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  1. Chlorella vulgaris triggers apoptosis in hepatocarcinogenesis-induced rats*

    Science.gov (United States)

    Mohd Azamai, Emey Suhana; Sulaiman, Suhaniza; Mohd Habib, Shafina Hanim; Looi, Mee Lee; Das, Srijit; Abdul Hamid, Nor Aini; Wan Ngah, Wan Zurinah; Mohd Yusof, Yasmin Anum

    2009-01-01

    Chlorella vulgaris (CV) has been reported to have antioxidant and anticancer properties. We evaluated the effect of CV on apoptotic regulator protein expression in liver cancer-induced rats. Male Wistar rats (200~250 g) were divided into eight groups: control group (normal diet), CDE group (choline deficient diet supplemented with ethionine in drinking water to induce hepatocarcinogenesis), CV groups with three different doses of CV (50, 150, and 300 mg/kg body weight), and CDE groups treated with different doses of CV (50, 150, and 300 mg/kg body weight). Rats were sacrificed at various weeks and liver tissues were embedded in paraffin blocks for immunohistochemistry studies. CV, at increasing doses, decreased the expression of anti-apoptotic protein, Bcl-2, but increased the expression of pro-apoptotic protein, caspase 8, in CDE rats, which was correlated with decreased hepatoctyes proliferation and increased apoptosis as determined by bromodeoxy-uridine (BrdU) labeling and terminal deoxynucleotidyl transferase mediated dUTP nick-end labeling (TUNEL) assay, respectively. Our study shows that CV has definite chemopreventive effect by inducing apoptosis via decreasing the expression of Bcl-2 and increasing the expression of caspase 8 in hepatocarcinogenesis-induced rats. PMID:19198018

  2. Tomato oleoresin inhibits DNA damage but not diethylnitrosamine-induced rat hepatocarcinogenesis.

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    Scolastici, Clarissa; Lopes, Gisele A D; Barbisan, Luís F; Salvadori, Daisy M F

    2008-06-01

    Various studies have shown that lycopene, a non-provitamin A carotenoid, exerts antioxidant, antimutagenic and anticarcinogenic activities in different in vitro and in vivo systems. However, the results concerning its chemopreventive potential on rat hepatocarcinogenesis are ambiguous. The aim of the present study was to investigate the antigenotoxic and anticarcinogenic effects of dietary tomato oleoresin adjusted to lycopene concentration at 30, 100 or 300 ppm (administered 2 weeks before and during or 8 weeks after carcinogen exposure) on liver of male Wistar rats treated with a single intraperitoneal dose of 20 or 100mg/kg of diethylnitrosamine (DEN), respectively. The level of DNA damage in liver cells and the development of putative preneoplastic single hepatocytes, minifoci and foci of altered hepatocytes (FHA) positive for glutathione S-transferase (GST-P) were used as endpoints. Significant reduction of DNA damage was detected when the highest lycopene concentration was administered before and during the DEN exposure (20mg/kg). However, the results also showed that lycopene consumption did not reduce cell proliferation in normal hepatocytes or the growth of initiated hepatocytes into minifoci positive for GST-P during early regenerative response after 70% partial hepatectomy, or the number and area of GST-P positive FHA induced by DEN (100mg/kg) at the end of week 10. Taken together, the data suggest a chemopreventive effect of tomato oleoresin against DNA damage induced by DEN but no clear effectiveness in initiating or promoting phases of rat hepatocarcinogenesis.

  3. Inhibition by cysteamine of hepatocarcinogenesis induced by N-nitrosomorpholine in Sprague-Dawley rats

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    Tatsuta, M.; Iishi, H.; Baba, M. (Center for Adult Diseases, Osaka (Japan))

    1989-09-15

    The effect of cysteamine (2-aminoethanethiol hydrochloride) on hepatocarcinogenesis induced by N-nitrosomorpholine (NNM) was investigated in male Sprague-Dawley rats. Rats received alternate-day s.c. injections of cysteamine, and beginning in experimental week 3 were given drinking water containing NNM for 8 weeks. Pre-neoplastic and neoplastic lesions staining positive for gamma-glutamyl transpeptidase (GGT) or glucose-6-phosphate dehydrogenase (G6PD) were examined by histochemical techniques. In week 18, quantitative histological analysis showed that prolonged administration of cysteamine resulted in a significant reduction in the number of GGT-positive and G6PD-positive hepatic lesions. Histologically, hepatocellular carcinomas were significantly fewer and smaller in GGT-positive and G6PD-positive lesions in rats treated with cysteamine than in untreated rats. Administration of cysteamine also caused a significant decrease in the liver norepinephrine concentration and in the labelling indices of pre-neoplastic lesions and the surrounding liver. Our findings indicate that cysteamine inhibits hepatocarcinogenesis; this may be related to its reducing effect on norepinephrine concentration in the liver and its subsequent inhibition of cell proliferation in neoplastic lesions and surrounding hepatocytes.

  4. SCD1 Expression is dispensable for hepatocarcinogenesis induced by AKT and Ras oncogenes in mice.

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    Lei Li

    Full Text Available Increased de novo lipogenesis is one of the major metabolic events in cancer. In human hepatocellular carcinoma (HCC, de novo lipogenesis has been found to be increased and associated with the activation of AKT/mTOR signaling. In mice, overexpression of an activated form of AKT results in increased lipogenesis and hepatic steatosis, ultimately leading to liver tumor development. Hepatocarcinogenesis is dramatically accelerated when AKT is co-expressed with an oncogenic form of N-Ras. SCD1, the major isoform of stearoyl-CoA desaturases, catalyzing the conversion of saturated fatty acids (SFA into monounsaturated fatty acids (MUFA, is a key enzyme involved in de novo lipogenesis. While many studies demonstrated the requirement of SCD1 for tumor cell growth in vitro, whether SCD1 is necessary for tumor development in vivo has not been previously investigated. Here, we show that genetic ablation of SCD1 neither inhibits lipogenesis and hepatic steatosis in AKT-overexpressing mice nor affects liver tumor development in mice co-expressing AKT and Ras oncogenes. Molecular analysis showed that SCD2 was strongly upregulated in liver tumors from AKT/Ras injected SCD1(-/- mice. Noticeably, concomitant silencing of SCD1 and SCD2 genes was highly detrimental for the growth of AKT/Ras cells in vitro. Altogether, our study provides the evidence, for the first time, that SCD1 expression is dispensable for AKT/mTOR-dependent hepatic steatosis and AKT/Ras-induced hepatocarcinogenesis in mice. Complete inhibition of stearoyl-CoA desaturase activity may be required to efficiently suppress liver tumor development.

  5. Studies on the biological functions of CPS1 in AFB1 induced hepatocarcinogenesis.

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    Yang, Chi; Fu, Rao; Zhuang, Zhenhong; Wang, Shihua

    2016-10-10

    Carbamyl phosphate synthetase 1 (CPS1) was down-regulated in hepatocellular carcinoma (HCC), as treated by aflatoxin B1 (AFB1), a potent hepatocarcinogenesis mycotoxin. In this study, we firstly confirmed that AFB1 down-regulated the expression of CPS1 in a dose-dependent manner. At the meantime, both siRNA knock down of CPS1 and AFB1 treatment inhibited cell proliferation, and induced cell apoptosis. To further analysis the function of CPS1, the interacting proteins of CPS1 were searched by Co-IP, and three interacting proteins including type II cytoskeletal 1 (KRT1), albumin (ALB), and ubiquitin C (UBC) were found. Both KRT1 and ALB were new interacting proteins for CPS1. Our further study showed that CPS1 was regulating interacted and colocalized with KRT1 and ALB, and the intensity correlation was changed by AFB1. KRT1, ALB and CPS1 were all reported to play an important role in differentiation and tissue specialization. These results may offer an increasing understand that CPS1 might have a function in differentiation. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Potential chemoprevention of diethylnitrosamine-induced hepatocarcinogenesis in rats: myrrh (Commiphora molmol) vs. turmeric (Curcuma longa).

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    El-Shahat, Mohamed; El-Abd, Sabah; Alkafafy, Mohamed; El-Khatib, Gamal

    2012-09-01

    The aim of the present study was to assess the potential chemopreventive effects of myrrh (Commiphora molmol) vs. turmeric (Curcuma longa) in hepatocarcinogenic rats induced by a single intraperitoneal injection of diethylnitrosamine (DENA) (200 mg/kg body weight). Ninety male Wistar rats used in this study were randomly divided into six equal groups (n=15). Group 1 rats served as negative controls; group 2 received a single i.p. injection of DENA and served as positive controls. Rats in both groups were fed on basal diet. Group 3 rats were fed a diet containing 5% turmeric, whereas group 4 rats were fed a diet containing 2% myrrh. Rats in groups 5 and 6 received a single i.p. injection of DENA and were fed diets containing 5% turmeric and 2% myrrh, respectively. The study demonstrated that DENA caused a significant increase in serum indices of liver enzymes and also severe histological and immunohistochemical changes in hepatic tissues. These included disorganized hepatic parenchyma, appearance of pseudoacinar and trabecular arrays of hepatocytes and alterations in CD10-immunoreactivity. Dietary supplementation of turmeric relatively improved the biochemical parameters to values approximating those of the negative controls and delayed the initiation of carcinogenesis. In contrast, myrrh did not improve the biochemical parameters or delay the hepatocarcinogenesis. Both turmeric and myrrh induced significant biochemical and histological changes in non-treated rats. In conclusion, DENA significantly changes the biological enzymatic activities in serum and the integrity of hepatic tissues. Phytochemicals with potential hepatoprotective effects must be applied cautiously owing to their potential hepatotoxicity. Copyright © 2011 Elsevier GmbH. All rights reserved.

  7. Potency of Semecarpus anacardium Linn. nut milk extract against aflatoxin B(1)-induced hepatocarcinogenesis: reflection on microsomal biotransformation enzymes.

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    Premalatha, B; Sachdanandam, P

    2000-08-01

    The effect of Semecarpus anacardium Linn. nut milk extract on host detoxification system in aflatoxin B(1) induced hepatocellular carcinoma, which is a vital mechanism in cancer treatment, was studied in male albino rats. Oral administration of nut extract (200 mg kg(-1)body weight per day for 14 days) is found to be highly effective in inducing phase I and phase II biotransformation enzymes. The obtained results have shown an overall decrease of liver microsomal cytochrome P450, cytochrome b5, NADPH-cytochrome P450 reductase, NADH-cytochrome b5 reductase, and aniline hydroxylase with a subsequent decrease of phase II enzymes, glutathione-S-transferase and UDP-glucuronyl transferase in cancer-bearing animals. The Semecarpus anacardium nut extract affords anticancer activity by enhancing both phase I and phase II enzymes to near normal levels. We propose that, much of the anticarcinogenic potency of Semecarpus anacardium nut extract on aflatoxin B(1)-induced hepatocarcinogenesis is mediated through the induction of hepatic biotransformation enzymes. Copyright 2000 Academic Press.

  8. Protection against diethylnitrosoamine-induced hepatocarcinogenesis by an indigenous medicine comprised of Nigella sativa, Hemidesmus indicus and Smilax glabra: a preliminary study

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    Wickramasinghe Nalinie

    2003-01-01

    Full Text Available Abstract Background A decoction comprised of Nigella sativa seeds, Hemidesmus indicus root and Smilax glabra rhizome is used to treat cancer patients in Sri Lanka. However, the anti-carcinogenic properties of this decoction have not been experimentally confirmed. The purpose of this study was to determine whether the above decoction could protect against chemically induce hepatocarcinogenesis. Methods The effects of this decoction on diethylnitrosamine (DEN induced hepatocarcinogenesis were examined in male Wistar rats using the medium term bioassay system of Ito, based on a 2-step model of hepatocarcinogenesis. Rats were randomly divided into 6 groups of 10 each. Groups 1 to 4 were injected with DEN (200 mg/kg to initiate carcinogenesis. Twenty-four hours later groups 1 and 2 were administered the decoction at 4 g/kg body weight/day (dose 1 and 6 g/kg body weight/day (dose 2, respectively. Group 3 and group 4 were given distilled water instead of the decoction and a suspension of garlic powder (20 g/kg body weight/day in distilled water (positive control, respectively. Group 5 and 6 were injected with normal saline and twenty-four hours later group 5 was given distilled water (normal control while group 6 was given decoction dose 2 (decoction control. Oral feeding continued for two weeks after which all rats were subjected to 2/3 partial hepatectomy to promote carcinogenesis. Oral feeding continued for eight more weeks. At the end of the 10th week, rats were sacrificed and samples of livers taken for immunohistochemical studies. Carcinogenic potential was scored by comparing the number, area and staining intensity of glutathione S-transferase placental form (GST-P positive foci and the number of cells/cm2 of the positive foci in the livers of the six groups of rats. Results The number and area of DEN-mediated GST-P positive foci, number of cells/cm2 of foci and staining intensity of the foci were significantly (P > 0.001 reduced by the

  9. Role of Oxidative Stress in Hepatocarcinogenesis Induced by Hepatitis C Virus

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    Kyoko Tsukiyama-Kohara

    2012-11-01

    Full Text Available Hepatitis C virus (HCV easily establishes chronic hepatitis, cirrhosis, and hepatocellular carcinoma (HCC. During the progression of HCV infections, reactive oxygen species (ROS are generated, and these ROS then induce significant DNA damage. The role of ROS in the pathogenesis of HCV infection is still not fully understood. Recently, we found that HCV induced the expression of 3β-hydroxysterol ∆24-reductase (DHCR24. We also found that a HCV responsive region is present in the 5'-flanking genomic promoter region of DHCR24 and the HCV responsive region was characterized as (−167/−140. Moreover, the transcription factor Sp1 was found to bind to this region in response to oxidative stress under the regulation of ataxia telangiectasia mutated (ATM kinase. Overexpression of DHCR24 impaired p53 activity by suppression of acetylation and increased interaction with MDM2. This impairment of p53 suppressed the hydrogen peroxide-induced apoptotic response in hepatocytes. Thus, a target of oxidative stress in HCV infection is DHCR24 through Sp1, which suppresses apoptotic responses and increases tumorigenicity.

  10. Hepatoprotective effect of engineered silver nanoparticles coated bioactive compounds against diethylnitrosamine induced hepatocarcinogenesis in experimental mice.

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    Prasannaraj, Govindaraj; Venkatachalam, Perumal

    2017-02-01

    Nanoparticle based drug delivery can rapidly improves the therapeutic potential of anti-cancer agents. The present study focused to evaluate the hepatoprotective activity of silver nanoparticles (AgNPs) synthesized using aqueous extracts of Andrographis paniculata leaves (ApAgNPs) and Semecarpus anacardium nuts (SaAgNPs) against diethylnitrosamine (DEN) induced liver cancer in mice model. The physico-chemical properties of synthesized AgNPs were characterized by Fourier transform infrared (FTIR) spectroscopy, Transmission Electron Microscopy (TEM), Selected Area Electron Diffraction (SAED), X-ray Diffraction (XRD), Energy Dispersive X-ray (EDX) spectrum, Zeta potential and Dynamic Light Scattering (DLS) analysis. The surface plasmon resonance (SPR) absorption spectrum revealed a strong peak at 420nm for both SaAgNPs and ApAgNPs. FTIR results exhibited the presence of possible functional groups in the synthesized AgNPs. TEM analysis determined the hexagonal, and spherical shape of the synthesized silver nanoparticles. The XRD and SAED pattern confirmed the crystalline nature and crystalline size of the AgNPs. EDX result clearly showed strong silver signals in the range between 2 and 4keV. Zeta potential measurements indicated a sharp peak at -3.93 and -13.8mV for ApAgNPs and SaAgNPs, respectively. DLS measurement expressed the particle size distribution was 70 and 60nm for ApAgNPs and SaAgNPs, respectively. DEN (20mg/kg b.wt.) was subjected to induce liver cancer in mice for 8weeks and treated with biosynthesized silver nanoparticles. Interestingly, ApAgNPs and SaAgNPs treated DEN induced animal groups show a decreased level of aspartate amino transferase (AST), alanine amino transferase (ALT), serum glutamate oxaloacetate transaminase (SGOT), serum glutamate pyruvate transaminase (SGPT) activity and elevated level of catalase (CAT), glutathione peroxidase (GPx), glutathione S-transferase (GST) and superoxide dismutase (SOD) activity over untreated DEN control

  11. Modulatory role of vanadium on trace element profile in diethylnitrosamine-induced rat hepatocarcinogenesis

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    Chakraborty, A.; Selvaraj, S.; Sudarshan, M.; Dutta, R. K.; Ghugre, S. S.; Chintalapudi, S. N.

    2000-09-01

    Particle-induced X-ray emission (PIXE) analysis was employed in the present study to investigate the chemopreventive potential of vanadium in influencing trace elemental profile and antioxidant status in chemical carcinogenesis. The elements with Z=15-40 were studied. Data reveal remarkable alterations in elemental composition in the hepatic tissue of diethylnitrosamine (DENA)-induced Sprague-Dawley male rats (intraperitoneal (ip) dose: 200 mg/kg body weight) after four weeks of induction. Several elements like Mn, Cu, Zn, Rb showed large depletion while other elements like Fe, Ca, K, Br showed large enhancement in comparison to that of the normal control animals. These elements compete for binding sites in the cell, change its enzymatic activity and exert direct or indirect action on the carcinogenic process. Supplementary vanadium (0.5 ppm ad libitum in drinking water) has shown effective modulation by alteration in the concentration of trace elements in the tumorigenic tissue ( Phomeostasis, a parameter of importance in cancer prevention research.

  12. Fourier Transform Infrared Spectroscopic Studies on Modulation of N-Nitrosodiethylamine-Induced Hepatocarcinogenesis by Azadirachta indica.

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    Bharati, Sanjay; Rishi, Parveen; Koul, Ashwani

    2015-01-01

    Fourier transform infrared spectroscopy was employed in the present study to obtain information about the molecular composition of hepatic tumor versus hepatic tissue. A hepatic cancer model was developed by administering N-nitrosodiethylamine (NDEA) to male Balb/c mice. The results revealed that NDEA-induced hepatic cancer tumor tissue had altered molecular composition compared with normal liver tissue. Compared with the normal tissue, the saturation level of membrane phospholipids was observed to be decreased in tumors along with an abnormal distribution of protein secondary structures. A significant decrease in glycogen and a significant increase in total nucleic acid content were also observed in tumor cells. The administration of aqueous Azadirachta indica leaf extract (AAILE) prior to NDEA treatment resulted in the normalization of saturation levels in phospholipids and total nucleic acid content and in the distribution of protein secondary structures in tumors. A significant increase in the amount of stored glycogen was observed in AAILE cotreated tumors compared with NDEA-induced tumors, which might indicate that AAILE cotreatment impeded the ability of tumor cells to consume glucose at a faster rate. The normalization of molecular composition upon AAILE cotreatment in hepatic tumors might indicate that AAILE hampered the process of evolution of tumors, which could be responsible for its observed chemopreventive action.

  13. Melatonin Activates Endoplasmic Reticulum Stress and Apoptosis in Rats with Diethylnitrosamine-Induced Hepatocarcinogenesis.

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    Andrea Janz Moreira

    Full Text Available Hepatocellular carcinoma (HCC is one of the most lethal human cancers worldwide because of its high incidence, its metastatic potential and the low efficacy of conventional treatment. Inactivation of apoptosis is implicated in tumour progression and chemotherapy resistance, and has been linked to the presence of endoplasmic reticulum stress. Melatonin, the main product of the pineal gland, exerts anti-proliferative, pro-apoptotic and anti-angiogenic effects in HCC cells, but these effects still need to be confirmed in animal models. Male Wistar rats in treatment groups received diethylnitrosamine (DEN 50 mg/kg intraperitoneally twice/once a week for 18 weeks. Melatonin was given in drinking water at 1 mg/kg/d, beginning 5 or 12 weeks after the start of DEN administration. Melatonin improved survival rates and successfully attenuated liver injury, as shown by histopathology, decreased levels of serum transaminases and reduced expression of placental glutathione S-transferase. Furthermore, melatonin treatment resulted in a significant increase of caspase 3, 8 and 9 activities, polyadenosine diphosphate (ADP ribose polymerase (PARP cleavage, and Bcl-associated X protein (Bax/Bcl-2 ratio. Cytochrome c, p53 and Fas-L protein concentration were also significantly enhanced by melatonin. Melatonin induced an increased expression of activating transcription factor 6 (ATF6, C/EBP-homologous protein (CHOP and immunoglobulin heavy chain-binding protein (BiP, while cyclooxygenase (COX-2 expression decreased. Data obtained suggest that induction of apoptosis and ER stress contribute to the beneficial effects of melatonin in rats with DEN-induced HCC.

  14. Aspects of Experimental Hepatocarcinogenesis

    African Journals Online (AJOL)

    1974-04-06

    Apr 6, 1974 ... The remaining articles in this series are: Part Il-Hyperplastic nodules; Part Ill-Iron overload and hepatocarcinogenesis; Part IV-Changes in the liver fol- lowing cessation of carcinogen administration; Part V-. The ultrastructural morphology of early hepatocellular carcinomas. EXPERIMENTAL METHOD.

  15. Water extracts of cabbage and kale inhibit ex vivo H2O2-induced DNA damage but not rat hepatocarcinogenesis

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    M.A. Horst

    2010-03-01

    Full Text Available The chemopreventive potential of water extracts of the Brassica vegetables cabbage and kale was evaluated by administering their aqueous extracts in drinking water ad libitum to Wistar rats submitted to Ito’s hepatocarcinogenesis model (CB group and K group, respectively - 14 rats per group. Animals submitted to this same model and treated with water were used as controls (W group - 15 rats. Treatment with the vegetable extracts did not inhibit (P > 0.05 placental glutathione S-transferase-positive preneoplastic lesions (PNL. The number of apoptotic bodies did not differ (P > 0.05 among the experimental groups. Ex vivo hydrogen peroxide treatment of rat livers resulted in lower (P < 0.05 DNA strand breakage in cabbage- (107.6 ± 7.8 µm and kale- (110.8 ± 10.0 µm treated animals compared with control (120.9 ± 12.7 µm, as evaluated by the single cell gel (comet assay. Treatment with cabbage (2 ± 0.3 µg/g or kale (4 ± 0.2 µg/g resulted in increased (P < 0.05 hepatic lutein concentration compared with control (0.5 ± 0.07 µg/g. Despite the absence of inhibitory effects of cabbage and kale aqueous extracts on PNL, these Brassica vegetables presented protection against DNA damage, an effect possibly related to increased hepatic lutein concentrations. However, it must be pointed out that the cause-effect relationship between lutein levels and protection is hypothetical and remains to be demonstrated.

  16. Hesperidin protects against chemically induced hepatocarcinogenesis via modulation of Nrf2/ARE/HO-1, PPARγ and TGF-β1/Smad3 signaling, and amelioration of oxidative stress and inflammation.

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    Mahmoud, Ayman M; Mohammed, Hanaa M; Khadrawy, Sally M; Galaly, Sanaa R

    2017-11-01

    Hesperidin is a plant-derived bioflavonoid with promising antitumor efficacy, though the underlying mechanisms of action remain poorly elucidated. Thus, we evaluated the in vivo chemopreventive effect of hesperidin against diethylnitrosamine (DEN)-induced hepatocarcinogenesis. We demonstrated the modulatory effect of hesperidin on Nrf2/ARE/HO-1, PPARγ and TGF-β1/Smad3 signaling. Hepatocarcinogenesis was initiated with DEN and promoted with carbon tetrachloride (CCl 4 ). DEN/CCl 4 -induced rats were treated with 50 and 100 mg/kg hesperidin throughout the experiment. The results revealed that hesperidin significantly reduced circulating liver function marker enzymes, bilirubin, tumor markers and tumor necrosis factor alpha. Hesperidin prevented liver morphological damage, proliferating cell nuclear antigen (PCNA) expression and oxidative stress as evidenced by the reduced lipid peroxidation and enhanced antioxidant defenses. Liver NF-κB and TGF-β1 expression, and Smad3 phosphorylation were significantly up-regulated in DEN/CCl 4 -induced rats. Hesperidin dramatically abolished NF-κB and TGF-β1/Smad3 signaling as well as collagen deposition in the liver of DEN/CCl 4 -induced rats. In addition, hesperidin markedly up-regulated the expression of Nrf2, HO-1 and PPARγ in the liver of DEN/CCl 4 -induced rats. In conclusion, hesperidin can inhibit hepatocarcinogenesis by suppressing oxidative stress, inflammation, cell proliferation, TGF-β1/Smad3 signaling and collagen deposition. These effects are suggested to be mediated by activating Nrf2/ARE/HO-1 and PPARγ pathways. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. L-carnitine inhibits hepatocarcinogenesis via protection of mitochondria.

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    Chang, Baojun; Nishikawa, Manabu; Nishiguchi, Shuhei; Inoue, Masayasu

    2005-02-20

    Hepatocellular carcinoma is usually preceded by chronic inflammation. However, the molecular mechanism in hepatocarcinogenesis is not well known. Recently, we reported that mitochondrial dysfunction plays an important role in hepatocarcinogenesis via the production of free radicals. Furthermore, we proved that L-carnitine effectively protects mitochondrial function in vivo. Therefore, we investigated whether long-term administration of L-carnitine could prevent hepatitis and subsequent hepatocellular carcinoma in Long-Evans Cinnamon rats that are often analyzed as a model of hepatocarcinogenesis. The results indicated that oxidative stress elicited from abnormally accumulated copper increased the amount of free fatty acids, thereby inducing mitochondrial dysfunction, resulting in cell death and enhanced secondary generation of reactive oxygen species, which were significantly inhibited by carnitine treatment. Finally, the occurrence of placental glutathione S-transferase-positive foci as a marker for preneoplastic lesions and hepatocarcinogenesis were significantly inhibited by L-carnitine. These facts suggest that mitochondrial injury plays an essential role in the development of hepatocarcinogenesis and that the clinical use of carnitine has excellent therapeutic potential in individuals with chronic hepatitis. (c) 2004 Wiley-Liss, Inc.

  18. Hesperetin conjugated PEGylated gold nanoparticles exploring the potential role in anti-inflammation and anti-proliferation during diethylnitrosamine-induced hepatocarcinogenesis in rats

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    Gokuladhas Krishnan

    2017-09-01

    Full Text Available Liver cancer is the fifth most common cancer and one of the leading causes of death in the world, and second most common cause of death in men. Natural products emerge as the most enduring approaches in the development of anticancer targeting drug. Hesperetin (HP, one of the abundant flavonoids found naturally in citrus fruits, has received considerable attention in anti-cancer promotion and progression. The present study was conducted to decipher the role of 0.5 ml hesperetin conjugated gold nanoparticles (Au-mPEG(5000-S-HP NPs during diethylnitrosamine (DEN-induced hepatocarcinogenesis in male Wistar albino rats and shows the better antioxidant that possesses anti-inflammatory, anti-proliferation and anticarcinogenic properties and may modulate signaling pathways. The confirmation of polymer functionalized gold nanoparticles and drug loaded polymer gold nanoparticles were characterized by HR-TEM with EDAX, and DLS with Zeta potential techniques. The drug encapsulation efficiency and release properties were carried out in PBS at pH 7.4 for Au- mPEG(5000-S-HP and compared with the control pure hesperetin (HP. Here, we review the role of mast cell counts, tumor necrosis factor alpha (TNF-α, transcription factor nuclear factor-κB (NF-κB, levels of glycoconjugates, proliferating cell nuclear antigen (PCNA and argyrophilic nucleolar organizing regions, are the master regulator of inflammation and proliferation, in the development of hepatocellular injury, liver fibrosis and HCC. DEN-administered animals showed increased mast cell counts, tumor necrosis factor alpha, transcription factor nuclear factor-κB, glycoconjugates, proliferating cell nuclear antigen, and argyrophilic nucleolar organizing regions. Whereas Au-mPEG(5000-S-HP NPs supplementation considerably suppressed all the above abnormalities. These results suggest that the Au-mPEG(5000-S-HP NPs exhibited the better potential anticancer activity by inhibiting cell inflammation and

  19. Early life exposure to a rodent carcinogen propiconazole fungicide induces oxidative stress and hepatocarcinogenesis in medaka fish

    Energy Technology Data Exchange (ETDEWEB)

    Tu, Tzu-Yi; Hong, Chwan-Yang [Department of Agricultural Chemistry, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan (China); Sasado, Takao [Laboratory of Bioresources, National Institute for Basic Biology, Okazaki (Japan); Kashiwada, Shosaku [Research Center for Life and Environmental Sciences, Department of Life Sciences, the Toyo University, Gunma (Japan); Chen, Pei-Jen, E-mail: chenpj@ntu.edu.tw [Department of Agricultural Chemistry, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan (China)

    2016-01-15

    Highlights: • Propiconazole initiates ROS-induced oxidative stress and damage in medaka fish. • Early life exposure to propiconazole increases incidence of hepatocarcionogensis in p53{sup −/−} medaka. • Oxidative stress and CYP induction involved in p53 regulation are key events in propiconazole-induced hepatotumorigenesis. • Propiconazole-induced toxic response in medaka is compatible with that in rodents. - Abstract: Conazole pollution is an emerging concern to human health and environmental safety because of the broad use of conazole fungicides in agriculture and medicine and their frequent occurrence in aquifers. The agricultural pesticide propiconazole has received much regulatory interest because it is a known rodent carcinogen with evidence of multiple adverse effects in mammals and non-targeted organisms. However, the carcinogenic effect and associated mechanism of propiconazole in fish under microgram-per-liter levels of environmental-relevant exposure remains unclear. To explore whether early life of propiconzaole exposure would induce oxidative stress and latent carcinogenic effects in fish, we continuously exposed larvae of wild type or p53{sup −/−} mutant of medaka fish (Oryzias latipes) to propiconazole (2.5–250 μg/L) for 3, 7, 14 or 28 days and assessed liver histopathology and/or the oxidative stress response and gene expression during exposure and throughout adulthood. Propiconazole dose-dependently induced reactive oxygen species (ROS) level, altered homeostasis of antioxidant superoxide dismutase, catalase and glutathione S-transferase and caused lipid and protein peroxidation during early life exposure in wild type medaka. Such exposure also significantly upregulated gene expression of the cytochrome P450 CYP1A, but marginally suppressed that of tumor suppressor p53 in adults. Furthermore, histopathology revealed that p53{sup −/−} mutant medaka with early life exposure to propiconazole showed increased incidence of

  20. Genetic alterations and epigenetic changes in hepatocarcinogenesis

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    Luz Stella Hoyos Giraldo

    2007-02-01

    Full Text Available

    Hepatocarcinogenesis as hepatocellular carcinoma (HCC is associated with background of chronic liver disease usually in association with cirrhosis, marked hepatic fibrosis, hepatitis B virus (HBV and/or hepatitis virus (HCV infection, chronic inflammation, Aflatoxin B1(AFB1 exposure, chronic alcoholism, metabolic disorder of the liver and necroinflamatory liver disease. Hepatocarcinogenesis involve two mechanisms, genetic alterations (with changes in the cell's DNA sequence and epigenetic changes (without changes in the cell's DNA sequence, but changes in the pattern of gene expression that can persist through one or more generations (somatic sense. Hepatocarcinogenesis is associated with activation of oncogenes and decreased expression of tumor suppressor genes (TSG; include those involved in cell cycle control, apoptosis, DNA repair, immortalization and angiogenesis. AFB1 is metabolized in the liver into a potent carcinogen, aflatoxin 8, 9-epoxide, which is detoxified by epoxide hydrolase (EPHX and glutathione S-transferase M1 (GSTM1.

    A failure of detoxification processes can allow to mutagenic metabolite to bind to DNA and inducing P53 mutation. Genetic polymorphism of EPHX and GSTM1 can make individuals more susceptible to AFB1. Epigenetic inactivation of GSTP1 by promoter hypermethylation plays a role in the development of HCC because, it leads that electrophilic metabolite increase DNA damage and mutations. HBV DNA integration into the host chromosomal DNA of hepatocytes has been detected in HBV-related HCC.

    DNA tumor viruses cause cancer mainly by interfering with cell cycle controls, and activating the cell's replication machinery by blocking the action of key TSG. HBx protein is a

  1. Nrf2 Mutagenic Activation Drives Hepatocarcinogenesis.

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    Ngo, Hoang Kieu Chi; Kim, Do-Hee; Cha, Young-Nam; Na, Hye-Kyung; Surh, Young-Joon

    2017-09-15

    Nrf2, a master regulator of oxidative stress, is considered a prominent target for prevention of hepatocellular carcinoma (HCC), one of the leading causes of cancer-related deaths worldwide. Here we report that Nrf2-deficient mice resisted diethylnitrosamine (DEN)-induced hepatocarcinogenesis without affecting P450-mediated metabolic activation of DEN. Nrf2 expression, nuclear translocation, and transcriptional activity were enhanced in liver tumors. Overactivated Nrf2 was required for hepatoma growth in DEN-induced HCC. Following DEN treatment, Nrf2 genetic disruption reduced expression of pentose phosphate pathway-related enzymes, the depletion of which has been associated with an amelioration of HCC incidence. Conversely, enhanced Nrf2 activity was attributable to alterations in the ability to bind its endogenous inhibitor Keap1. Our findings provide a mechanistic rationale for Nrf2 blockade to prevent and possibly treat liver cancer. Cancer Res; 77(18); 4797-808. ©2017 AACR. ©2017 American Association for Cancer Research.

