops by Korean listeners

    Science.gov (United States)

    Han, Jeong-Im

    2002-05-01

    This paper reports results of an experiment examining Korean listeners' perception of English intrusive stops in nasal-obstruent clusters. The experiment tests (1) how often intrusive stops are perceived; (2) how language-specific syllable structure constraints influence the perception, given the fact that Korean does not allow consonant clusters in syllable onsets and codas; (3) whether even the perception of phonetic variables like intrusive stops, not phonemes, could be improved by learning. Ninety English non-words with a monosyllable structure of CVC1C2 were created, where C1=/m,n,N/, and C2=/p,k,s/. The stimuli including additional 90 filler items were recorded by three native English speakers and one representative data among them was given to three groups of native Korean listeners in terms of their English proficiency. Each was asked to monitor the target sounds [Warner and Weber, J. Phonetics 29, 23-52 (2001)]. The preliminary results show that identification of intrusive stops in English is totally dependent on Korean syllable structure, so even stimuli with strong acoustic cues were misparsed. Nonetheless, there's a high correlation between perception of intrusive stops and listeners' English proficiency, showing the possibility of the improvement of perception by learning.

  6. Orthodontic intrusive movement to reduce infrabony defects in periodontal pacients

    Directory of Open Access Journals (Sweden)

    Aldrieli Regina Ambrósio

    2008-01-01

    Full Text Available The adult tends to be an excellent orthodontic patient, because he/she is motivated and cooperative. Nevertheless, many adult patientspresent periodontal problems. Intrusive movement is usually necessary against an area with infrabony defects, and in order for treatmentto be successful, it is necessary for all related aspects to be well understood. The aim of this study was to discuss the feasibility and efficacy of orthodontic intrusion as a means of reducing infrabony defects caused by periodontal disease. The methodology used was reviewed in the literature, from which articles were selected using the MEDLINE, LILACS and BBO databases. After periodontal treatment and maintenance with suitable bacterial plaque control has been performed, orthodontic treatment with intrusive tooth movement can be performed in case of pathological tooth migration and extrusion. The segmented arch technique is the most indicated for intruding teeth with infrabony defects because it is capable of developing light and continuous forces. Furthermore, although studies did not confirm, they suggested that orthodontic intrusion could lead to the formation of new periodontal support tissue. With a multidisciplinary approach, it is possible to successfully perform intrusion movements in teeth that present infrabony defects, provided that periodontal inflammation has been treated and the patient presents an excellent level of plaque control. Among the benefits of this approach are: better appearance, better access to dental hygiene, restitution of incisal occlusion and reduction in non axial load.

  7. Distributed intrusion detection for mobile ad hoc networks

    Institute of Scientific and Technical Information of China (English)

    Yi Ping; Jiang Xinghao; Wu Yue; Liu Ning

    2008-01-01

    Mobile ad hoc networking(MANET)has become an exciting and important technology in recent years,because of the rapid proliferation of wireless devices.Mobile ad hoc networks is highly vulnerable to attacks due to the open medium,dynamically changing network topology,cooperative algorithms,and lack of centralized monitoring and management point.The traditional way of protecting networks with firewalls and encryption software is no longer sufficient and effective for those features.A distributed intrusion detection approach based on timed automata is given.A cluster-based detection scheme is presented,where periodically a node is elected as the monitor node for a cluster.These monitor nodes can not only make local intrusion detection decisions,but also cooperatively take part in global intrusion detection.And then the timed automata is constructed by the way of manually abstracting the correct behaviours of the node according to the routing protocol of dynamic source routing(DSR).The monitor nodes can verify the behaviour of every nodes by timed automata,and validly detect real-time attacks without signatures of intrusion or trained data.Compared with the architecture where each node is its own IDS agent,the approach is much more efficient while maintaining the same level of effectiveness.Finally,the intrusion detection method is evaluated through simulation experiments.

  8. Studies of an expanded trinucleotide repeat in transgenic mice

    Energy Technology Data Exchange (ETDEWEB)

    Bingham, P.; Wang, S.; Merry, D. [Univ. of Pennsylvania, Philadelphia, PA (United States)

    1994-09-01

    Spinal and bulbar muscular atrophy (SBMA) is a progressive motor neuron disease caused by expansion of a trinucleotide repeat in the androgen receptor gene (AR{sup exp}). AR{sup exp} repeats expand further or contract in approximately 25% of transmissions. Analogous {open_quotes}dynamic mutations{close_quotes} have been reported in other expanded trinucleotide repeat disorders. We have been developing a mouse model of this disease using a transgenic approach. Expression of the SBMA AR was documented in transgenic mice with an inducible promoter. No phenotypic effects of transgene expression were observed. We have extended our previous results on stability of the expanded trinucleotide repeat in transgenic mice in two lines carrying AR{sup exp}. Tail DNA was amplified by PCR using primers spanning the repeat on 60 AR{sup exp} transgenic mice from four different transgenic lines. Migration of the PCR product through an acrylamide gel showed no change of the 45 CAG repeat length in any progeny. Similarly, PCR products from 23 normal repeat transgenics showed no change from the repeat length of the original construct. Unlike the disease allele in humans, the expanded repeat AR cDNA in transgenic mice showed no change in repeat length with transmission. The relative stability of CAG repeats seen in the transgenic mice may indicate either differences in the fidelity of replicative enzymes, or differences in error identification and repair between mice and humans. Integration site or structural properties of the transgene itself might also play a role.

  9. Intrusions in Episodic Memory: Reconsolidation or Interference?

    Science.gov (United States)

    Klingmüller, Angela; Caplan, Jeremy B.; Sommer, Tobias

    2017-01-01

    It would be profoundly important if reconsolidation research in animals and other memory domains generalized to human episodic memory. A 3-d-list-discrimination procedure, based on free recall of objects, with a contextual reminder cue (the testing room), has been thought to demonstrate reconsolidation of human episodic memory (as noted in a…

  10. SEAWATER INTRUSION TYPES AND REGIONAL DIVISIONS IN THE SOUTHERN COAST OF LAIZHOU BAY

    Institute of Scientific and Technical Information of China (English)

    孟广兰; 韩有松; 王少青; 王珍岩

    2002-01-01

    The southern coast of Laizhou Bay, Bohai Sea, is one of the areas in China most seriously impacted by seawater intrusion. Based on the sources of intruding waterbedies, seawater intrusion can be divided into two types: intrusion of saline water derived from modern seawater, and intrusion of subsurface brine and saline water derived from paleo-seawater in shallow Quaternary sediments. There are some distinct differences in their formation, mechanism and damage. The subsurface brine intrusion is a special type, which can cause very serious disaster. The coastal landform and the Quaternary hydrogeological environment are predominant factors in the classification of seawater intrusion types. Various coastal environments in different coastal sections result in three types of intrusion: seawater intrusion, saline groundwater intrusion, and mixed seawater and saline water intrusion, in the southern coast of Laizhou Bay, which can be divided into four areas: the sea-water intrusion area in the northern Laizhou City coast, the mixed seawater and saline groundwater intrusion area in the Baisha River-Jiaolai River mouth plain area, the mixed seawater and saline groundwater intrusion area in the Weihe River mouth plain area northern Changyi county coast, and the saline ground-water intrusion area in the northern Shouguang plains.

  11. Distress and recurrence of intrusive thoughts in younger and older adults.

    Science.gov (United States)

    Magee, Joshua C; Teachman, Bethany A

    2012-03-01

    The current study incorporated a life span perspective into existing theories of intrusive thoughts to examine age-related differences in the difficulty controlling intrusive thoughts, the distress following intrusive thought recurrences, and the meanings assigned to these recurrences. Younger (N = 51) and older (N = 49) community adults were randomly assigned to suppress (i.e., keep out of mind) or monitor an intrusive thought. Participants rated their positive and negative affect throughout engagement with the intrusive thought, and they also rated the meanings they gave to recurrences of their everyday intrusive thoughts. The results demonstrated that older adults tended to perceive greater difficulty with controlling the intrusive thought than younger adults despite the fact that they did not differ in the actual recurrence of the intrusive thought. With regard to distress, older adults experienced steadier levels of positive affect than younger adults throughout engagement with the intrusive thought. However, older adults also reported greater residual negative affect after engaging with the intrusive thought than younger adults. Finally, older and younger adults appeared to assign meanings to recurrences of intrusive thoughts in line with age-relevant concerns. Specifically, older adults were prone to interpret the recurrence of intrusive thoughts as a sign of cognitive decline, but they were less likely than younger adults to see intrusive thoughts as a sign of moral failure. Together, these results highlight a range of potential risk and protective factors in older adults for experiencing emotion dysregulation after intrusive thoughts.