  2. Possible quantum mechanical mechanism for hepatocarcinogenesis

    Science.gov (United States)

    Torres-Vega, G.; Godina-Nava, J. J.; Morales-Peñaloza, A.; Jiménez-García, M. N.

    2012-10-01

    We describe a method to study the effects of an extremely low frequency electromagnetic field (ELF-EMF) on the development of preneoplastic lesions in experimental hepatocarcinogenesis. The method uses the dual Lanczos transformation theory to diagonalize the Liouville superoperator that describe the evolution of a radical pair. We illustrate this procedure with a simple two level system.

  3. Flash-induced fading: Dependence on colour and shape similarity

    NARCIS (Netherlands)

    Vergeer, M.; Lier, R.J. van

    2005-01-01

    We investigated the effects of perceptual grouping by colour and shape similarity on flash-induced perceptual fading. This flash-induced fading effect (Kanai et al, 2003 Journal of Cognitive Neuroscience 15 664 - 672) is considered as a time-locked variant of the Troxler effect. In the original

  4. Graphemes Sharing Phonetic Features Tend to Induce Similar Synesthetic Colors

    Science.gov (United States)

    Kang, Mi-Jeong; Kim, Yeseul; Shin, Ji-Young; Kim, Chai-Youn

    2017-01-01

    Individuals with grapheme-color synesthesia experience idiosyncratic colors when viewing achromatic letters or digits. Despite large individual differences in grapheme-color association, synesthetes tend to associate graphemes sharing a perceptual feature with similar synesthetic colors. Sound has been suggested as one such feature. In the present study, we investigated whether graphemes of which representative phonemes have similar phonetic features tend to be associated with analogous synesthetic colors. We tested five Korean multilingual synesthetes on a color-matching task using graphemes from Korean, English, and Japanese orthography. We then compared the similarity of synesthetic colors induced by those characters sharing a phonetic feature. Results showed that graphemes associated with the same phonetic feature tend to induce synesthetic color in both within- and cross-script analyses. Moreover, this tendency was consistent for graphemes that are not transliterable into each other as well as graphemes that are. These results suggest that it is the perceptual—i.e., phonetic—properties associated with graphemes, not just conceptual associations such as transliteration, that determine synesthetic color. PMID:28348537

  5. Liver-specific expressions of HBx and src in the p53 mutant trigger hepatocarcinogenesis in zebrafish.

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    Jeng-Wei Lu

    Full Text Available Hepatocarcinogenesis is a multistep process that starts from fatty liver and transitions to fibrosis and, finally, into cancer. Many etiological factors, including hepatitis B virus X antigen (HBx and p53 mutations, have been implicated in hepatocarcinogenesis. However, potential synergistic effects between these two factors and the underlying mechanisms by which they promote hepatocarcinogenesis are still unclear. In this report, we show that the synergistic action of HBx and p53 mutation triggers progressive hepatocellular carcinoma (HCC formation via src activation in zebrafish. Liver-specific expression of HBx in wild-type zebrafish caused steatosis, fibrosis and glycogen accumulation. However, the induction of tumorigenesis by HBx was only observed in p53 mutant fish and occurred in association with the up-regulation and activation of the src tyrosine kinase pathway. Furthermore, the overexpression of src in p53 mutant zebrafish also caused hyperplasia, HCC, and sarcomatoid HCC, which were accompanied by increased levels of the signaling proteins p-erk, p-akt, myc, jnk1 and vegf. Increased expression levels of lipogenic factors and the genes involved in lipid metabolism and glycogen storage were detected during the early stages of hepatocarcinogenesis in the HBx and src transgenic zebrafish. The up-regulation of genes involved in cell cycle regulation, tumor progression and other molecular hallmarks of human liver cancer were found at later stages in both HBx and src transgenic, p53 mutant zebrafish. Together, our study demonstrates that HBx and src overexpression induced hepatocarcinogenesis in p53 mutant zebrafish. This phenomenon mimics human HCC formation and provides potential in vivo platforms for drug screening for therapies for human liver cancer.

  6. Deregulation of Epigenetic Mechanisms by the Hepatitis B Virus X Protein in Hepatocarcinogenesis

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    Ourania M. Andrisani

    2013-03-01

    Full Text Available This review focuses on the significance of deregulation of epigenetic mechanisms by the hepatitis B virus (HBV X protein in hepatocarcinogenesis and HBV replication. Epigenetic mechanisms, DNA methylation, and specific histone modifications, e.g., trimethylation of H3 on lysine-27 or lysine-4, maintain ‘cellular memory’ by silencing expression of lineage-inducing factors in stem cells and conversely, of pluripotency factors in differentiated cells. The X protein has been reported to induce expression of DNA methyltransferases (DNMTs, likely promoting epigenetic changes during hepatocarcinogenesis. Furthermore, in cellular and animal models of X-mediated oncogenic transformation, protein levels of chromatin modifying proteins Suz12 and Znf198 are down-regulated. Suz12 is essential for the Polycomb Repressive Complex 2 (PRC2 mediating the repressive trimethylation of H3 on lysine-27 (H3K27me3. Znf198, stabilizes the LSD1-CoREST-HDAC complex that removes, via lysine demethylase1 (LSD1, the activating trimethylation of H3 on lysine-4 (H3K4me3. Down-regulation of Suz12 also occurs in liver tumors of woodchucks chronically infected by woodchuck hepatitis virus, an animal model recapitulating HBV-mediated hepatocarcinogenesis in humans. Significantly, subgroups of HBV-induced liver cancer re-express hepatoblast and fetal markers, and imprinted genes, suggesting hepatocyte reprogramming during oncogenic transformation. Lastly, down-regulation of Suz12 and Znf198 enhances HBV replication. Collectively, these observations suggest deregulation of epigenetic mechanisms by HBV X protein influences both the viral cycle and the host cell.

  7. Deregulation of epigenetic mechanisms by the hepatitis B virus X protein in hepatocarcinogenesis.

    Science.gov (United States)

    Andrisani, Ourania M

    2013-03-18

    This review focuses on the significance of deregulation of epigenetic mechanisms by the hepatitis B virus (HBV) X protein in hepatocarcinogenesis and HBV replication. Epigenetic mechanisms, DNA methylation, and specific histone modifications, e.g., trimethylation of H3 on lysine-27 or lysine-4, maintain 'cellular memory' by silencing expression of lineage-inducing factors in stem cells and conversely, of pluripotency factors in differentiated cells. The X protein has been reported to induce expression of DNA methyltransferases (DNMTs), likely promoting epigenetic changes during hepatocarcinogenesis. Furthermore, in cellular and animal models of X-mediated oncogenic transformation, protein levels of chromatin modifying proteins Suz12 and Znf198 are down-regulated. Suz12 is essential for the Polycomb Repressive Complex 2 (PRC2) mediating the repressive trimethylation of H3 on lysine-27 (H3K27me3). Znf198, stabilizes the LSD1-CoREST-HDAC complex that removes, via lysine demethylase1 (LSD1), the activating trimethylation of H3 on lysine-4 (H3K4me3). Down-regulation of Suz12 also occurs in liver tumors of woodchucks chronically infected by woodchuck hepatitis virus, an animal model recapitulating HBV-mediated hepatocarcinogenesis in humans. Significantly, subgroups of HBV-induced liver cancer re-express hepatoblast and fetal markers, and imprinted genes, suggesting hepatocyte reprogramming during oncogenic transformation. Lastly, down-regulation of Suz12 and Znf198 enhances HBV replication. Collectively, these observations suggest deregulation of epigenetic mechanisms by HBV X protein influences both the viral cycle and the host cell.

  8. Pomegranate-mediated chemoprevention of experimental hepatocarcinogenesis involves Nrf2-regulated antioxidant mechanisms

    Science.gov (United States)

    Bishayee, Anupam; Bhatia, Deepak; Thoppil, Roslin J.; Darvesh, Altaf S.; Nevo, Eviatar; Lansky, Ephraim P.

    2011-01-01

    Hepatocellular carcinoma (HCC), one of the most prevalent and lethal cancers, has shown an alarming rise in the USA. Without effective therapy for HCC, novel chemopreventive strategies may effectively circumvent the current morbidity and mortality. Oxidative stress predisposes to hepatocarcinogenesis and is the major driving force of HCC. Pomegranate, an ancient fruit, is gaining tremendous attention due to its powerful antioxidant properties. Here, we examined mechanism-based chemopreventive potential of a pomegranate emulsion (PE) against dietary carcinogen diethylnitrosamine (DENA)-induced rat hepatocarcinogenesis that mimics human HCC. PE treatment (1 or 10 g/kg), started 4 weeks prior to the DENA challenge and continued for 18 weeks thereafter, showed striking chemopreventive activity demonstrated by reduced incidence, number, multiplicity, size and volume of hepatic nodules, precursors of HCC. Both doses of PE significantly attenuated the number and area of γ-glutamyl transpeptidase-positive hepatic foci compared with the DENA control. PE also attenuated DENA-induced hepatic lipid peroxidation and protein oxidation. Mechanistic studies revealed that PE elevated gene expression of an array of hepatic antioxidant and carcinogen detoxifying enzymes in DENA-exposed animals. PE elevated protein and messenger RNA expression of the hepatic nuclear factor E2-related factor 2 (Nrf2). Our results provide substantial evidence, for the first time, that pomegranate constituents afford chemoprevention of hepatocarcinogenesis possibly through potent antioxidant activity achieved by upregulation of several housekeeping genes under the control of Nrf2 without toxicity. The outcome of this study strongly supports the development of pomegranate-derived products in the prevention and treatment of human HCC, which remains a devastating disease. PMID:21389260

  9. Cyclooxygenase 2 and Prostaglandin E2 are not Involved in N-Nitrosodiethylamine-Initiated Early Rat Hepatocarcinogenesis

    Science.gov (United States)

    Ogawa, Kumiko; Pitchakarn, Pornsiri; Takahashi, Satoru; Asamoto, Makoto; Shirai, Tomoyuki

    2009-01-01

    The present study was undertaken to investigate the effect of dietary supplementation with nimesulide or eugenol on N-nitrosodiethylamine (DEN)-initiated early hepatocarcinogenesis in F344 male rats. Both compounds did not alter the expression of cytochrome P450 (CYP) 2E1, the enzyme that plays a major role in the activation of DEN to genotoxic products; however, nimesulide induced the expression of CYP1A1. Western blot analysis revealed that COX-1 and COX-2 protein expressions were not modulated by DEN compared with normal controls. Furthermore, post-initiation feeding with nimesulide or eugenol did not modulate COX-2 protein expression in normal or DEN-treated rats, whereas eugenol significantly increased the liver prostaglandin E2 (PGE2) levels of DEN-injected animals compared with the DEN controls. Ultimately, nimesulide or eugenol did not modify DEN-induced hepatocarcinogenesis as evidenced by insignificant changes in the number and size of preneoplastic placental glutathione S-transferase (GST-P) positive liver foci compared with the DEN controls. These results suggest that COX-2, as well as prostaglandin E2, may play no role in the post-initiation development of DEN-induced rat hepatocarcinogenesis at an early stage. PMID:22272001

  10. Molecular basis of hepatitis C virus -associated hepatocarcinogenesis

    Directory of Open Access Journals (Sweden)

    Isabelle Chemin

    2007-02-01

    Full Text Available

    In areas with an intermediate rate of Hepatocellular Carcinoma (HCC such as Western Europe and Japan, hepatitis C is the predominant cause, whereas in low rate areas such as Western Europe and North USA, HCC is often related to other factors as alcoholic liver disease. There is a rising incidence in HCC in developed countries during the last two decades, due to the increasing rate of hepatitis C infection and improvement of the clinical management of cirrhosis (most of the time appear after cirrhosis, the total number of HCC cases annually registered should be multiplied by 3 until 2020.

    The pathogenesis of HCC in HCV infection has extensively been analysed. Hepatitis C virus-induced chronic inflammation and the effects of cytokines in the development of fibrosis and liver cell proliferation are considered as one of the major pathogenic mechanisms. Increasing experimental evidence suggests that HCV contributes to HCC by directly modulating pathways that promote the malignant transformation of hepatocytes. Hepatitis C virus is an RNA virus that does not integrate into the host genome but HCV proteins interact with many host-cell factors well beyond their roles in the viral life cycle and are involved in a wide range of activities at least in vitro, including cell signalling, transcription, cell proliferation, apoptosis, membrane rearrangements, vesicular trafficking and translational regulation. At least four of the HCV gene products, namely HCV core, NS3, NS4B and NS5A, have been shown to exhibit transformation potential in tissue culture and several potentially oncogenic pathways have been shown to be altered by the expression of HCV proteins. Both HCV core and NS5A induce the accumulation of wild-type betacatenin and the Wnt-beta-catenin pathway emerges as a common target

  11. Persistent activation of NF-kappaB related to IkappaB's degradation profiles during early chemical hepatocarcinogenesis

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    García-Román Rebeca

    2007-04-01

    Full Text Available Abstract Background To define the NF-kappaB activation in early stages of hepatocarcinogenesis and its IkappaB's degradation profiles in comparison to sole liver regeneration. Methods Western-blot and EMSA analyses were performed for the NF-kappaB activation. The transcriptional activity of NF-kappaB was determined by RT-PCR of the IkappaB-α mRNA. The IkappaB's degradation proteins were determined by Western-blot assay. Results We demonstrated the persistent activation of NF-kappaB during early stages of hepatocarcinogenesis, which reached maximal level 30 min after partial hepatectomy. The DNA binding and transcriptional activity of NF-kappaB, were sustained during early steps of hepatocarcinogenesis in comparison to only partial hepatectomy, which displayed a transitory NF-kappaB activation. In early stages of hepatocarconogenesis, the IkappaB-α degradation turned out to be acute and transitory, but the low levels of IkappaB-β persisted even 15 days after partial hepatectomy. Interestingly, IkappaB-β degradation is not induced after sole partial hepatectomy. Conclusion We propose that during liver regeneration, the transitory stimulation of the transcription factor response, assures blockade of NF-kappaB until recovery of the total mass of the liver and the persistent NF-kappaB activation in early hepatocarcinogenesis may be due to IkappaB-β and IkappaB-α degradation, mainly IkappaB-β degradation, which contributes to gene transcription related to proliferation required for neoplasic progression.

  12. Identification of the Differential Expression Profiles of Serum and Tissue Proteins During Rat Hepatocarcinogenesis.

    Science.gov (United States)

    Sheng, Xia; Huang, Tao; Qin, Jianmin; Yang, Lin; Sa, Zhong-Qiu; Li, Qi

    2018-01-01

    The pathogenesis of hepatocellular carcinoma is complex and not fully known yet. This study aims to screen and identify the differentially expressed proteins in peripheral blood and liver tissue samples from rat hepatocellular carcinoma and to further clarify the pathogenesis and discover the specific tumor markers and molecular targets of hepatocellular carcinoma. The hepatocellular carcinoma model of Wistar rats were induced by chemical carcinogen. The serum and liver tissue samples were obtained after induction for 2, 4, 8, 14, 18, and 21 weeks. The results showed that the clusterin (IPI00198667), heat shock protein a8 (IPI00208205), and N-myc downstream-regulated gene-2 (IPI00382069) being closely related to hepatocarcinogenesis were eventually identified from the 30 different proteins. As the time progressed, the serum levels of clusterin and heat shock protein a8 increased gradually during induced liver cancer in rats. However, the serum N-myc downstream-regulated gene 2 level in induced liver cancer in rats underwent biphasic changes, and the serum N-myc downstream-regulated gene 2 level decreased at the 8th week, increased at the 14th week, and then decreased significantly. Statistical difference occurred in protein expression of clusterin and heat shock protein a8 in liver tissues at the different time points. In the liver tissues, the N-myc downstream-regulated gene 2 level decreased gradually at the 8th week, increased gradually at the 14th week, and then decreased significantly after 14 weeks. The study demonstrated that heat shock protein a8, clusterin, and N-myc downstream-regulated gene 2 participated in the process of abnormal cell division, proliferation, and carcinogenesis of liver cells during hepatocarcinogenesis.

  13. Proton-Induced X-ray Emission (PIXE Analysis and DNA-chain Break study in rat hepatocarcinogenesis: A possible chemopreventive role by combined supplementation of vanadium and beta-carotene

    Directory of Open Access Journals (Sweden)

    Kanjilal NB

    2005-05-01

    Full Text Available Abstract Combined effect of vanadium and beta-carotene on rat liver DNA-chain break and Proton induced X-ray emission (PIXE analysis was studied during a necrogenic dose (200 mg/kg of body weight of Diethyl Nitrosamine (DENA induced rat liver carcinogenesis. Morphological and histopathological changes were observed as an end point biomarker. Supplementation of vanadium (0.5 ppm ad libitum in drinking water and beta-carotene in the basal diet (120 mg/Kg of body weight were performed four weeks before DENA treatment and continued till the end of the experiment (16 weeks. PIXE analysis revealed the restoration of near normal value of zinc, copper, and iron, which were substantially altered when compared to carcinogen treated groups. Supplementation of both vanadium and beta-carotene four weeks before DENA injection was found to offer significant (64.73%, P

  14. Dectin-1 Regulates Hepatic Fibrosis and Hepatocarcinogenesis by Suppressing TLR4 Signaling Pathways

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    Lena Seifert

    2015-12-01

    Full Text Available Dectin-1 is a C-type lectin receptor critical in anti-fungal immunity, but Dectin-1 has not been linked to regulation of sterile inflammation or oncogenesis. We found that Dectin-1 expression is upregulated in hepatic fibrosis and liver cancer. However, Dectin-1 deletion exacerbates liver fibro-inflammatory disease and accelerates hepatocarcinogenesis. Mechanistically, we found that Dectin-1 protects against chronic liver disease by suppressing TLR4 signaling in hepatic inflammatory and stellate cells. Accordingly, Dectin-1–/– mice exhibited augmented cytokine production and reduced survival in lipopolysaccharide (LPS-mediated sepsis, whereas Dectin-1 activation was protective. We showed that Dectin-1 inhibits TLR4 signaling by mitigating TLR4 and CD14 expression, which are regulated by Dectin-1-dependent macrophage colony stimulating factor (M-CSF expression. Our study suggests that Dectin-1 is an attractive target for experimental therapeutics in hepatic fibrosis and neoplastic transformation. More broadly, our work deciphers critical cross-talk between pattern recognition receptors and implicates a role for Dectin-1 in suppression of sterile inflammation, inflammation-induced oncogenesis, and LPS-mediated sepsis.

  15. Modulation of radical pairs dynamics immersed in an ELF-EMF: The effect on hepatocarcinogenesis

    Science.gov (United States)

    López-Riquelme, G. O.; López-Sandoval, E.; Vera-Aguilar, E.; Godina-Nava, J. J.

    2015-01-01

    The most suitable mechanism of action of electromagnetic fields (EMF) on biological systems is the effect on the radical pair (RP) recombination through the Zeeman effect and hyperfine interaction, which changes the rate of reactions or the product distribution. Enzyme reactions with RP intermediates can be altered by EMF, like those catalyzed by cytochrome P450 enzymes (CYP450), a heme-thiolate family protein that detoxifies xenobiotics and involved in chemical carcinogenesis. CYP450 activate chemical carcinogens producing an enormous amount of free radicals, which damage the DNA resulting in the malignant transformation of cells. During the activation, CYP450 produce spin-correlated RP intermediates that can either go to recombination or to continue the catalytic process. As CYP450 are electron carrier proteins, it is possible that RP intermediates may be affected by EMF. It was previously found that periodic treatment with extremely low frequency electromagnetic fields (ELF-EMF) inhibits more than 50% the number and area of preneoplastic lesions in rats with chemically induced hepatocarcinogenesis through reduction of cell proliferation. In this work, we developed a quantum mechanical model based on RP mechanism in order to explain the experimental effects of ELF-EMF on the free radicals produced in the early stages of chemical carcinogenesis.

  16. Dectin-1 Regulates Hepatic Fibrosis and Hepatocarcinogenesis by Suppressing TLR4 Signaling Pathways.

    Science.gov (United States)

    Seifert, Lena; Deutsch, Michael; Alothman, Sara; Alqunaibit, Dalia; Werba, Gregor; Pansari, Mridul; Pergamo, Matthew; Ochi, Atsuo; Torres-Hernandez, Alejandro; Levie, Elliot; Tippens, Daniel; Greco, Stephanie H; Tiwari, Shaun; Ly, Nancy Ngoc Giao; Eisenthal, Andrew; van Heerden, Eliza; Avanzi, Antonina; Barilla, Rocky; Zambirinis, Constantinos P; Rendon, Mauricio; Daley, Donnele; Pachter, H Leon; Hajdu, Cristina; Miller, George

    2015-12-01

    Dectin-1 is a C-type lectin receptor critical in anti-fungal immunity, but Dectin-1 has not been linked to regulation of sterile inflammation or oncogenesis. We found that Dectin-1 expression is upregulated in hepatic fibrosis and liver cancer. However, Dectin-1 deletion exacerbates liver fibro-inflammatory disease and accelerates hepatocarcinogenesis. Mechanistically, we found that Dectin-1 protects against chronic liver disease by suppressing TLR4 signaling in hepatic inflammatory and stellate cells. Accordingly, Dectin-1(-/-) mice exhibited augmented cytokine production and reduced survival in lipopolysaccharide (LPS)-mediated sepsis, whereas Dectin-1 activation was protective. We showed that Dectin-1 inhibits TLR4 signaling by mitigating TLR4 and CD14 expression, which are regulated by Dectin-1-dependent macrophage colony stimulating factor (M-CSF) expression. Our study suggests that Dectin-1 is an attractive target for experimental therapeutics in hepatic fibrosis and neoplastic transformation. More broadly, our work deciphers critical cross-talk between pattern recognition receptors and implicates a role for Dectin-1 in suppression of sterile inflammation, inflammation-induced oncogenesis, and LPS-mediated sepsis. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  17. Heat Shock Response Associated with Hepatocarcinogenesis in a Murine Model of Hereditary Tyrosinemia Type I

    Energy Technology Data Exchange (ETDEWEB)

    Angileri, Francesca; Morrow, Geneviève; Roy, Vincent; Orejuela, Diana; Tanguay, Robert M., E-mail: robert.tanguay@ibis.ulaval.ca [Laboratory of Cell and Developmental Genetics, Department of Molecular Biology, Medical Biochemistry and Pathology, Institut de Biologie Intégrative et des Systèmes (IBIS) and PROTEO, 1030 avenue de la médecine, Université Laval, Québec G1V 0A6 (Canada)

    2014-04-23

    Hereditary Tyrosinemia type 1 (HT1) is a metabolic liver disease caused by genetic defects of fumarylacetoacetate hydrolase (FAH), an enzyme necessary to complete the breakdown of tyrosine. The severe hepatic dysfunction caused by the lack of this enzyme is prevented by the therapeutic use of NTBC (2-[2-nitro-4-(trifluoromethyl)benzoyl]cyclohexane-1,3-dione). However despite the treatment, chronic hepatopathy and development of hepatocellular carcinoma (HCC) are still observed in some HT1 patients. Growing evidence show the important role of heat shock proteins (HSPs) in many cellular processes and their involvement in pathological diseases including cancer. Their survival-promoting effect by modulation of the apoptotic machinery is often correlated with poor prognosis and resistance to therapy in a number of cancers. Here, we sought to gain insight into the pathophysiological mechanisms associated with liver dysfunction and tumor development in a murine model of HT1. Differential gene expression patterns in livers of mice under HT1 stress, induced by drug retrieval, have shown deregulation of stress and cell death resistance genes. Among them, genes coding for HSPB and HSPA members, and for anti-apoptotic BCL-2 related mitochondrial proteins were associated with the hepatocarcinogenetic process. Our data highlight the variation of stress pathways related to HT1 hepatocarcinogenesis suggesting the role of HSPs in rendering tyrosinemia-affected liver susceptible to the development of HCC.

  18. Lignocellulolytic mutants of Pleurotus ostreatus induced by gamma-ray radiation and their genetic similarities

    Science.gov (United States)

    Lee, Y.-K.; Chang, H.-H.; Kim, J.-S.; Kim, J. K.; Lee, K.-S.

    2000-02-01

    To induce the lignocellulolytic mutants of Pleurotus ostreatus, the mycelia were irradiated by gamma-ray radiation to doses of 1-2 kGy. Five strains were isolated by the criteria of clamp connection, fruiting body formation, growth rate and activities of extracellular enzymes. All isolated strains were able to form the fruiting bodies and grew similarly to the control. The extracellular enzymes activities in liquid media of isolated strains were up to 10 times higher than the control. Genetic similarities of the isolated strains ranged from 64.4% to 93.3% of the control. From these results, it seems that the genetic diversity of P. ostreatus could be changed and useful strains be induced by gamma-ray radiation to recycle or reuse biowastes.

  19. Lignocellulolytic mutants of Pleurotus ostreatus induced by gamma-ray radiation and their genetic similarities

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y-K. E-mail: yklee@nanum.kaeri.re.kr; Chang, H-H.; Kim, J-S.; Kim, J.K.; Lee, K-S

    2000-02-01

    To induce the lignocellulolytic mutants of Pleurotus ostreatus, the mycelia were irradiated by gamma-ray radiation to doses of 1-2 kGy. Five strains were isolated by the criteria of clamp connection, fruiting body formation, growth rate and activities of extracellular enzymes. All isolated strains were able to form the fruiting bodies and grew similarly to the control. The extracellular enzymes activities in liquid media of isolated strains were up to 10 times higher than the control. Genetic similarities of the isolated strains ranged from 64.4% to 93.3% of the control. From these results, it seems that the genetic diversity of P. ostreatus could be changed and useful strains be induced by gamma-ray radiation to recycle or reuse biowastes. (author)

  20. Exploration of Deregulated Long Non-Coding RNAs in Association with Hepatocarcinogenesis and Survival

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Jing, E-mail: js2182@cumc.columbia.edu [Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032 (United States); Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 (United States); Siegel, Abby B. [Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 (United States); Department of Medicine, Columbia University Medical Center, New York, NY 10032 (United States); Remotti, Helen [Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 (United States); Wang, Qiao; Shen, Yueyue [Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032 (United States); Santella, Regina M. [Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032 (United States); Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 (United States)

    2015-09-10

    Long non-coding RNAs (lncRNAs) are larger than 200 nucleotides in length and pervasively expressed across the genome. An increasing number of studies indicate that lncRNA transcripts play integral regulatory roles in cellular growth, division, differentiation and apoptosis. Deregulated lncRNAs have been observed in a variety of human cancers, including hepatocellular carcinoma (HCC). We determined the expression profiles of 90 lncRNAs for 65 paired HCC tumor and adjacent non-tumor tissues, and 55 lncRNAs were expressed in over 90% of samples. Eight lncRNAs were significantly down-regulated in HCC tumor compared to non-tumor tissues (p < 0.05), but no lncRNA achieved statistical significance after Bonferroni correction for multiple comparisons. Within tumor tissues, carrying more aberrant lncRNAs (6–7) was associated with a borderline significant reduction in survival (HR = 8.5, 95% CI: 1.0–72.5). The predictive accuracy depicted by the AUC was 0.93 for HCC survival when using seven deregulated lncRNAs (likelihood ratio test p = 0.001), which was similar to that combining the seven lncRNAs with tumor size and treatment (AUC = 0.96, sensitivity = 87%, specificity = 87%). These data suggest the potential association of deregulated lncRNAs with hepatocarcinogenesis and HCC survival.

  1. Similar metabolic changes induced by HIPVs exposure as herbivore in Ammopiptanthus mongolicus.

    Science.gov (United States)

    Sun, Jingru; Zhang, Xiao; Cao, Chuanjian; Mei, Xindi; Wang, Ningning; Yan, Suli; Zong, Shixiang; Luo, Youqing; Yang, Haijun; Shen, Yingbai

    2014-01-01

    Herbivore-induced plant volatiles (HIPVs) are important compounds to prim neighboring undamaged plants; however, the mechanism for this priming process remains unclear. To reveal metabolic changes in plants exposed to HIPVs, metabolism of leaves and roots of Ammopiptanthus mongolicus seedlings exposed to HIPVs released from conspecific plants infested with larvae of Orgyia ericae were analyzed together with control and infested seedlings using nuclear magnetic resonance (NMR)-based metabolic technology and multi variate data analysis. Results presented showed that HIPVs exposure led to similar but specific metabolic changes compared with those induced by infestation in both leaves and roots. Furthermore, both HIPVs exposure and herbivore attack resulted in metabolic changes involving a series of primary and secondary metabolites in both leaves and roots. Taken together, these results suggested that priming of yet-damaged plants may be achieved by reconfiguring metabolic pathways in leaves and roots to make similar concentrations for all metabolites as those in seedlings infested. Therefore, we propose that improved readiness of defense induction of primed plants toward subsequent herbivore attack may be based on the similar metabolic profiling induced by HIPVs exposure as those caused by herbivore.

  2. Similar metabolic changes induced by HIPVs exposure as herbivore in Ammopiptanthus mongolicus.

    Directory of Open Access Journals (Sweden)

    Jingru Sun

    Full Text Available Herbivore-induced plant volatiles (HIPVs are important compounds to prim neighboring undamaged plants; however, the mechanism for this priming process remains unclear. To reveal metabolic changes in plants exposed to HIPVs, metabolism of leaves and roots of Ammopiptanthus mongolicus seedlings exposed to HIPVs released from conspecific plants infested with larvae of Orgyia ericae were analyzed together with control and infested seedlings using nuclear magnetic resonance (NMR-based metabolic technology and multi variate data analysis. Results presented showed that HIPVs exposure led to similar but specific metabolic changes compared with those induced by infestation in both leaves and roots. Furthermore, both HIPVs exposure and herbivore attack resulted in metabolic changes involving a series of primary and secondary metabolites in both leaves and roots. Taken together, these results suggested that priming of yet-damaged plants may be achieved by reconfiguring metabolic pathways in leaves and roots to make similar concentrations for all metabolites as those in seedlings infested. Therefore, we propose that improved readiness of defense induction of primed plants toward subsequent herbivore attack may be based on the similar metabolic profiling induced by HIPVs exposure as those caused by herbivore.

  3. Keratin 19 epithelial patterns in cirrhotic stroma parallel hepatocarcinogenesis.

    Science.gov (United States)

    Lennerz, Jochen K M; Chapman, William C; Brunt, Elizabeth M

    2011-08-01

    Cirrhotic septa harbor vessels and inflammatory, fibrogenic, and ductular epithelial cells, collectively referred to as the ductular reaction (DR). Lack of the DR in the stromal compartment around hepatocellular carcinoma (HCC) has been documented; however, the relationship of epithelial keratin 19 (K19) structures to progression of intralesional carcinogenesis has not been explored. K19 immunoreactivity in the stromal compartment around 176 nodules in cirrhotic explants was examined. Quantitative differences (P transforming growth factor-β signaling components (TGFβR1, SMAD3, and pSMAD2/3) demonstrated increased percentages of pSMAD2/3 around DN when compared with CN (P identity as an underlying mechanism for the reproducible extralesional K19 pattern that parallels progressive stages of intranodular hepatocarcinogenesis. Paracrine signaling is proposed as a link that emphasizes the importance of the epithelial-stromal compartment in malignant progression of HCC in cirrhosis. Copyright © 2011 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  4. Promotion of hepatocarcinogenesis by suxibuzone in rats initiated with 3'-methyl-4-dimethylaminoazobenzene.

    Science.gov (United States)

    Yanagi, S; Sakamoto, M; Takahashi, S; Tsutsumi, M; Konishi, Y; Shibata, K; Kamiya, T

    1987-07-01

    Among phenylbutazone (PZ) and its related compounds, suxibuzone (SUX) caused the most extensive decrease in pyruvate kinase (PK) activity with lower toxicity. Therefore, we studied the effect of SUX on rat hepatocarcinogenesis to confirm our assumption that an agent which causes a prolonged decrease in PK activity in rat liver promotes hepatocarcinogenesis. For initiation rats were fed a diet containing 0.06% 3'-methyl-4-dimethylaminoazobenzene (3'-Me-DAB) for 4 weeks. At the end of 53 weeks of the experiment the incidences of liver tumors were 14.3 and 70.0% in the rats fed basal diet and in the rats fed 0.5% SUX diet, respectively, after the initiation. No tumors were observed in rats fed the SUX diet without the initiation. The result shows that SUX promotes hepatocarcinogenesis and supports the above assumption.

  5. RISM: Single-Modal Image Registration via Rank-Induced Similarity Measure.

    Science.gov (United States)

    Ghaffari, Aboozar; Fatemizadeh, Emad

    2015-12-01

    Similarity measure is an important block in image registration. Most traditional intensity-based similarity measures (e.g., sum-of-squared-difference, correlation coefficient, and mutual information) assume a stationary image and pixel-by-pixel independence. These similarity measures ignore the correlation between pixel intensities; hence, perfect image registration cannot be achieved, especially in the presence of spatially varying intensity distortions. Here, we assume that spatially varying intensity distortion (such as bias field) is a low-rank matrix. Based on this assumption, we formulate the image registration problem as a nonlinear and low-rank matrix decomposition (NLLRMD). Therefore, image registration and correction of spatially varying intensity distortion are simultaneously achieved. We illustrate the uniqueness of NLLRMD, and therefore, we propose the rank of difference image as a robust similarity in the presence of spatially varying intensity distortion. Finally, by incorporating the Gaussian noise, we introduce rank-induced similarity measure based on the singular values of the difference image. This measure produces clinically acceptable registration results on both simulated and real-world problems examined in this paper, and outperforms other state-of-the-art measures such as the residual complexity approach.

  6. Effect of prolyl hydroxylase domain 2 haplodeficiency on liver progenitor cell characteristics in early mouse hepatocarcinogenesis

    Science.gov (United States)

    Bogaerts, Eliene; Paridaens, Annelies; Verhelst, Xavier; Carmeliet, Peter; Geerts, Anja; Van Vlierberghe, Hans; Devisscher, Lindsey

    2016-01-01

    Activation of the hypoxia-inducible factor (HIF)-pathway in hepatocellular carcinoma (HCC) induces therapy resistant tumours, characterized by increased liver progenitor cell (LPCs) characteristics and poor prognosis. We previously reported corresponding results in mice with HCC in which hypoxia was mimicked by prolyl hydroxylase domain (PHD) inhibition. Here, we aimed at investigating whether induction of LPC characteristics occurs during the onset of hepatocarcinogenesis and if this is associated with activation of Notch signalling. Dietheylnitrosamine (DEN) was used to induce hepatic tumours in PHD2 haplodeficient (PHD2+/-) mice which were euthanized at 5, 10, 15 and 17 weeks following DEN during neoplastic transformation, before tumour formation. Neoplasia and mRNA expression of LPC and Notch markers were evaluated by histology and qPCR on isolated livers. PHD2 haplodeficiency resulted in enhanced expression of HIF target genes after 17 weeks of DEN compared to wild type (WT) littermates but had no effect on the onset of neoplastic transformation. The mRNA expression of Afp and Epcam was increased at all time points following DEN whereas CK19, Prom1 and Notch3 were increased after 17 weeks of DEN, without difference between PHD2+/- and WT mice. MDR1 mRNA expression was increased in all DEN treated mice compared to saline control with increased expression in PHD2+/- compared to WT from 15 weeks. These results indicate that the effects of PHD2 haplodeficiency on the expression of LPC and Notch markers manifest during tumour nodule formation and not early on during neoplastic transformation. PMID:28337100

  7. Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes

    DEFF Research Database (Denmark)

    Väremo, Leif; Henriksen, Tora Ida; Scheele, Camilla

    2017-01-01

    used to characterize the different myocytes. RESULTS: We found that the transcriptional program associated with obesity alone was strikingly similar to that induced specifically by T2D. We identified a candidate epigenetic mechanism, H3K27me3 histone methylation, mediating these transcriptional...... in sphingolipid metabolism was transcriptionally regulated. CONCLUSIONS: Our findings identify inherent characteristics in myocytes, as a memory of the in vivo phenotype, without the influence from a diabetic or obese extracellular environment, highlighting their importance in the development of T2D....

  8. Plant defenses against parasitic plants show similarities to those induced by herbivores and pathogens.

    Science.gov (United States)

    Runyon, Justin B; Mescher, Mark C; De Moraes, Consuelo M

    2010-08-01

    Herbivores and pathogens come quickly to mind when one thinks of the biotic challenges faced by plants. Important but less appreciated enemies are parasitic plants, which can have important consequences for the fitness and survival of their hosts. Our knowledge of plant perception, signaling, and response to herbivores and pathogens has expanded rapidly in recent years, but information is generally lacking for parasitic species. In a recent paper we reported that some of the same defense responses induced by herbivores and pathogens--notably increases in jasmonic acid (JA), salicylic acid (SA), and a hypersensitive-like response (HLR)--also occur in tomato plants upon attack by the parasitic plant Cuscuta pentagona (field dodder). Parasitism induced a distinct pattern of JA and SA accumulation, and growth trials using genetically-altered tomato hosts suggested that both JA and SA govern effective defenses against the parasite, though the extent of the response varied with host plant age. Here we discuss similarities between the induced responses we observed in response to Cuscuta parasitism to those previously described for herbivores and pathogens and present new data showing that trichomes should be added to the list of plant defenses that act against multiple enemies and across Kingdoms.

  9. Botanical and biological pesticides elicit a similar Induced Systemic Response in tomato (Solanum lycopersicum) secondary metabolism.

    Science.gov (United States)

    Pretali, Luca; Bernardo, Letizia; Butterfield, Timothy S; Trevisan, Marco; Lucini, Luigi

    2016-10-01

    Natural pesticides have attracted substantial interest due to the increase in organic agriculture and enhanced attention to environmental pollution. Plant Growth Promoting Bacteria (PGPB) are applied for both disease control and growth enhancement; PGPBs are known to elicit Induced Systemic Response (ISR) in plants. However, less is known about the effect of botanical pesticides, such as the azadirachtin-containing neem extracts, on plant metabolism. This study aimed to investigate the effects of foliar application of the above-mentioned natural pesticides on the metabolic profiling of tomato. Leaf application of Bacillus subtilis fostered Induced Systemic Resistance (ISR) in treated plants via the Jasmonic acid pathway, and enhanced production of secondary metabolites such as flavonoids, phytoalexins and auxins. Changes in sterols and terpenes, as well as an increase in glucosinolates were also observed. Interestingly, azadirachtin-treated tomatoes also showed an increase in ISR and our results revealed that most of the enriched metabolites are shared with a B. subtilis treatment, suggesting conserved biochemical responses. These (un)expected findings indicate that plants are not insensitive to application of natural pesticide and while Azadirachtin is applied as a direct pesticide, it also stimulates a defense response in tomatoes very similar to B. subtilis induced ISR. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Biodentine and mineral trioxide aggregate induce similar cellular responses in a fibroblast cell line.

    Science.gov (United States)

    Corral Nuñez, Camila M; Bosomworth, Helen J; Field, Claire; Whitworth, John M; Valentine, Ruth A

    2014-03-01

    The aim of this study was to assess the cell viability and messenger RNA expression of interleukin (IL)-1α and IL-6 in 3T3 fibroblast cells when in direct contact with Biodentine (Septodont, Saint Maur de Fossés, France) and mineral trioxide aggregate (MTA). Biodentine and MTA were coated onto coverslips and allowed to set. An uncoated coverslip and one coated with GC Fuji IX (GC Corporation, Tokyo, Japan) were used as controls. Coverslips were cultured with 3T3 fibroblast cells. Cell viability was assessed quantitatively using AlamarBlue dye (Serotec, Oxford, UK) after 3, 6, 24, and 72 hours. Morphologic cell changes of 3T3 cells in contact with BD and MTA were observed by scanning electron microscopy, and cytokine expression was assessed at the messenger RNA level by semiquantitative reverse-transcription polymerase chain reaction after 3 and 24 hours of direct contact with the materials. Cells in contact with Biodentine and MTA showed similar viability to untreated control cells at all time points, with the exception of 6 hours when viability was decreased with both treatments. Examination by scanning electron microscopy revealed cells adhering to most of the Biodentine surface after 24 hours. However, for MTA samples, significantly fewer cells were observed. The messenger RNA expression of IL-1α and IL-6 by cells in contact with Biodentine was similar to cells in contact with MTA. Biodentine and MTA showed similar cytotoxicity and induced a similar pattern of cytokine expression. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  11. Gene silencing of Nox4 by CpG island methylation during hepatocarcinogenesis in rats

    Directory of Open Access Journals (Sweden)

    Guadalupe S. López-Álvarez

    2017-01-01

    Full Text Available The association between the downregulation of genes and DNA methylation in their CpG islands has been extensively studied as a mechanism that favors carcinogenesis. The objective of this study was to analyze the methylation of a set of genes selected based on their microarray expression profiles during the process of hepatocarcinogenesis. Rats were euthanized at: 24 h, 7, 11, 16 and 30 days and 5, 9, 12 and 18 months post-treatment. We evaluated the methylation status in the CpG islands of four deregulated genes (Casp3, Cldn1, Pex11a and Nox4 using methylation-sensitive high-resolution melting technology for the samples obtained from different stages of hepatocarcinogenesis. We did not observe methylation in Casp3, Cldn1 or Pex11a. However, Nox4 exhibited altered methylation patterns, reaching a maximum of 10%, even during the early stages of hepatocarcinogenesis. We observed downregulation of mRNA and protein of Nox4 (97.5% and 40%, respectively after the first carcinogenic stimulus relative to the untreated samples. Our results suggest that Nox4 downregulation is associated with DNA methylation of the CpG island in its promoter. We propose that methylation is a mechanism that can silence the expression of Nox4, which could contribute to the acquisition of neoplastic characteristics during hepatocarcinogenesis in rats.

  12. Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes

    DEFF Research Database (Denmark)

    Väremo, Leif; Henriksen, Tora Ida; Scheele, Camilla

    2017-01-01

    BACKGROUND: Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to the disease alone. Therefore, here we set out to identify and characterize...... used to characterize the different myocytes. RESULTS: We found that the transcriptional program associated with obesity alone was strikingly similar to that induced specifically by T2D. We identified a candidate epigenetic mechanism, H3K27me3 histone methylation, mediating these transcriptional...... in sphingolipid metabolism was transcriptionally regulated. CONCLUSIONS: Our findings identify inherent characteristics in myocytes, as a memory of the in vivo phenotype, without the influence from a diabetic or obese extracellular environment, highlighting their importance in the development of T2D....

  13. Inhibition of Hepatocarcinogenesis by ArtinM via Anti-proliferative and Pro-apoptotic Mechanisms.

    Science.gov (United States)

    Braz, Mariana M; Roque-Barreira, Maria Cristina; Ramalho, Fernando S; Oliveira, Carlos A; Augusto, Marlei J; Ramalho, Leandra N Z

    ArtinM is a d-mannose-binding lectin found in the seeds of Artocarpus heterophyllus (jackfruit) that interacts with N-glycans, that is associated with receptors on the surface of phagocytic cells and induces the production of inflammatory mediators. Some of them are especially important because they may be required for antitumor immune response. This study aimed to evaluate the effect of ArtinM on hepatocellular preneoplastic foci. Wistar rats received 50 mg/kg of diethyl-nitrosamine (DEN) intraperitoneal weekly for 12 weeks. From the 14th week, the treated animals received 50 μg/kg of ArtinM subcutaneous every 2 weeks until the 18th week, whereas control animals were injected with vehicle alone. Preneoplastic-related factors were estimated using histological, western blotting and RT-PCR analysis. In comparison to the groups exposed to DEN, the ArtinM-treated rats showed diminution of preneoplastic foci, decreased expression of proliferating cell nuclear antigen (PCNA), increased number of nuclear p21 and p27 stained cells, augmented number of apoptotic cells, increased expression of p53, p42/44 MAPK and p21 proteins, reduced cyclin D1 (CCND1) protein levels and increased expression of TNFα and IFNγ genes. No difference was observed in interleukin 12 (IL12) protein levels. These findings indicate that ArtinM may provide protection against hepatocarcinogenesis as a result of the induction of cell-cycle blockage and pro-apoptotic mechanisms. Copyright © 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  14. Downregulation of TMEM70 in Rat Liver Cells After Hepatocarcinogen Treatment Related to the Warburg Effect in Hepatocarcinogenesis Producing GST-P-Expressing Proliferative Lesions.

    Science.gov (United States)

    Mizukami, Sayaka; Watanabe, Yousuke; Nakajima, Kota; Hasegawa-Baba, Yasuko; Jin, Meilan; Yoshida, Toshinori; Shibutani, Makoto

    2017-09-01

    We previously observed downregulation of mitochondrial oxidative phosphorylation-related protein, TMEM70, which is suggestive of disrupted cellular senescence, in GST-P-expressing (+) proliferative lesions from early hepatocarcinogenesis stages in rats. The present study investigated the immunohistochemical relationship between TMEM70 downregulation and cellular metabolic changes in carcinogenic processes, as well as the onset of the liver cell respiratory changes after repeated hepatocarcinogen treatment in rats. At the early hepatocarcinogenesis stage in a 2-stage model, GST-P+ preneoplastic lesions showing TMEM70 downregulation also downregulated the mitochondrial ATPase, ATPB, but upregulated glycolysis-related glucose transporter member 1 (GLUT1) and glucose-6-phosphate dehydrogenase, suggesting a metabolic shift from oxidative phosphorylation to glycolysis, known as the Warburg effect. Combined downregulation of TMEM70 and ATPB increased proliferation activity in GST-P+ preneoplastic lesions, suggesting cell proliferation facilitation by reducing mitochondrial respiration. Concurrent GLUT1-upregulation and TMEM70-downregulation increased nuclear phosphorylated c-MYC+ cells in GST-P+ preneoplastic lesions, suggesting c-MYC-mediated transcription facilitation to promote glycolysis and cell proliferation. The TMEM70-related metabolic shift was enhanced in GST-P+ neoplastic lesions, suggesting a contribution to tumor progression. Conversely, the TMEM70-related metabolic shift was lacking in peroxisome proliferator-activated receptor-α agonist-induced hepatocarcinogenesis, as well as in carcinogenic processes targeting other organs. Transcript expression analysis following 28- and 90-day repeated hepatocarcinogen treatment showed downregulation of Tmem70 from day 28 and upregulation of Pkm and Myc at day 90, suggesting early onset of a catastrophic cellular senescence-related metabolic shift beginning from depressed mitochondrial respiration in the liver. These

  15. Primary EBV infection induces an expression profile distinct from other viruses but similar to hemophagocytic syndromes.

    Directory of Open Access Journals (Sweden)

    Samantha K Dunmire

    Full Text Available Epstein-Barr Virus (EBV causes infectious mononucleosis and establishes lifelong infection associated with cancer and autoimmune disease. To better understand immunity to EBV, we performed a prospective study of natural infection in healthy humans. Transcriptome analysis defined a striking and reproducible expression profile during acute infection but no lasting gene changes were apparent during latent infection. Comparing the EBV response profile to multiple other acute viral infections, including influenza A (influenza, respiratory syncytial virus (RSV, human rhinovirus (HRV, attenuated yellow fever virus (YFV, and Dengue fever virus (DENV, revealed similarity only to DENV. The signature shared by EBV and DENV was also present in patients with hemophagocytic syndromes, suggesting these two viruses cause uncontrolled inflammatory responses. Interestingly, while EBV induced a strong type I interferon response, a subset of interferon induced genes, including MX1, HERC5, and OAS1, were not upregulated, suggesting a mechanism by which viral antagonism of immunity results in a profound inflammatory response. These data provide an important first description of the response to a natural herpesvirus infection in humans.

  16. Immunization of mice with LRP4 induces myasthenia similar to MuSK-associated myasthenia gravis.

    Science.gov (United States)

    Mori, Shuuichi; Motohashi, Norio; Takashima, Rumi; Kishi, Masahiko; Nishimune, Hiroshi; Shigemoto, Kazuhiro

    2017-11-01

    Since the first report of experimental animal models of myasthenia gravis (MG) with autoantibodies against low-density lipoprotein receptor-related protein 4 (LRP4), there have not been any major reports replicating the pathogenicity of anti-LRP4 antibodies (Abs). Recent clinical studies have cast doubt on the specificity and pathogenicity of anti-LRP4 antibodies for MG, highlighting the need for further research. In this study, we purified antigens corresponding to the extracellular region of human LRP4 stably expressed with chaperones in 293 cells and used these antigens to immunize female A/J mice. Immunization with LRP4 protein caused mice to develop myasthenia having similar electrophysiological and histological features as are observed in MG patients with circulating Abs against muscle-specific kinase (MuSK). Our results clearly demonstrate that active immunization of mice with LRP4 proteins causes myasthenia similar to the MG induced by anti-MuSK Abs. Further experimental and clinical studies are required to prove the pathogenicity of anti-LRP4 Abs in MG patients. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  17. Histogenesis of bile duct-like cells proliferating during ethionine hepatocarcinogenesis. Evidence for a biliary epithelial nature of oval cells.

    Science.gov (United States)

    Lenzi, R; Liu, M H; Tarsetti, F; Slott, P A; Alpini, G; Zhai, W R; Paronetto, F; Lenzen, R; Tavoloni, N

    1992-03-01

    The origin of bile duct-like cells (oval cells) proliferating during chemical hepatocarcinogenesis is highly controversial. To illuminate this issue, we induced oval cell proliferation by feeding rats a choline-devoid diet containing 0.1% ethionine (CDE), a hepatocarcinogenic diet, for up to 60 days. At various times we studied 1) oval cell morphology by light and electron microscopy, 2) the immunohistochemical expression of albumin and intermediate filament proteins by the various hepatic cells, 3) hepatic incorporation of [3H]thymidine by histoautoradiography, 4) the fractional area occupied by duct-like structures in liver cross sections, 5) the biliary tree volume in vivo to establish the possible continuity of the proliferated structures to the existing biliary lumina, and 6) spontaneous bile flow rate and the choleretic responsiveness to the hormone secretin, which stimulates ductular secretory activity. The results demonstrated the following: 1) oval cells resemble bile duct cells with respect to their histologic and ultrastructural appearance and their formation of duct-like structures; 2) as normal and hyperplastic bile duct cells induced by bile duct ligation, oval cells are positive for cytokeratins 7 and 19 (markers of glandular epithelia) and 8 and 18 (markers of simple epithelia) and are negative for vimentin and desmin, markers of mesenchymal and muscular differentiation, respectively; 3) in general, oval cells are negative for albumin, which is expressive of hepatocyte lineage, even though a few are positive for this protein, particularly those morphologically resembling small hepatocytes; 4) after initiation of the CDE diet, DNA synthesis begins in biliary epithelial cells; and 5) the degree of oval cell proliferation parallels the increase in biliary tree volume, spontaneous bile flow rate, and responsiveness to secretin choleresis, as in bile duct cell hyperplasia induced by biliary obstruction. Although the involvement of a periductular

  18. The Lymphocytes Stimulation Induced DNA Release, a Phenomenon Similar to NETosis.

    Science.gov (United States)

    Rocha Arrieta, Y C; Rojas, M; Vasquez, G; Lopez, J

    2017-10-01

    The release of DNA into the extracellular milieu by neutrophil during a process called NETosis has been postulated as an additional source of autoantigens; a process believed to be important in the pathogenesis of some autoimmune disease, such as systemic lupus erythematosus (SLE). However, it is not established if the B and T cells undergo the release of DNA to the extracellular milleu, in response to different stimuli. In this study, it was observed that the treatment of B and T cells with PMA, ionomycin and the serum from patients with SLE induced the extracellular DNA presence in B and T cells. These findings suggest that the phenomenon were similar to those observed in neutrophil's Etosis; B and T cells also released their DNA into the extracellular milieu. The findings express that serum from patients with SLE and SLEDAI ≤ 8 triggers the release of extracellular DNA in neutrophils, B and T cells, that suggested the presence of soluble factors in the serum that favoured this phenomenon. © 2017 The Foundation for the Scandinavian Journal of Immunology.

  19. Low-Grade Dysplastic Nodules Revealed as the Tipping Point during Multistep Hepatocarcinogenesis by Dynamic Network Biomarkers.

    Science.gov (United States)

    Lu, Lina; Jiang, Zhonglin; Dai, Yulin; Chen, Luonan

    2017-10-13

    Hepatocellular carcinoma (HCC) is a complex disease with a multi-step carcinogenic process from preneoplastic lesions, including cirrhosis, low-grade dysplastic nodules (LGDNs), and high-grade dysplastic nodules (HGDNs) to HCC. There is only an elemental understanding of its molecular pathogenesis, for which a key problem is to identify when and how the critical transition happens during the HCC initiation period at a molecular level. In this work, for the first time, we revealed that LGDNs is the tipping point (i.e., pre-HCC state rather than HCC state) of hepatocarcinogenesis based on a series of gene expression profiles by a new mathematical model termed dynamic network biomarkers (DNB)-a group of dominant genes or molecules for the transition. Different from the conventional biomarkers based on the differential expressions of the observed genes (or molecules) for diagnosing a disease state, the DNB model exploits collective fluctuations and correlations of the observed genes, thereby predicting the imminent disease state or diagnosing the critical state. Our results show that DNB composed of 59 genes signals the tipping point of HCC (i.e., LGDNs). On the other hand, there are a large number of differentially expressed genes between cirrhosis and HGDNs, which highlighted the stark differences or drastic changes before and after the tipping point or LGDNs, implying the 59 DNB members serving as the early-warning signals of the upcoming drastic deterioration for HCC. We further identified the biological pathways responsible for this transition, such as the type I interferon signaling pathway, Janus kinase-signal transducers and activators of transcription (JAK-STAT) signaling pathway, transforming growth factor (TGF)-β signaling pathway, retinoic acid-inducible gene I (RIG-I)-like receptor signaling pathway, cell adhesion molecules, and cell cycle. In particular, pathways related to immune system reactions and cell adhesion were downregulated, and pathways

  20. Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.

    Science.gov (United States)

    Väremo, Leif; Henriksen, Tora Ida; Scheele, Camilla; Broholm, Christa; Pedersen, Maria; Uhlén, Mathias; Pedersen, Bente Klarlund; Nielsen, Jens

    2017-05-25

    Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to the disease alone. Therefore, here we set out to identify and characterize intrinsic properties of myocytes, associated independently with T2D or obesity. We generated and analyzed RNA-seq data from primary differentiated myotubes from 24 human subjects, using a factorial design (healthy/T2D and non-obese/obese), to determine the influence of each specific factor on genome-wide transcription. This setup enabled us to identify intrinsic properties, originating from muscle precursor cells and retained in the corresponding myocytes. Bioinformatic and statistical methods, including differential expression analysis, gene-set analysis, and metabolic network analysis, were used to characterize the different myocytes. We found that the transcriptional program associated with obesity alone was strikingly similar to that induced specifically by T2D. We identified a candidate epigenetic mechanism, H3K27me3 histone methylation, mediating these transcriptional signatures. T2D and obesity were independently associated with dysregulated myogenesis, down-regulated muscle function, and up-regulation of inflammation and extracellular matrix components. Metabolic network analysis identified that in T2D but not obesity a specific metabolite subnetwork involved in sphingolipid metabolism was transcriptionally regulated. Our findings identify inherent characteristics in myocytes, as a memory of the in vivo phenotype, without the influence from a diabetic or obese extracellular environment, highlighting their importance in the development of T2D.

  1. Intermittent and continuous high-intensity exercise training induce similar acute but different chronic muscle adaptations.

    Science.gov (United States)

    Cochran, Andrew J R; Percival, Michael E; Tricarico, Steven; Little, Jonathan P; Cermak, Naomi; Gillen, Jenna B; Tarnopolsky, Mark A; Gibala, Martin J

    2014-05-01

    High-intensity interval training (HIIT) performed in an 'all-out' manner (e.g. repeated Wingate tests) is a time-efficient strategy to induce skeletal muscle remodelling towards a more oxidative phenotype. A fundamental question that remains unclear, however, is whether the intermittent or 'pulsed' nature of the stimulus is critical to the adaptive response. In study 1, we examined whether the activation of signalling cascades linked to mitochondrial biogenesis was dependent on the manner in which an acute high-intensity exercise stimulus was applied. Subjects performed either four 30 s Wingate tests interspersed with 4 min of rest (INT) or a bout of continuous exercise (CONT) that was matched for total work (67 ± 7 kJ) and which required ∼4 min to complete as fast as possible. Both protocols elicited similar increases in markers of adenosine monophosphate-activated protein kinase (AMPK) and p38 mitogen-activated protein kinase activation, as well as Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) mRNA expression (main effects for time, P ≤ 0.05). In study 2, we determined whether 6 weeks of the CONT protocol (3 days per week) would increase skeletal muscle mitochondrial content to a similar extent to what we have previously reported after 6 weeks of INT. Despite similar acute signalling responses to the CONT and INT protocols, training with CONT did not increase the maximal activity or protein content of a range of mitochondrial markers. However, peak oxygen uptake was higher after CONT training (from 45.7 ± 5.4 to 48.3 ± 6.5 ml kg(-1) min(-1); P < 0.05) and 250 kJ time trial performance was improved (from 26:32 ± 4:48 to 23:55 ± 4:16 min:s; P < 0.001) in our recreationally active participants. We conclude that the intermittent nature of the stimulus is important for maximizing skeletal muscle adaptations to low-volume, all-out HIIT. Despite the lack of skeletal muscle mitochondrial adaptations

  2. CAMK2γ Antagonizes mTORC1 Activation during Hepatocarcinogenesis

    OpenAIRE

    Meng, Zhipeng; Ma, Xiaoxiao; Du, Juan; Wang, Xiaoqiong; He, Min; Gu, Ying; Zhang, Jiawei; Han, Weidong; Fang, Zhipeng; Gan, Xiaoxian; Van Ness, Carl; Fu, Xianghui; Schones, Dustin E.; Xu, Rongzhen; Huang, Wendong

    2016-01-01

    Hepatocellular carcinoma (HCC) is one of the most deadly cancers that still lacks effective treatments. Dysregulation of kinase signaling has frequently been reported to contribute to HCC. In this study, we used bioinformatic approaches to identify kinases that regulate gene expression changes in human HCCs and two murine HCC models. We identified a role for calcium/calmodulin-dependent protein kinases II gamma isoform (CAMK2γ) in hepatocarcinogenesis. CAMK2γ −/− mice displayed severely enhan...

  3. How to Differentiate Borderline Hepatic Nodules in Hepatocarcinogenesis: Emphasis on Imaging Diagnosis.

    Science.gov (United States)

    Park, Hyun Jeong; Choi, Byung Ihn; Lee, Eun Sun; Park, Sung Bin; Lee, Jong Beum

    2017-06-01

    Rapid advances in liver imaging have improved the evaluation of hepatocarcinogenesis and early diagnosis and treatment of hepatocellular carcinoma (HCC). In this situation, detection of early-stage HCC in its development is important for the improvement of patient survival and optimal treatment strategies. Because early HCCs are considered precursors of progressed HCC, precise differentiation between a dysplastic nodule (DN), especially a high-grade DN, and early HCC is important. In clinical practice, these nodules are frequently called "borderline hepatic nodules." This article discusses radiological and pathological characteristics of these borderline hepatic nodules and offers an understanding of multistep hepatocarcinogenesis by focusing on the descriptions of the imaging changes in the progression of DN and early HCC. Detection and accurate diagnosis of borderline hepatic nodules are still a challenge with contrast enhanced ultrasonography, CT, and MRI with extracellular contrast agents. However, gadoxetic acid-enhanced MRI may be useful for improving the diagnosis of these borderline nodules. Since there is a net effect of incomplete neoangiogenesis and decreased portal venous flow in the early stage of hepatocarcinogenesis, borderline hepatic nodules commonly show iso- or hypovascularity. Therefore, precise differentiation of these nodules remains a challenging issue. In MRI using hepatobiliary contrast agents, signal intensity of HCCs on hepatobiliary phase (HBP) is regarded as a potential imaging biomarker. Borderline hepatic nodules are seen as nonhypervascular and hypointense nodules on the HBP, which is important for predicting tumor behavior and determining appropriate therapeutic strategies.

  4. RIP3 Inhibits Inflammatory Hepatocarcinogenesis but Promotes Cholestasis by Controlling Caspase-8- and JNK-Dependent Compensatory Cell Proliferation

    Directory of Open Access Journals (Sweden)

    Mihael Vucur

    2013-08-01

    Full Text Available For years, the term “apoptosis” was used synonymously with programmed cell death. However, it was recently discovered that receptor interacting protein 3 (RIP3-dependent “necroptosis” represents an alternative programmed cell death pathway activated in many inflamed tissues. Here, we show in a genetic model of chronic hepatic inflammation that activation of RIP3 limits immune responses and compensatory proliferation of liver parenchymal cells (LPC by inhibiting Caspase-8-dependent activation of Jun-(N-terminal kinase in LPC and nonparenchymal liver cells. In this way, RIP3 inhibits intrahepatic tumor growth and impedes the Caspase-8-dependent establishment of specific chromosomal aberrations that mediate resistance to tumor-necrosis-factor-induced apoptosis and underlie hepatocarcinogenesis. Moreover, RIP3 promotes the development of jaundice and cholestasis, because its activation suppresses compensatory proliferation of cholangiocytes and hepatic stem cells. These findings demonstrate a function of RIP3 in regulating carcinogenesis and cholestasis. Controlling RIP3 or Caspase-8 might represent a chemopreventive or therapeutic strategy against hepatocellular carcinoma and biliary disease.

  5. Similar cold stress induces sex-specific neuroendocrine and working memory responses.

    Science.gov (United States)

    Solianik, Rima; Skurvydas, Albertas; Urboniene, Daiva; Eimantas, Nerijus; Daniuseviciute, Laura; Brazaitis, Marius

    2015-01-01

    Men have higher cold-induced neuroendocrine response than women; nevertheless, it is not known whether a different stress hormone rise elicits different effects on cognition during whole body cooling. The objective was to compare the effect of cold-induced neuroendocrine responses on the performance of working memory sensitive tasks between men and women. The cold stress continued until rectal temperature reached 35.5 degree C or for a maximum of 170 min. Working memory performance and stress hormone concentrations were monitored. During cold stress, body temperature variables dropped in all subjects (P stress raised plasma epinephrine and serum cortisol levels only in men (P stress adversely affected memory performance in men but not in women (P stress in men and women induces sex-specific neuroendocrine and working memory responses.

  6. Ventilator-induced Lung Injury : Similarity and Differences between Children and Adults

    NARCIS (Netherlands)

    Kneyber, Martin C.J.; Zhang, Haibo; Slutsky, Arthur S.

    2014-01-01

    It is well established that mechanical ventilation can injure the lung, producing an entity known as ventilator-induced lung injury (VILI). There are various forms of VILI, including volutrauma (i.e., injury caused by overdistending the lung), atelectrauma (injury due to repeated opening/closing of

  7. Tactile Perception and Friction-Induced Vibrations: Discrimination of Similarly Patterned Wood-Like Surfaces.

    Science.gov (United States)

    Dacleu Ndengue, Jessica; Cesini, Ilaria; Faucheu, Jenny; Chatelet, Eric; Zahouani, Hassan; Delafosse, David; Massi, Francesco

    2017-01-01

    The tactile perception of a surface texture is mediated by factors such as material, topography, and vibrations induced by the sliding contact. In this paper, sensory characterizations are developed together with topographical and tribo-tactile characterizations to relate perceived features with objective measurements of tribological and dynamic signals. Two sets of surface samples are used in this study: the first set is made of a commercial floor covering tiles that aim at counter-typing natural wood flooring, with both a visual and a tactile texture mimicking wood. A second set is custom-made by replicating the first set using a plain purple polyurethane resin. The comparison between tribo-tactile signals and sensory analysis allowed the identification of objective indices for textures with slight topographical differences. Even though the topography of the replicated samples is the same as their corresponding commercial products, the fact that the material is different, induces differences in the contact and vibrational parameters. This in turn modifies the discrimination performances during the sensory experiment. Tactile characteristics collected during sensory procedures are found to be in agreement with objective indices such as friction coefficients and induced vibrations.

  8. Inflammasome priming is similar for francisella species that differentially induce inflammasome activation.

    Directory of Open Access Journals (Sweden)

    Mohammed G Ghonime

    Full Text Available Inflammasome activation is a two-step process where step one, priming, prepares the inflammasome for its subsequent activation, by step two. Classically step one can be induced by LPS priming followed by step two, high dose ATP. Furthermore, when IL-18 processing is used as the inflammasome readout, priming occurs before new protein synthesis. In this context, how intracellular pathogens such as Francisella activate the inflammasome is incompletely understood, particularly regarding the relative importance of priming versus activation steps. To better understand these events we compared Francisella strains that differ in virulence and ability to induce inflammasome activation for their relative effects on step one vs. step two. When using the rapid priming model, i.e., 30 min priming by live or heat killed Francisella strains (step 1, followed by ATP (step 2, we found no difference in IL-18 release, p20 caspase-1 release and ASC oligomerization between Francisella strains (F. novicida, F. holarctica -LVS and F. tularensis Schu S4. This priming is fast, independent of bacteria viability, internalization and phagosome escape, but requires TLR2-mediated ERK phosphorylation. In contrast to their efficient priming capacity, Francisella strains LVS and Schu S4 were impaired in inflammasome triggering compared to F. novicida. Thus, observed differences in inflammasome activation by F. novicida, LVS and Schu S4 depend not on differences in priming but rather on their propensity to trigger the primed inflammasome.