  12. A simulation/optimization study to assess seawater intrusion management strategies for the Gaza Strip coastal aquifer (Palestine)

    Science.gov (United States)

    Dentoni, Marta; Deidda, Roberto; Paniconi, Claudio; Qahman, Khalid; Lecca, Giuditta

    2015-03-01

    Seawater intrusion is one of the major threats to freshwater resources in coastal areas, often exacerbated by groundwater overexploitation. Mitigation measures are needed to properly manage aquifers, and to restore groundwater quality. This study integrates three computational tools into a unified framework to investigate seawater intrusion in coastal areas and to assess strategies for managing groundwater resources under natural and human-induced stresses. The three components are a three-dimensional hydrogeological model for density-dependent variably saturated flow and miscible salt transport, an automatic calibration procedure that uses state variable outputs from the model to estimate selected model parameters, and an optimization module that couples a genetic algorithm with the simulation model. The computational system is used to rank alternative strategies for mitigation of seawater intrusion, taking into account conflicting objectives and problem constraints. It is applied to the Gaza Strip (Palestine) coastal aquifer to identify a feasible groundwater management strategy for the period 2011-2020. The optimized solution is able to: (1) keep overall future abstraction from municipal groundwater wells close to the user-defined maximum level, (2) increase the average groundwater heads, and (3) lower both the total mass of salt extracted and the extent of the areas affected by seawater intrusion.

  13. A phase 1 study evaluating the pharmacokinetics, safety and tolerability of repeat dosing with a human IL-13 antibody (CAT-354 in subjects with asthma

    Directory of Open Access Journals (Sweden)

    Roskos Lorin

    2010-01-01

    Full Text Available Abstract Background IL-13 has been implicated in the development of airway inflammation and hyperresponsiveness. This study investigated the multiple-dose pharmacokinetics and safety profile of human anti-IL-13 antibody (CAT-354 in adults with asthma. Methods This was a multiple-dose, randomised, double-blind, placebo-controlled phase 1 study in asthmatics (forced expiratory volume in 1 second [FEV1] ≥ 80% predicted. Subjects were randomised to receive three intravenous infusions of CAT-354 (1 mg/kg, 5 mg/kg or 10 mg/kg or placebo at 28-day intervals. Blood samples were taken for pharmacokinetic measurements. Safety was assessed by adverse events, vital signs, ECGs, laboratory and pulmonary function parameters. Results Twenty-three subjects (aged 21-60 years, FEV1 88-95% predicted received ≥ 1 dose of study medication. The half-life of CAT-354 was 12-17 days and was dose-independent. The maximum serum concentration and area under the curve were dose-dependent. Clearance (2.2-2.6 mL/day/kg and volume of distribution (44-57 mL/kg were both low and dose-independent. The observed maximum serum concentration after each dose increased slightly from dose 1 through dose 3 at all dose levels, consistent with an accumulation ratio of 1.4 to 1.7 for area under the curve. Most adverse events were deemed mild to moderate and unrelated to study medication. One SAE was reported and deemed unrelated to study drug. There were no effects of clinical concern for vital signs, ECG, laboratory or pulmonary parameters. Conclusions CAT-354 exhibited linear pharmacokinetics and an acceptable safety profile. These findings suggest that at the doses tested, CAT-354 can be safely administered in multiple doses to patients with asthma. Trial registration NCT00974675.

  14. Repeatability of Cryogenic Multilayer Insulation

    Science.gov (United States)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

    2017-01-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between multiple identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five GRC provided coupons with 25 layers was shown to be +/- 8.4 whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0. A second group of 10 coupons have been fabricated by Yetispace and tested by Florida State University, through the first 4 tests, the repeatability has been shown to be +/- 16. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  15. A Cooperative Network Intrusion detection Based on Fuzzy SVMs

    Directory of Open Access Journals (Sweden)

    Shaohua Teng

    2010-04-01

    Full Text Available There is a large number of noise in the data obtained from network, which deteriorates intrusion detection performance. To delete the noise data, data preprocessing is done before the construction of hyperplane in support vector machine (SVM. By introducing fuzzy theory into SVM, a new method is proposed for network intrusion detection.  Because the attack behavior is different for different network protocol, a different fuzzy membership function is formatted, such that for each class of protocol there is a SVM. To implement this approach, a fuzzy SVM-based cooperative network intrusion detection system with multi-agent architecture is presented. It is composed of three types of agents corresponding to TCP, UDP, and ICMP protocols, respectively. Simulation experiments are done by using KDD CUP 1999 data set, results show that the training time is significantly shortened, storage space requirement is reduced, and classification accuracy is improved.

  16. Intrusion detection based on system calls and homogeneous Markov chains

    Institute of Scientific and Technical Information of China (English)

    Tian Xinguang; Duan Miyi; Sun Chunlai; Li Wenfa

    2008-01-01

    A novel method for detecting anomalous program behavior is presented, which is applicable to hostbased intrusion detection systems that monitor system call activities. The method constructs a homogeneous Markov chain model to characterize the normal behavior of a privileged program, and associates the states of the Markov chain with the unique system calls in the training data. At the detection stage, the probabilities that the Markov chain model supports the system call sequences generated by the program are computed. A low probability indicates an anomalous sequence that may result from intrusive activities. Then a decision rule based on the number of anomalous sequences in a locality frame is adopted to classify the program's behavior. The method gives attention to both computational efficiency and detection accuracy, and is especially suitable for on-line detection. It has been applied to practical host-based intrusion detection systems.

  17. CUSUM-Based Intrusion Detection Mechanism for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Bishan Ying

    2014-01-01

    Full Text Available The nature of wireless sensor networks (WSNs makes them very vulnerable to adversary's malicious attacks. Therefore, network security is an important issue to WSNs. Due to the constraints of WSN, intrusion detection in WSNs is a challengeable task. In this paper, we present a novel intrusion detection mechanism for WSNs, which is composed of a secure data communication algorithm and an intrusion detection algorithm. The major contribution of this paper is that we propose an original secure mechanism to defend WSNs against malicious attacks by using the information generated during data communication. The approach is able to protect the data communication in a WSN even if some sensor nodes are compromised by adversary. The proposed approach is easy to be implemented and performed in resource-constrained WSN. We also evaluate the proposed approach by a simulation experiment and analyze the simulation results in detail.

  18. Physical model simulations of seawater intrusion in unconfined aquifer

    Directory of Open Access Journals (Sweden)

    Tanapol Sriapai

    2012-12-01

    Full Text Available The objective of this study is to simulate the seawater intrusion into unconfined aquifer near shoreline and to assessthe effectiveness of its controlling methods by using scaled-down physical models. The intrusion controlled methods studiedhere include fresh water injection, saltwater extraction, and subsurface barrier. The results indicate that under natural dynamicequilibrium between the recharge of fresh water and the intrusion well agree with the Ghyben-Herzberg mathematical solution.Fresh water pumping from the aquifer notably move the fresh-salt water interface toward the pumping well, depending on thepumping rates and the head differences (h between the aquifer recharge and the salt water level. The fresh water injectionmethod is more favorable than the salt water extraction and subsurface barrier method. The fresh water injection rate of about10% of the usage rate can effectively push the interface toward the shoreline, and keeping the pumping well free of salinity.

  19. Hybrid Intrusion Detection and Prediction multiAgent System HIDPAS

    CERN Document Server

    Jemili, Farah; Ahmed, Mohamed Ben

    2009-01-01

    This paper proposes an intrusion detection and prediction system based on uncertain and imprecise inference networks and its implementation. Giving a historic of sessions, it is about proposing a method of supervised learning doubled of a classifier permitting to extract the necessary knowledge in order to identify the presence or not of an intrusion in a session and in the positive case to recognize its type and to predict the possible intrusions that will follow it. The proposed system takes into account the uncertainty and imprecision that can affect the statistical data of the historic. The systematic utilization of an unique probability distribution to represent this type of knowledge supposes a too rich subjective information and risk to be in part arbitrary. One of the first objectives of this work was therefore to permit the consistency between the manner of which we represent information and information which we really dispose.

  20. Intrusion Awareness Based on Data Fusion and SVM Classification

    Directory of Open Access Journals (Sweden)

    Ramnaresh Sharma

    2012-06-01

    Full Text Available Network intrusion awareness is important factor for risk analysis of network security. In the current decade various method and framework are available for intrusion detection and security awareness. Some method based on knowledge discovery process and some framework based on neural network. These entire model take rule based decision for the generation of security alerts. In this paper we proposed a novel method for intrusion awareness using data fusion and SVM classification. Data fusion work on the biases of features gathering of event. Support vector machine is super classifier of data. Here we used SVM for the detection of closed item of ruled based technique. Our proposed method simulate on KDD1999 DARPA data set and get better empirical evaluation result in comparison of rule based technique and neural network model.

  1. Intrusion Awareness Based on Data Fusion and SVM Classification

    Directory of Open Access Journals (Sweden)

    Ramnaresh Sharma

    2012-06-01

    Full Text Available Network intrusion awareness is important factor forrisk analysis of network security. In the currentdecade various method and framework are availablefor intrusion detection and security awareness.Some method based on knowledge discovery processand some framework based on neural network.These entire model take rule based decision for thegeneration of security alerts. In this paper weproposed a novel method for intrusion awarenessusing data fusion and SVM classification. Datafusion work on the biases of features gathering ofevent. Support vector machine is super classifier ofdata. Here we used SVM for the detection of closeditem of ruled based technique. Our proposedmethod simulate on KDD1999 DARPA data set andget better empirical evaluation result in comparisonof rule based technique and neural network model.