  9. Two genes with similarity to bacterial response regulators are rapidly and specifically induced by cytokinin in Arabidopsis

    Science.gov (United States)

    Brandstatter, I.; Kieber, J. J.; Evans, M. L. (Principal Investigator)

    1998-01-01

    Cytokinins are central regulators of plant growth and development, but little is known about their mode of action. By using differential display, we identified a gene, IBC6 (for induced by cytokinin), from etiolated Arabidopsis seedlings, that is induced rapidly by cytokinin. The steady state level of IBC6 mRNA was elevated within 10 min by the exogenous application of cytokinin, and this induction did not require de novo protein synthesis. IBC6 was not induced by other plant hormones or by light. A second Arabidopsis gene with a sequence highly similar to IBC6 was identified. This IBC7 gene also was induced by cytokinin, although with somewhat slower kinetics and to a lesser extent. The pattern of expression of the two genes was similar, with higher expression in leaves, rachises, and flowers and lower transcript levels in roots and siliques. Sequence analysis revealed that IBC6 and IBC7 are similar to the receiver domain of bacterial two-component response regulators. This homology, coupled with previously published work on the CKI1 histidine kinase homolog, suggests that these proteins may play a role in early cytokinin signaling.

  10. Ecto- and endoparasite induce similar chemical and brain neurogenomic responses in the honey bee (Apis mellifera)

    Science.gov (United States)

    2013-01-01

    Background Exclusion from a social group is an effective way to avoid parasite transmission. This type of social removal has also been proposed as a form of collective defense, or social immunity, in eusocial insect groups. If parasitic modification of host behavior is widespread in social insects, the underlying physiological and neuronal mechanisms remain to be investigated. We studied this phenomenon in honey bees parasitized by the mite Varroa destructor or microsporidia Nosema ceranae, which make bees leave the hive precociously. We characterized the chemical, behavioral and neurogenomic changes in parasitized bees, and compared the effects of both parasites. Results Analysis of cuticular hydrocarbon (CHC) profiles by gas chromatography coupled with mass spectrophotometry (GC-MS) showed changes in honey bees parasitized by either Nosema ceranae or Varroa destructor after 5 days of infestation. Levels of 10-HDA, an antiseptic important for social immunity, did not change in response to parasitism. Behavioral analysis of N. ceranae- or V. destructor- parasitized bees revealed no significant differences in their behavioral acts or social interactions with nestmates. Digital gene expression (DGE) analysis of parasitized honey bee brains demonstrated that, despite the difference in developmental stage at which the bee is parasitized, Nosema and Varroa-infested bees shared more gene changes with each other than with honey bee brain expression gene sets for forager or nurse castes. Conclusions Parasitism by Nosema or Varroa induces changes to both the CHC profiles on the surface of the bee and transcriptomic profiles in the brain, but within the social context of the hive, does not result in observable effects on her behavior or behavior towards her. While parasitized bees are reported to leave the hive as foragers, their brain transcription profiles suggest that their behavior is not driven by the same molecular pathways that induce foraging behavior. PMID:23866001

  11. Electroencephalogram Similarity Analysis Using Temporal and Spectral Dynamics Analysis for Propofol and Desflurane Induced Unconsciousness

    Directory of Open Access Journals (Sweden)

    Quan Liu

    2018-01-01

    Full Text Available Important information about the state dynamics of the brain during anesthesia is unraveled by Electroencephalogram (EEG approaches. Patterns that are observed through EEG related to neural circuit mechanism under different molecular targets dependent anesthetics have recently attracted much attention. Propofol, a Gamma-amino butyric acid, is known with evidently increasing alpha oscillation. Desflurane shares the same receptor action and should be similar to propofol. To explore their dynamics, EEG under routine surgery level anesthetic depth is analyzed using multitaper spectral method from two groups: propofol (n = 28 and desflurane (n = 23. The time-varying spectrum comparison was undertaken to characterize their properties. Results show that both of the agents are dominated by slow and alpha waves. Especially, for increased alpha band feature, propofol unconsciousness shows maximum power at about 10 Hz (mean ± SD; frequency: 10.2 ± 1.4 Hz; peak power, −14.0 ± 1.6 dB, while it is approximate about 8 Hz (mean ± SD; frequency: 8.3 ± 1.3 Hz; peak power, −13.8 ± 1.6 dB for desflurane with significantly lower frequency-resolved spectra for this band. In addition, the mean power of propofol is much higher from alpha to gamma band, including slow oscillation than that of desflurane. The patterns might give us an EEG biomarker for specific anesthetic. This study suggests that both of the anesthetics exhibit similar spectral dynamics, which could provide insight into some common neural circuit mechanism. However, differences between them also indicate their uniqueness where relevant.

  12. Early TBI-induced cytokine alterations are similarly detected by two distinct methods of multiplex assay.

    Directory of Open Access Journals (Sweden)

    Sanjib eMukherjee

    2011-09-01

    Full Text Available Annually, more than a million persons experience traumatic brain injury (TBI in the US and a substantial proportion of this population develop debilitating neurological disorders, such as, paralysis, cognitive deficits and epilepsy. Despite the long-standing knowledge of the risks associated with TBI, no effective biomarkers or interventions exist. Recent evidence suggests a role for inflammatory modulators in TBI-induced neurological impairments. Current technological advances allow for the simultaneous analysis of the precise spatial and temporal expression patterns of numerous proteins in single samples which ultimately can lead to the development of novel treatments. Thus, the present study examined 23 different cytokines, including chemokines, in the ipsi and contralateral cerebral cortex of rats at 24 hours after a Fluid Percussion Injury (FPI. Furthermore, the estimation of cytokines were performed in a newly developed multiplex assay instrument, MAGPIX (Luminex Corp and compared with an established instrument, Bio-Plex (Bio-Rad, in order to validate the newly developed instrument. The results show numerous inflammatory changes in the ipsi and contralateral side after FPI that were consistently reported by both technologies.

  13. Early Trichinella spiralis and Trichinella nativa infections induce similar gene expression profiles in rat jejunal mucosa.

    Science.gov (United States)

    Airas, Niina; Näreaho, Anu; Lindén, Jere; Valo, Erkka; Hautaniemi, Sampsa; Jokelainen, Pikka; Sukura, Antti

    2013-10-01

    Trichinella spiralis causes a significantly higher parasite burden in rat muscle than Trichinella nativa. To assess whether the difference in infectivity is due to the early intestinal response, we analyzed gene expression changes in the rat jejunum during Trichinella infection with a whole-genome microarray. The rats were euthanized on day five of infection, and their jejunal mucosa was sampled for microarray analysis. In addition, intestinal histology and hematology were examined. Against our expectations, the gene expression changes were similar in both T.nativa- and T. spiralis-infected groups. The two groups were hence pooled, and in the combined Trichinella-infected group, 551 genes were overexpressed and 427 underexpressed when compared to controls (false discovery rate ≤ 0.001 and fold change at least 2 in either direction). Pathway analysis identified seven pathways significantly associated with Trichinella infection (p Trichinella infection caused complex gene expression changes that indicate a host response to tissue damage in the mucosa of the jejunum, but the changes were not notably dependent on the studied species of Trichinella. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. RNA interference and dietary inhibitors induce a similar compensation response in Tribolium castaneum larvae.

    Science.gov (United States)

    Perkin, L C; Elpidina, E N; Oppert, B

    2017-02-01

    Tribolium castaneum is a major agriculture pest damaging stored grains and cereal products. The T. castaneum genome contains 26 cysteine peptidase genes, mostly cathepsins L and B, and seven have a major role in digestion. We targeted the expression of the most highly expressed cathepsin L gene on chromosome 10, TC011001, by RNA interference (RNAi), using double-stranded RNA (dsRNA) constructs of different regions of the gene (3', middle, 5' and entire coding regions). RNA sequencing and quantitation (RNA-seq) was used to evaluate knockdown and specificity amongst the treatments. Overall, target gene expression decreased in all treatment groups, but was more severe and specific in dsRNA targeting the 3' and entire coding regions, encoding the proteolytic active site in the enzyme. Additional cysteine cathepsin genes also were down-regulated (off-target effects), but some were up-regulated in response to RNAi treatment. Notably, some serine peptidase genes were increased in expression, especially in dsRNA targeting 5' and middle regions, and the response was similar to the effects of dietary cysteine protease inhibitors. We manually annotated these serine peptidase genes to gain insight into function and relevance to the RNAi study. The data indicate that T. castaneum larvae compensate for the loss of digestive peptidase activity in the larval gut, regardless of the mechanism of disruption. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

  15. Similarities between exercise-induced hypoalgesia and conditioned pain modulation in humans.

    Science.gov (United States)

    Vaegter, Henrik Bjarke; Handberg, Gitte; Graven-Nielsen, Thomas

    2014-01-01

    Pain inhibitory mechanisms are often assessed by paradigms of exercise-induced hypoalgesia (EIH) and conditioned pain modulation (CPM). In this study it was hypothesized that the spatial and temporal manifestations of EIH and CPM were comparable. The participants were 80 healthy subjects (40 females), between 18 and 65 years of age in this randomized, repeated-measures cross-over trial that involved data collection on 2 different days. CPM was assessed by 2 different cold pressor tests (hand and foot). EIH was assessed by 2 intensities of aerobic bicycling exercises and 2 intensities of isometric muscle contraction exercises (arm and leg). Pressure pain thresholds (PPTs) were recorded before, during, after, and 15 minutes after conditioning/exercise at sites local to and remote from the extremity used for cold pressor stimulation and exercise. PPTs increased at local as well as at remote sites during both cold pressor tests and after all of the exercise conditions except low-intensity bicycling. EIH after bicycling was higher in women than in men. CPM and the EIH responses after isometric exercises were comparable in men and women and were not affected by age. The EIH response was larger in the exercising body part compared with nonexercising body parts for all exercise conditions. High-intensity exercise produced greater EIH responses than did low-intensity exercise. The change in PPTs during cold pressor tests and the change in PPTs after exercises were not correlated. The CPM response was not dominated by local manifestations, and the effect was seen only during the stimulation, whereas exercise had larger local manifestations, and the effects were also found after exercise. Copyright © 2013 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

  16. Homogeneous generation of iDA neurons with high similarity to bona fide DA neurons using a drug inducible system.

    Science.gov (United States)

    Park, Hanseul; Kim, Hongwon; Yoo, Junsang; Lee, Jaekwang; Choi, Hwan; Baek, Soonbong; Lee, C Justin; Kim, Janghwan; Lengner, Christopher J; Sung, Jung-Suk; Kim, Jongpil

    2015-12-01

    Recent work generating induced dopaminergic (iDA) neurons using direct lineage reprogramming potentially provides a novel platform for the study and treatment Parkinson's disease (PD). However, one of the most important issues for iDA-based applications is the degree to which iDA neurons resemble the molecular and functional properties of their endogenous DA neuron counterparts. Here we report that the homogeneity of the reprogramming gene expression system is critical for the generation of iDA neuron cultures that are highly similar to endogenous DA neurons. We employed an inducible system that carries iDA-inducing factors as defined transgenes for direct lineage reprogramming to iDA neurons. This system circumvents the need for viral transduction, enabling a more efficient and reproducible reprogramming process for the generation of genetically homogenous iDA neurons. We showed that this inducible system generates iDA neurons with high similarity to their bona fide in vivo counterparts in comparison to direct infection methods. Thus, our results suggest that homogenous expression of exogenous genes in direct lineage reprogramming is critical for the generation of high quality iDA neuron cultures, making such culture systems a valuable resource for iDA-based drug screening and, ultimately, potential therapeutic intervention in PD. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Redox proteomics screening cellular factors associated with oxidative stress in hepatocarcinogenesis.

    Science.gov (United States)

    Zhou, Li; Wen, Ji; Huang, Zhao; Nice, Edouard C; Huang, Canhua; Zhang, Haiyuan; Li, Qifu

    2017-03-01

    Liver cancer is a major global health problem being the sixth most common cancer and the third cause of cancer-related death, with hepatocellular carcinoma (HCC) representing more than 90% of primary liver cancers. Mounting evidence suggests that, compared with their normal counterparts, many types of cancer cell have increased levels of ROS. Therefore, cancer cells need to combat high levels of ROS, especially at early stages of tumor development. Recent studies have revealed that ROS-mediated regulation of redox-sensitive proteins (redox sensors) is involved in the pathogenesis and/or progression of many human diseases, including cancer. Unraveling the altered functions of redox sensors and the underlying mechanisms in hepatocarcinogenesis is critical for the development of novel cancer therapeutics. For this reason, redox proteomics has been developed for the high-throughput screening of redox sensors, which will benefit the development of novel therapeutic strategies for the treatment of HCC. In this review, we will briefly introduce several novel redox proteomics techniques that are currently available to study various oxidative modifications in hepatocarcinogenesis and summarize the most important discoveries in the study of redox processes related to the development and progression of HCC. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Unfolding stabilities of two structurally similar proteins as probed by temperature-induced and force-induced molecular dynamics simulations.

    Science.gov (United States)

    Gorai, Biswajit; Prabhavadhni, Arasu; Sivaraman, Thirunavukkarasu

    2015-09-01

    Unfolding stabilities of two homologous proteins, cardiotoxin III and short-neurotoxin (SNTX) belonging to three-finger toxin (TFT) superfamily, have been probed by means of molecular dynamics (MD) simulations. Combined analysis of data obtained from steered MD and all-atom MD simulations at various temperatures in near physiological conditions on the proteins suggested that overall structural stabilities of the two proteins were different from each other and the MD results are consistent with experimental data of the proteins reported in the literature. Rationalization for the differential structural stabilities of the structurally similar proteins has been chiefly attributed to the differences in the structural contacts between C- and N-termini regions in their three-dimensional structures, and the findings endorse the 'CN network' hypothesis proposed to qualitatively analyse the thermodynamic stabilities of proteins belonging to TFT superfamily of snake venoms. Moreover, the 'CN network' hypothesis has been revisited and the present study suggested that 'CN network' should be accounted in terms of 'structural contacts' and 'structural strengths' in order to precisely describe order of structural stabilities of TFTs.

  19. Intermittent whole-body cold immersion induces similar thermal stress but different motor and cognitive responses between males and females.

    Science.gov (United States)

    Solianik, Rima; Skurvydas, Albertas; Mickevičienė, Dalia; Brazaitis, Marius

    2014-10-01

    The main aim of this study was to compare the thermal responses and the responses of cognitive and motor functions to intermittent cold stress between males and females. The intermittent cold stress continued until rectal temperature (TRE) reached 35.5°C or for a maximum of 170 min. Thermal response and motor and cognitive performance were monitored. During intermittent cold stress, body temperature variables decreased in all subjects (P differ between sexes. The presence of fast and slow cooling types for participants with similar effect on physiological variables were observed; thus the different rate coolers were grouped together and were attributed only sex specific responses. Overall, TRE cooling rate and cold strain index did not differ between sexes. Maximal voluntary contraction (MVC) decreased after intermittent cold exposure only in males (P differ between sexes. The effects of intermittent cold stress on electrically evoked muscle properties, spinal (H-reflex), and supraspinal (V-waves) reflexes did not differ between sexes. Intermittent cold-induced cognitive perturbation of attention and memory task performance was greater in males (P males and females experience similar thermal stress induced by intermittent whole-body cold immersion. Although no sex-specific differences were observed in muscle EMG activity, involuntary muscle properties, spinal and supraspinal reflexes, some of the sex differences observed (e.g., lower isometric MVC and greater cognitive perturbation in males) support the view of sex-specific physiological responses to core temperature decrease. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Deep brain stimulation in rats: different targets induce similar antidepressant-like effects but influence different circuits.

    Science.gov (United States)

    Hamani, Clement; Amorim, Beatriz O; Wheeler, Anne L; Diwan, Mustansir; Driesslein, Klaus; Covolan, Luciene; Butson, Christopher R; Nobrega, José N

    2014-11-01

    Recent studies in patients with treatment-resistant depression have shown similar results with the use of deep brain stimulation (DBS) in the subcallosal cingulate gyrus (SCG), ventral capsule/ventral striatum (VC/VS) and nucleus accumbens (Acb). As these brain regions are interconnected, one hypothesis is that by stimulating these targets one would just be influencing different relays in the same circuitry. We investigate behavioral, immediate early gene expression, and functional connectivity changes in rats given DBS in homologous regions, namely the ventromedial prefrontal cortex (vmPFC), white matter fibers of the frontal region (WMF) and nucleus accumbens. We found that DBS delivered to the vmPFC, Acb but not WMF induced significant antidepressant-like effects in the FST (31%, 44%, and 17% reduction in immobility compared to controls). Despite these findings, stimulation applied to these three targets induced distinct patterns of regional activity and functional connectivity. While animals given vmPFC DBS had increased cortical zif268 expression, changes after Acb stimulation were primarily observed in subcortical structures. In animals receiving WMF DBS, both cortical and subcortical structures at a distance from the target were influenced by stimulation. In regard to functional connectivity, DBS in all targets decreased intercorrelations among cortical areas. This is in contrast to the clear differences observed in subcortical connectivity, which was reduced after vmPFC DBS but increased in rats receiving Acb or WMF stimulation. In conclusion, results from our study suggest that, despite similar antidepressant-like effects, stimulation of the vmPFC, WMF and Acb induces distinct changes in regional brain activity and functional connectivity. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Lycopene and tomato powder supplementation similarly inhibit high-fat diet induced obesity, inflammatory response, and associated metabolic disorders.

    Science.gov (United States)

    Fenni, Soumia; Hammou, Habib; Astier, Julien; Bonnet, Lauriane; Karkeni, Esma; Couturier, Charlène; Tourniaire, Franck; Landrier, Jean-François

    2017-09-01

    Several studies have linked the high intake of lycopene or tomatoes products with lower risk for metabolic diseases. The aim of the present study was to evaluate and to compare the effect of lycopene and tomato powder on obesity-associated disorders. Male C57BL/J6 mice were assigned into four groups to receive: control diet (CD), high fat diet (HFD), high fat diet supplemented with lycopene or with tomato powder (TP) for 12 weeks. In HFD condition, lycopene and TP supplementation significantly reduced adiposity index, organ, and relative organ weights, serum triglycerides, free fatty acids, 8-iso-prostaglandin GF2α and improved glucose homeostasis, but did not affect total body weight. Lycopene and TP supplementation prevented HFD-induced hepatosteatosis and hypertrophy of adipocytes. Lycopene and TP decreased HFD-induced proinflammatory cytokine mRNA expression in the liver and in the epididymal adipose tissue. The anti-inflammatory effect of lycopene and TP was related to a reduction in the phosphorylation levels of IκB, and p65, and resulted in a decrease of inflammatory proteins in adipose tissue. These results suggest that lycopene or TP supplementation display similar beneficial health effects that could be particularly relevant in the context of nutritional approaches to fight obesity-associated pathologies. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Additive-induced aggregate changes of two structurally similar dyes in aqueous solutions: A comparative photophysical study

    Science.gov (United States)

    Ghanadzadeh Gilani, A.; Poormohammadi-Ahandani, Z.; Kian, R.

    2018-01-01

    Absorption and emission spectral characteristics of the two structurally similar phenothiazine dyes, azure B and toluidine blue, in aqueous solutions of the two sets of molecular additives (ureas and monosaccharides) were studied as a function of the dye and additive concentrations. The absorption spectra of the dyes were also studied in pure tetramethylurea with an aprotic nature. The spectral data were analyzed using DECOM Program. The dimer structure of the interacting molecules in these dyes was discussed using the exciton model. The urea class of additives was found to act as water structure-breakers over the range of studied concentration. The carbohydrate additives were found to act as water structure-breakers at low concentrations. However, the water structure breaking process may be disfavored by the additive-additive interactions at higher concentrations. It can be concluded that at low additive concentrations, the main driving force for breaking the dye association is water-additive interaction, which disrupts the water hydrogen bonds induced by the additives. However, at the high additive concentrations, the different phenomena including additive-additive and additive-dye interactions can change the structure, strength, and aggregative properties of the dyes. Finally, the urea in water induces noticeably fluorescence quenching in emission spectra of both the dyes.

  3. Hepatitis, rash and eosinophilia following trichloroethylene exposure: a case report and speculation on mechanistic similarity to halothane induced hepatitis.

    Science.gov (United States)

    Bond, G R

    1996-01-01

    A previously healthy 30-year-old male began work as a degreaser. The solvent used in the degreasing operation was trichloroethylene. Over the next month he experienced symptoms of weakness, dizziness, decreased appetite, nausea, abdominal pain, diarrhea, fever, chills, dry skin, red rash with bumps, peeling face, and itching. At that time he had marked liver enzyme elevation without evidence of cholestasis. CBC was remarkable for a significant number of atypical lymphocytes. Two weeks later his liver enzymes showed a marked reduction in ALT from a peak of 1250 IU to 717 IU. Tests for Hepatitis A, B, and C, CMV, HIV1 were all negative. The night following his first day back at work he had a recurrence of a red, diffuse rash without any consumption of alcohol. The rash caused tremendous itching. Over the next few days off work the rash continued and peeled. Physical examination one week after re-exposure was remarkable for diffuse, erythematous rash; some peeling skin and pitting edema to the knees. ALT was 517 IU/L. White blood cell count was 10,100/mm3 with 27% eosinophilia. This patient had possibly experienced sensitization to trichloroethylene, or more likely, to one of its metabolites. Similar symptoms attributed to trichloroethylene have been reported in only a few other patients. Patch testing with trichloroethylene and its metabolites may better clarify a causal relationship in future patients. If an immune mechanism is involved it may be similar to one postulated for halothane induced hepatitis.

  4. Global transcriptional profiles of beating clusters derived from human induced pluripotent stem cells and embryonic stem cells are highly similar

    Directory of Open Access Journals (Sweden)

    Gupta Manoj K

    2010-09-01

    Full Text Available Abstract Background Functional and molecular integrity of cardiomyocytes (CMs derived from induced pluripotent stem (iPS cells is essential for their use in tissue repair, disease modelling and drug screening. In this study we compared global transcriptomes of beating clusters (BCs microdissected from differentiating human iPS cells and embryonic stem (ES cells. Results Hierarchical clustering and principal component analysis revealed that iPS-BCs and ES-BCs cluster together, are similarly enriched for cardiospecific genes and differ in expression of only 1.9% of present transcripts. Similarly, sarcomeric organization, electrophysiological properties and calcium handling of iPS-CMs were indistinguishable from those of ES-CMs. Gene ontology analysis revealed that among 204 genes that were upregulated in iPS-BCs vs ES-BCs the processes related to extracellular matrix, cell adhesion and tissue development were overrepresented. Interestingly, 47 of 106 genes that were upregulated in undifferentiated iPS vs ES cells remained enriched in iPS-BCs vs ES-BCs. Most of these genes were found to be highly expressed in fibroblasts used for reprogramming and 34% overlapped with the recently reported iPS cell-enriched genes. Conclusions These data suggest that iPS-BCs are transcriptionally highly similar to ES-BCs. However, iPS-BCs appear to share some somatic cell signature with undifferentiated iPS cells. Thus, iPS-BCs may not be perfectly identical to ES-BCs. These minor differences in the expression profiles may occur due to differential cellular composition of iPS-BCs and ES-BCs, due to retention of some genetic profile of somatic cells in differentiated iPS cell-derivatives, or both.

  5. Cross-taxa similarities in affect-induced changes of vocal behavior and voice in arboreal monkeys.

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    Alban Lemasson

    Full Text Available Measuring the affective state of an individual across species with comparable non-invasive methods is a current challenge in animal communication research. This study aims to explore to which extent affect intensity is conveyed in the vocal behaviours of three nonhuman primate species (Campbell's monkeys, De Brazza's monkeys, red-capped mangabeys, which vary in body size, ecological niche and social system. Similarly in the three species, we experimentally induced a change in captive social groups' affect by locking all group members together in their outside enclosure. The two experimental conditions which varied in affect intensity consisted in imposing a pre-reunion 90 mn-separation by splitting up the respective group into two subgroups (High affect condition or not (Low affect condition. We measured call rates as well as voice features at the time of reunion in both conditions. The three studied species reacted in a very similar way. Across species, call rates changed significantly between the behaviourally defined states. Furthermore, contact call duration and, to some extent, voice pitch increased. Our results suggest, for the first time in arboreal Old World monkeys, that affect intensity is conveyed reliably in vocal behaviour and specific acoustic characteristics of voice, irrespective of body size and ecological niche differences between species. Cross-taxa similarities in acoustic cues of affect intensity point to phylogenetic constraints and inheritance from a common ancestor, whereas variations in vocal behaviour and affect intensity-related acoustic cues between species may be an adaptation to specific social requirements and depend on social systems. Our findings as well as a comparison with published works on acoustic communication in other vertebrate groups support the hypothesis that affect intensity in human voice originates from precursors already found deep inside the vertebrate phylogeny.

  6. Nitrosative stress and apoptosis in non-anemic healthy rats induced by intravenous iron sucrose similars versus iron sucrose originator.

    Science.gov (United States)

    Toblli, Jorge E; Cao, Gabriel; Angerosa, Margarita

    2015-04-01

    Iron can both induce and inhibit nitrosative stress. Intracellular iron levels play an important role in nitric oxide (NO(•)) signaling mechanisms. Depending on various factors, such as the cell's redox state and transition metal levels, NO(•) generation may lead to lipid peroxidation and DNA damage as well as both anti- and pro-apoptotic effects. Administration of intravenous iron sucrose originator (IS(ORIG)) has been shown not to cause significant tyrosine nitration or significantly increased caspase 3 levels in non-anemic rats. In this study, the potential of several marketed iron sucrose similars (ISSs) to induce tyrosine nitration and caspase 3 expression in non-anemic rats was assessed. Although the physico-chemical properties of most of the analyzed ISSs complied with the United States Pharmacopeia for iron sucrose injection, all ISSs resulted in higher levels of tyrosine nitration and increased the expression of caspase 3 versus IS(ORIG). Moreover, significant differences were detected in tissue iron distribution between IS(ORIG)- and ISS-treated animals. In general, ISORIG resulted in higher levels of ferritin deposits versus ISSs whereas ISSs showed higher Prussian blue-stainable iron(III) deposits than IS(ORIG). This result suggests that some iron from ISSs bypassed the tightly regulated pathway through resident macrophages of the liver, spleen and bone marrow thus, ending up in the cellular compartment that favors oxidative and or nitrosative stress as well as apoptosis. The results also confirm that polynuclear iron(III)-oxyhydroxide carbohydrates, such as iron sucrose, cannot be fully characterized by physico-chemical methods alone.

  7. Genome-Wide Expression of MicroRNAs Is Regulated by DNA Methylation in Hepatocarcinogenesis

    Directory of Open Access Journals (Sweden)

    Jing Shen

    2015-01-01

    Full Text Available Background. Previous studies, including ours, have examined the regulation of microRNAs (miRNAs by DNA methylation, but whether this regulation occurs at a genome-wide level in hepatocellular carcinoma (HCC is unclear. Subjects/Methods. Using a two-phase study design, we conducted genome-wide screening for DNA methylation and miRNA expression to explore the potential role of methylation alterations in miRNAs regulation. Results. We found that expressions of 25 miRNAs were statistically significantly different between tumor and nontumor tissues and perfectly differentiated HCC tumor from nontumor. Six miRNAs were overexpressed, and 19 were repressed in tumors. Among 133 miRNAs with inverse correlations between methylation and expression, 8 miRNAs (6% showed statistically significant differences in expression between tumor and nontumor tissues. Six miRNAs were validated in 56 additional paired HCC tissues, and significant inverse correlations were observed for miR-125b and miR-199a, which is consistent with the inactive chromatin pattern found in HepG2 cells. Conclusion. These data suggest that the expressions of miR-125b and miR-199a are dramatically regulated by DNA hypermethylation that plays a key role in hepatocarcinogenesis.

  8. Diagnosis and management of amiodarone-induced thyrotoxicosis: similarities and differences between North American and European thyroidologists

    NARCIS (Netherlands)

    Tanda, Maria Laura; Piantanida, Eliana; Lai, Adriana; Liparulo, Luigi; Sassi, Lorenza; Bogazzi, Fausto; Wiersinga, Wilmar M.; Braverman, Lewis E.; Martino, Enio; Bartalena, Luigi

    2008-01-01

    OBJECTIVE: To investigate how North American thyroidologists assess and treat amiodarone-induced thyrotoxicosis (AIT) and to compare the results with those of the same questionnaire-based survey previously carried out among European thyroidologists. DESIGN: Members of the American Thyroid

  9. Ceramide-enriched LDL induces cytokine release through TLR4 and CD14 in monocytes. Similarities with electronegative LDL.

    Science.gov (United States)

    Estruch, Montserrat; Sánchez-Quesada, Jose Luis; Ordóñez-Llanos, Jordi; Benítez, Sonia

    2014-01-01

    In vitro ceramide-enriched LDL (CER-LDL) reproduces most of the properties of electronegative LDL (LDL(-)), a heterogeneous subfraction of LDL found in plasma. LDL(-) comprises several modifications of LDL and has an increased content in ceramide (CER). It promotes cytokine release in monocytes through CD14 and TLR4. CER-LDL also induces cytokine release in these cells but the mechanism is unknown. To evaluate TLR4 and CD14 as the putative receptors involved in cytokine release induced by CER-LDL. CER-LDL was obtained by incubating native LDL with CER-enriched liposomes. CER content in CER-LDL was assessed by thin layer chromatography of lipid extracts. CER-LDL and LDL(-) were incubated for 20 h with human monocytes in the presence or absence of a TLR4 signaling inhibitor. Both LDLs were also incubated with two human monocytic cell lines, normal and THP1 overexpressing CD14 (THP1-CD14) cells. The release of IL-6, IL-10 and MCP-1 was evaluated by ELISA in culture medium. The release of IL-6, IL-10 and MCP-1 induced by CER-LDL in monocytes was inhibited by VIPER (90% inhibition), a specific TLR4 inhibitor. The cytokine release induced by CER-LDL was negligible in THP1, cells presenting a very low CD14 expression. In contrast, the induction of cytokine release in THP1-CD14 was high and dependent on the CER content in LDL. CER-LDL induces IL-6, IL-10 and MCP-1 release through the activation of CD14 and TLR4 in monocytes, reproducing the behavior of LDL(-). The increased content of CER in LDL(-) is then related to the inflammatory action of LDL(-). Copyright © 2013 Sociedad Española de Arteriosclerosis. Published by Elsevier España. All rights reserved.

  10. The uptake transporter OATP8 expression decreases during multistep hepatocarcinogenesis: correlation with gadoxetic acid enhanced MR imaging

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    Kitao, Azusa; Matsui, Osamu; Yoneda, Norihide; Kozaka, Kazuto; Shinmura, Rieko; Koda, Wataru; Kobayashi, Satoshi; Gabata, Toshifumi [Kanazawa University Graduate School of Medical Science, Department of Radiology, Kanazawa (Japan); Zen, Yoh [Kanazawa University Graduate School of Medical Science, Human Pathology, Kanazawa (Japan); King' s College Hospital, Institute of Liver Studies, London (United Kingdom); Yamashita, Tatsuya; Kaneko, Shuichi [Kanazawa University Graduate School of Medical Science, Gastroenterology, Kanazawa (Japan); Nakanuma, Yasuni [Kanazawa University Graduate School of Medical Science, Human Pathology, Kanazawa (Japan)

    2011-10-15

    To clarify the changes in organic anion-transporting polypeptide 8 (OATP8) expression and enhancement ratio on gadoxetic acid-enhanced MR imaging in hepatocellular nodules during multistep hepatocarcinogenesis. In imaging analysis, we focused on 71 surgically resected hepatocellular carcinomas (well, moderately and poorly differentiated HCCs) and 1 dysplastic nodule (DN). We examined the enhancement ratio in the hepatobiliary phase of gadoxetic acid enhanced MR imaging [(1/postcontrast T1 value-1/precontrast T1 value)/(1/precontrast T1 value)], then analysed the correlation among the enhancement ratio, tumour differentiation grade and intensity of immunohistochemical OATP8 expression. In pathological analysis, we focused on surgically resected 190 hepatocellular nodules: low-grade DNs, high-grade DNs, early HCCs, well-differentiated, moderately differentiated and poorly differentiated HCCs, including cases without gadoxetic acid-enhanced MR imaging. We evaluated the correlation between the immunohistochemical OATP8 expression and the tumour differentiation grade. The enhancement ratio of HCCs decreased in accordance with the decline in tumour differentiation (P < 0.0001, R = 0.28) and with the decline of OATP8 expression (P < 0.0001, R = 0.81). The immunohistochemical OATP8 expression decreased from low-grade DNs to poorly differentiated HCCs (P < 0.0001, R = 0.15). The immunohistochemical expression of OATP8 significantly decreases during multistep hepatocarcinogenesis, which may explain the decrease in enhancement ratio on gadoxetic acid-enhanced MR imaging. (orig.)

  11. General relativistic self-similar waves that induce an anomalous acceleration into the standard model of cosmology

    CERN Document Server

    Smoller, Joel

    2012-01-01

    We prove that the Einstein equations in Standard Schwarzschild Coordinates close to form a system of three ordinary differential equations for a family of spherically symmetric, self-similar expansion waves, and the critical ($k=0$) Friedmann universe associated with the pure radiation phase of the Standard Model of Cosmology (FRW), is embedded as a single point in this family. Removing a scaling law and imposing regularity at the center, we prove that the family reduces to an implicitly defined one parameter family of distinct spacetimes determined by the value of a new {\\it acceleration parameter} $a$, such that $a=1$ corresponds to FRW. We prove that all self-similar spacetimes in the family are distinct from the non-critical $k\

  12. Yes-associated protein/TEA domain family member and hepatocyte nuclear factor 4-alpha (HNF4α) repress reciprocally to regulate hepatocarcinogenesis in rats and mice.

    Science.gov (United States)

    Cai, Wang-Yu; Lin, Ling-Yun; Hao, Han; Zhang, Sai-Man; Ma, Fei; Hong, Xin-Xin; Zhang, Hui; Liu, Qing-Feng; Ye, Guo-Dong; Sun, Guang-Bin; Liu, Yun-Jia; Li, Sheng-Nan; Xie, Yuan-Yuan; Cai, Jian-Chun; Li, Bo-An

    2017-04-01

    Great progress has been achieved in the study of Hippo signaling in regulating tumorigenesis; however, the downstream molecular events that mediate this process have not been completely defined. Moreover, regulation of Hippo signaling during tumorigenesis in hepatocellular carcinoma (HCC) remains largely unknown. In the present study, we systematically investigated the relationship between Yes-associated protein/TEA domain family member (YAP-TEAD) and hepatocyte nuclear factor 4-alpha (HNF4α) in the hepatocarcinogenesis of HCC cells. Our results indicated that HNF4α expression was negatively regulated by YAP1 in HCC cells by a ubiquitin proteasome pathway. By contrast, HNF4α was found to directly associate with TEAD4 to compete with YAP1 for binding to TEAD4, thus inhibiting the transcriptional activity of YAP-TEAD and expression of their target genes. Moreover, overexpression of HNF4α was found to significantly compromise YAP-TEAD-induced HCC cell proliferation and stem cell expansion. Finally, we documented the regulatory mechanism between YAP-TEAD and HNF4α in rat and mouse tumor models, which confirmed our in vitro results. There is a double-negative feedback mechanism that controls TEAD-YAP and HNF4α expression in vitro and in vivo, thereby regulating cellular proliferation and differentiation. Given that YAP acts as a dominant oncogene in HCC and plays a crucial role in stem cell homeostasis and tissue regeneration, manipulating the interaction between YAP, TEADs, and HNF4α may provide a new approach for HCC treatment and regenerative medicine. (Hepatology 2017;65:1206-1221). © 2016 by the American Association for the Study of Liver Diseases.

  13. Low Glucose Concentrations Induce a Similar Inflammatory Response in Monocytes from Type 2 Diabetic Patients and Healthy Subjects

    Directory of Open Access Journals (Sweden)

    Francesco Piarulli

    2017-01-01

    Full Text Available This study aims to assess the proinflammatory interleukin 1β (IL-1β and anti-inflammatory IL-10 production by monocytes from 38 patients with type 2 diabetes and 31 controls in different glucose concentrations. Monocytes were incubated in low (2.5 mmol/L-, normal (5.0 mmol/L-, and high (20 mmol/L-glucose conditions in the presence and absence of lipopolysaccharide (LPS. Monocytes from both patients and controls only produced a significant increase in IL-1β in low-glucose conditions (p<0.01, and this phenomenon was amplified in the presence of LPS, while it was not seen in normal- or high-glucose conditions, not even in the presence of LPS stimulation. There was no increase in IL-10 production by monocytes from either diabetic patients or controls using whatever glucose concentrations, except when treated with LPS in normal-glucose conditions. These findings seem to suggest that low-glucose conditions induce an inflammatory response in monocytes in all individuals, as an intrinsic capacity of this cell line. On the other hand, monocytes only retain their anti-inflammatory ability in response to known inflammatory stimuli such as LPS, under normal-glucose concentrations. In conclusion, human monocytes express an inflammatory pattern in low-glucose conditions in vitro. This response could contribute to explaining the higher cardiovascular risk induced by hypoglycemia in diabetic patients.

  14. Low- and high-volume strength training induces similar neuromuscular improvements in muscle quality in elderly women.

    Science.gov (United States)

    Radaelli, Regis; Botton, Cíntia E; Wilhelm, Eurico N; Bottaro, Martim; Lacerda, Fabiano; Gaya, Anelise; Moraes, Kelly; Peruzzolo, Amanda; Brown, Lee E; Pinto, Ronei Silveira

    2013-08-01

    The aim of this study was to compare the effects of low- and high-volume strength training on strength, muscle activation and muscle thickness (MT) of the lower- and upper-body, and on muscle quality (MQ) of the lower-body in older women. Twenty apparently healthy elderly women were randomly assigned into two groups: low-volume (LV, n=11) and high-volume (HV, n=9). The LV group performed one-set of each exercise, while the HV group performed three-sets of each exercise, twice weekly for 13 weeks. MQ was measured by echo intensity obtained by ultrasonography (MQEI), strength per unit of muscle mass (MQST), and strength per unit of muscle mass adjusted with an allometric scale (MQAS). Following training, there was a significant increase (p≤0.001) in knee extension 1-RM (31.8±20.5% for LV and 38.3±7.3% for HV) and in elbow flexion 1-RM (25.1±9.5% for LV and 26.6±8.9% for HV) and in isometric maximal strength of the lower-body (p≤0.05) and upper-body (p≤0.001), with no difference between groups. The maximal electromyographic activation for both groups increased significantly (p≤0.05) in the vastus medialis and biceps brachii, with no difference between groups. All MT measurements of the lower- and upper-body increased similarly in both groups (p≤0.001). Similar improvements were also observed in MQEI (p≤0.01), MQST, and MQAS (p≤0.001) for both groups. These results demonstrate that low- and high-volume strength training promote similar increases in neuromuscular adaptations of the lower- and upper-body, and in MQ of the lower-body in elderly women. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Ketamine-induced apoptosis in the mouse cerebral cortex follows similar characteristic of physiological apoptosis and can be regulated by neuronal activity.

    Science.gov (United States)

    Wang, Qi; Shen, Feng-Yan; Zou, Rong; Zheng, Jing-Jing; Yu, Xiang; Wang, Ying-Wei

    2017-06-17

    The effects of general anesthetics on inducing neuronal apoptosis during early brain development are well-documented. However, since physiological apoptosis also occurs during this developmental window, it is important to determine whether anesthesia-induced apoptosis targets the same cell population as physiological apoptosis or different cell types altogether. To provide an adequate plane of surgery, ketamine was co-administered with dexmedetomidine. The apoptotic neurons in the mouse primary somatosensory cortex (S1) were quantitated by immunohistochemistry. To explore the effect of neural activity on ketamine-induced apoptosis, the approaches of Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) and an environmental enrichment (EE) were performed. Ketamine-induced apoptosis in S1 is most prominent at postnatal days 5 and 7 (P5 - P7), and becomes insignificant by P12. Physiological and ketamine-induced apoptosis follow similar developmental patterns, mostly comprised of layer V pyramidal neurons at P5 and shifting to mostly layer II to IV GABAergic neurons by P9. Changes in neuronal activity induced by the DREADD system bidirectionally regulated the pattern of ketamine-induced apoptosis, with reduced activity inducing increased apoptosis and shifting the lamination pattern to a more immature form. Importantly, rearing mice in an EE significantly reduced the magnitude of ketamine-induced apoptosis and shifted its developmental pattern to a more mature form. Together, these results demonstrate that lamination pattern and cell-type dependent vulnerability to ketamine-induced apoptosis follow the physiological apoptosis pattern and are age- and activity-dependent. Naturally elevating neuronal activity is a possible method for reducing the adverse effects of general anesthesia.

  16. Gender-specific cold responses induce a similar body-cooling rate but different neuroendocrine and immune responses.

    Science.gov (United States)

    Solianik, Rima; Skurvydas, Albertas; Vitkauskienė, Astra; Brazaitis, Marius

    2014-08-01

    This study investigated whether there are any gender differences in body-heating strategies during cold stress and whether the immune and neuroendocrine responses to physiological stress differ between men and women. Thirty-two participants (18 men and 14 women) were exposed to acute cold stress by immersion to the manubrium level in 14 °C water. The cold stress continued until rectal temperature (TRE) reached 35.5 °C or for a maximum of 170 min. The responses to cold stress of various indicators of body temperature, insulation, metabolism, shivering, stress, and endocrine and immune function were compared between men and women. During cold stress, TRE and muscle and mean skin temperatures decreased in all subjects (Pcold strain did not differ between men and women, but men exhibited larger changes in the indicators of neuroendocrine (epinephrine level) and in immune (tumor necrosis factor-α level) responses (both Pcold stress, whereas women exhibited a greater insulative response. Despite the similar experience of cold strain in men and women, the neuroendocrine and immune responses were larger in men. Contrary to our expectations, the cooling rate was similar in men and women. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. A novel human protease similar to the interleukin-1 beta converting enzyme induces apoptosis in transfected cells.

    Science.gov (United States)

    Faucheu, C; Diu, A; Chan, A W; Blanchet, A M; Miossec, C; Hervé, F; Collard-Dutilleul, V; Gu, Y; Aldape, R A; Lippke, J A

    1995-05-01

    We have identified a novel cDNA encoding a protein (named TX) with > 50% overall sequence identity with the interleukin-1 beta converting enzyme (ICE) and approximately 30% sequence identity with the ICE homologs NEDD-2/ICH-1L and CED-3. A computer homology model of TX was constructed based on the X-ray coordinates of the ICE crystal recently published. This model suggests that TX is a cysteine protease, with the P1 aspartic acid substrate specificity retained. Transfection experiments demonstrate that TX is a protease which is able to cleave itself and the p30 ICE precursor, but not to generate mature IL-1 beta from pro-IL-1 beta. In addition, this protein induces apoptosis in transfected COS cells. TX therefore delineates a new member of the growing Ice/ced-3 gene family coding for proteases with cytokine processing activity or involved in programmed cell death.

  18. Ultrasound accelerates thrombolysis of acutely induced platelet-rich thrombi similar to those in acute myocardial infarction.

    Science.gov (United States)

    Kawata, Hiroyuki; Naya, Noriyuki; Takemoto, Yasuhiro; Uemura, Shiro; Nakajima, Tamio; Horii, Manabu; Takeda, Yukiji; Fujimoto, Shinichi; Yamashita, Atsushi; Asada, Yujiro; Saito, Yoshihiko

    2007-10-01

    Although sonothrombolysis has been studied for development of recanalization that is safer and more efficacious than the methods currently used, there have been no studies of the efficacy of sonothrombolysis for the platelet-rich thrombi that typically cause acute myocardial infarction (AMI). The effects of adding ultrasound (US) to pharmacological lysis of platelet-rich thrombi was examined in a rabbit model of femoral artery occlusion. In 35 rabbits, the right femoral artery was balloon-injured repeatedly at 4-week intervals to induce platelet-rich thrombi. Two hours after the induction of occlusive thrombi, 27,500 IU/kg tissue plasminogen activator (tPA) were injected via an ear vein, with or without transcutaneous US (continuous wave, 1 MHz, 0.75 W/cm2), or 13,750 IU/kg tPA was administered with US (n=10). Significantly higher rates of successful thrombolysis (Thrombolysis In Myocardial Infarction grade 3) were observed with US (90.0%) than without it (10.0%), irrespective of the dose of tPA used (pdissolution of thrombi. However, the thrombi were not affected by US alone (n=5). US facilitates thrombolysis of platelet-rich thrombi and could be a useful component of thrombolytic therapy following AMI.

  19. Induced Neurocysticercosis in Rhesus Monkeys (Macaca mulatta Produces Clinical Signs and Lesions Similar to Natural Disease in Man

    Directory of Open Access Journals (Sweden)

    N. Chowdhury

    2014-01-01

    Full Text Available Neurocysticercosis is a serious endemic zoonosis resulting in increased cases of seizure and epilepsy in humans. The genesis of clinical manifestations of the disease through experimental animal models is poorly exploited. The monkeys may prove useful for the purpose due to their behavior and cognitive responses mimicking man. In this study, neurocysticercosis was induced in two rhesus monkeys each with 12,000 and 6,000 eggs, whereas three monkeys were given placebo. The monkeys given higher dose developed hyperexcitability, epileptic seizures, muscular tremors, digital cramps at 10 DPI, and finally paralysis of limbs, followed by death on 67 DPI, whereas the monkeys given lower dose showed delayed and milder clinical signs. On necropsy, all the infected monkeys showed numerous cysticerci in the brain. Histopathologically, heavily infected monkeys revealed liquefactive necrosis and formation of irregular cystic cavities lined by atrophied parenchymal septa with remnants of neuropil of the cerebrum. In contrast, the monkeys infected with lower dose showed formation of typical foreign body granulomas characterized by central liquefaction surrounded by chronic inflammatory response. It was concluded that the inflammatory and immune response exerted by the host against cysticerci, in turn, led to histopathological lesions and the resultant clinical signs thereof.

  20. Relationship of hepatocarcinogenicity and hepatocellular proliferation induced by mutagenic noncarcinogens vs carcinogens. II. 1- vs 2-nitropropane.

    Science.gov (United States)

    Cunningham, M L; Matthews, H B

    1991-09-15

    2-Nitropropane (2-NP) is mutagenic in a number of short-term mutagenicity assays in vitro and in vivo, and is a potent hepatocarcinogen in rats. A structural isomer, 1-nitropropane (1-NP), is mutagenic in V79 cells and can induce unscheduled DNA synthesis in rat hepatocytes, yet did not induce tumors in rats following chronic exposure. We examined the correlation of cell proliferation and hepatocarcinogenesis induced by this mutagenic noncarcinogen-carcinogen pair in a rat liver proliferation model. Rats were exposed to gavage doses of 0.5, 1, or 2 mmol/kg of 1-NP or 2-NP daily for 10 days; the highest two dose groups were similar to the doses used in the carcinogenesis bioassay. Cell proliferation was quantitated by incorporation of bromodeoxyuridine, detected immunohistochemically, into newly synthesized DNA. Animals exposed to the vehicle exhibited a labeling index (LI) of approximately 1.9% and animals exposed to CCL4 had a LI of approximately 30%. Rats exposed to the hepatocarcinogen 2-NP exhibited a dose-related increase in LI to 6.3 and 11% at the 1 and 2 mmol/kg doses, respectively, and no increase above control at the 0.5 mmol/kg exposure level. Animals exposed to the noncarcinogenic isomer 1-NP showed no statistically significant increase in LI above controls at any dose level tested. Serum chemistries were consistent with mild to moderate decreases in hepatocellular function, cholestasis, and necrosis following 2-NP exposure, but only minimal effects were observed, probably due to slight dehydration resulting from 1-NP exposure. These data indicate a positive association between increased cell proliferation and hepatocarcinogenesis induced by these two nitropropane isomers.

  1. Comparison of oxidative stress and inflammation induced by different intravenous iron sucrose similar preparations in a rat model.

    Science.gov (United States)

    Toblli, Jorge Eduardo; Cao, Gabriel; Oliveri, Leda; Angerosa, Margarita

    2012-02-01

    Iron sucrose originator (IS(ORIG)) has been used to treat iron deficiency and iron deficiency anemia for decades. Iron sucrose similars (ISSs) have recently entered the market. In this non-clinical study of non-anemic rats, five doses (40 mg iron/kg body weight) of six ISSs marketed in Asian countries, IS(ORIG) or saline solution (control) were administered intravenously over four weeks to compare their toxicologic effects. Vasodilatory effects, impaired renal function and hepatic damage were only observed in the ISS groups. Significantly elevated serum iron and transferrin saturation levels were observed in the ISS groups suggesting a higher release of iron resulting in higher amounts of non-transferrin bound (free) iron compared to IS(ORIG). This might explain the elevated oxidative stress and increased levels of inflammatory markers and antioxidant enzymes in the liver, heart and kidneys of ISS-treated animals. Physico-chemical analyses showed that the molecular structure of most of the ISSs differed greatly from that of the IS(ORIG). These differences may be responsible for the organ damage and oxidative stress observed in the ISS groups. Significant differences were also found between different lots of a single ISS product. In contrast, polarographic analyses of three different IS(ORIG) lots were identical, indicating that the molecular structure and thus the manufacturing process for IS(ORIG) is highly consistent. Data from this study suggest that ISSs and IS(ORIG) differ significantly. Therefore, before widespread use of these products it would be prudent to evaluate additional non-clinical and/or clinical data proving the safety, therapeutic equivalence and interchangeability of ISSs with IS(ORIG). © 2012 Bentham Science Publishers

  2. Similar protective immunity induced by an inactivated enterovirus 71 (EV71) vaccine in neonatal rhesus macaques and children.

    Science.gov (United States)

    Zhang, Ying; Wang, Lichun; Liao, Yun; Liu, Longding; Ma, Kaili; Yang, Erxia; Wang, Jingjing; Che, Yanchun; Jiang, Li; Pu, Jing; Guo, Lei; Feng, Min; Liang, Yan; Cui, Wei; Yang, Huai; Li, Qihan

    2015-11-17

    During the development of enterovirus 71 (EV71) inactivated vaccine for preventing human hand, foot and mouth diseases (HFMD) by EV71 infection, an effective animal model is presumed to be significant and necessary. Our previous study demonstrated that the vesicles in oral regions and limbs potentially associated with viremia, which are the typical manifestations of HFMD, and remarkable pathologic changes were identified in various tissues of neonatal rhesus macaque during EV71 infection. Although an immune response in terms of neutralizing antibody and T cell memory was observed in animals infected by the virus or stimulated by viral antigen, whether such a response could be considered as an indicator to justify the immune response in individuals vaccinated or infected in a pandemic needs to be investigated. Here, a comparative analysis of the neutralizing antibody response and IFN-γ-specific T cell response in vaccinated neonatal rhesus macaques and a human clinical trial with an EV71 inactivated vaccine was performed, and the results showed the identical tendency and increased level of neutralizing antibody and the IFN-γ-specific T cell response stimulated by the EV71 antigen peptide. Importantly, the clinical protective efficacy against virus infection by the elicited immune response in the immunized population compared with the placebo control and the up-modulated gene profile associated with immune activation were similar to those in infected macaques. Further safety verification of this vaccine in neonatal rhesus macaques and children confirmed the potential use of the macaque as a reliable model for the evaluation of an EV71 candidate vaccine. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. A single dose of inactivated hepatitis A vaccine promotes HAV-specific memory cellular response similar to that induced by a natural infection.

    Science.gov (United States)

    Melgaço, Juliana Gil; Morgado, Lucas Nóbrega; Santiago, Marta Almeida; Oliveira, Jaqueline Mendes de; Lewis-Ximenez, Lia Laura; Hasselmann, Bárbara; Cruz, Oswaldo Gonçalves; Pinto, Marcelo Alves; Vitral, Claudia Lamarca

    2015-07-31

    Based on current studies on the effects of single dose vaccines on antibody production, Latin American countries have adopted a single dose vaccine program. However, no data are available on the activation of cellular response to a single dose of hepatitis A. Our study investigated the functional reactivity of the memory cell phenotype after hepatitis A virus (HAV) stimulation through administration of the first or second dose of HAV vaccine and compared the response to that of a baseline group to an initial natural infection. Proliferation assays showed that the first vaccine dose induced HAV-specific cellular response; this response was similar to that induced by a second dose or an initial natural infection. Thus, from the first dose to the second dose, increase in the frequencies of classical memory B cells, TCD8 cells, and central memory TCD4 and TCD8 cells were observed. Regarding cytokine production, increased IL-6, IL-10, TNF, and IFNγ levels were observed after vaccination. Our findings suggest that a single dose of HAV vaccine promotes HAV-specific memory cell response similar to that induced by a natural infection. The HAV-specific T cell immunity induced by primary vaccination persisted independently of the protective plasma antibody level. In addition, our results suggest that a single dose immunization system could serve as an alternative strategy for the prevention of hepatitis A in developing countries. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Dose-response modeling of early molecular and cellular key events in the CAR-mediated hepatocarcinogenesis pathway.

    Science.gov (United States)

    Geter, David R; Bhat, Virunya S; Gollapudi, B Bhaskar; Sura, Radhakrishna; Hester, Susan D

    2014-04-01

    Low-dose extrapolation and dose-related transitions are paramount in the ongoing debate regarding the quantification of cancer risks for nongenotoxic carcinogens. Phenobarbital (PB) is a prototypical nongenotoxic carcinogen that activates the constitutive androstane receptor (CAR) resulting in rodent liver tumors. In this study, male and female CD-1 mice administered dietary PB at 0, 0.15, 1.5, 15, 75, or 150 mg/kg-day for 2 or 7 days to characterize multiple apical and molecular endpoints below, at (∼75 mg/kg-day), and above the carcinogenic dose level of PB and examine these responses using benchmark dose modeling. Linear toxicokinetics were observed for all doses. Increased liver weight, hepatocellular hypertrophy, and mitotic figures were seen at 75 and 150 mg/kg-day. CAR activation, based on Cyp2b qPCR and pentoxyresorufin dealkylase activity, occurred at doses ≥ 1.5 mg/kg-day. The no-observable transcriptional effect level for global gene expression was 15 mg/kg-day. At 2 days, several xenobiotic metabolism and cell protective pathways were activated at lower doses and to a greater degree in females. However, hepatocellular proliferation, quantified by bromodeoxyuridine immunohistochemistry, was the most sensitive indicator of PB exposure with female mice more sensitive than males, contrary to sex-specific differences in sensitivity to hepatocarcinogenesis. Taken together, the identification of low-dose cellular and molecular transitions in the subtumorigenic dose range aids the understanding of early key events in CAR-mediated hepatocarcinogenesis.

  5. Similar to spironolactone, oxymatrine is protective in aldosterone-induced cardiomyocyte injury via inhibition of calpain and apoptosis-inducing factor signaling.

    Directory of Open Access Journals (Sweden)

    Ting-Ting Xiao

    Full Text Available Accumulating evidence indicates that oxymatrine (OMT possesses variously pharmacological properties, especially on the cardiovascular system. We previously demonstrated that activated calpain/apoptosis-inducing factor (AIF-mediated pathway was the key molecular mechanism in aldosterone (ALD induces cardiomyocytes apoptosis. In the present study, we extended the experimentation by investigating the effect of OMT on cardiomyocytes exposed to ALD, as compared to spironolactone (Spiro, a classical ALD receptor antagonist. Cardiomyocytes were pre-incubated with OMT, Spiro or vehicle for 1 h, and then, cardiomyocytes were exposed to ALD 24 h. The cell injury was evaluated by 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyltetrazolium bromide (MTT assay and lactate dehydrogenase (LDH leakage ratio. Apoptosis was determined by terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL assay, annexin V/PI staining, and relative caspase-3 activity assay. Furthermore, expression of pro-apoptotic proteins including truncated Bid (tBid, calpain and AIF were evaluated by western blot analysis. ALD stimulation increased cardiomyocytes apoptosis, caspase-3 activity and protein expression of calpain, tBid and AIF in the cytosol (p<0.05. Pre-incubated with cardiomyocytes injury and increased caspase-3 activity were significantly attenuated (p<0.05. Furthermore, OMT suppressed ALD-induced high expression of calpain and AIF. And these effects of OMT could be comparable to Spiro. These findings indicated that OMT might be a potential cardioprotective-agent against excessive ALD-induced cardiotoxicity, at least in part, mediated through inhibition of calpain/AIF signaling.

  6. Radiation-Induced Deletions in Mouse Spermatogonia are Usually Large (over 200 kb) and Contain Little Sequence Similarity at the Junctions.

    Science.gov (United States)

    Kodaira, Mieko; Asakawa, Jun-Ichi; Nakamura, Nori

    2017-06-01

    Ionizing radiation can induce mutations, and the majority of radiation-induced mutations in mammalian cells are deletions. The most critical types of radiation-induced DNA damage are DNA double-strand breaks, and these breaks are repaired by either the homologous recombination (HR) pathway or the non-homologous end joining (NHEJ) pathway. The HR pathway is not as mutagenic as the NHEJ pathway, and it is expected that radiation-induced deletions would usually have little sequence similarity around the deletion junction points. Here we report sequence data from the regions around the rejoined junctions of 33 de novo copy-number mutations (27 deletions and 6 duplications) obtained from offspring sired by male mice that were irradiated at the spermatogonia stage and from nonirradiated controls. The results indicate that deletions can be classified into three major groups. In group 1, nine deletions were found to share long blocks of similar sequences (200-6,000 bp) at the junctions and the deletion size varied extensively (1 kb to 2 Mb) (e.g., illegitimate recombination). In group 2, five deletions shared short identical sequences (0-7 bp) at the junctions, and the deletion sizes were shorter than 200 kb (e.g., micro-homology-mediated repair). Additional three-deletion candidates of this group were also found but turned out to be inherited from mosaic parents. They are therefore not included in germline mutations. In group 3, twelve deletions shared little sequence similarity (only 0-2 bp) at the junctions (likely due to NHEJ repair) and deletion sizes were longer than 200 kb. Group 1 consisted of deletions found in both spontaneous and irradiated genomes and thus, were probably caused by spontaneous events during meiosis or DNA replication. Group 2 consisted mainly of deletions found in nonexposed genomes. Group 3 consisted primarily of deletions that occurred in the irradiated genomes. Among the duplications, we found no indication of any association with radiation

  7. Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase.

    Science.gov (United States)

    Andreevskaya, Margarita; Johansson, Per; Jääskeläinen, Elina; Rämö, Tanja; Ritari, Jarmo; Paulin, Lars; Björkroth, Johanna; Auvinen, Petri

    2016-08-03

    Lactobacillus oligofermentans has been mostly isolated from cold-stored packaged meat products in connection with their spoilage, but its precise role in meat spoilage is unknown. It belongs to the L. vaccinostercus group of obligate heterofermentative lactobacilli that generally ferment pentoses (e.g. xylose and ribose) more efficiently than hexoses (e.g. glucose). However, more efficient hexose utilization can be induced. The regulation mechanisms of the carbohydrate catabolism in such bacteria have been scarcely studied. To address this question, we provided the complete genome sequence of L. oligofermentans LMG 22743(T) and generated time course transcriptomes during its growth on glucose, ribose and xylose. The genome was manually annotated and its main functional features were examined. L. oligofermentans was confirmed to be able to efficiently utilize several hexoses and maltose, which is, presumably, induced by its repeated cultivation with glucose in vitro. Unexpectedly, in the beginning of the exponential growth phase, glucose- and xylose-induced transcriptome responses were more similar, whereas toward the end of the growth phase xylose and ribose transcriptomes became more alike. The promoter regions of genes simultaneously upregulated both on glucose and xylose in comparison with ribose (particularly, hexose and xylose utilization genes) were found to be enriched in the CcpA- binding site. Transcriptionally, no glucose-induced carbon catabolite repression was detected. The catabolism of glucose, which requires initial oxidation, led to significant overexpression of the NAD(P)H re-oxidation genes, the upstream regions of which were found to contain a motif, which was highly similar to a Rex repressor binding site. This paper presents the second complete genome and the first study of carbohydrate catabolism-dependent transcriptome response for a member of the L. vaccinostercus group. The transcriptomic changes detected in L. oligofermentans for growth

  8. RNA helicase DEAD box protein 5 regulates Polycomb repressive complex 2/Hox transcript antisense intergenic RNA function in hepatitis B virus infection and hepatocarcinogenesis.

    Science.gov (United States)

    Zhang, Hao; Xing, Zheng; Mani, Saravana Kumar Kailasam; Bancel, Brigitte; Durantel, David; Zoulim, Fabien; Tran, Elizabeth J; Merle, Philippe; Andrisani, Ourania

    2016-10-01

    Chronic hepatitis B virus (HBV) infection is a major factor in hepatocellular carcinoma (HCC) pathogenesis by a mechanism not yet understood. Elucidating mechanisms of HBV-mediated hepatocarcinogenesis is needed to gain insights into classification and treatment of HCC. In HBV replicating cells, including virus-associated HCCs, suppressor of zeste 12 homolog (SUZ12), a core subunit of Polycomb repressive complex2 (PRC2), undergoes proteasomal degradation. This process requires the long noncoding RNA, Hox transcript antisense intergenic RNA (HOTAIR). Intriguingly, HOTAIR interacts with PRC2 and also binds RNA-binding E3 ligases, serving as a ubiquitination scaffold. Herein, we identified the RNA helicase, DEAD box protein 5 (DDX5), as a regulator of SUZ12 stability and PRC2-mediated gene repression, acting by regulating RNA-protein complexes formed with HOTAIR. Specifically, knockdown of DDX5 and/or HOTAIR enabled reexpression of PRC2-repressed genes epithelial cell adhesion molecule (EpCAM) and pluripotency genes. Also, knockdown of DDX5 enhanced transcription from the HBV minichromosome. The helicase activity of DDX5 stabilized SUZ12- and PRC2-mediated gene silencing, by displacing the RNA-binding E3 ligase, Mex-3 RNA-binding family member B (Mex3b), from HOTAIR. Conversely, ectopic expression of Mex3b ubiquitinated SUZ12, displaced DDX5 from HOTAIR, and induced SUZ12 down-regulation. In G2 phase of cells expressing the HBV X protein (HBx), SUZ12 preferentially associated with Mex3b, but not DDX5, resulting in de-repression of PRC2 targets, including EpCAM and pluripotency genes. Significantly, liver tumors from HBx/c-myc bitransgenic mice and chronically HBV-infected patients exhibited a strong negative correlation between DDX5 messenger RNA levels, pluripotency gene expression, and liver tumor differentiation. Notably, chronically infected HBV patients with HCC expressing reduced DDX5 exhibited poor prognosis after tumor resection, identifying DDX5 as an

  9. Rates of clinically apparent heparin-induced thrombocytopenia for unfractionated heparin vs. low molecular weight heparin in non-surgical patients are low and similar

    Directory of Open Access Journals (Sweden)

    Gerber Jonathan

    2005-04-01

    Full Text Available Abstract With the growing use of low-molecular-weight heparins (LMWH for the treatment and prevention of venous thromboembolism (VTE, it is important to provide an evidence-based comparison with unfractionated heparin (UFH concerning rates of heparin-induced thrombocytopenia (HIT. Such comparisons are essential in clinical decision-making and cost-modeling. In this paper we review data regarding non-surgical (medical patients. We conclude that the lack of uniform evaluation and standardized testing for HIT in the current literature precludes making a reliable estimate of the relative risk of HIT in UFH vs. LMWH in either the treatment or prevention of VTE in non-surgical patients. However, current data suggest that the risk of thrombocytopenia and HIT is low and similar for non-surgical patients who receive either LMWH or UFH.

  10. In Vivo Detection of c-MET Expression in a Rat Hepatocarcinogenesis Model Using Molecularly Targeted Magnetic Resonance Imaging

    Directory of Open Access Journals (Sweden)

    Rheal A. Towner

    2007-01-01

    Full Text Available The multifunctional growth factor scatter factor/hepatocyte growth factor and its tyrosine kinase receptor, c-MET, have been implicated in the genesis and malignant progression of numerous human malignancies, including hepatocellular carcinomas. The incidence of hepatocellular carcinomas in the United States has increased noticeably over the past two decades and is listed as the fifth major cancer in men worldwide. In this study, we used a choline-deficient l-amino acid (CDAA-defined rat hepatocarcinogenesis model to visualize increased in vivo expression of the c-MET antigen in neoplastic lesion formation with the use of a super paramagnetic iron oxide (SPIO–anti-c-MET molecularly targeted magnetic resonance imaging (MRI contrast agent. SPIO–anti-c-MET was used for the first time to detect overexpression of c-MET in neoplastic nodules and tumors within the livers of CDAA-treated rats, as determined by a decrease in MRI signal intensity and a decrease in regional T2 values. Specificity for the binding of the molecularly targeted anti-c-MET contrast agent was determined using rat hepatoma (H4-II-E-C3 cell cultures and immunofluorescence microscopic imaging of the targeting agents within neoplastic liver tissue 1 to 2 hours following intravenous administration of SPIO–anti-c-MET and MRI investigation. This method has the ability to visualize in vivo the overexpression of c-MET at early developmental stages of tumor formation.