  2. HYBRID ARCHITECTURE FOR DISTRIBUTED INTRUSION DETECTION SYSTEM IN WIRELESS NETWORK

    Directory of Open Access Journals (Sweden)

    Seyedeh Yasaman Rashida

    2013-06-01

    Full Text Available In order to the rapid growth of the network application, new kinds of network attacks are emerging endlessly. So it is critical to protect the networks from attackers and the Intrusion detection technology becomes popular. Therefore, it is necessary that this security concern must be articulate right from the beginning of the network design and deployment. The intrusion detection technology is the process of identifying network activity that can lead to a compromise of security policy. Lot of work has been done in detection of intruders. But the solutions are not satisfactory. In this paper, we propose a novel Distributed Intrusion Detection System using Multi Agent In order to decrease false alarms and manage misuse and anomaly detects.

  3. Research of Intrusion Detection Technology and its Formal Modeling

    Directory of Open Access Journals (Sweden)

    PENG Yali

    2009-10-01

    Full Text Available The intrusion detection technology is one of the most important dynamic security technologies, which can be used in the critical security system construction and the basic service protection. Apparently, applying formal specification to the procedure of developing an intrusion detection system can fulfill their security requirement and win the confidence of users of the secured systems. Taking a DDoS intrusion detection system as an example, we establish integrity sub-regular database through analyzing the default characteristics and universal characteristics in communication of DDoS attack, which can guarantee fast and effective detection in each appeared DDoS attack. At the same time, we use the association rules mining algorithm mine new rules and their association pattern to detect the unknown attack, and illustrate how Z can be used to specify and model the security-critical systems.

  4. Alerts Visualization and Clustering in Network-based Intrusion Detection

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Dr. Li [University of Tennessee; Gasior, Wade C [ORNL; Dasireddy, Swetha [University of Tennessee

    2010-04-01

    Today's Intrusion detection systems when deployed on a busy network overload the network with huge number of alerts. This behavior of producing too much raw information makes it less effective. We propose a system which takes both raw data and Snort alerts to visualize and analyze possible intrusions in a network. Then we present with two models for the visualization of clustered alerts. Our first model gives the network administrator with the logical topology of the network and detailed information of each node that involves its associated alerts and connections. In the second model, flocking model, presents the network administrator with the visual representation of IDS data in which each alert is represented in different color and the alerts with maximum similarity move together. This gives network administrator with the idea of detecting various of intrusions through visualizing the alert patterns.

  5. Basement influences on dolomite-hosted vertical sedimentary intrusions in marine erg-margin deposits from the Pennsylvanian of Northern Wyoming (USA)

    Science.gov (United States)

    Blanchard, Sébastien; Frank, Tracy D.; Fielding, Christopher R.

    2016-06-01

    Understanding soft-sediment deformation structures and their triggers can help in assessing the influence of tectonics, climate, and diagenesis on the stratigraphic record. Such features commonly record processes that would not otherwise be preserved. The description of soft-sediment deformation in Pennsylvanian deposits of the western United States, characterized by orbitally driven alternations between eolian sandstones, marine dolomites, and shales, has been limited to contorted cross-beds. We document discordant, sheet-like sedimentary intrusions in three marine intervals over a 45-km-wide area. Intrusions consist of very well to moderately cemented, very fine to fine-grained quartz sandstone. Body widths range from 5 to 50 cm, and heights up to 2 m. The orientations of 103 vertical bodies were measured. Based on upward- and downward-tapering, and the presence of deformed, microfractured fragments of host rocks, these intrusions are interpreted to result from seismically induced fluidization of water-saturated sands. Their sheet-like morphology indicates injection through fractures. Two predominant directions (WNW-ESE and N-S) were recognized and interpreted as pre-injection fracture sets. Folding of surrounding layers around the intrusions suggests negligible compaction prior to injection, indicating penecontemporaneous or shallow burial fluidization. The intraplate location of Wyoming implies that seismicity did not originate at a plate boundary. The area within which intrusions are found is crossed by a zone characterized by localized development of thick eolian stories at the top of the formation, interpreted to reflect the rejuvenation of a basement lineament. The seismically active character of lineaments may explain overpressure and fluidization, substantiating the notion that Precambrian structures repeatedly affected Phanerozoic sedimentation. Similar intrusive features may be wrongly identified or overlooked in deposits of arid environments, but their

  6. Repeated whole cigarette smoke exposure alters cell differentiation and augments secretion of inflammatory mediators in air-liquid interface three-dimensional co-culture model of human bronchial tissue.

    Science.gov (United States)

    Ishikawa, Shinkichi; Ito, Shigeaki

    2017-02-01

    In vitro models of human bronchial epithelium are useful for toxicological testing because of their resemblance to in vivo tissue. We constructed a model of human bronchial tissue which has a fibroblast layer embedded in a collagen matrix directly below a fully-differentiated epithelial cell layer. The model was applied to whole cigarette smoke (CS) exposure repeatedly from an air-liquid interface culture while bronchial epithelial cells were differentiating. The effects of CS exposure on differentiation were determined by histological and gene expression analyses on culture day 21. We found a decrease in ciliated cells and perturbation of goblet cell differentiation. We also analyzed the effects of CS exposure on the inflammatory response, and observed a significant increase in secretion of IL-8, GRO-α, IL-1β, and GM-CSF. Interestingly, secretion of these mediators was augmented with repetition of whole CS exposure. Our data demonstrate the usefulness of our bronchial tissue model for in vitro testing and the importance of exposure repetition in perturbing the differentiation and inflammation processes.

  7. How stratospheric are deep stratospheric intrusions? LUAMI 2008

    Science.gov (United States)

    Trickl, Thomas; Vogelmann, Hannes; Fix, Andreas; Schäfler, Andreas; Wirth, Martin; Calpini, Bertrand; Levrat, Gilbert; Romanens, Gonzague; Apituley, Arnoud; Wilson, Keith M.; Begbie, Robert; Reichardt, Jens; Vömel, Holger; Sprenger, Michael

    2016-07-01

    A large-scale comparison of water-vapour vertical-sounding instruments took place over central Europe on 17 October 2008, during a rather homogeneous deep stratospheric intrusion event (LUAMI, Lindenberg Upper-Air Methods Intercomparison). The measurements were carried out at four observational sites: Payerne (Switzerland), Bilthoven (the Netherlands), Lindenberg (north-eastern Germany), and the Zugspitze mountain (Garmisch-Partenkichen, German Alps), and by an airborne water-vapour lidar system creating a transect of humidity profiles between all four stations. A high data quality was verified that strongly underlines the scientific findings. The intrusion layer was very dry with a minimum mixing ratios of 0 to 35 ppm on its lower west side, but did not drop below 120 ppm on the higher-lying east side (Lindenberg). The dryness hardens the findings of a preceding study ("Part 1", Trickl et al., 2014) that, e.g., 73 % of deep intrusions reaching the German Alps and travelling 6 days or less exhibit minimum mixing ratios of 50 ppm and less. These low values reflect values found in the lowermost stratosphere and indicate very slow mixing with tropospheric air during the downward transport to the lower troposphere. The peak ozone values were around 70 ppb, confirming the idea that intrusion layers depart from the lowermost edge of the stratosphere. The data suggest an increase of ozone from the lower to the higher edge of the intrusion layer. This behaviour is also confirmed by stratospheric aerosol caught in the layer. Both observations are in agreement with the idea that sections of the vertical distributions of these constituents in the source region were transferred to central Europe without major change. LAGRANTO trajectory calculations demonstrated a rather shallow outflow from the stratosphere just above the dynamical tropopause, for the first time confirming the conclusions in "Part 1" from the Zugspitze CO observations. The trajectories qualitatively explain

  8. Repeats in transforming acidic coiled-coil (TACC) genes.

    Science.gov (United States)

    Trivedi, Seema

    2013-06-01

    Transforming acidic coiled-coil proteins (TACC1, 2, and 3) are essential proteins associated with the assembly of spindle microtubules and maintenance of bipolarity. Dysregulation of TACCs is associated with tumorigenesis, but studies of microsatellite instability in TACC genes have not been extensive. Microsatellite or simple sequence repeat instability is known to cause many types of cancer. The present in silico analysis of SSRs in human TACC gene sequences shows the presence of mono- to hexa-nucleotide repeats, with the highest densities found for mono- and di-nucleotide repeats. Density of repeats is higher in introns than in exons. Some of the repeats are present in regulatory regions and retained introns. Human TACC genes show conservation of many repeat classes. Microsatellites in TACC genes could be valuable markers for monitoring numerical chromosomal aberrations and or cancer.

  9. Role of DNA Polymerases in Repeat-Mediated Genome Instability

    Directory of Open Access Journals (Sweden)

    Kartik A. Shah

    2012-11-01

    Full Text Available Expansions of simple DNA repeats cause numerous hereditary diseases in humans. We analyzed the role of DNA polymerases in the instability of Friedreich’s ataxia (GAAn repeats in a yeast experimental system. The elementary step of expansion corresponded to ∼160 bp in the wild-type strain, matching the size of Okazaki fragments in yeast. This step increased when DNA polymerase α was mutated, suggesting a link between the scale of expansions and Okazaki fragment size. Expandable repeats strongly elevated the rate of mutations at substantial distances around them, a phenomenon we call repeat-induced mutagenesis (RIM. Notably, defects in the replicative DNA polymerases δ and ∊ strongly increased rates for both repeat expansions and RIM. The increases in repeat-mediated instability observed in DNA polymerase δ mutants depended on translesion DNA polymerases. We conclude that repeat expansions and RIM are two sides of the same replicative mechanism.