  11. Human induced pluripotent stem cell lines show stress defense mechanisms and mitochondrial regulation similar to those of human embryonic stem cells.

    Science.gov (United States)

    Armstrong, Lyle; Tilgner, Katarzyna; Saretzki, Gabriele; Atkinson, Stuart P; Stojkovic, Miodrag; Moreno, Ruben; Przyborski, Stefan; Lako, Majlinda

    2010-04-01

    The generation of induced pluripotent stem cells (iPSC) has enormous potential for the development of patient-specific regenerative medicine. Human embryonic stem cells (hESC) are able to defend their genomic integrity by maintaining low levels of reactive oxygen species (ROS) through a combination of enhanced removal capacity and limited production of these molecules. Such limited ROS production stems partly from the small number of mitochondria present in hESC; thus, it was important to determine that human iPSC (hiPSC) generation is able to eliminate the extra mitochondria present in the parental fibroblasts (reminiscent of "bottleneck" situation after fertilization) and to show that hiPSC have antioxidant defenses similar to hESC. We were able to generate seven hiPSC lines from adult human dermal fibroblasts and have fully characterized two of those clones. Both hiPSC clones express pluripotency markers and are able to differentiate in vitro into cells belonging to all three germ layers. One of these clones is able to produce fully differentiated teratoma, whereas the other hiPSC clone is unable to silence the viral expression of OCT4 and c-MYC, produce fully differentiated teratoma, and unable to downregulate the expression of some of the pluripotency genes during the differentiation process. In spite of these differences, both clones show ROS stress defense mechanisms and mitochondrial biogenesis similar to hESC. Together our data suggest that, during the reprogramming process, certain cellular mechanisms are in place to ensure that hiPSC are provided with the same defense mechanisms against accumulation of ROS as the hESC.

  12. Amiodarone Induces Overexpression of Similar to Versican b to Repress the EGFR/Gsk3b/Snail Signaling Axis during Cardiac Valve Formation of Zebrafish Embryos.

    Science.gov (United States)

    Lee, Hung-Chieh; Lo, Hao-Chan; Lo, Dao-Ming; Su, Mai-Yan; Hu, Jia-Rung; Wu, Chin-Chieh; Chang, Sheng-Nan; Dai, Ming-Shen; Tsai, Chia-Ti; Tsai, Huai-Jen

    2015-01-01

    Although Amiodarone, a class III antiarrhythmic drug, inhibits zebrafish cardiac valve formation, the detailed molecular pathway is still unclear. Here, we proved that Amiodarone acts as an upstream regulator, stimulating similar to versican b (s-vcanb) overexpression at zebrafish embryonic heart and promoting cdh-5 overexpression by inhibiting snail1b at atrioventricular canal (AVC), thus blocking invagination of endocardial cells and, as a result, preventing the formation of cardiac valves. A closer investigation showed that an intricate set of signaling events ultimately caused the up-regulation of cdh5. In particular, we investigated the role of EGFR signaling and the activity of Gsk3b. It was found that knockdown of EGFR signaling resulted in phenotypes similar to those of Amiodarone-treated embryos. Since the reduced phosphorylation of EGFR was rescued by knockdown of s-vcanb, it was concluded that the inhibition of EGFR activity by Amiodarone is s-vcanb-dependent. Moreover, the activity of Gsk3b, a downstream effector of EGFR, was greatly increased in both Amiodarone-treated embryos and EGFR-inhibited embryos. Therefore, it was concluded that reduced EGFR signaling induced by Amiodarone treatment results in the inhibition of Snail functions through increased Gsk3b activity, which, in turn, reduces snail1b expression, leading to the up-regulation the cdh5 at the AVC, finally resulting in defective formation of valves. This signaling cascade implicates the EGFR/Gsk3b/Snail axis as the molecular basis for the inhibition of cardiac valve formation by Amiodarone.

  13. Heterogeneous hCG and hMG commercial preparations result in different intracellular signalling but induce a similar long-term progesterone response in vitro.

    Science.gov (United States)

    Riccetti, Laura; Klett, Danièle; Ayoub, Mohammed Akli; Boulo, Thomas; Pignatti, Elisa; Tagliavini, Simonetta; Varani, Manuela; Trenti, Tommaso; Nicoli, Alessia; Capodanno, Francesco; La Sala, Giovanni Battista; Reiter, Eric; Simoni, Manuela; Casarini, Livio

    2017-10-01

    Are four urinary hCG/menotropin (hMG) and one recombinant preparation characterized by different molecular features and do they mediate specific intracellular signaling and steroidogenesis? hCG and hMG preparations have heterogeneous compositions and mediate preparation-specific cell signaling and early steroidogenesis, although similar progesterone plateau levels are achieved in 24 h-treated human primary granulosa cells in vitro. hCG is the pregnancy hormone marketed as a drug for ARTs to induce final oocyte maturation and ovulation, and to support FSH action. Several hCG formulations are commercially available, differing in source, purification methods and biochemical composition. Commercial hCG preparations for ART or research purposes were compared in vitro. The different preparations were quantified by immunoassay with calibration against the hCG standard (Fifth IS; NIBSC 07/364). Immunoreactivity patterns, isoelectric points and oligosaccharide contents of hCGs were evaluated using reducing and non-reducing Western blotting, capillary isoelectric-focusing immunoassay and lectin-ELISA, respectively. Functional studies were performed in order to evaluate intracellular and total cAMP, progesterone production and β-arrestin 2 recruitment by ELISA and BRET, in both human primary granulosa lutein cells (hGLC) and luteinizing hormone (LH)/hCG receptor (LHCGR)-transfected HEK293 cells, stimulated by increasing hormone concentrations. Statistical analysis was performed using two-way ANOVA and Bonferroni post-test or Mann-Whitney's U-test as appropriate. Heterogeneous profiles were found among preparations, revealing specific molecular weight patterns (20-75 KDa range), isoelectric points (4.0-9.0 pI range) and lectin binding (P hCG/hMG preparations is provided in International Units (IU) by in-vivo bioassay and calibration against an International Standard, although it is an unsuitable unit of measure for in-vitro studies. The re-calibration against recombinant h

  14. Sonicated and stirred copper oxide nanoparticles induce similar toxicity and pro-inflammatory response in N-hTERT keratinocytes and SZ95 sebocytes

    Science.gov (United States)

    Piret, Jean-Pascal; Mejia, Jorge; Lucas, Stéphane; Zouboulis, Christos C.; Saout, Christelle; Toussaint, Olivier

    2014-04-01

    The potential toxic and pro-inflammatory effects of rod-shaped copper oxide (CuO) nanoparticles (NPs; 10 ± 3 nm in thickness and 74 ± 17 nm in length) were studied on N-hTERT keratinocytes and SZ95 sebocytes and on reconstructed human epidermis. Non-sonicated and sonicated CuO NPs induced similar cellular toxicity. The toxic effect of CuO NPs (non-sonicated and sonicated) was more pronounced in keratinocytes than in sebocytes. Pro-oxidant effects of CuO NPs were demonstrated by showing increase in the production of reactive oxygen species and decrease of cellular glutathione. In addition, DNA-binding activities suggested that redox-sensitive transcription factors Nrf2 and NF-κB were implicated in the response of keratinocytes to CuO NPs. Transcriptomic analysis showed an increase in the abundance of transcript species coding for pro-inflammatory interleukins (e.g. IL-8 and IL-1α) and chemokines. In reconstituted human epidermis exposed topically to raw CuO NPs, no effect on the integrity, viability and inflammatory response was noticed.

  15. Allospecific CD8 T suppressor cells induced by multiple MLC stimulation or priming in the presence of ILT3.Fc have similar gene expression profiles.

    Science.gov (United States)

    Chen, Ling; Xu, Zheng; Chang, Chris; Ho, Sophey; Liu, Zhuoru; Vlad, George; Cortesini, Raffaello; Clynes, Raphael A; Luo, Yun; Suciu-Foca, Nicole

    2014-02-01

    Alloantigen specific CD8 T suppressor cells can be generated in vitro either by multiple stimulations of CD3 T cells with allogeneic APC or by single stimulation in primary MLC containing recombinant ILT3.Fc protein. The aim of the present study was to determine whether multiple MLC stimulation induced in CD8(+) CD28(-) T suppressor cells molecular changes that are similar to those observed in CD8 T suppressor cells from primary MLC containing ILT3.Fc protein. Our study demonstrates that the characteristic signatures of CD8 T suppressor cells, generated by either of these methods are the same consisting of up-regulation of the BCL6 transcriptional repressor and down-regulation of inflammatory microRNAs, miR-21, miR-30b, miR-146a, and miR-155 expression. In conclusion microRNAs which are increased under inflammatory conditions in activated CD4 and CD8 T cells with helper or cytotoxic function show low levels of expression in CD8 T cells which have acquired antigen-specific suppressor activity. Copyright © 2014. Published by Elsevier Inc.

  16. Dietary lycopene and tomato extract supplementations inhibit nonalcoholic steatohepatitis-promoted hepatocarcinogenesis in rats

    Science.gov (United States)

    Epidemiological and experimental studies provide supportive evidence that lycopene (LY), a major carotenoid from tomatoes and tomato products, may act as a chemopreventive agent against certain types of cancers. We recently showed that high-fat diet (HFD)-induced nonalcoholic steatohepatitis (NASH) ...

  17. Med1 subunit of the mediator complex in nuclear receptor-regulated energy metabolism, liver regeneration, and hepatocarcinogenesis.

    Science.gov (United States)

    Jia, Yuzhi; Viswakarma, Navin; Reddy, Janardan K

    2014-01-01

    Several nuclear receptors regulate diverse metabolic functions that impact on critical biological processes, such as development, differentiation, cellular regeneration, and neoplastic conversion. In the liver, some members of the nuclear receptor family, such as peroxisome proliferator-activated receptors (PPARs), constitutive androstane receptor (CAR), farnesoid X receptor (FXR), liver X receptor (LXR), pregnane X receptor (PXR), glucocorticoid receptor (GR), and others, regulate energy homeostasis, the formation and excretion of bile acids, and detoxification of xenobiotics. Excess energy burning resulting from increases in fatty acid oxidation systems in liver generates reactive oxygen species, and the resulting oxidative damage influences liver regeneration and liver tumor development. These nuclear receptors are important sensors of exogenous activators as well as receptor-specific endogenous ligands. In this regard, gene knockout mouse models revealed that some lipid-metabolizing enzymes generate PPARα-activating ligands, while others such as ACOX1 (fatty acyl-CoA oxidase1) inactivate these endogenous PPARα activators. In the absence of ACOX1, the unmetabolized ACOX1 substrates cause sustained activation of PPARα, and the resulting increase in energy burning leads to hepatocarcinogenesis. Ligand-activated nuclear receptors recruit the multisubunit Mediator complex for RNA polymerase II-dependent gene transcription. Evidence indicates that the Med1 subunit of the Mediator is essential for PPARα, PPARγ, CAR, and GR signaling in liver. Med1 null hepatocytes fail to respond to PPARα activators in that these cells do not show induction of peroxisome proliferation and increases in fatty acid oxidation enzymes. Med1-deficient hepatocytes show no increase in cell proliferation and do not give rise to liver tumors. Identification of nuclear receptor-specific coactivators and Mediator subunits should further our understanding of the complexities of metabolic

  18. Phytophthora megakarya and P. palmivora, Causal Agents of Black Pod Rot, Induce Similar Plant Defense Responses Late during Infection of Susceptible Cacao Pods

    Science.gov (United States)

    Ali, Shahin S.; Shao, Jonathan; Lary, David J.; Strem, Mary D.; Meinhardt, Lyndel W.; Bailey, Bryan A.

    2017-01-01

    Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) cause black pod rot of Theobroma cacao L. (cacao). Of these two clade 4 species, Pmeg is more virulent and is displacing Ppal in many cacao production areas in Africa. Symptoms and species specific sporangia production were compared when the two species were co-inoculated onto pod pieces in staggered 24 h time intervals. Pmeg sporangia were predominantly recovered from pod pieces with unwounded surfaces even when inoculated 24 h after Ppal. On wounded surfaces, sporangia of Ppal were predominantly recovered if the two species were simultaneously applied or Ppal was applied first but not if Pmeg was applied first. Pmeg demonstrated an advantage over Ppal when infecting un-wounded surfaces while Ppal had the advantage when infecting wounded surfaces. RNA-Seq was carried out on RNA isolated from control and Pmeg and Ppal infected pod pieces 3 days post inoculation to assess their abilities to alter/suppress cacao defense. Expression of 4,482 and 5,264 cacao genes was altered after Pmeg and Ppal infection, respectively, with most genes responding to both species. Neural network self-organizing map analyses separated the cacao RNA-Seq gene expression profiles into 24 classes, 6 of which were largely induced in response to infection. Using KEGG analysis, subsets of genes composing interrelated pathways leading to phenylpropanoid biosynthesis, ethylene and jasmonic acid biosynthesis and action, plant defense signal transduction, and endocytosis showed induction in response to infection. A large subset of genes encoding putative Pr-proteins also showed differential expression in response to infection. A subset of 36 cacao genes was used to validate the RNA-Seq expression data and compare infection induced gene expression patterns in leaves and wounded and unwounded pod husks. Expression patterns between RNA-Seq and RT-qPCR were generally reproducible. The level and timing of altered gene expression was

  19. Phytophthora megakarya and P. palmivora, Causal Agents of Black Pod Rot, Induce Similar Plant Defense Responses Late during Infection of Susceptible Cacao Pods.

    Science.gov (United States)

    Ali, Shahin S; Shao, Jonathan; Lary, David J; Strem, Mary D; Meinhardt, Lyndel W; Bailey, Bryan A

    2017-01-01

    Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) cause black pod rot of Theobroma cacao L. (cacao). Of these two clade 4 species, Pmeg is more virulent and is displacing Ppal in many cacao production areas in Africa. Symptoms and species specific sporangia production were compared when the two species were co-inoculated onto pod pieces in staggered 24 h time intervals. Pmeg sporangia were predominantly recovered from pod pieces with unwounded surfaces even when inoculated 24 h after Ppal. On wounded surfaces, sporangia of Ppal were predominantly recovered if the two species were simultaneously applied or Ppal was applied first but not if Pmeg was applied first. Pmeg demonstrated an advantage over Ppal when infecting un-wounded surfaces while Ppal had the advantage when infecting wounded surfaces. RNA-Seq was carried out on RNA isolated from control and Pmeg and Ppal infected pod pieces 3 days post inoculation to assess their abilities to alter/suppress cacao defense. Expression of 4,482 and 5,264 cacao genes was altered after Pmeg and Ppal infection, respectively, with most genes responding to both species. Neural network self-organizing map analyses separated the cacao RNA-Seq gene expression profiles into 24 classes, 6 of which were largely induced in response to infection. Using KEGG analysis, subsets of genes composing interrelated pathways leading to phenylpropanoid biosynthesis, ethylene and jasmonic acid biosynthesis and action, plant defense signal transduction, and endocytosis showed induction in response to infection. A large subset of genes encoding putative Pr-proteins also showed differential expression in response to infection. A subset of 36 cacao genes was used to validate the RNA-Seq expression data and compare infection induced gene expression patterns in leaves and wounded and unwounded pod husks. Expression patterns between RNA-Seq and RT-qPCR were generally reproducible. The level and timing of altered gene expression was

  20. IgE and allergen-specific immunotherapy-induced IgG4 recognize similar epitopes of Bet v 1, the major allergen of birch pollen.

    Science.gov (United States)

    Groh, N; von Loetzen, C S; Subbarayal, B; Möbs, C; Vogel, L; Hoffmann, A; Fötisch, K; Koutsouridou, A; Randow, S; Völker, E; Seutter von Loetzen, A; Rösch, P; Vieths, S; Pfützner, W; Bohle, B; Schiller, D

    2017-05-01

    Allergen-specific immunotherapy (AIT) with birch pollen generates Bet v 1-specific immunoglobulin (Ig)G4 which blocks IgE-mediated hypersensitivity mechanisms. Whether IgG4 specific for Bet v 1a competes with IgE for identical epitopes or whether novel epitope specificities of IgG4 antibodies are developed is under debate. We sought to analyze the epitope specificities of IgE and IgG4 antibodies from sera of patients who received AIT. 15 sera of patients (13/15 received AIT) with Bet v 1a-specific IgE and IgG4 were analyzed. The structural arrangements of recombinant (r)Bet v 1a and rBet v 1a_11x , modified in five potential epitopes, were analyzed by circular dichroism and nuclear magnetic resonance spectroscopy. IgE binding to Bet v 1 was assessed by ELISA and mediator release assays. Competitive binding of monoclonal antibodies specific for Bet v 1a and serum IgE/IgG4 to rBet v 1a and serum antibody binding to a non-allergenic Bet v 1-type model protein presenting an individual epitope for IgE was analyzed in ELISA and western blot. rBet v 1a_11x had a Bet v 1a - similar secondary and tertiary structure. Monomeric dispersion of rBet v 1a_11x was concentration and buffer-dependent. Up to 1500-fold increase in the EC50 for IgE-mediated mediator release induced by rBet v 1a_11x was determined. The reduction of IgE and IgG4 binding to rBet v 1a_11x was comparable in 67% (10/15) of sera. Bet v 1a-specific monoclonal antibodies inhibited binding of serum IgE and IgG4 to 66.1% and 64.9%, respectively. Serum IgE and IgG4 bound specifically to an individual epitope presented by our model protein in 33% (5/15) of sera. Patients receiving AIT develop Bet v 1a-specific IgG4 which competes with IgE for partly identical or largely overlapping epitopes. The similarities of epitopes for IgE and IgG4 might stimulate the development of epitope-specific diagnostics and therapeutics. © 2016 John Wiley & Sons Ltd.

  1. Impact of epidermal growth factor receptor and transforming growth factor-α on hepatitis C virus-induced hepatocarcinogenesis.

    Science.gov (United States)

    Badawy, Afkar Abdel-Ghany; El-Hindawi, Ali; Hammam, Olfat; Moussa, Mona; Gabal, Samia; Said, Noha

    2015-10-01

    Epidermal growth factor receptor system plays a central hepato-protective and pro-regenerative role in liver. Transforming growth factor-α (TGF-α) is an important autocrine growth regulator of hepatocytes that plays a role in development of hepatocellular carcinoma (HCC) among patients with chronic hepatitis C (CHC). This study was done on 40 core liver biopsies from patients with CHC, 20 liver specimens from HCC cases on top of CHC as well as five normal controls. All were immunohistochemically stained with epidermal growth factor receptor (EGFR) and TGF-α antibodies. Some selected HCC cases were submitted for FISH technique to detect EGFR gene alteration. By immunohistochemistry EGFR and TGF-α were overexpressed in HCC and cirrhotic cases compared to CHC cases without cirrhosis. Also, their expression was stronger in CHC cases with higher grades of activity and stages of fibrosis compared to lower ones. FISH positive results for EGFR were detected in 33.3% of the examined HCC cases. EGFR and TGF-α can be used as predictive markers for activity, fibrosis, and carcinogenesis in CHC patients. Overexpression of EGFR in HCC patients can be promising in selecting those who can get benefit from anti-EGFR target therapy. © 2015 APMIS. Published by John Wiley & Sons Ltd.

  2. Similar changes in muscle lipid metabolism are induced by chronic high-fructose feeding and high-fat feeding in C57BL/J6 mice.

    Science.gov (United States)

    Song, Guang-Yao; Ren, Lu-Ping; Chen, Shu-Chun; Wang, Chao; Liu, Na; Wei, Li-Min; Li, Fan; Sun, Wen; Peng, Lan-Bo; Tang, Yong

    2012-12-01

    The aim of the present study was to investigate the effects of high fructose and high fat feeding on muscle lipid metabolism and to illustrate the mechanisms by which the two different dietary factors induce muscle lipid accumulation. C57BL/J6 mice were fed either a standard, high-fructose (HFru) or high-fat diet. After 16 weeks feeding, mice were killed and plasma triglyceride (TG) and free fatty acid (FFA) levels were detected. In addition, muscle TG and long chain acyl CoA (LCACoA) content was determined, glucose tolerance was evaluated and the protein content of fatty acid translocase CD36 (FATCD36) in muscle was measured. Mitochondrial oxidative function in the muscle was evaluated by estimating the activity of oxidative enzymes, namely cytochrome oxidase (COx), citrate synthase (CS) and β-hydroxyacyl CoA dehydrogenase (β-HAD), and the muscle protein content of carnitine palmitoyltransferase-1 (CPT-1), cyclo-oxygenase (COX)-1 and proliferator-activated receptor coactivator (PGC)-1α was determined. Finally, sterol regulatory element-binding protein-1c (SREBP-1c) gene expression and fatty acid synthase (FAS) protein content were determined in muscle tissues. After 16 weeks, plasma TG and FFA levels were significantly increased in both the HFru and HF groups. In addition, mice in both groups exhibited significant increases in muscle TG and LCACoA content. Compared with mice fed the standard diet (control group), those in the HFru and HF groups developed glucose intolerance and exhibited increased FATCD36 protein levels, enzyme activity related to fatty acid utilization in the mitochondria and protein expressions of CPT-1, COX-1 and PGC-1α in muscle tissue. Finally, mice in both the HFru and HF groups exhibited increase SREBP-1c expression and FAS protein content. In conclusion, high fructose and high fat feeding lead to similar changes in muscle lipid metabolism in C57BL/J6 mice. Lipid accumulation in the muscle may be associated with increased expression

  3. Effect of dietary antioxidants on the promotion of hepatocarcinogenesis by PCBs

    Energy Technology Data Exchange (ETDEWEB)

    Glauert, H.; Tharappel, J.; Stemm, D.; Spear, B. [Univ. of Kentucky, Lexington, KY (United States); Lehmler, H.J.; Robertson, L. [Univ. of Iowa, Iowa City, IA (United States)

    2004-09-15

    Mixtures of halogenated biphenyls as well as many individual congeners have been reported to be promoters of carcinogenesis in various liver tumor models. However, their mechanism of action is not known. A number of mechanisms have been investigated, including direct effects on signal transduction pathways, induction of oxidative stress, effects on vitamin A metabolism, and effects on intercellular communication. One mechanism by which PCBs may promote hepatic tumors is by inducing oxidative damage in the liver. Forms of oxidative damage that may be important are the induction of lipid peroxidation, the induction of oxidative DNA damage, and the alteration of gene expression. One possible mechanism for inhibiting the promoting activity of PCBs may be to increase the concentration of antioxidants in the diet. In this study, we examined if dietary selenium or antioxidant phytochemicals could inhibit the hepatic promoting activity of PCBs in rats.

  4. Interferon-microRNA signalling drives liver precancerous lesion formation and hepatocarcinogenesis.

    Science.gov (United States)

    Yang, Yingcheng; Lin, Ximeng; Lu, Xinyuan; Luo, Guijuan; Zeng, Tao; Tang, Jing; Jiang, Feng; Li, Liang; Cui, Xiuliang; Huang, Wentao; Hou, Guojun; Chen, Xin; Ouyang, Qing; Tang, Shanhua; Sun, Huanlin; Chen, Luonan; Gonzalez, Frank J; Wu, Mengchao; Cong, Wenming; Chen, Lei; Wang, Hongyang

    2016-07-01

    Precancerous lesion, a well-established histopathologically premalignant tissue with the highest risk for tumourigenesis, develops preferentially from activation of DNA damage checkpoint and persistent inflammation. However, little is known about the mechanisms by which precancerous lesions are initiated and their physiological significance. Laser capture microdissection was used to acquire matched normal liver, precancerous lesion and tumour tissues. miR-484(-/-), Ifnar1(-/-) and Tgfbr2(△hep) mice were employed to determine the critical role of the interferon (IFN)-microRNA pathway in precancerous lesion formation and tumourigenesis. RNA immunoprecipitation (RIP), pull-down and chromatin immunoprecipitation (ChIP) assays were applied to explore the underlying mechanisms. miR-484 is highly expressed in over 88% liver samples clinically. DEN-induced precancerous lesions and hepatocellular carcinoma were dramatically impaired in miR-484(-/-) mice. Mechanistically, ectopic expression of miR-484 initiates tumourigenesis and cell malignant transformation through synergistic activation of the transforming growth factor-β/Gli and nuclear factor-κB/type I IFN pathways. Specific acetylation of H3K27 is indispensable for basal IFN-induced continuous transcription of miR-484 and cell transformation. Convincingly, formation of precancerous lesions were significantly attenuated in both Tgfbr2(△hep) and Ifnar1(-/-) mice. These findings demonstrate a new protumourigenic axis involving type I IFN-microRNA signalling, providing a potential therapeutic strategy to manipulate or reverse liver precancerous lesions and tumourigenesis. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  5. Phenolic extract of Dialium guineense pulp enhances reactive oxygen species detoxification in aflatoxin B₁ hepatocarcinogenesis.

    Science.gov (United States)

    Adeleye, Abdulwasiu O; Ajiboye, Taofeek O; Iliasu, Ganiyat A; Abdussalam, Folakemi A; Balogun, Abdulazeez; Ojewuyi, Oluwayemisi B; Yakubu, Musa T

    2014-08-01

    This study investigated the effect of Dialium guineense pulp phenolic extract on aflatoxin B1 (AFB1)-induced oxidative imbalance in rat liver. Reactive oxygen species (ROS) scavenging potentials of free and bound phenolic extract of D. guineense (0.2-1.0 mg/mL) were investigated in vitro using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical, superoxide ion (O2(-)), hydrogen peroxide (H2O2), hydroxyl radical, and ferric ion reducing system. In the in vivo study, 35 animals were randomized into seven groups of five rats each. Free and bound phenolic extract (1 mg/mL) produced 66.42% and 93.08%, 57.1% and 86.0%, 62.0% and 90.05%, and 60.11% and 72.37% scavenging effect on DPPH radical, O2(-) radical, H2O2, and hydroxyl radical, while ferric ion was significantly reduced. An AFB1-mediated decrease in the activities of ROS detoxifying enzymes (superoxide dismutase, catalase, glutathione peroxidase, glutathione reductase, and glucose 6 phosphate dehydrogenase) was significantly attenuated (P<.05). AFB1-mediated elevation in the concentrations of oxidative stress biomarkers; malondialdehyde, conjugated dienes, lipid hydroperoxides, protein carbonyl, and percentage DNA fragmentation were significantly lowered by D. guineense phenolic extract (P<.05). Overall, the in vitro and in vivo effects suggest that D. guineense phenolic extract elicited ROS scavenging and detoxification potentials, as well as the capability of preventing lipid peroxidation, protein oxidation, and DNA fragmentation.

  6. Epigenetic Activation of Wnt/β-Catenin Signaling in NAFLD-Associated Hepatocarcinogenesis

    Directory of Open Access Journals (Sweden)

    Yuan Tian

    2016-08-01

    Full Text Available Non-alcoholic fatty liver disease (NAFLD, characterized by fat accumulation in liver, is closely associated with central obesity, over-nutrition and other features of metabolic syndrome, which elevate the risk of developing hepatocellular carcinoma (HCC. The Wnt/β-catenin signaling pathway plays a significant role in the physiology and pathology of liver. Up to half of HCC patients have activation of Wnt/β-catenin signaling. However, the mutation frequencies of CTNNB1 (encoding β-catenin protein or other antagonists targeting Wnt/β-catenin signaling are low in HCC patients, suggesting that genetic mutations are not the major factor driving abnormal β-catenin activities in HCC. Emerging evidence has demonstrated that obesity-induced metabolic pathways can deregulate chromatin modifiers such as histone deacetylase 8 to trigger undesired global epigenetic changes, thereby modifying gene expression program which contributes to oncogenic signaling. This review focuses on the aberrant epigenetic activation of Wnt/β-catenin in the development of NAFLD-associated HCC. A deeper understanding of the molecular mechanisms underlying such deregulation may shed light on the identification of novel druggable epigenetic targets for the prevention and/or treatment of HCC in obese and diabetic patients.

  7. Epigenetic Activation of Wnt/β-Catenin Signaling in NAFLD-Associated Hepatocarcinogenesis.

    Science.gov (United States)

    Tian, Yuan; Mok, Myth T S; Yang, Pengyuan; Cheng, Alfred S L

    2016-08-20

    Non-alcoholic fatty liver disease (NAFLD), characterized by fat accumulation in liver, is closely associated with central obesity, over-nutrition and other features of metabolic syndrome, which elevate the risk of developing hepatocellular carcinoma (HCC). The Wnt/β-catenin signaling pathway plays a significant role in the physiology and pathology of liver. Up to half of HCC patients have activation of Wnt/β-catenin signaling. However, the mutation frequencies of CTNNB1 (encoding β-catenin protein) or other antagonists targeting Wnt/β-catenin signaling are low in HCC patients, suggesting that genetic mutations are not the major factor driving abnormal β-catenin activities in HCC. Emerging evidence has demonstrated that obesity-induced metabolic pathways can deregulate chromatin modifiers such as histone deacetylase 8 to trigger undesired global epigenetic changes, thereby modifying gene expression program which contributes to oncogenic signaling. This review focuses on the aberrant epigenetic activation of Wnt/β-catenin in the development of NAFLD-associated HCC. A deeper understanding of the molecular mechanisms underlying such deregulation may shed light on the identification of novel druggable epigenetic targets for the prevention and/or treatment of HCC in obese and diabetic patients.

  8. INTRACEREBROVENTRICULAR APPLICATION OF COMPETITIVE AND NONCOMPETITIVE NMDA ANTAGONISTS INDUCE SIMILAR EFFECTS UPON RAT HIPPOCAMPAL ELECTROENCEPHALOGRAM AND LOCAL CEREBRAL GLUCOSE-UTILIZATION

    NARCIS (Netherlands)

    BODDEKE, HWGM; WIEDERHOLD, KH; PALACIOS, JM

    1992-01-01

    In this study we have used electrophysiological and metabolic markers to investigate the effects of competitive and non-competitive NMDA antagonists in rats after central or peripheral administration. The non-competitive antagonist, MK-801, induced dose-dependent suppression of rat hippocampal EEG

  9. Intracerebroventricular application of competitive and non-competitive NMDA antagonists induce similar effects upon rat hippocampal electroencephalogram and local cerebral glucose utilization

    NARCIS (Netherlands)

    Boddeke, H.W.G.M.; Wiederhold, K.H.; Palacios, J.M.

    1992-01-01

    In this study we have used electrophysiological and metabolic markers to investigate the effects of competitive and non-competitive NMDA antagonists in rats after central or peripheral administration. The non-competitive antagonist, MK-801, induced dose-dependent suppression of rat hippocampal EEG

  10. Both food restriction and high-fat diet during gestation induce low birth weight and altered physical activity in adult rat offspring: the "Similarities in the Inequalities" model.

    Science.gov (United States)

    Cunha, Fábio da Silva; Dalle Molle, Roberta; Portella, André Krumel; Benetti, Carla da Silva; Noschang, Cristie; Goldani, Marcelo Zubaran; Silveira, Patrícia Pelufo

    2015-01-01

    We have previously described a theoretical model in humans, called "Similarities in the Inequalities", in which extremely unequal social backgrounds coexist in a complex scenario promoting similar health outcomes in adulthood. Based on the potential applicability of and to further explore the "similarities in the inequalities" phenomenon, this study used a rat model to investigate the effect of different nutritional backgrounds during gestation on the willingness of offspring to engage in physical activity in adulthood. Sprague-Dawley rats were time mated and randomly allocated to one of three dietary groups: Control (Adlib), receiving standard laboratory chow ad libitum; 50% food restricted (FR), receiving 50% of the ad libitum-fed dam's habitual intake; or high-fat diet (HF), receiving a diet containing 23% fat. The diets were provided from day 10 of pregnancy until weaning. Within 24 hours of birth, pups were cross-fostered to other dams, forming the following groups: Adlib_Adlib, FR_Adlib, and HF_Adlib. Maternal chow consumption and weight gain, and offspring birth weight, growth, physical activity (one week of free exercise in running wheels), abdominal adiposity and biochemical data were evaluated. Western blot was performed to assess D2 receptors in the dorsal striatum. The "similarities in the inequalities" effect was observed on birth weight (both FR and HF groups were smaller than the Adlib group at birth) and physical activity (both FR_Adlib and HF_Adlib groups were different from the Adlib_Adlib group, with less active males and more active females). Our findings contribute to the view that health inequalities in fetal life may program the health outcomes manifested in offspring adult life (such as altered physical activity and metabolic parameters), probably through different biological mechanisms.

  11. Both food restriction and high-fat diet during gestation induce low birth weight and altered physical activity in adult rat offspring: the "Similarities in the Inequalities" model.

    Directory of Open Access Journals (Sweden)

    Fábio da Silva Cunha

    Full Text Available We have previously described a theoretical model in humans, called "Similarities in the Inequalities", in which extremely unequal social backgrounds coexist in a complex scenario promoting similar health outcomes in adulthood. Based on the potential applicability of and to further explore the "similarities in the inequalities" phenomenon, this study used a rat model to investigate the effect of different nutritional backgrounds during gestation on the willingness of offspring to engage in physical activity in adulthood. Sprague-Dawley rats were time mated and randomly allocated to one of three dietary groups: Control (Adlib, receiving standard laboratory chow ad libitum; 50% food restricted (FR, receiving 50% of the ad libitum-fed dam's habitual intake; or high-fat diet (HF, receiving a diet containing 23% fat. The diets were provided from day 10 of pregnancy until weaning. Within 24 hours of birth, pups were cross-fostered to other dams, forming the following groups: Adlib_Adlib, FR_Adlib, and HF_Adlib. Maternal chow consumption and weight gain, and offspring birth weight, growth, physical activity (one week of free exercise in running wheels, abdominal adiposity and biochemical data were evaluated. Western blot was performed to assess D2 receptors in the dorsal striatum. The "similarities in the inequalities" effect was observed on birth weight (both FR and HF groups were smaller than the Adlib group at birth and physical activity (both FR_Adlib and HF_Adlib groups were different from the Adlib_Adlib group, with less active males and more active females. Our findings contribute to the view that health inequalities in fetal life may program the health outcomes manifested in offspring adult life (such as altered physical activity and metabolic parameters, probably through different biological mechanisms.

  12. Vitamin K3 and vitamin C alone or in combination induced apoptosis in leukemia cells by a similar oxidative stress signalling mechanism

    Directory of Open Access Journals (Sweden)

    Velez-Pardo Carlos

    2011-06-01

    Full Text Available Abstract Background Secondary therapy-related acute lymphoblastic leukemia might emerge following chemotherapy and/or radiotherapy for primary malignancies. Therefore, other alternatives should be pursued to treat leukemia. Results It is shown that vitamin K3- or vitamin C- induced apoptosis in leukemia cells by oxidative stress mechanism involving superoxide anion radical and hydrogen peroxide generation, activation of NF-κB, p53, c-Jun, protease caspase-3 activation and mitochondria depolarization leading to nuclei fragmentation. Cell death was more prominent when Jurkat and K562 cells are exposed to VC and VK3 in a ratio 1000:1 (10 mM: 10 μM or 100:1 (300 μM: 3 μM, respectively. Conclusion We provide for the first time in vitro evidence supporting a causative role for oxidative stress in VK3- and VC-induced apoptosis in Jurkat and K562 cells in a domino-like mechanism. Altogether these data suggest that VK3 and VC should be useful in the treatment of leukemia.

  13. Redox-related metabolites and gene expression modulated by sugar in sunflower leaves: similarities with Sunflower chlorotic mottle virus-induced symptom.

    Science.gov (United States)

    Rodríguez, Marianela; Muñoz, Nacira; Lenardon, Sergio; Lascano, Ramiro

    2013-01-01

    Sugars are part of an integrated redox system, since they are key regulators of respiration and photosynthesis, and therefore of the levels of reducing power, ATP and ROS. These elements are major determinants of the cellular redox state, which is involved in the perception and regulation of many endogenous and environmental stimuli. Our previous findings suggested that early sugar increase produced during compatible Sunflower chlorotic mottle virus (SuCMoV) infection might modulate chlorotic symptom development through redox state alteration in sunflower. The purpose of this work was to characterize redox-related metabolites and gene expression changes associated with high sugar availability and symptom development induced by SuCMoV. The results show that sugar caused an increase in glutathione, ascorbate, pyridine nucleotides, and ATP. In addition, higher sugar availability reduced hydrogen peroxide and ΦPSII. This finding suggests that high sugar availability would be associated with cellular redox alteration and photoinhibitory process. The expression of the genes analyzed was also strongly affected by sugar, such as the down-regulation of psbA and up-regulation of psbO and cp29. The expression level of cytoplasmic (apx-1 and gr)- and chloroplastic (Fe-sod)-targeted genes was also significantly enhanced in sugar-treated leaves. Therefore, all these responses suggest that sugars induce chloroplastic redox state alteration with photoinhibition process that could be contributing to chlorotic symptom development during SuCMoV infection.

  14. Subcutaneous bortezomib in multiple myeloma patients induces similar therapeutic response rates as intravenous application but it does not reduce the incidence of peripheral neuropathy.

    Directory of Open Access Journals (Sweden)

    Jiri Minarik

    Full Text Available Subcutaneous (SC application of bortezomib has been recently introduced as a new application route in multiple myeloma (MM patients. We performed an analysis to compare the outcomes of bortezomib-based therapy in multiple myeloma (MM patients treated using either intravenous (IV or subcutaneous (SC route of administration.During January 2012 through December 2013, we performed a retrospective analysis of 446 patients with MM treated with bortezomib-based regimens (either once weekly - 63% or twice weekly - 27% in both, the first line setting, and in relapse, with separate analysis of patients undergoing autologous stem cell transplantation. We assessed the response rates and toxicity profiles in both, IV and SC route of bortezomib administration.The response rates in both IV and SC arm were similar with overall response rate 71.7% vs 70.7%, complete remissions in 13.9% vs 8.6%, very good partial remissions in 30.8% vs 34.5% and partial remissions in 27% vs 27.6%. The most frequent grade ≥ 3 toxicities were anemia, thrombocytopenia and neutropenia, with no significant differences between IV and SC group. There were no significant differences in the rate of peripheral neuropathy (PN. PN of any grade was present in 48% in the IV arm and in 41% in the SC arm. PN grade ≥ 2 was present in 20% vs 18% and PN grade ≥ 3 was present in 6% vs 4%.We conclude that subcutaneous application of bortezomib has similar therapeutic outcomes and toxicity profile as intravenous route of application. In our cohort there was no difference in the incidence of PN, suggesting that PN is dose dependent and might be reduced by lower intensity schemes rather than by the route of administration.

  15. RARα2 and PML-RAR similarities in the control of basal and retinoic acid induced myeloid maturation of acute myeloid leukemia cells

    Science.gov (United States)

    Gianni, Maurizio; Fratelli, Maddalena; Bolis, Marco; Kurosaki, Mami; Zanetti, Adriana; Paroni, Gabriela; Rambaldi, Alessandro; Borleri, Gianmaria; Rochette-Egly, Cecile; Terao, Mineko; Garattini, Enrico

    2017-01-01

    Treatment of acute promyelocytic leukemia (APL) with all-trans retinoic acid (ATRA) is the first example of targeted therapy. In fact, the oncogenic fusion-protein (PML-RAR) typical of this leukemia contains the retinoid-nuclear-receptor RARα. PML-RAR is responsible for the differentiation block of the leukemic blast. Besides PML-RAR, two endogenous RARα proteins are present in APL blasts, i.e. RARα1 and RARα2. We developed different cell populations characterized by PML-RAR, RARα2 and RARα1 knock-down in the APL-derived NB4 cell-line. Unexpectedly, silencing of PML-RAR and RARα2 results in similar increases in the constitutive expression of several granulocytic differentiation markers. This is accompanied by enhanced expression of the same granulocytic markers upon exposure of the NB4 blasts to ATRA. Silencing of PML-RAR and RARα2 causes also similar perturbations in the whole genome gene-expression profiles of vehicle and ATRA treated NB4 cells. Unlike PML-RAR and RARα2, RARα1 knock-down blocks ATRA-dependent induction of several granulocytic differentiation markers. Many of the effects on myeloid differentiation are confirmed by over-expression of RARα2 in NB4 cells. RARα2 action on myeloid differentiation does not require the presence of PML-RAR, as it is recapitulated also upon knock-down in PML-RAR-negative HL-60 cells. Thus, relative to RARα1, PML-RAR and RARα2 exert opposite effects on APL-cell differentiation. These contrasting actions may be related to the fact that both PML-RAR and RARα2 interact with and inhibit the transcriptional activity of RARα1. The interaction surface is located in the carboxy-terminal domain containing the D/E/F regions and it is influenced by phosphorylation of Ser-369 of RARα1. PMID:27419624

  16. Reverse translation of the rodent 5C-CPT reveals that the impaired attention of people with schizophrenia is similar to scopolamine-induced deficits in mice.

    Science.gov (United States)

    Young, J W; Geyer, M A; Rissling, A J; Sharp, R F; Eyler, L T; Asgaard, G L; Light, G A

    2013-11-12

    Attentional dysfunction in schizophrenia (SZ) is a core deficit that contributes to multiple cognitive deficits and the resulting functional disability. However, developing procognitive therapeutics for neuropsychiatric disorders have been limited by a 'translational gap'--a lack of cognitive paradigms having cross-species translational validity and relevance. The present study was designed to perform an initial validation of the cross-species homology of the 5-choice Continuous Performance Test (5C-CPT) in healthy nonpsychiatric comparison subjects (NCS), SZ patients and mice under pharmacologic challenge. The 5C-CPT performance in SZ patients (n=20) was compared with age-matched NCS (n=23). The effects of the general muscarinic receptor antagonist scopolamine on mice (n=21) performing the 5C-CPT were also assessed. SZ subjects exhibited significantly impaired attention in the 5C-CPT, driven by reduced target detection over time and nonsignificantly increased impulsive responding. Similarly, scopolamine significantly impaired attention in mice, driven by reduced target detection and nonsignificantly increased impulsive responding. Scopolamine also negatively affected accuracy and speed of responding in mice, although these measures failed to differentiate SZ vs. NCS. Thus, mice treated with scopolamine exhibited similar impairments in vigilance as seen in SZ, although the differences between the behavioral profiles warrant further study. The availability of rodent and human versions of this paradigm provides an opportunity to: (1) investigate the neuroanatomic, neurochemical and genomic architecture of abnormalities in attention observed in clinical populations such as SZ; (2) develop and refine animal models of cognitive impairments; and (3) improve cross-species translational testing for the development of treatments for these impairments.

  17. Molecular structural differences between low methoxy pectins induced by pectin methyl esterase II: effects on texture, release and perception of aroma in gels of similar modulus of elasticity.

    Science.gov (United States)

    Kim, Yang; Kim, Young-Suk; Yoo, Sang-Ho; Kim, Kwang-Ok

    2014-02-15

    Six low-methoxy pectins with different degrees of methylesterification and amidation, and molecular weights were used to prepare gels with similar moduli of elasticity by varying the concentrations of pectin and calcium phosphate. Five aroma compounds were added to the gels and their sensory textural properties, release and perception of aromas were investigated. Sensory firmness, springiness, adhesiveness, chewiness and cohesiveness differed according to the gel type, even though the moduli of elasticity were not significantly different (p<0.05). Release and perception of aromas also displayed significant difference according to the gel type (p<0.05). Low-methoxy amidated pectin exhibited the lowest release and perception for all the aroma compounds, while pectin-methylesterase-treated pectin gels exhibited relatively higher aroma release and perception. These results showed that the structural properties of pectins and gelling factors that increase the non-polar character of the gel matrices could decrease the release and perception of aromas in pectin gel systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Lead induces similar gene expression changes in brains of gestationally exposed adult mice and in neurons differentiated from mouse embryonic stem cells.

    Directory of Open Access Journals (Sweden)

    Francisco Javier Sánchez-Martín

    Full Text Available Exposure to environmental toxicants during embryonic life causes changes in the expression of developmental genes that may last for a lifetime and adversely affect the exposed individual. Developmental exposure to lead (Pb, an ubiquitous environmental contaminant, causes deficits in cognitive functions and IQ, behavioral effects, and attention deficit hyperactivity disorder (ADHD. Long-term effects observed after early life exposure to Pb include reduction of gray matter, alteration of myelin structure, and increment of criminal behavior in adults. Despite growing research interest, the molecular mechanisms responsible for the effects of lead in the central nervous system are still largely unknown. To study the molecular changes due to Pb exposure during neurodevelopment, we exposed mice to Pb in utero and examined the expression of neural markers, neurotrophins, transcription factors and glutamate-related genes in hippocampus, cortex, and thalamus at postnatal day 60. We found that hippocampus was the area where gene expression changes due to Pb exposure were more pronounced. To recapitulate gestational Pb exposure in vitro, we differentiated mouse embryonic stem cells (ESC into neurons and treated ESC-derived neurons with Pb for the length of the differentiation process. These neurons expressed the characteristic neuronal markers Tubb3, Syp, Gap43, Hud, Ngn1, Vglut1 (a marker of glutamatergic neurons, and all the glutamate receptor subunits, but not the glial marker Gafp. Importantly, several of the changes observed in Pb-exposed mouse brains in vivo were also observed in Pb-treated ESC-derived neurons, including those affecting expression of Ngn1, Bdnf exon IV, Grin1, Grin2D, Grik5, Gria4, and Grm6. We conclude that our ESC-derived model of toxicant exposure during neural differentiation promises to be a useful model to analyze mechanisms of neurotoxicity induced by Pb and other environmental agents.

  19. Morphology transition of raft-model membrane induced by osmotic pressure: Formation of double-layered vesicle similar to an endo- and/or exocytosis

    Energy Technology Data Exchange (ETDEWEB)

    Onai, Teruaki; Hirai, Mitsuhiro, E-mail: mhirai@fs.aramaki.gunma-u.ac.j [Department of Physics, Gunma University, Maebashi 371-8510 (Japan)

    2010-10-01

    The effect of osmotic pressure on the structure of large uni-lamellar vesicle (LUV) of the lipid mixtures of monosialoganglioside (G{sub M1})-cholesterol-dioleoyl-phosphatidylcholine (DOPC) was studies by using wide-angle X-ray scattering (WAXS) method. The molar ratios of the mixtures were 0.1/0.1/1, 0/0.1/1, and 0/0/1. The ternary lipid mixture is a model of lipid rafts. The value of osmotic pressure was varied from 0 to 4.16x10{sup 5} N/m{sup 2} by adding the polyvinylpyrrolidone (PVP) in the range from 0 to 25 % w/v. In the case of the mixtures without G{sub M1}, the rise of the osmotic pressure just enhances the multi-lamellar stacking with deceasing the inter-lamellar spacing. On the other hand, the mixture containing G{sub M1} shows the structural transition from a uni-lamellar vesicle to a double-layered vesicle (a liposome including a smaller one inside) by the rise of osmotic pressure. In this morphology transition the total surface area of the double-layered vesicle is mostly as same as that of the LUV at the initial state. The polar head region of G{sub M1} is bulky and highly hydrophilic due to the oligosaccharide chain containing a sialic acid residue. Then, the present results suggest that the existence of G{sub M1} in the outer-leaflet of the LUV is essentially important for such a double-layered vesicle formation. Alternatively, a phenomenon similar to an endo- and/or exocytosis in cells can be caused simply by a variation of osmotic pressure.

  20. Promoter-region hypermethylation and expression downregulation of Yy1 (Yin yang 1) in preneoplastic liver lesions in a thioacetamide rat hepatocarcinogenesis model

    Energy Technology Data Exchange (ETDEWEB)

    Abe, Hajime [Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509 (Japan); Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193 (Japan); Ogawa, Takashi; Wang, Liyun [Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509 (Japan); Kimura, Masayuki; Tanaka, Takeshi; Morita, Reiko [Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509 (Japan); Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193 (Japan); Yoshida, Toshinori [Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509 (Japan); Shibutani, Makoto, E-mail: mshibuta@cc.tuat.ac.jp [Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509 (Japan)

    2014-11-01

    Thioacetamide (TAA) has been used to develop a rodent model for hepatocarcinogenesis. To determine the genes with epigenetic modifications in early hepatocarcinogenesis, we did a genome-wide scan for hypermethylated promoter regions using CpG island microarrays in TAA-promoted rat liver tissue. Eight genes were selected based on the microarray profile; of these, Yy1 and Wdr45b were confirmed to be hypermethylated by methylation-specific polymerase chain reaction (PCR) and pyrosequencing and downregulated by real-time reverse transcription PCR. Non-neoplastic liver cells had nuclear Yy1 immunoreactivity, while preneoplastic foci with glutathione S-transferase placental form (GST-P) immunoreactivity had decreased Yy1 immunoreactivity. The incidence of these foci was proportional to the dose of TAA administered. Co-expression analysis of gene products downstream of Yy1 revealed increased nuclear phospho-c-Myc{sup +} foci as well as nuclear and cytoplasmic p21{sup Cip1+} foci in Yy1{sup −} or GST-P{sup +} foci in response to TAA-promotion dose. Although the absolute number of cells was low, the incidence of death receptor 5{sup −} foci was increased in Yy1{sup −} foci in proportion to the TAA dose. Yy1{sup −}/GST-P{sup +} foci revealed a higher number of proliferating cell nuclear antigen (PCNA)-immunoreactive cells than Yy1{sup +}/GST-P{sup +} foci, while cleaved caspase-3{sup +} cells were unchanged between Yy1{sup –}/GST-P{sup +} and Yy1{sup +}/GST-P{sup +} foci. In the case of Wdr45b, most GST-P{sup +} foci were Wdr45b{sup –} and were not increased by TAA promotion. These results suggest involvement of Yy1 in the epigenetic gene regulation at the early stages of TAA promoted cell proliferation and concomitant cell cycle arrest in preneoplastic lesions. - Highlights: • Epigenetically downregulated genes were searched in TAA-promnoted rat livers. • Yy1 and Wdr45b showed promoter-region hypermethylation and mRNA downregulation. • TAA promoted

  1. Similarity transformations of MAPs

    Directory of Open Access Journals (Sweden)

    Andersen Allan T.

    1999-01-01

    Full Text Available We introduce the notion of similar Markovian Arrival Processes (MAPs and show that the event stationary point processes related to two similar MAPs are stochastically equivalent. This holds true for the time stationary point processes too. We show that several well known stochastical equivalences as e.g. that between the H 2 renewal process and the Interrupted Poisson Process (IPP can be expressed by the similarity transformations of MAPs. In the appendix the valid region of similarity transformations for two-state MAPs is characterized.

  2. Similarity after Goodman

    NARCIS (Netherlands)

    Decock, L.B.; Douven, I.

    2011-01-01

    In a famous critique, Goodman dismissed similarity as a slippery and both philosophically and scientifically useless notion. We revisit his critique in the light of important recent work on similarity in psychology and cognitive science. Specifically, we use Tversky's influential set-theoretic

  3. Judgments of brand similarity

    NARCIS (Netherlands)

    Bijmolt, THA; Wedel, M; Pieters, RGM; DeSarbo, WS

    This paper provides empirical insight into the way consumers make pairwise similarity judgments between brands, and how familiarity with the brands, serial position of the pair in a sequence, and the presentation format affect these judgments. Within the similarity judgment process both the

  4. Similarity Measure of Graphs

    Directory of Open Access Journals (Sweden)

    Amine Labriji

    2017-07-01

    Full Text Available The topic of identifying the similarity of graphs was considered as highly recommended research field in the Web semantic, artificial intelligence, the shape recognition and information research. One of the fundamental problems of graph databases is finding similar graphs to a graph query. Existing approaches dealing with this problem are usually based on the nodes and arcs of the two graphs, regardless of parental semantic links. For instance, a common connection is not identified as being part of the similarity of two graphs in cases like two graphs without common concepts, the measure of similarity based on the union of two graphs, or the one based on the notion of maximum common sub-graph (SCM, or the distance of edition of graphs. This leads to an inadequate situation in the context of information research. To overcome this problem, we suggest a new measure of similarity between graphs, based on the similarity measure of Wu and Palmer. We have shown that this new measure satisfies the properties of a measure of similarities and we applied this new measure on examples. The results show that our measure provides a run time with a gain of time compared to existing approaches. In addition, we compared the relevance of the similarity values obtained, it appears that this new graphs measure is advantageous and  offers a contribution to solving the problem mentioned above.

  5. New Similarity Functions

    DEFF Research Database (Denmark)

    Yazdani, Hossein; Ortiz-Arroyo, Daniel; Kwasnicka, Halina

    2016-01-01

    spaces, in addition to their similarity in the vector space. Prioritized Weighted Feature Distance (PWFD) works similarly as WFD, but provides the ability to give priorities to desirable features. The accuracy of the proposed functions are compared with other similarity functions on several data sets......In data science, there are important parameters that affect the accuracy of the algorithms used. Some of these parameters are: the type of data objects, the membership assignments, and distance or similarity functions. This paper discusses similarity functions as fundamental elements in membership...... assignments. The paper introduces Weighted Feature Distance (WFD), and Prioritized Weighted Feature Distance (PWFD), two new distance functions that take into account the diversity in feature spaces. WFD functions perform better in supervised and unsupervised methods by comparing data objects on their feature...

  6. The BH3-only protein BID impairs the p38-mediated stress response and promotes hepatocarcinogenesis during chronic liver injury in mice.

    Science.gov (United States)

    Orlik, Johanna; Schüngel, Sven; Buitrago-Molina, Laura Elisa; Marhenke, Silke; Geffers, Robert; Endig, Jessica; Lobschat, Katharina; Rössler, Stephanie; Goeppert, Benjamin; Manns, Michael P; Gross, Atan; Vogel, Arndt

    2015-09-01

    Apoptosis is critical for maintaining tissue homeostasis, and apoptosis evasion is considered as a hallmark of cancer. However, increasing evidence also suggests that proapoptotic molecules can contribute to the development of cancer, including liver cancer. The aim of this study was to further clarify the role of the proapoptotic B-cell lymphoma 2 homology domain 3 (BH3)-only protein BH3 interacting-domain death agonist (BID) for chronic liver injury (CLI) and hepatocarcinogenesis (HCG). Loss of BID significantly delayed tumor development in two mouse models of Fah-mediated and HBsTg-driven HCG, suggesting a tumor-promoting effect of BID. Liver injury as well as basal and mitogen-stimulated hepatocyte proliferation were not modulated by BID. Moreover, there was no in vivo or in vitro evidence that BID was involved in DNA damage response in hepatocytes and hepatoma cells. Our data revealed that CLI was associated with strong activation of oxidative stress (OS) response and that BID impaired full activation of p38 after OS. We provide evidence that the tumor-promoting function of BID in CLI is not related to enhanced proliferation or an impaired DNA damage response. In contrast, BID suppresses p38 activity and facilitates malignant transformation of hepatocytes. © 2015 by the American Association for the Study of Liver Diseases.

  7. A dual and opposite effect of Calendula officinalis flower extract: chemoprotector and promoter in a rat hepatocarcinogenesis model.

    Science.gov (United States)

    Barajas-Farias, L M; Pérez-Carreón, J I; Arce-Popoca, E; Fattel-Fazenda, S; Alemán-Lazarini, L; Hernández-García, S; Salcido-Neyoy, M; Cruz-Jiménez, F G; Camacho, J; Villa-Treviño, S

    2006-02-01

    Calendula officinalis extracts have protective and cytotoxic effects. We previously reported the dual activity of C. officinalis in primary rat hepatocyte cultures treated with N-nitrosodiethylamine. At nM concentrations it was anti-genotoxic while at microM concentrations it exhibited genotoxic effects. Here we tested the activity of Calendula officinalis in vivo in male Fischer 344 rats initiated with N-nitrosodiethylamine, promoted with 2-acetylaminofluorene, and 70 % partially hepatectomized. Liver gamma-glutamyltranspeptidase positively altered hepatocyte foci 25 days after initiation were our end point. The protective effect of C. officinalis started at 0.1 mg/kg concentration, increased at 0.5 mg/kg and reached its maximum at 2.5 mg/kg, when it decreased the area and number of altered foci by 55 % and 49 %, respectively, in comparison with rats treated only with carcinogen. At 5 mg/kg the number and area of altered hepatocyte foci were still lower, but almost reached the figures of carcinogen-treated rats. Ten and 20 mg/kg doses produced a notorious increment in the area and number of altered hepatic foci, and at 40 mg/kg of extract the increment was 40 % and 53 %, respectively. Additionally, when 2-acetylaminofluorene was substituted by a 40 mg/kg C. officinalis extract, a promoting effect was observed with increments of 175 % and 266 % in area and number of altered hepatocyte foci with respect to controls. When N-nitrosodiethylamine was substituted by 40 mg/kg of extract, the latter did not show initiator activity. In summary, we showed a protecting activity of C. officinalis at low doses, but doses above 10 mg/kg increased altered hepatocyte foci. This dual effect is an example of the phenomenon of hormesis. Furthermore, 40 mg/kg of dry weight extract administered instead of 2-acetylaminofluorene induced a clear promoting activity. These in vivo results are similar and consistent with those reported by us in primary rat liver cell cultures.

  8. The semantic similarity ensemble

    Directory of Open Access Journals (Sweden)

    Andrea Ballatore

    2013-12-01

    Full Text Available Computational measures of semantic similarity between geographic terms provide valuable support across geographic information retrieval, data mining, and information integration. To date, a wide variety of approaches to geo-semantic similarity have been devised. A judgment of similarity is not intrinsically right or wrong, but obtains a certain degree of cognitive plausibility, depending on how closely it mimics human behavior. Thus selecting the most appropriate measure for a specific task is a significant challenge. To address this issue, we make an analogy between computational similarity measures and soliciting domain expert opinions, which incorporate a subjective set of beliefs, perceptions, hypotheses, and epistemic biases. Following this analogy, we define the semantic similarity ensemble (SSE as a composition of different similarity measures, acting as a panel of experts having to reach a decision on the semantic similarity of a set of geographic terms. The approach is evaluated in comparison to human judgments, and results indicate that an SSE performs better than the average of its parts. Although the best member tends to outperform the ensemble, all ensembles outperform the average performance of each ensemble's member. Hence, in contexts where the best measure is unknown, the ensemble provides a more cognitively plausible approach.

  9. Additive Similarity Trees

    Science.gov (United States)

    Sattath, Shmuel; Tversky, Amos

    1977-01-01

    Tree representations of similarity data are investigated. Hierarchical clustering is critically examined, and a more general procedure, called the additive tree, is presented. The additive tree representation is then compared to multidimensional scaling. (Author/JKS)

  10. Gender similarities and differences.

    Science.gov (United States)

    Hyde, Janet Shibley

    2014-01-01

    Whether men and women are fundamentally different or similar has been debated for more than a century. This review summarizes major theories designed to explain gender differences: evolutionary theories, cognitive social learning theory, sociocultural theory, and expectancy-value theory. The gender similarities hypothesis raises the possibility of theorizing gender similarities. Statistical methods for the analysis of gender differences and similarities are reviewed, including effect sizes, meta-analysis, taxometric analysis, and equivalence testing. Then, relying mainly on evidence from meta-analyses, gender differences are reviewed in cognitive performance (e.g., math performance), personality and social behaviors (e.g., temperament, emotions, aggression, and leadership), and psychological well-being. The evidence on gender differences in variance is summarized. The final sections explore applications of intersectionality and directions for future research.

  11. Identification of a second family of genes in Moniliophthora perniciosa, the causal agent of witches' broom disease in cacao, encoding necrosis-inducing proteins similar to cerato-platanins.

    Science.gov (United States)

    Zaparoli, Gustavo; Cabrera, Odalys García; Medrano, Francisco Javier; Tiburcio, Ricardo; Lacerda, Gustavo; Pereira, Gonçalo Guimarães

    2009-01-01

    The hemibiotrophic basidiomycete Moniliophthora perniciosa is the causal agent of witches' broom disease in cacao. This is a dimorphic species, with monokaryotic hyphae during the biotrophic phase, which is converted to dikaryotic mycelia during the saprophytic phase. The infection in pod is characterized by the formation of hypertrophic and hyperplasic tissues in the biotrophic phase, which is followed by necrosis and complete degradation of the organ. We found at least five sequences in the fungal genome encoding putative proteins similar to cerato-platanin (CP)-like proteins, a novel class of proteins initially found in the phytopathogen Ceratocystis fimbriata. One M. perniciosa CP gene (MpCP1) was expressed in vitro and proved to have necrosis-inducing ability in tobacco and cacao leaves. The protein is present in solution as dimers and is able to recover necrosis activity after heat treatment. Transcription analysis ex planta showed that MpCP1 is more expressed in biotrophic-like mycelia than saprotrophic mycelia. The necrosis profile presented is different from that caused by M. perniciosa necrosis and ethylene-inducing proteins (MpNEPs), another family of elicitors expressed by M. perniciosa. Remarkably, a mixture of MpCP1 with MpNEP2 led to a synergistic necrosis effect very similar to that found in naturally infected plants. This is the first report of a basidiomycete presenting both NEP1-like proteins (NLPs) and CPs in its genome.

  12. De novo deposition of laminin-positive basement membrane in vitro by normal hepatocytes and during hepatocarcinogenesis

    DEFF Research Database (Denmark)

    Albrechtsen, R; Wewer, U M; Thorgeirsson, S S

    1988-01-01

    De novo formation of laminin-positive basement membranes was found to be a distinct morphologic feature of diethylnitrosamine/phenobarbital-induced hepatocellular carcinomas of the rat. The first appearance of extracellularly located laminin occurred in the preneoplastic liver lesions (correspond......De novo formation of laminin-positive basement membranes was found to be a distinct morphologic feature of diethylnitrosamine/phenobarbital-induced hepatocellular carcinomas of the rat. The first appearance of extracellularly located laminin occurred in the preneoplastic liver lesions...

  13. Similarity or difference?

    DEFF Research Database (Denmark)

    Villadsen, Anders Ryom

    2013-01-01

    While the organizational structures and strategies of public organizations have attracted substantial research attention among public management scholars, little research has explored how these organizational core dimensions are interconnected and influenced by pressures for similarity....... In this paper I address this topic by exploring the relation between expenditure strategy isomorphism and structure isomorphism in Danish municipalities. Different literatures suggest that organizations exist in concurrent pressures for being similar to and different from other organizations in their field...... of action. It is theorized that to meet this challenge organizations may substitute increased similarity on one core dimension for increased idiosyncrasy on another, but only after a certain level of isomorphism is reached. Results of quantitative analyses support this theory and show that an inverse U...

  14. Incremental Similarity and Turbulence

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole E.; Hedevang, Emil; Schmiegel, Jürgen

    This paper discusses the mathematical representation of an empirically observed phenomenon, referred to as Incremental Similarity. We discuss this feature from the viewpoint of stochastic processes and present a variety of non-trivial examples, including those that are of relevance for turbulence...

  15. Upregulation of heat shock protein 70 and the differential protein expression induced by tumor necrosis factor-alpha enhances migration and inhibits apoptosis of hepatocellular carcinoma cell HepG2

    OpenAIRE

    Huang, Bee-Piao; Lin, Chun-Shiang; Wang, Chau-Jong; Kao, Shao-Hsuan

    2017-01-01

    Tumor necrosis factor alpha (TNF?) plays diverse roles in liver damage and hepatocarcinogenesis with its multipotent bioactivity. However, the influence of TNF? on protein expression of hepatocellular carcinoma (HCC) is incompletely understood. Therefore, we aimed to investigate the differential protein expression of HCC in response to TNF? stimulus. We observed that HepG2 cell revealed a higher resistance to TNF?-induced apoptosis as compared to the non-tumorigenic hepatocyte THLE-2. By usin...

  16. More Similar Than Different

    DEFF Research Database (Denmark)

    Pedersen, Mogens Jin

    2015-01-01

    What role do employee features play into the success of different personnel management practices for serving high performance? Using data from a randomized survey experiment among 5,982 individuals of all ages, this article examines how gender conditions the compliance effects of different...... incentive treatments—each relating to the basic content of distinct types of personnel management practices. The findings show that males and females are more similar than different in terms of the incentive treatments’ effects: Significant average effects are found for three out of five incentive...

  17. Similar or different?

    DEFF Research Database (Denmark)

    Cornér, Solveig; Pyhältö, Kirsi; Peltonen, Jouni

    2018-01-01

    experienced by PhD students within the same discipline. This study explores the support experiences of 381 PhD students within the humanities and social sciences from three research-intensive universities in Denmark (n=145) and Finland (n=236). The mixed methods design was utilized. The data were collected...... counter partners, whereas the Finnish students perceived lower levels of instrumental support than the Danish students. The findings imply that seemingly similar contexts hold valid differences in experienced social support and educational strategies at the PhD level.......Previous research has identified researcher community and supervisory support as key determinants of the doctoral journey contributing to students’ persistence and robustness. However, we still know little about cross-cultural variation in the researcher community and supervisory support...