  10. Power-Aware Intrusion Detection in Mobile Ad Hoc Networks

    Science.gov (United States)

    Şen, Sevil; Clark, John A.; Tapiador, Juan E.

    Mobile ad hoc networks (MANETs) are a highly promising new form of networking. However they are more vulnerable to attacks than wired networks. In addition, conventional intrusion detection systems (IDS) are ineffective and inefficient for highly dynamic and resource-constrained environments. Achieving an effective operational MANET requires tradeoffs to be made between functional and non-functional criteria. In this paper we show how Genetic Programming (GP) together with a Multi-Objective Evolutionary Algorithm (MOEA) can be used to synthesise intrusion detection programs that make optimal tradeoffs between security criteria and the power they consume.

  11. A national inventory of seawater intrusion vulnerability for Australia

    Directory of Open Access Journals (Sweden)

    Leanne K. Morgan

    2015-09-01

    New hydrological insights for the region: The combination of methods identified areas of highest risk to SWI including unconfined aquifers at Derby (WA and Esperance (WA, and confined aquifers at Esperance (WA and Adelaide (SA. The combination of analytic and qualitative approaches offers a more comprehensive and less subjective seawater intrusion characterization than arises from applying the methods in isolation, thereby imparting enhanced confidence in the outcomes. Importantly, active seawater intrusion conditions occur in many of Australia’s confined coastal aquifers, obviating the use of the analytical solution, and suggesting that offshore groundwater resources provide significant contributions to these systems.

  12. Hybrid Optimization of Support Vector Machine for Intrusion Detection

    Institute of Scientific and Technical Information of China (English)

    XI Fu-li; YU Song-nian; HAO Wei

    2005-01-01

    Support vector machine (SVM) technique has recently become a research focus in intrusion detection field for its better generalization performance when given less priori knowledge than other soft-computing techniques. But the randomicity of parameter selection in its implement often prevents it achieving expected performance. By utilizing genetic algorithm (GA) to optimize the parameters in data preprocessing and the training model of SVM simultaneously, a hybrid optimization algorithm is proposed in the paper to address this problem. The experimental results demonstrate that it's an effective method and can improve the perfornance of SVM-based intrusion detection system further.

  13. Research and Implementation of Unsupervised Clustering-Based Intrusion Detection

    Institute of Scientific and Technical Information of China (English)

    Luo Min; Zhang Huan-guo; Wang Li-na

    2003-01-01

    An unsupervised clustering-based intrusion de tection algorithm is discussed in this paper. The basic idea of the algorithm is to produce the cluster by comparing the distances of unlabeled training data sets. With the classified data instances, anomaly data clusters can be easily identified by normal cluster ratio and the identified cluster can be used in real data detection. The benefit of the algorithm is that it doesnt need labeled training data sets. The experiment concludes that this approach can detect unknown intrusions efficiently in the real network connections via using the data sets of KDD99.

  14. Research and Implementation of Unsupervised Clustering-Based Intrusion Detection

    Institute of Scientific and Technical Information of China (English)

    LuoMin; ZhangHuan-guo; WangLi-na

    2003-01-01

    An unsupervised clustering-based intrusion detection algorithm is discussed in this paper. The basic idea of the algorithm is to produce the cluster by comparing the distances of unlabeled training data sets. With the classified data instances, anomaly data clusters can be easily identified by normal duster ratio and the identified cluster can be used in real data detection. The benefit of the algorithm is that it doesn't need labeled training data sets. The experiment coneludes that this approach can detect unknown intrusions efficiently in the real network connections via using the data sets of KDD99.

  15. Enhancing collaborative intrusion detection networks against insider attacks using supervised intrusion sensitivity-based trust management model

    DEFF Research Database (Denmark)

    Li, Wenjuan; Meng, Weizhi; Kwok, Lam-For

    2017-01-01

    To defend against complex attacks, collaborative intrusion detection networks (CIDNs) have been developed to enhance the detection accuracy, which enable an IDS to collect information and learn experience from others. However, this kind of networks is vulnerable to malicious nodes which...... of intrusion sensitivity based on expert knowledge. In the evaluation, we compare the performance of three different supervised classifiers in assigning sensitivity values and investigate our trust model under different attack scenarios and in a real wireless sensor network. Experimental results indicate...... are utilized by insider attacks (e.g., betrayal attacks). In our previous research, we developed a notion of intrusion sensitivity and identified that it can help improve the detection of insider attacks, whereas it is still a challenge for these nodes to automatically assign the values. In this article, we...

  16. SEAWATER INTRUSION TYPES AND REGIONAL DIVISIONS IN THE SOUTHERN COAST OF LAIZHOU BAY

    Institute of Scientific and Technical Information of China (English)

    孟广兰; 韩有松; 王少青; 王珍岩

    2002-01-01

    The southern coast of Laizhou Bay, Bohai Sea, is one of the areas in China most seriously impacted by seawater intrusion. Based on the sources of intruding wate rbodies, seawater intrusion can be divided into two types: intrusion of saline water derived from modern seawater, and intrusion of subsurface brine and saline water derived from paleo-seawater in shallow Quaternary sediments. There are so me distinct differences in their formation, mechanism and damage. The subsurface brine intrusion is a special typ e, which can cause very serious disaster.The coastal landform and the Quaternary hydrogeological environment are pr edominant factors in the classification of seawater intrusion types. Various coastal environments in diff erent coastal sections result in three types of intrusion: seawater intrusion, saline groundwater intrusion, and mixed seawater and saline water intrusion, in the southern coast of Laizhou Bay, which can be divided into four areas: the seawater intrusion area in the northern Laizhou City coast, the mixed seawater and saline groundwater in trusion area in the Baisha River-Jiaolai River mouth plain area, the mixed seawater and saline groundwater intrus ion area in the Weihe River mouth plain area northern Changyi county coast, and the saline groundwater intrusion area in the northern Shouguang plains.

  17. Episodic intrusion, internal differentiation, and hydrothermal alteration of the miocene tatoosh intrusive suite south of Mount Rainier, Washington

    Science.gov (United States)

    du Bray, E.A.; Bacon, C.R.; John, D.A.; Wooden, J.L.; Mazdab, F.K.

    2011-01-01

    The Miocene Tatoosh intrusive suite south of Mount Rainier is composed of three broadly granodioritic plutons that are manifestations of ancestral Cascades arc magmatism. Tatoosh intrusive suite plutons have individually diagnostic characteristics, including texture, mineralogy, and geochemistry, and apparently lack internal contacts. New ion-microprobe U-Pb zircon ages indicate crystallization of the Stevens pluton ca. 19.2 Ma, Reflection-Pyramid pluton ca. 18.5 Ma, and Nisqually pluton ca. 17.5 Ma. The Stevens pluton includes rare, statistically distinct ca. 20.1 Ma zircon antecrysts. Wide-ranging zircon rare earth element (REE), Hf, U, and Th concentrations suggest late crystallization from variably evolved residual liquids. Zircon Eu/Eu*-Hf covariation is distinct for each of the Reflection-Pyramid, Nisqually, and Stevens plutons. Although most Tatoosh intrusive suite rocks have been affected by weak hydrothermal alteration, and sparse mineralized veins cut some of these rocks, significant base or precious metal mineralization is absent. At the time of shallow emplacement, each of these magma bodies was largely homogeneous in bulk composition and petrographic features, but, prior to final solidification, each of the Tatoosh intrusive suite plutons developed internal compositional variation. Geochemical and petrographic trends within each pluton are most consistent with differential loss of residual melt, possibly represented by late aplite dikes or erupted as rhyolite, from crystal-rich magma. Crystal-rich magma that formed each pluton evidently accumulated in reservoirs below the present level of exposure and then intruded to a shallow depth. Assembled by episodic intrusion, the Tatoosh intrusive suite may be representative of midsized composite plutonic complexes beneath arc volcanoes. ?? 2011 Geological Society of America.

  18. Hydrodynamic modeling of the intrusion phenomenon in water distribution systems; Modelacion hidrodinamica del fenomeno de intrusion en tuberia de abastecimiento

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Jimenez, Petra Amparo; Mora-Rodriguez, Jose de Jesus; Perez-Garcia, Rafael; Martinez-Solano, F. Javier [Universidad Politecnica de Valencia (Spain)

    2008-10-15

    This paper describes a strategy for the hydrodynamic modeling of the pathogen intrusion phenomenon in water distribution systems by the combination of a breakage with a depression situation. This scenario will be modeled computationally and experimentally. The phenomenon to be represented by both simulations is the same: the entrance of an external volume into the circulation of a main volume, known as a pathogen intrusion, as long as the main volume is potable water. To this end, a prototype and a computational model based on Computational Fluid Dynamics (CFD) are used, which allow visualizing the fields of speeds and pressures in a simulated form. With the comparison of the results of both models, conclusions will be drawn on the detail of the studied pathogen intrusion phenomenon. [Spanish] En el presente documento se describe una estrategia de modelacion del fenomeno hidrodinamico de la intrusion patogena en redes de distribucion de agua por combinacion de una rotura con una situacion de depresion. Este escenario sera modelado computacional y experimentalmente. El fenomeno que se desea representar con ambas simulaciones es el mismo: la entrada de un caudal externo a una conduccion para la que circula un caudal principal, denominado intrusion patogena, siempre y cuando el caudal principal sea agua potable. Para ello se dispone de un prototipo y un modelo computacional basado en la Dinamica de Fluidos Computacional (DFC de aqui en adelante), que permite visualizar los campos de velocidades y presiones de forma simulada. Con la comparacion de los resultados de ambos modelos se extraeran conclusiones sobre el detalle del fenomeno de la intrusion patogena estudiado.

  19. Geology and Geochemistry of Reworking Gold Deposits in Intrusive Rocks of China—Ⅰ. Features of the Intrusive Rocks

    Institute of Scientific and Technical Information of China (English)

    王秀璋; 程景平; 等

    1998-01-01

    Most gold deposits in intrusive rocks were formed as a result of reworking processes.the intrusive rocks containing gold deposits and consisting of ultramafic-mafic,intermediateacid and alkaline rocks of the Archean,Proterozoic,Caledonian,Hercynian and Yenshanian periods occur in cratons,activated zones of cratons and fold belts.Among them,ultramaficmafic rocks,diorite,alkaline rocks,and anorthosite are products of remelting in the mantle or mantle-crust or mantle with crustal contamination,However,auriferous intermediate-acid rocks are products of metasomatic-remelting in auriferous volcainc rocks or auriferous volcanosedimentary rocks in the deep crust.

  20. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  1. Quality control during repeated fryings

    Directory of Open Access Journals (Sweden)

    Cuesta, C.

    1998-08-01

    Full Text Available Most of the debate ¡s about how the slow or frequent turnover of fresh fat affects the deterioration, of fat used in frying. Then, the modification of different oils used in repeated fryings of potatoes without or with turnover of fresh oil, under similar frying conditions, was evaluated by two criteria: by measuring the total polar component isolated by column chromatography and by the evaluation of the specific compounds related to thermoxidative and hydrolytic alteration by High Performance Size Exclusion Chromatography (HPSEC. The results indicate that with frequent turnover of fresh oil, the critical level of 25% of polar material is rarely reached, and there are fewer problems with fat deterioration because the frying tended to increase the level of polar material and thermoxidative compounds (polymers and dimers of triglycerides and oxidized triglycerides in the fryer oil during the first fryings, followed by minor changes and a tendency to reach a near-steady state in successive fryings. However, in repeated frying of potatoes using a null turnover the alteration rate was higher being linear the relationship found between polar material or the different thermoxidative compounds and the number of fryings. On the other hand chemical reactions produced during deep-fat frying can be minimized by using proper oils. In addition the increased level of consumers awareness toward fat composition and its impact on human health could had an impact on the selection of fats for snacks and for industry. In this way monoenic fats are the most adequate from a nutritional point of view and for its oxidative stability during frying.

  2. Lunar Intrusive Domes on the Floor of Grimaldi and Near Aristillus

    Science.gov (United States)

    Wöhler, C.; Lena, R.; Pau, K. C.

    2010-03-01

    In this contribution we examine two large lunar domes of probably intrusive origin. The morphometric properties of the domes are derived, and geophysical parameters (intrusion depth, magma pressure) are estimated based on modelling.

  3. The effect of intrusive orthodontic force on dental pulp of adults versus adolescents

    Directory of Open Access Journals (Sweden)

    Mostafa Abtahi

    2016-01-01

    Conclusion: Mild intrusive force in closed apex teeth causes no significant histologic changes in adolescents and adults. However, it seems that inflammatory-related histologic pulpal changes are more severe in adults after one month of intrusion.

  4. Enhancing Battlemind: Preventing PTSD by Coping with Intrusive Thoughts

    Science.gov (United States)

    2014-05-01

    normative across varied populations, those experiencing intrusive thoughts often report that the thoughts are disturbing, and they fear Coping With...tests of a cognitive model of generalized anxiety disorder: Metacognitions and worry in GAD, panic disorder, social phobia , depression, and nonpatients

  5. Revisiting anomaly-based network intrusion detection systems

    NARCIS (Netherlands)

    Bolzoni, Damiano

    2009-01-01

    Intrusion detection systems (IDSs) are well-known and widely-deployed security tools to detect cyber-attacks and malicious activities in computer systems and networks. A signature-based IDS works similar to anti-virus software. It employs a signature database of known attacks, and a successful match

  6. MULTI SCALE TIME SERIES PREDICTION FOR INTRUSION DETECTION

    Directory of Open Access Journals (Sweden)

    G. Palanivel

    2014-01-01

    Full Text Available We propose an anomaly-based network intrusion detection system, which analyzes traffic features to detect anomalies. The proposed system can be used both in online as well as off-line mode for detecting deviations from the expected behavior. Although our approach uses network packet or flow data, it is general enough to be adaptable for use with any other network variable, which may be used as a signal for anomaly detection. It differs from most existing approaches in its use of wavelet transform for generating different time scales for a signal and using these scales as an input to a two-stage neural network predictor. The predictor predicts the expected signal value and labels considerable deviations from this value as anomalies. The primary contribution of our work would be to empirically evaluate the effectiveness of multi resolution analysis as an input to neural network prediction engine specifically for the purpose of intrusion detection. The role of Intrusion Detection Systems (IDSs, as special-purpose devices to detect anomalies and attacks in a network, is becoming more important. First, anomaly-based methods cannot achieve an outstanding performance without a comprehensive labeled and up-to-date training set with all different attack types, which is very costly and time-consuming to create if not impossible. Second, efficient and effective fusion of several detection technologies becomes a big challenge for building an operational hybrid intrusion detection system.

  7. An Overview of IP Flow-Based Intrusion Detection

    NARCIS (Netherlands)

    Sperotto, Anna; Schaffrath, Gregor; Sadre, Ramin; Morariu, Cristian; Pras, Aiko; Stiller, Burkhard

    2010-01-01

    Intrusion detection is an important area of research. Traditionally, the approach taken to find attacks is to inspect the contents of every packet. However, packet inspection cannot easily be performed at high-speeds. Therefore, researchers and operators started investigating alternative approaches,

  8. SSHCure: SSH Intrusion Detection using NetFlow and IPFIX

    NARCIS (Netherlands)

    Hendriks, Luuk; Hofstede, Rick; Sperotto, Anna; Pras, Aiko

    2014-01-01

    With this poster, we present our SSH Intrusion Detection System named SSHCure: it is the first IDS capable of distinguishing successful attacks from unsuccessful attacks, thus detecting actual compromises. As powerful as SSH is to administrators, as attractive it is to anyone with malicious intents.

  9. Neural Network Based Intrusion Detection System for Critical Infrastructures

    Energy Technology Data Exchange (ETDEWEB)

    Todd Vollmer; Ondrej Linda; Milos Manic

    2009-07-01

    Resiliency and security in control systems such as SCADA and Nuclear plant’s in today’s world of hackers and malware are a relevant concern. Computer systems used within critical infrastructures to control physical functions are not immune to the threat of cyber attacks and may be potentially vulnerable. Tailoring an intrusion detection system to the specifics of critical infrastructures can significantly improve the security of such systems. The IDS-NNM – Intrusion Detection System using Neural Network based Modeling, is presented in this paper. The main contributions of this work are: 1) the use and analyses of real network data (data recorded from an existing critical infrastructure); 2) the development of a specific window based feature extraction technique; 3) the construction of training dataset using randomly generated intrusion vectors; 4) the use of a combination of two neural network learning algorithms – the Error-Back Propagation and Levenberg-Marquardt, for normal behavior modeling. The presented algorithm was evaluated on previously unseen network data. The IDS-NNM algorithm proved to be capable of capturing all intrusion attempts presented in the network communication while not generating any false alerts.

  10. Misleading reconstruction of seawater intrusion via integral depth sampling

    Science.gov (United States)

    Colombani, N.; Volta, G.; Osti, A.; Mastrocicco, M.

    2016-05-01

    Saltwater intrusion in coastal aquifers is an urgent issue for the actual and future groundwater supply and a detailed characterization of groundwater quality with depth is a fundamental prerequisite to correctly distinguish salinization processes. In this study, interpolated Cl- maps of the Po River delta coastal aquifer (Italy), gained with Integrated Depth Sampling (IDS) and Multi-Level Sampling (MLS) techniques, are compared. The data set used to build up the IDS and MLS interpolated Cl- maps come from numerous monitoring campaigns on surface and ground waters, covering the time frame from 2010 to 2014. The IDS interpolated Cl- map recalls the phenomenon of actual seawater intrusion, with Cl- concentration never exceeding that of seawater and the absence of hypersaline groundwater all over the study area. On the contrary, in the MLS interpolated Cl- maps the lower portion of the unconfined aquifer presents hypersaline groundwater making it necessary to consider salinization processes other than actual seawater intrusion, like upward flux from a saline aquitard. Results demonstrate the obligation of using MLS in reconstructing a reliable representation of the distribution of salinity, especially in areas where the density contrast between fresh and saline groundwater is large. Implications of the reported field case are not limited to the local situation but have a wider significance, since the IDS technique is often employed in saltwater intrusion monitoring even in recent works, with detrimental effect on the sustainable water resource management of coastal aquifers.

  11. Predicting The Intrusion Layer From Deep Ocean Oil Spills

    Science.gov (United States)

    Wang, Dayang; Chow, Aaron; Adams, E. Eric

    2015-11-01

    Oil spills from deep ocean blowout events motivate our study of multiphase plumes in a water column. Key to understanding the long-term fate of these plumes is the ability to predict the depth and persistence of intrusion layers. While intrusion layers from multiphase plumes have been studied under stagnant conditions, their behavior in the presence of crossflow, especially in mild crossflow, remains poorly understood. The classical classification of plume behavior identifies two regimes: crossflow-dominant and stratification-dominant--but it does not account for the interplay between the two effects, leaving the transition region unexplored. We conduct laboratory tank experiments to investigate the behavior of intrusion layers under the simultaneous action of crossflow and stratification. Our experiments use an inverted frame of reference, using glass beads with a range of sizes to simulate oil droplets. We find that crossflow creates enhanced mixing, which in turn leads to a shallower intrusion layer of the released fluid (correspondingly, a deeper layer in the case of a deep ocean blowout). We develop a mathematical formulation that extends previous models to account for crossflow effects, and use field observations to validate the analytical and experimental findings.

  12. Tracking salinity intrusions in a coastal forested freshwater wetland system

    Science.gov (United States)

    Anand D. Jayakaran; Thomas M. Williams; William H. Conner

    2016-01-01

    Coastal forested freshwater wetlands are sentinel sites for salinity intrusions associated with large, tidally influenced, storm-driven or drought-induced incursions of estuarine waters into freshwater ecosystems. These incursions may also be exacerbated by rising sea levels associated with climate change.

  13. Extension by faulting, stretching and magma intrusion in Ethiopia

    Science.gov (United States)

    Bastow, I. D.; Keir, D.

    2012-12-01

    The 2001-2004 Ethiopia Afar Geoscientific Lithospheric Experiment showed that high seismic wavespeed, dense, mafic crustal intrusions exist beneath many zones of Quaternary magmatism in the Main Ethiopian rift, and that crustal thinning is minimal. From these observations, a consensus quickly emerged that extension presently occurs not by ductile stretching and brittle faulting but by magma intrusion. Striking InSAR images and accompanying seismic data from the 2005 Afar diking episode provided further compelling evidence in support of the magma assisted rifting hypothesis. Patterns of mantle seismic anisotropy, constrained by a combination of body and surface-wave analysis showed that melt intrusion likely also plays an important role in accommodating extension at greater depths in the extending plate. Evidence from further north in Afar, however, where crustal thickness decreases abruptly into the Danakil Depression, is not so easily explained by the magma assisted rifting hypothesis. Subsidence of the newly forming margin towards and below sea level, and eruption of voluminous basalt flows, is likely the result of late-stage thinning of the heavily intruded, weakened plate just before the onset of seafloor spreading. Faulting, stretching and magma intrusion are thus each important, but at different times during breakup. Combining, not isolating, these mechanisms of strain in new rifting models and appreciating how plate strength varies during rifting is essential in developing a clearer understanding of the incomplete geological record that documents continental breakup over time.

  14. A novel feature selection approach for intrusion detection data classification

    NARCIS (Netherlands)

    Ambusaidi, Mohammed A.; He, Xiangjian; Tan, Zhiyuan; Nanda, Priyadarsi; Lu, Liang Fu; Nagar, Upasana T.

    2014-01-01

    Intrusion Detection Systems (IDSs) play a significant role in monitoring and analyzing daily activities occurring in computer systems to detect occurrences of security threats. However, the routinely produced analytical data from computer networks are usually of very huge in size. This creates a

  15. Sensitivity analysis on parameters and processes affecting vapor intrusion risk

    NARCIS (Netherlands)

    Picone, S.; Valstar, J.R.; Gaans, van P.; Grotenhuis, J.T.C.; Rijnaarts, H.H.M.

    2012-01-01

    A one-dimensional numerical model was developed and used to identify the key processes controlling vapor intrusion risks by means of a sensitivity analysis. The model simulates the fate of a dissolved volatile organic compound present below the ventilated crawl space of a house. In contrast to the v

  16. Boosting Web Intrusion Detection Systems by Inferring Positive Signatures

    NARCIS (Netherlands)

    Bolzoni, D.; Etalle, Sandro

    2008-01-01

    We present a new approach to anomaly-based network intrusion detection for web applications. This approach is based on dividing the input parameters of the monitored web application in two groups: the "regular" and the "irregular" ones, and applying a new method for anomaly detection on the

  17. SSHCure: a flow-based SSH intrusion detection system

    NARCIS (Netherlands)

    Hellemons, Laurens; Hendriks, Luuk; Hofstede, Rick; Sperotto, Anna; Sadre, Ramin; Pras, Aiko

    2012-01-01

    SSH attacks are a main area of concern for network managers, due to the danger associated with a successful compromise. Detecting these attacks, and possibly compromised victims, is therefore a crucial activity. Most existing network intrusion detection systems designed for this purpose rely on the

  18. Poseidon: a 2-tier anomaly-based intrusion detection system

    NARCIS (Netherlands)

    Bolzoni, Damiano; Zambon, Emmanuele; Etalle, Sandro; Hartel, Pieter

    2005-01-01

    We present Poseidon, a new anomaly based intrusion detection system. Poseidon is payload-based, and presents a two-tier architecture: the first stage consists of a Self-Organizing Map, while the second one is a modified PAYL system. Our benchmarks on the 1999 DARPA data set show a higher detection r

  19. Evaluation of of μ-controller PIR Intrusion Detector

    African Journals Online (AJOL)

    PROF. OLIVER OSUAGWA

    West African Journal of Industrial & Academic Research Vol.15 No.1 December 2015. 3 ... Intrusion detection is simply the process of recognizing that an object is located in a place ... the specific application and operational ... Figure 1: Block Diagram Showing Design Modules and the ..... Engineering Science Invention, Vol.

  20. Network Intrusion Detection System Based On Machine Learning Algorithms

    Directory of Open Access Journals (Sweden)

    Vipin Das

    2010-12-01

    Full Text Available Network and system security is of paramount importance in the present data communication environment. Hackers and intruders can create many successful attempts to cause the crash of the networks and web services by unauthorized intrusion. New threats and associated solutions to prevent these threats are emerging together with the secured system evolution. Intrusion Detection Systems (IDS are one of these solutions. The main function of Intrusion Detection System is to protect the resources from threats. It analyzes and predicts the behaviours of users, and then these behaviours will be considered an attack or a normal behaviour. We use Rough Set Theory (RST and Support Vector Machine (SVM to detect network intrusions. First, packets are captured from the network, RST is used to pre-process the data and reduce the dimensions. The features selected by RST will be sent to SVM model to learn and test respectively. The method is effective to decrease the space density of data. The experiments compare the results with Principal Component Analysis (PCA and show RST and SVM schema could reduce the false positive rate and increase the accuracy.

  1. Neural Network Based Intrusion Detection System for Critical Infrastructures

    Energy Technology Data Exchange (ETDEWEB)

    Todd Vollmer; Ondrej Linda; Milos Manic

    2009-07-01

    Resiliency and security in control systems such as SCADA and Nuclear plant’s in today’s world of hackers and malware are a relevant concern. Computer systems used within critical infrastructures to control physical functions are not immune to the threat of cyber attacks and may be potentially vulnerable. Tailoring an intrusion detection system to the specifics of critical infrastructures can significantly improve the security of such systems. The IDS-NNM – Intrusion Detection System using Neural Network based Modeling, is presented in this paper. The main contributions of this work are: 1) the use and analyses of real network data (data recorded from an existing critical infrastructure); 2) the development of a specific window based feature extraction technique; 3) the construction of training dataset using randomly generated intrusion vectors; 4) the use of a combination of two neural network learning algorithms – the Error-Back Propagation and Levenberg-Marquardt, for normal behavior modeling. The presented algorithm was evaluated on previously unseen network data. The IDS-NNM algorithm proved to be capable of capturing all intrusion attempts presented in the network communication while not generating any false alerts.

  2. Corporate Mergers in the Publishing Industry: Helpful or Intrusive?

    Science.gov (United States)

    Rudman, Herbert C.

    1990-01-01

    Examines the effects of corporate mergers in the publishing industry on the publishing of textbooks and standardized tests. Concludes that restructuring, acquisitions, and mergers have an intrusive effect on established practices of academic publishing and may severely limit the access of scholars to the academic marketplace. (FMW)

  3. Mitigating Intrusion and Vulnerabilities in Cognitive Radio Networks

    Directory of Open Access Journals (Sweden)

    I. Ohaeri

    Full Text Available The deployment of Cognitive Radio Networks has been greatly hindered in spite of its potentials by the rate at which intrusions and vulnerabilities replicate within every domain of the network. Cognitive Radio Network is expected to drive the next generat ...

  4. Implementation of Network Intrusion Detection System Based on Density-based Outliers Mining

    Institute of Scientific and Technical Information of China (English)

    Huang,Guangqiu; Peng,Xuyou; LV,Dingquan

    2005-01-01

    The paper puts forward a new method of densitybased anomaly data mining, the method is used to design the engine of network intrusion detection system (NIDS), thus a new NIDS is constructed based on the engine. The NIDS can find new unknown intrusion behaviors, which are used to updated the intrusion rule-base, based on which intrusion detections can be carried out online by the BM pattern match algorithm. Finally all modules of the NIDS are described by formalized language.

  5. Network Intrusion Detection Using FP Tree Rules

    Directory of Open Access Journals (Sweden)

    P Srinivasulu

    2009-07-01

    Full Text Available In the faceless world of the Internet, online fraud is one of the greatest reasons of loss for web merchants. Advanced solutions are needed to protect e-businesses from the constant problems of fraud. Many popular fraud detection algorithms require supervised training, which needs human intervention to prepare training cases. Since it is quite often for an online transaction database to have Terabyte-level storage, human investigation to identify fraudulent transactions is very costly. This paper describes the automatic design of user profiling method for the purpose of fraud detection. We use a FP (Frequent Pattern Tree rule-learning algorithm to adaptively profile legitimate customer behavior in a transaction database. Then the incoming transactions are compared against the user profile to uncover the anomalies. The anomaly outputs are used as input to an accumulation system for combining evidence to generate high-confidence fraud alert value. Favorable experimental results are presented.

  6. Network Intrusion Detection Using FP Tree Rules

    CERN Document Server

    Srinivasulu, P; Babu, I Ramesh

    2010-01-01

    In the faceless world of the Internet,online fraud is one of the greatest reasons of loss for web merchants.Advanced solutions are needed to protect e businesses from the constant problems of fraud.Many popular fraud detection algorithms require supervised training,which needs human intervention to prepare training cases.Since it is quite often for an online transaction database to ha e Terabyte level storage,human investigation to identify fraudulent transactions is very costly.This paper describes the automatic design of user profiling method for the purpose of fraud detection.We use a FP (Frequent Pattern) Tree rule learning algorithm to adaptively profile legitimate customer behavior in a transaction database.Then the incoming transactions are compared against the user profile to uncover the anomalies The anomaly outputs are used as input to an accumulation system for combining evidence to generate high confidence fraud alert value. Favorable experimental results are presented.

  7. Intrusion Detection Systems with Live Knowledge System

    Science.gov (United States)

    2016-05-31

    node. Figure 3 describes the result of modified nodes from the original RDR rule tree. Red - coloured ‘X’ sign represents the stopping rule, and the...RDR rule tree, where red -circled nodes indicate those nodes with poor prediction of accuracy. DISTRIBUTION A. Approved for public release...green- coloured boxes describe the refined rule. However, when human knowledge is applied to those incorrectly classified data, not all of the

  8. Intrusions of a drowsy mind: Neural markers of phenomenological unpredictability

    Directory of Open Access Journals (Sweden)

    Valdas eNoreika

    2015-03-01

    Full Text Available The transition from a relaxed to a drowsy state of mind is often accompanied by hypnagogic experiences: most commonly, perceptual imagery, but also linguistic intrusions, i.e. the sudden emergence of unpredictable anomalies in the stream of inner speech. This study has sought to describe the contents of such intrusions, to verify their association with the progression of sleep onset, and to investigate the electroencephalographic processes associated with linguistic intrusions as opposed to more common hypnagogic perceptual imagery. A single participant attended 10 experimental sessions in the EEG laboratory, where he was allowed to drift into a drowsy state of mind, while maintaining metacognition of his own experiences. Once a linguistic intrusion or a noticeable perceptual image occurred, the participant pressed a button and reported it verbally. An increase in the EEG-defined depth of drowsiness as assessed by the Hori system of sleep onset was observed in the last 20 sec before a button press. Likewise, EEG Dimension of Activation values decreased before the button press, indicating that the occurrence of cognitively incongruous experiences coincides with the rapid change of EEG predictability patterns. EEG hemispheric asymmetry analysis showed that linguistic intrusions had a higher alpha and gamma power in the left hemisphere electrodes, whereas perceptual imagery reports were associated with a higher beta power over the right hemisphere. These findings indicate that the modality as well as the incongruence of drowsiness-related hypnagogic experiences is strongly associated with distinct EEG signatures in this participant. Sleep onset may provide a unique possibility to study the neural mechanisms accompanying the fragmentation of the stream of consciousness in healthy individuals.

  9. Intrusions of autobiographical memories in individuals reporting childhood emotional maltreatment

    Directory of Open Access Journals (Sweden)

    Philip Spinhoven

    2011-09-01

    Full Text Available During childhood emotional maltreatment (CEM negative attitudes are provided to the child (e.g., “you are worthless”. These negative attitudes may result in emotion inhibition strategies in order to avoid thinking of memories of CEM, such as thought suppression. However, thought suppression may paradoxically enhance occurrences (i.e., intrusions of these memories, which may occur immediately or sometime after active suppression of these memories.Until now, studies that examined suppressive coping styles in individuals reporting CEM have utilized self-report questionnaires. Therefore, it is unclear what the consequences will be of emotion inhibition styles on the intrusion of autobiographical memories in individuals reporting CEM.Using a thought suppression task, this study aimed to investigate the experience of intrusions during suppression of, and when no longer instructed to actively suppress, positive and negative autobiographical memories in individuals reporting Low, Moderate, and Severe CEM compared to No Abuse (total N = 83.We found no group differences during active suppression of negative and positive autobiographical memories. However, when individuals reporting Severe CEM were no longer instructed to suppress thinking about the memory, individuals reporting No Abuse, Low CEM, or Moderate CEM reported fewer intrusions of both positive and negative autobiographical memories than individuals reporting Severe CEM. Finally, we found that intrusions of negative memories are strongly related with psychiatric distress.The present study results provide initial insights into the cognitive mechanisms that may underlie the consequences of childhood emotional maltreatment and suggests avenues for successful interventions.For the abstract or full text in other languages, please see Supplementary files under Reading Tools online

  10. Geochronologic, Isotopic, and Trace Element Constraints on Zircon Recycling in Sierra Crest Intrusive Suites, Sierra Nevada Batholith, USA

    Science.gov (United States)

    Miller, J. S.; Lackey, J.; Memeti, V.; Hirt, W. H.; Wooden, J. L.

    2011-12-01

    megacryst-bearing intrusions all point to initial zircon undersaturation in magmas feeding the intrusions, and late crystallization of zircon at low temperature (low Tzrn,Ti, high Hf, low Th/U) in the presence of titanite, which exerts strong control on the overall REE budget but particularly the MREEs. When considered with the age and isotope data, these trace element characteristics pose a conundrum. The megacryst-bearing intrusions are not minimum-melt compositions; therefore, the zircons must have grown at high crystal fractions in residual low-T melt, at which point mixing would have been severely impeded. And yet, the age and isotopic variability at the hand sample and crystal scale require repeated mixing of zircons from distinct increments of magma (antecryst recycling). This suggests repeated thawing (by new magma inputs and with significant fluid) and mechanical destabilization of stiff crystal mush that was thermally buffered near the wet granite solidus.

  11. Application of a Hidden Bayes Naive Multiclass Classifier in Network Intrusion Detection

    Science.gov (United States)

    Koc, Levent

    2013-01-01

    With increasing Internet connectivity and traffic volume, recent intrusion incidents have reemphasized the importance of network intrusion detection systems for combating increasingly sophisticated network attacks. Techniques such as pattern recognition and the data mining of network events are often used by intrusion detection systems to classify…

  12. A reactive transport investigation of a seawater intrusion experiment in a shallow aquifer, Skansehage Denmark

    DEFF Research Database (Denmark)

    Christensen, Flemming Damgaard; Engesgaard, Peter Knudegaard; Kipp, K.L.

    2001-01-01

    Previous investigations on seawater intrusion have mainly focused on either the physical density flow system with transport of a single non-reactive species or focused on the geochemical aspects neglecting density effects. This study focuses on both the geochemical and physical aspects of seawater...... intrusion and their interaction during an intrusion experiment in a shallow, small-scale coastal aquifer in Denmark....

  13. Molecular characterization of tat gene and long terminal repeat region of human immunodeficiency virus type-1 detected among the injecting drug users (IDUs) of Manipur, India: identification of BC recombinants.

    Science.gov (United States)

    Mullick, Ranajoy; Sengupta, Satarupa; Sarkar, Kamalesh; Chakrabarti, Sekhar

    2010-02-01

    The tat gene of human immunodeficiency virus type-1 (HIV-1) is responsible for the initiation and elongation of viral transcription through the LTR (long terminal repeat) transactivation process. Our study included structural and functional analyses of the tat gene and LTR region of 35 injecting drug users (IDUs) from Manipur (a north-eastern state in India and a potential source of HIV-1 recombinants) in order to search for the recombinants and variation in the transactivation process if any due to recombination. Analysis showed prevalence of subtype C with few BC recombinants for the tat gene showing identical recombination breakpoints. Phylogenetic analysis of the LTR region of those IDU strains showed strong resemblance to Indian subtype C forming a completely separate cluster from the other global C LTR sequences. The TAR element (transactivator response region) in all the LTR sequences was fairly conserved. Further study of the transactivation rate of the C and BC tat for the Manipur C LTR showed almost equal transactivity in both the cases. This is the first report of characterisation of tat gene and LTR region of HIV-1 samples among IDUs from north-eastern India.

  14. Assessment of the safety of hydrogenated resistant maltodextrin: reverse mutation assay, acute and 90-day subchronic repeated oral toxicity in rats, and acute no-effect level for diarrhea in humans.

    Science.gov (United States)

    Yoshikawa, Yuko; Kishimoto, Yuka; Tagami, Hiroyuki; Kanahori, Sumiko

    2013-01-01

    A series of safety assessments were performed on hydrogenated resistant maltodextrin prepared by converting the reducing terminal glucose of resistant maltodextrin into sorbitol. The reverse mutation assay did not show mutagenicity. Acute and 90-day subchronic oral toxicity studies in rats showed no death was observed in any groups, including the group receiving the highest single dose of 10 g/kg body weight or the highest dose of 5 g/kg body weight per day for 90 days. Mucous or watery stools were observed in the hydrogenated resistant maltodextrin treatment group on the acute study, which were transient and were associated with the osmotic pressure caused by intake of the high concentrations. Subchronic study showed dose-dependent increases in the weights of cecum alone, cecal contents alone, and cecum with cecal contents as well as hypertrophy of the cecal mucosal epithelium, which are considered to be common physiological responses after intake of indigestible carbohydrates. These results indicated that the no observed adverse effect level (NOAEL) of hydrogenated resistant maltodextrin was 10 g/kg body weight or more on the acute oral toxicity study and 5.0 g/kg body weight/day or more on the 90-day subchronic repeated oral toxicity study in rats. Further study performed in healthy adult humans showed that the acute no-effect level of hydrogenated resistant maltodextrin for diarrhea was 0.8 g/kg body weight for men and more than 1.0 g/kg body weight for women. The results of the current safety assessment studies suggest that hydrogenated resistant maltodextrin is safe for human consumption.

  15. Use of multiple-locus variable-number of tandem repeats analysis (MLVA) to investigate genetic diversity of Salmonella enterica subsp. enterica serovar Typhimurium isolates from human, food, and veterinary sources.

    Science.gov (United States)

    Mateva, Gergana; Pedersen, Karl; Sørensen, Gitte; Asseva, Galina; Daskalov, Hristo; Petrov, Petar; Kantardjiev, Todor; Alexandar, Irina; Löfström, Charlotta

    2017-08-23

    Salmonella enterica subspecies enterica serovar Typhimurium is the most common zoonotic pathogen in Bulgaria. To allow efficient outbreak investigations and surveillance in the food chain, accurate and discriminatory methods for typing are needed. This study evaluated the use of multiple-locus variable-number of tandem repeats analysis (MLVA) and compared results with antimicrobial resistance (AMR) determinations for 100 S. Typhimurium strains isolated in Bulgaria during 2008-2012 (50 veterinary/food and 50 human isolates). Results showed that isolates were divided into 80 and 34 groups using MLVA and AMR, respectively. Simpson's index of diversity was determined to 0.994 ± 0.003 and 0.945 ± 0.012. The most frequently encountered MLVA profiles were 3-11-9-NA-211 (n = 5); 3-12-9-NA-211 (n = 3); 3-12-11-21-311 (n = 3); 3-17-10-NA-311 (n = 3); 2-20-9-7-212 (n = 3); and 2-23-NA-NA-111 (n = 3). No clustering of isolates related to susceptibility/resistance to antimicrobials, source of isolation, or year of isolation was observed. Some MLVA types were found in both human and veterinary/food isolates, indicating a possible route of transmission. A majority (83%) of the isolates were found to be resistant against at least one antimicrobial and 44% against ≥4 antimicrobials. Further studies are needed to verify MLVA usefulness over a longer period of time and with more isolates, including outbreak strains. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  16. 1420 Ma diabasic intrusives from the Mesoproterozoic Singhora Group, Chhattisgarh Supergroup, India: Implications towards non-plume intrusive activity

    Indian Academy of Sciences (India)

    Priyabrata Das; Kaushik Das; Partha Pratim Chakraborty; S Balakrishnan

    2011-04-01

    Besides offering significant clues towards tracking the geochemical evolution of the mantle and architectural reconstruction of different ‘supercontinent’, geochronological and geochemical appraisal of igneous inputs are also important to bracket the depositional time frame of any lithopackage, particularly, the unfossiliferous sedimentary successions. The present study deals with diabasic intrusive within Mesoproterozoic Saraipalli Formation, which is an argillaceous constituent present at the basal part of nearly 400 m thick four-tiered unmetamorphosed but deformed sedimentary succession of Singhora Group, Chhattisgarh Supergroup, central India. The SE–NW trending intrusive comprises mainly of plagioclase and augite together with minor orthopyroxene, biotite and opaque minerals. Though some plagioclase laths are partially sericitized, the ophitic-to-subophitic texture of the rock is well preserved. Major and trace element geochemical data indicate that this intrusive is basalt-to-basaltic andesite in character and of subalkaline basalt affinity. Multi-element plot shows overall LILE-enrichment and enrichment of Pb and slight depletion of Nb and P, coupled with moderate La/Nb and Th/Nb ratios. Zr, Y and Nb ternary diagrams plot in the fields of within plate basalt. Selected HFSE ratios indicate a non-plume source with crustal assimilation/sediment mixing. Sm–Nd and Rb–Sr isotope data show that the intrusive has Srinitial and Ndinitial of 0.709377–0.706672 and 0.510919–0.510815, respectively. Positive tNd [t = 1420 Ma] values (+0.3 to + 2.3) indicate depleted isotopic nature of their protolith. The calculated DM age is 1.7–1.9 Ga. The mineral-whole rock isochron data (Sm–Nd systematics) of the intrusive implies an emplacement age of ca. 1420 Ma. Considering synchronous terrain boundary shear zone development in Bastar craton on the southeastern part of the Singhora basin, mafic magmatism in Eastern Ghats and large-scale basic intrusion in Sausar

  17. Expansion of protein domain repeats.

    Directory of Open Access Journals (Sweden)

    Asa K Björklund

    2006-08-01

    Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

  18. Syn-collision Hairhan layered intrusion, Lakes Zone, Western Mongolia

    Science.gov (United States)

    Vishnevskiy, A. V.; Izokh, A. E.; Kalugin, V. M.; Gertner, I. F.

    2012-04-01

    In the structure of the Lakes Zone of Western Mongolia, which is reconstructed as the Early Cambrian island arc (Lakes island arc terrane), there are several groups of contiguous space gabbroic intrusions, merged in Hirgisnuur complex. The largest (70 km2) is Hairhan intrusion, located in the central part of the Lake Zone in the Bumbat-Hairhan ridge. The structure of the intrusion disturbed by later tectonic movements and the subsequent formation of Cambrian granitoids Tohtoginshil complex. The structures of the body are two groups of rocks: layered series and marginal facies, fragmentary spread to the periphery of intrusion. Gabbronorites of marginal facies have intrusive contacts with the sedimentary rocks of Early Cambrian age Burgastay formation. The marginal facies, apparent thickness which is 1.5 km, is composed primarily of non-olivine gabbronorites in which there is trachytoid and sometimes bedding. Layered series composes the central part of the Hairhan intrusion, the direction of layering has a northwest strike, coaxial with the long axis of the intrusion. The lower part of the layered series consists mainly troctolites with minor olivine gabbroids. The upper part of the layered series consists mainly of olivine gabbro, troctolite occur here less frequently also observed small schlieren anorthosites. Of particular interest is the horizon taxitic gabbro and being above it - the horizon orbicular gabbro at the top of the layered series. The rocks are widely manifested magmatic disruptive and plastic deformation - both macro and micro levels. They are expressed in the collapse of layering of elements in small folds of varying amplitude (typically to a few tens centimeters), often passing into areas and zones taxitic disruption. The greatest number of these structural elements characteristic of the upper part of the layered series, including the orbicular gabbro and troctolites taxitic horizons. These features indicate intensive tectonic processes that

  19. DWI Repeaters and Non-Repeaters: A Comparison.

    Science.gov (United States)

    Weeber, Stan

    1981-01-01

    Discussed how driving-while-intoxicated (DWI) repeaters differed signigicantly from nonrepeaters on 4 of 23 variables tested. Repeaters were more likely to have zero or two dependent children, attend church frequently, drink occasionally and have one or more arrests for public intoxication. (Author)

  20. To Repeat or Not to Repeat a Course

    Science.gov (United States)

    Armstrong, Michael J.; Biktimirov, Ernest N.

    2013-01-01

    The difficult transition from high school to university means that many students need to repeat (retake) 1 or more of their university courses. The authors examine the performance of students repeating first-year core courses in an undergraduate business program. They used data from university records for 116 students who took a total of 232…