  18. Intranodular signal intensity analysis of hypovascular high-risk borderline lesions of HCC that illustrate multi-step hepatocarcinogenesis within the nodule on Gd–EOB–DTPA-enhanced MRI

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Satoshi, E-mail: satoshik@staff.kanazawa-u.ac.jp [Dept of Radiology, Kanazawa University School of Medicine, 13-1, Takara Machi, Kanazawa 920-8641 (Japan); Matsui, Osamu, E-mail: matsuio@med.kanazawa-u.ac.jp [Dept of Radiology, Kanazawa University School of Medicine, 13-1, Takara Machi, Kanazawa 920-8641 (Japan); Gabata, Toshifumi, E-mail: gabata@med.kanazawa-u.ac.jp [Dept of Radiology, Kanazawa University School of Medicine, 13-1, Takara Machi, Kanazawa 920-8641 (Japan); Koda, Wataru, E-mail: wkoda@staff.kanazawa-u.ac.jp [Dept of Radiology, Kanazawa University School of Medicine, 13-1, Takara Machi, Kanazawa 920-8641 (Japan); Minami, Tetsuya, E-mail: tminami@staff.kanazawa-u.ac.jp [Dept of Radiology, Kanazawa University School of Medicine, 13-1, Takara Machi, Kanazawa 920-8641 (Japan); Ryu, Yasuji, E-mail: yryu-kanazawa@umin.ac.jp [Dept of Radiology, Kanazawa University School of Medicine, 13-1, Takara Machi, Kanazawa 920-8641 (Japan); Kozaka, Kazuto, E-mail: k-kozaka@staff.kanazawa-u.ac.jp [Dept of Radiology, Kanazawa University School of Medicine, 13-1, Takara Machi, Kanazawa 920-8641 (Japan); Kitao, Azusa, E-mail: azusa@med.kanazawa-u.ac.jp [Dept of Radiology, Kanazawa University School of Medicine, 13-1, Takara Machi, Kanazawa 920-8641 (Japan)

    2012-12-15

    Objectives: To analyze intranodular signal intensity pattern of hypovascular high-risk borderline lesions of HCC that illustrate multi-step hepatocarcinogenesis within the nodule on Gd–EOB–DTPA-enhanced MRI. Methods: A total of 73 nodules showing hypervascular foci in hypovascular high-risk borderline lesions identified by angiography-assisted CT were included in this study. The intranodular signal intensities of both the hypervascular foci and the hypovascular high-risk borderline lesions were evaluated on hepatobiliary-phase EOB-enhanced MRI obtained 20 min after intravenous injection of contrast media. Results: Among 59 hypervascular foci within hypointense hypovascular high-risk borderline lesions, 6 showed more hypointensity, 32 isointensity, and 21 hyperintensity compared to the surrounding hypointense, hypovascular portion of the nodules. Among 14 hypervascular foci within isointense hypovascular high-risk borderline lesions, 5 showed isointensity, and 9 hypointensity compared to the surrounding isointense hypovascular high-risk borderline lesions. No hypervascular foci showed hyperintensity compared to the surrounding isointense hypovascular high-risk borderline lesions. Conclusions: In most of the hypovascular high-risk borderline lesions containing hypervascular foci within the nodule, the signal intensity was decreased in hypervascular foci as compared with hypovascular high-risk borderline lesions and the surrounding background liver parenchyma. This supports the concept of signal intensity decrease during the dedifferentiation process in multistep hepatocarcinogenesis. However, around 30% of the nodules did not follow this rule, and hypervascular foci showed hyperintensity relative to the hypovascular high-risk borderline lesions.

  19. Extracellular matrix dynamics in hepatocarcinogenesis: a comparative proteomics study of PDGFC transgenic and Pten null mouse models.

    Directory of Open Access Journals (Sweden)

    Keane K Y Lai

    2011-06-01

    Full Text Available We are reporting qualitative and quantitative changes of the extracellular matrix (ECM and associated receptor proteomes, occurring during the transition from liver fibrosis and steatohepatitis to hepatocellular carcinoma (HCC. We compared two mouse models relevant to human HCC: PDGFC transgenic (Tg and Pten null mice, models of disease progression from fibrosis and steatohepatitis to HCC. Using mass spectrometry, we identified in the liver of both models proteins for 26 collagen-encoding genes, providing the first evidence of expression at the protein level for 16 collagens. We also identified post-transcriptional protein variants for six collagens and lysine hydroxylation modifications for 14 collagens. Tumor-associated collagen proteomes were similar in both models with increased expression of collagens type IV, VI, VII, X, XIV, XV, XVI, and XVIII. Splice variants for Col4a2, Col6a2, Col6a3 were co-upregulated while only the short form of Col18a1 increased in the tumors. We also identified tumor specific increases of nidogen 1, decorin, perlecan, and of six laminin subunits. The changes in these non-collagenous ECM proteins were similar in both models with the exception of laminin β3, detected specifically in the Pten null tumors. Pdgfa and Pdgfc mRNA expression was increased in the Pten null liver, a possible mechanism for the similarity in ECM composition observed in the tumors of both models. In contrast and besides the strong up-regulation of integrin α5 protein observed in the liver tumors of both models, the expression of the six other integrins identified was specific to each model, with integrins α2b, α3, α6, and β1 up-regulated in Pten null tumors and integrins α8 and β5 up-regulated in the PDGFC Tg tumors. In conclusion, HCC-associated ECM proteins and ECM-integrin networks, common or specific to HCC subtypes, were identified, providing a unique foundation to using ECM composition for HCC classification, diagnosis

  20. Quantum mechanical model for the anticarcinogenic effect of extremely-low-frequency electromagnetic fields on early chemical hepatocarcinogenesis

    Science.gov (United States)

    Godina-Nava, Juan José; Torres-Vega, Gabino; López-Riquelme, Germán Octavio; López-Sandoval, Eduardo; Samana, Arturo Rodolfo; García Velasco, Fermín; Hernández-Aguilar, Claudia; Domínguez-Pacheco, Arturo

    2017-02-01

    Using the conventional Haberkorn approach, it is evaluated the recombination of the radical pair (RP) singlet spin state to study theoretically the cytoprotective effect of an extremely-low-frequency electromagnetic field (ELF-EMF) on early stages of hepatic cancer chemically induced in rats. The proposal is that ELF-EMF modulates the interconversion rate of singlet and triplet spin states of the RP populations modifying the products from the metabolization of carcinogens. Previously, we found that the daily treatment with ELF-EMF 120 Hz inhibited the number and area of preneoplastic lesions in chemical carcinogenesis. The singlet spin population is evaluated diagonalizing the spin density matrix through the Lanczos method in a radical pair mechanism (RPM). Using four values of the interchange energy, we have studied the variations over the singlet population. The low magnetic field effect as a test of the influence over the enzymatic chemical reaction is evaluated calculating the quantum yield. Through a bootstrap technique the range is found for the singlet decay rate for the process. Applying the quantum measurements concept, we addressed the impact toward hepatic cells. The result contributes to improving our understanding of the chemical carcinogenesis process affected by charged particles that damage the DNA.

  1. Quantum mechanical model for the anticarcinogenic effect of extremely-low-frequency electromagnetic fields on early chemical hepatocarcinogenesis.

    Science.gov (United States)

    Godina-Nava, Juan José; Torres-Vega, Gabino; López-Riquelme, Germán Octavio; López-Sandoval, Eduardo; Samana, Arturo Rodolfo; García Velasco, Fermín; Hernández-Aguilar, Claudia; Domínguez-Pacheco, Arturo

    2017-02-01

    Using the conventional Haberkorn approach, it is evaluated the recombination of the radical pair (RP) singlet spin state to study theoretically the cytoprotective effect of an extremely-low-frequency electromagnetic field (ELF-EMF) on early stages of hepatic cancer chemically induced in rats. The proposal is that ELF-EMF modulates the interconversion rate of singlet and triplet spin states of the RP populations modifying the products from the metabolization of carcinogens. Previously, we found that the daily treatment with ELF-EMF 120 Hz inhibited the number and area of preneoplastic lesions in chemical carcinogenesis. The singlet spin population is evaluated diagonalizing the spin density matrix through the Lanczos method in a radical pair mechanism (RPM). Using four values of the interchange energy, we have studied the variations over the singlet population. The low magnetic field effect as a test of the influence over the enzymatic chemical reaction is evaluated calculating the quantum yield. Through a bootstrap technique the range is found for the singlet decay rate for the process. Applying the quantum measurements concept, we addressed the impact toward hepatic cells. The result contributes to improving our understanding of the chemical carcinogenesis process affected by charged particles that damage the DNA.

  2. Alcohol consumption promotes diethylnitrosamine-induced hepatocarcinogenesis in male mice through the activation of the Wnt/Beta-catenin signaling pathway

    Science.gov (United States)

    Although alcohol effects within the liver have been extensively studied, the complex mechanisms by which alcohol causes liver cancer are not well understood. It has been suggested that ethanol (EtOH) metabolism promotes tumor growth by increasing hepatocyte proliferation. In this study, we develop...

  3. On distributional assumptions and whitened cosine similarities

    DEFF Research Database (Denmark)

    Loog, Marco

    2008-01-01

    Recently, an interpretation of the whitened cosine similarity measure as a Bayes decision rule was proposed (C. Liu, "The Bayes Decision Rule Induced Similarity Measures,'' IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 29, no. 6, pp. 1086-1090, June 2007. This communication makes...... the observation that some of the distributional assumptions made to derive this measure are very restrictive and, considered simultaneously, even inconsistent....

  4. Similarity increases altruistic punishment in humans.

    Science.gov (United States)

    Mussweiler, Thomas; Ockenfels, Axel

    2013-11-26

    Humans are attracted to similar others. As a consequence, social networks are homogeneous in sociodemographic, intrapersonal, and other characteristics--a principle called homophily. Despite abundant evidence showing the importance of interpersonal similarity and homophily for human relationships, their behavioral correlates and cognitive foundations are poorly understood. Here, we show that perceived similarity substantially increases altruistic punishment, a key mechanism underlying human cooperation. We induced (dis)similarity perception by manipulating basic cognitive mechanisms in an economic cooperation game that included a punishment phase. We found that similarity-focused participants were more willing to punish others' uncooperative behavior. This influence of similarity is not explained by group identity, which has the opposite effect on altruistic punishment. Our findings demonstrate that pure similarity promotes reciprocity in ways known to encourage cooperation. At the same time, the increased willingness to punish norm violations among similarity-focused participants provides a rationale for why similar people are more likely to build stable social relationships. Finally, our findings show that altruistic punishment is differentially involved in encouraging cooperation under pure similarity vs. in-group conditions.

  5. Similar outcome despite slight clinical differences between lumbar radiculopathy induced by lateral versus medial disc herniations in patients without previous foraminal stenosis: a prospective cohort study with 1-year follow-up.

    Science.gov (United States)

    Mérot, Oriane A; Maugars, Yves M; Berthelot, Jean-Marie M

    2014-08-01

    lying or standing), but slight significant differences (t testlumbar spine (above L4-L5: 7/28 vs. 3/31), motor weakness was more frequent (25% vs. 3%), SLR was less restricted (65.0°±24.5° vs. 51.1°±25.7°), DN4 score of neuropathic pain was higher (4.4±2.1 vs. 3.2±1.8), anxiety level was higher (10.3±4.1 vs. 7.9±3.2), length of hospital stay was longer (5.7±2.4 days vs. 4.5±1.4 days), and physician's prognosis of a good outcome was poorer (6.6±2.2 vs. 8.0±1.6). However, at the end of follow-up (12.2±3.3 months), outcome was similar: 37% (vs. 41% for medial herniations) had transiently relapsed, 66% felt finally improved (vs. 63%), and walking capacity was nearly identical despite the fact that only 18% had to be operated (vs. 32% of those with medial herniations). Despite differences in clinical presentation, the outcome of radiculopathy induced by the more lateral lumbar disc herniations was not worse than the outcome of patients with only medial disc herniations. Previous claims of poorer outcome in foraminal herniations might be explained by the inclusion of patients with associated foraminal stenosis. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Curcumin Attenuates N-Nitrosodiethylamine-Induced Liver Injury in Mice by Utilizing the Method of Metabonomics.

    Science.gov (United States)

    Qiu, Peiyu; Sun, Jiachen; Man, Shuli; Yang, He; Ma, Long; Yu, Peng; Gao, Wenyuan

    2017-03-08

    N-Nitrosodiethylamine (DEN) exists as a food additive in cheddar cheese, processed meats, beer, water, and so forth. It is a potent hepatocarcinogen in animals and humans. Curcumin as a natural dietary compound decreased DEN-induced hepatocarcinogenesis in this research. According to the histopathological examination of liver tissues and biomarker detection in serum and livers, it was demonstrated that curcumin attenuated DEN-induced hepatocarcinogenesis through parts of regulating the oxidant stress enzymes (T-SOD and CAT), liver function (ALT and AST) and LDHA, AFP level, and COX-2/PGE2 pathway. Furthermore, curcumin attenuated metabolic disorders via increasing concentration of glucose and fructose, and decreasing levels of glycine and proline, and mRNA expression of GLUT1, PKM and FASN. Docking study indicated that curcumin presented strong affinity with key metabolism enzymes such as GLUT1, PKM, FASN and LDHA. There were a number of amino acid residues involved in curcumin-targeting enzymes of hydrogen bonds and hydrophobic interactions. All in all, curcumin exhibited a potent liver protective agent inhibiting chemically induced liver injury through suppressing liver cellular metabolism in the prospective application.

  7. A COMPARISON OF SEMANTIC SIMILARITY MODELS IN EVALUATING CONCEPT SIMILARITY

    Directory of Open Access Journals (Sweden)

    Q. X. Xu

    2012-08-01

    Full Text Available The semantic similarities are important in concept definition, recognition, categorization, interpretation, and integration. Many semantic similarity models have been established to evaluate semantic similarities of objects or/and concepts. To find out the suitability and performance of different models in evaluating concept similarities, we make a comparison of four main types of models in this paper: the geometric model, the feature model, the network model, and the transformational model. Fundamental principles and main characteristics of these models are introduced and compared firstly. Land use and land cover concepts of NLCD92 are employed as examples in the case study. The results demonstrate that correlations between these models are very high for a possible reason that all these models are designed to simulate the similarity judgement of human mind.

  8. Renewing the Respect for Similarity

    Directory of Open Access Journals (Sweden)

    Shimon eEdelman

    2012-07-01

    Full Text Available In psychology, the concept of similarity has traditionally evoked a mixture of respect, stemmingfrom its ubiquity and intuitive appeal, and concern, due to its dependence on the framing of the problemat hand and on its context. We argue for a renewed focus on similarity as an explanatory concept, bysurveying established results and new developments in the theory and methods of similarity-preservingassociative lookup and dimensionality reduction — critical components of many cognitive functions, aswell as of intelligent data management in computer vision. We focus in particular on the growing familyof algorithms that support associative memory by performing hashing that respects local similarity, andon the uses of similarity in representing structured objects and scenes. Insofar as these similarity-basedideas and methods are useful in cognitive modeling and in AI applications, they should be included inthe core conceptual toolkit of computational neuroscience.

  9. An n-3 PUFA-rich microalgal oil diet protects to a similar extent as a fish oil-rich diet against AOM-induced colonic aberrant crypt foci in male F344 rats

    NARCIS (Netherlands)

    Beelen, van V.A.; Spenkelink, A.; Mooibroek, H.; Sijtsma, L.; Bosch, H.J.; Rietjens, I.M.C.M.; Alink, G.M.

    2009-01-01

    The chemopreventive effects of high fat microalgal oil diet on azoxymethane (AOM)-induced colonic aberrant crypt foci (ACF) were studied in male Fischer 344 rats following 8 weeks of dietary treatment. These effects were compared to the effects of high fat fish oil and high fat corn oil diets to

  10. Dynamic similarity in erosional processes

    Science.gov (United States)

    Scheidegger, A.E.

    1963-01-01

    A study is made of the dynamic similarity conditions obtaining in a variety of erosional processes. The pertinent equations for each type of process are written in dimensionless form; the similarity conditions can then easily be deduced. The processes treated are: raindrop action, slope evolution and river erosion. ?? 1963 Istituto Geofisico Italiano.

  11. Fisetin Modulates Antioxidant Enzymes and Inflammatory Factors to Inhibit Aflatoxin-B1 Induced Hepatocellular Carcinoma in Rats

    Directory of Open Access Journals (Sweden)

    Brajesh Kumar Maurya

    2016-01-01

    Full Text Available Fisetin, a known antioxidant, has been found to be cytotoxic against certain cell lines. However, the mechanism by which it inhibits tumor growth in vivo remains unexplored. Recently, we have demonstrated that Aflatoxin-B1 (AFB1 induced hepatocarcinogenesis is associated with activation of oxidative stress-inflammatory pathway in rat liver. The present paper describes the effect of in vivo treatment with 20 mg/kg b.w. Fisetin on antioxidant enzymes vis-a-vis oxidative stress level and on the profile of certain proinflammatory cytokines in the hepatocellular carcinoma (HCC induced by two doses of 1 mg/kg b.w. AFB1 i.p. in rats. The reduced levels of most of the antioxidant enzymes, coinciding with the enhanced level of reactive oxygen species in the HCC liver, were observed to regain their normal profiles due to Fisetin treatment. Also, Fisetin treatment could normalize the enhanced expression of TNFα and IL1α, the two proinflammatory cytokines, reported to be involved in HCC pathogenesis. These observations were consistent with the regression of neoplastic lesion and declined GST-pi (placental type glutathione-S-transferase level, a HCC marker, in the liver of the Fisetin treated HCC rats. The findings suggest that Fisetin attenuates oxidative stress-inflammatory pathway of AFB1 induced hepatocarcinogenesis.

  12. Fisetin Modulates Antioxidant Enzymes and Inflammatory Factors to Inhibit Aflatoxin-B1 Induced Hepatocellular Carcinoma in Rats.

    Science.gov (United States)

    Maurya, Brajesh Kumar; Trigun, Surendra Kumar

    2016-01-01

    Fisetin, a known antioxidant, has been found to be cytotoxic against certain cell lines. However, the mechanism by which it inhibits tumor growth in vivo remains unexplored. Recently, we have demonstrated that Aflatoxin-B1 (AFB1) induced hepatocarcinogenesis is associated with activation of oxidative stress-inflammatory pathway in rat liver. The present paper describes the effect of in vivo treatment with 20 mg/kg b.w. Fisetin on antioxidant enzymes vis-a-vis oxidative stress level and on the profile of certain proinflammatory cytokines in the hepatocellular carcinoma (HCC) induced by two doses of 1 mg/kg b.w. AFB1 i.p. in rats. The reduced levels of most of the antioxidant enzymes, coinciding with the enhanced level of reactive oxygen species in the HCC liver, were observed to regain their normal profiles due to Fisetin treatment. Also, Fisetin treatment could normalize the enhanced expression of TNFα and IL1α, the two proinflammatory cytokines, reported to be involved in HCC pathogenesis. These observations were consistent with the regression of neoplastic lesion and declined GST-pi (placental type glutathione-S-transferase) level, a HCC marker, in the liver of the Fisetin treated HCC rats. The findings suggest that Fisetin attenuates oxidative stress-inflammatory pathway of AFB1 induced hepatocarcinogenesis.

  13. An n-3 PUFA-rich microalgal oil diet protects to a similar extent as a fish oil-rich diet against AOM-induced colonic aberrant crypt foci in F344 rats.

    Science.gov (United States)

    van Beelen, Vincent A; Spenkelink, Bert; Mooibroek, Hans; Sijtsma, Lolke; Bosch, Dirk; Rietjens, Ivonne M C M; Alink, Gerrit M

    2009-02-01

    The chemopreventive effects of high fat microalgal oil diet on azoxymethane (AOM)-induced colonic aberrant crypt foci (ACF) were studied in male Fischer 344 rats following 8 weeks of dietary treatment. These effects were compared to the effects of high fat fish oil and high fat corn oil diets to determine whether microalgal oil is a good alternative for fish oil regarding protection against colorectal cancer. Despite the difference in fatty acid composition and total amount of n-3 polyunsaturated fatty acids (PUFAs) between microalgal oil and fish oil, both these oils gave the same 50% reduction of AOM-induced ACF when compared to corn oil. To determine whether oxidative stress could play a role in the chemoprevention of colorectal cancer by n-3 PUFAs, feces and caecal content were examined using the TBA assay. The results showed that lipid peroxidation does occur in the gastrointestinal tract. As several lipid peroxidation products of n-3 PUFAs can induce phase II detoxifying enzymes by an EpRE-mediated pathway, the in vivo results suggest that this route may contribute to n-3 PUFA-mediated chemoprevention. All in all, n-3 PUFA-rich oil from microalgae is as good as fish oil regarding chemoprevention in the colon of the rat.

  14. Renewing the respect for similarity.

    Science.gov (United States)

    Edelman, Shimon; Shahbazi, Reza

    2012-01-01

    In psychology, the concept of similarity has traditionally evoked a mixture of respect, stemming from its ubiquity and intuitive appeal, and concern, due to its dependence on the framing of the problem at hand and on its context. We argue for a renewed focus on similarity as an explanatory concept, by surveying established results and new developments in the theory and methods of similarity-preserving associative lookup and dimensionality reduction-critical components of many cognitive functions, as well as of intelligent data management in computer vision. We focus in particular on the growing family of algorithms that support associative memory by performing hashing that respects local similarity, and on the uses of similarity in representing structured objects and scenes. Insofar as these similarity-based ideas and methods are useful in cognitive modeling and in AI applications, they should be included in the core conceptual toolkit of computational neuroscience. In support of this stance, the present paper (1) offers a discussion of conceptual, mathematical, computational, and empirical aspects of similarity, as applied to the problems of visual object and scene representation, recognition, and interpretation, (2) mentions some key computational problems arising in attempts to put similarity to use, along with their possible solutions, (3) briefly states a previously developed similarity-based framework for visual object representation, the Chorus of Prototypes, along with the empirical support it enjoys, (4) presents new mathematical insights into the effectiveness of this framework, derived from its relationship to locality-sensitive hashing (LSH) and to concomitant statistics, (5) introduces a new model, the Chorus of Relational Descriptors (ChoRD), that extends this framework to scene representation and interpretation, (6) describes its implementation and testing, and finally (7) suggests possible directions in which the present research program can be

  15. Self-similar aftershock rates

    CERN Document Server

    Davidsen, Jörn

    2016-01-01

    In many important systems exhibiting crackling noise --- intermittent avalanche-like relaxation response with power-law and, thus, self-similar distributed event sizes --- the "laws" for the rate of activity after large events are not consistent with the overall self-similar behavior expected on theoretical grounds. This is in particular true for the case of seismicity and a satisfying solution to this paradox has remained outstanding. Here, we propose a generalized description of the aftershock rates which is both self-similar and consistent with all other known self-similar features. Comparing our theoretical predictions with high resolution earthquake data from Southern California we find excellent agreement, providing in particular clear evidence for a unified description of aftershocks and foreshocks. This may offer an improved way of time-dependent seismic hazard assessment and earthquake forecasting.

  16. Method of similarity for cavitation

    Energy Technology Data Exchange (ETDEWEB)

    Espanet, L.; Tekatlian, A.; Barbier, D. [CEA/Cadarache, Dept. d' Etudes des Combustibles (DEC), 13 - Saint-Paul-lez-Durance (France); Gouin, H. [Aix-Marseille-3 Univ., 13 - Marseille (France). Laboratoire de Modelisation en Mecanique et Thermodynamique

    1998-07-01

    The knowledge of possible cavitation in subassembly nozzles of the fast reactor core implies the realization of a fluid dynamic model test. We propose a method of similarity based on the non-dimensionalization of the equation of motion for viscous capillarity fluid issued from the Cahn and Hilliard model. Taking into account the dissolved gas effect, a condition of compatibility is determined. This condition must be respected by the fluid in experiment, along with the scaling between the two similar flows. (author)

  17. Self-Similar Isentropic Implosions

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, M.; Amable, L.

    1980-07-01

    The self-similar compression of an isentropic spherical gas pellet Is analyzed for large values of the ratio of the final to initial densities. An asymptotic analysis provides the solution corresponding to a prescribed value of the final density when it is high. In addition an approximate solution is given when the specific heat ratio is not constant. The time evolution of the pressure on the outer surface leading to the self-similar solutions, is calculated for large density ratios. (Author)

  18. Pomegranate Bioactive Constituents Suppress Cell Proliferation and Induce Apoptosis in an Experimental Model of Hepatocellular Carcinoma: Role of Wnt/β-Catenin Signaling Pathway

    Directory of Open Access Journals (Sweden)

    Deepak Bhatia

    2013-01-01

    Full Text Available Hepatocellular carcinoma (HCC is the third leading cause of cancer-related death worldwide, and chemoprevention represents a viable approach in lowering the mortality of this disease. Pomegranate fruit, an abundant source of anti-inflammatory phytochemicals, is gaining tremendous attention for its wide-spectrum health benefits. We previously reported that a characterized pomegranate emulsion (PE prevents diethylnitrosamine (DENA-induced rat hepatocarcinogenesis though inhibition of nuclear factor-kappaB (NF-κB. Since NF-κB concurrently induces Wnt/β-catenin signaling implicated in cell proliferation, cell survival, and apoptosis evasion, we examined antiproliferative, apoptosis-inducing and Wnt/β-catenin signaling-modulatory mechanisms of PE during DENA rat hepatocarcinogenesis. PE (1 or 10 g/kg was administered 4 weeks before and 18 weeks following DENA exposure. There was a significant increase in hepatic proliferation (proliferating cell nuclear antigen and alteration in cell cycle progression (cyclin D1 due to DENA treatment, and PE dose dependently reversed these effects. PE substantially induced apoptosis by upregulating proapoptotic protein Bax and downregulating antiapoptotic protein Bcl-2. PE dose dependently reduced hepatic β-catenin and augmented glycogen synthase kinase-3β expression. Our study provides evidence that pomegranate phytochemicals exert chemoprevention of hepatic cancer through antiproliferative and proapoptotic mechanisms by modulating Wnt/β-catenin signaling. PE, thus, targets two interconnected molecular circuits (canonical NF-κB and Wnt/β-catenin pathways to exert chemoprevention of HCC.

  19. Photodynamic therapy using a novel irradiation source, LED lamp, is similarly effective to photodynamic therapy using diode laser or metal-halide lamp on DMBA- and TPA-induced mouse skin papillomas.

    Science.gov (United States)

    Takahashi, Hidetoshi; Nakajima, Susumu; Ogasawara, Koji; Asano, Ryuji; Nakae, Yoshinori; Sakata, Isao; Iizuka, Hajime

    2014-08-01

    Photodynamic therapy (PDT) is useful for superficial skin tumors such as actinic keratosis and Bowen disease. Although PDT is non-surgical and easily-performed treatment modality, irradiation apparatus is large and expensive. Using 7, 12-dimethylbenz[a]anthracene (DMBA) and 12-ο-tetradecanoylphorbol-13-acetate (TPA)-induced mouse skin papilloma model, we compared the efficacy of TONS501- and ALA-PDT with a LED lamp, a diode laser lamp or a metal-halide lamp on the skin tumor regression. TONS501-PDT using 660 nm LED lamp showed anti-tumor effect at 1 day following the irradiation and the maximal anti-tumor effect was observed at 3 days following the irradiation. There was no significant difference in the anti-tumor effects among TONS501-PDT using LED, TONS501-PDT using diode laser, and 5-aminolevulinic acid hydrochloride (ALA)-PDT using metal-halide lamp. Potent anti-tumor effect on DMBA- and TPA-induced mouse skin papilloma was observed by TONS501-PDT using 660 nm LED, which might be more useful for clinical applications. © 2014 Japanese Dermatological Association.

  20. Tensile strain and magnetic particle force application do not induce MAP3K8 and IL-1B differential gene expression in a similar manner to fluid shear stress in human mesenchymal stem cells.

    Science.gov (United States)

    Glossop, John R; Cartmell, Sarah H

    2010-10-01

    Mechanical forces, important in a variety of cellular processes, including proliferation, differentiation and gene expression, are also key in the development, remodelling and maintenance of load-bearing tissues such as cartilage and bone. Thus, there is great interest in using in vitro mechanical conditioning of mesenchymal stem cells (MSCs), multipotent adult stem cells, for tissue engineering of these tissues. In a previous gene expression study, we reported a potentially important role for mitogen-activated protein kinase kinase kinase 8 (MAP3K8) and interleukin-1β (IL-1B) in MAPK signalling in MSCs exposed to fluid shear stress. In this follow-up study, we examined the expression of these genes in MSCs exposed to other types of mechanical force: uniaxial tensile strain (3% cell elongation) and forces generated through the exposure of magnetic particle-labelled MSCs to an oscillating magnetic field (maximum field strength 90 mT). Exposure to both types of mechanical force for 1 h did not significantly alter the gene expression of MAP3K8 or IL-1B over the 24 h period subsequent to force exposure. These data demonstrate that uniaxial tensile strain and magnetic particle-based forces do not induce MAP3K8-related MAPK signalling in the same manner as does fluid flow-induced shear stress. This illustrates divergence in the process of mechanotransduction in mechanically stimulated MSCs. Copyright © 2010 John Wiley & Sons, Ltd.

  1. Domain similarity based orthology detection.

    Science.gov (United States)

    Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

    2015-05-13

    Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

  2. OGlcNAcylation and Phosphorylation Have Similar Structural Effects in α-Helices: Post-Translational Modifications as Inducible Start and Stop Signals in α-Helices, with Greater Structural Effects on Threonine Modification

    Science.gov (United States)

    2015-01-01

    OGlcNAcylation and phosphorylation are the major competing intracellular post-translational modifications of serine and threonine residues. The structural effects of both post-translational modifications on serine and threonine were examined within Baldwin model α-helical peptides (Ac-AKAAAAKAAAAKAAGY-NH2 or Ac-YGAKAAAAKAAAAKAA-NH2). At the N-terminus of an α-helix, both phosphorylation and OGlcNAcylation stabilized the α-helix relative to the free hydroxyls, with a larger induced structure for phosphorylation than for OGlcNAcylation, for the dianionic phosphate than for the monoanionic phosphate, and for modifications on threonine than for modifications on serine. Both phosphoserine and phosphothreonine resulted in peptides more α-helical than alanine at the N-terminus, with dianionic phosphothreonine the most α-helix-stabilizing residue here. In contrast, in the interior of the α-helix, both post-translational modifications were destabilizing with respect to the α-helix, with the greatest destabilization seen for threonine OGlcNAcylation at residue 5 and threonine phosphorylation at residue 10, with peptides containing either post-translational modification existing as random coils. At the C-terminus, both OGlcNAcylation and phosphorylation were destabilizing with respect to the α-helix, though the induced structural changes were less than in the interior of the α-helix. In general, the structural effects of modifications on threonine were greater than the effects on serine, because of both the lower α-helical propensity of Thr and the more defined induced structures upon modification of threonine than serine, suggesting threonine residues are particularly important loci for structural effects of post-translational modifications. The effects of serine and threonine post-translational modifications are analogous to the effects of proline on α-helices, with the effects of phosphothreonine being greater than those of proline throughout the α-helix. These

  3. Conversation level syntax similarity metric.

    Science.gov (United States)

    Boghrati, Reihane; Hoover, Joe; Johnson, Kate M; Garten, Justin; Dehghani, Morteza

    2017-07-11

    The syntax and semantics of human language can illuminate many individual psychological differences and important dimensions of social interaction. Accordingly, psychological and psycholinguistic research has begun incorporating sophisticated representations of semantic content to better understand the connection between word choice and psychological processes. In this work we introduce ConversAtion level Syntax SImilarity Metric (CASSIM), a novel method for calculating conversation-level syntax similarity. CASSIM estimates the syntax similarity between conversations by automatically generating syntactical representations of the sentences in conversation, estimating the structural differences between them, and calculating an optimized estimate of the conversation-level syntax similarity. After introducing and explaining this method, we report results from two method validation experiments (Study 1) and conduct a series of analyses with CASSIM to investigate syntax accommodation in social media discourse (Study 2). We run the same experiments using two well-known existing syntactic metrics, LSM and Coh-Metrix, and compare their results to CASSIM. Overall, our results indicate that CASSIM is able to reliably measure syntax similarity and to provide robust evidence of syntax accommodation within social media discourse.

  4. Visualizing multiple word similarity measures.

    Science.gov (United States)

    Kievit-Kylar, Brent; Jones, Michael N

    2012-09-01

    Although many recent advances have taken place in corpus-based tools, the techniques used to guide exploration and evaluation of these systems have advanced little. Typically, the plausibility of a semantic space is explored by sampling the nearest neighbors to a target word and evaluating the neighborhood on the basis of the modeler's intuition. Tools for visualization of these large-scale similarity spaces are nearly nonexistent. We present a new open-source tool to plot and visualize semantic spaces, thereby allowing researchers to rapidly explore patterns in visual data that describe the statistical relations between words. Words are visualized as nodes, and word similarities are shown as directed edges of varying strengths. The "Word-2-Word" visualization environment allows for easy manipulation of graph data to test word similarity measures on their own or in comparisons between multiple similarity metrics. The system contains a large library of statistical relationship models, along with an interface to teach them from various language sources. The modularity of the visualization environment allows for quick insertion of new similarity measures so as to compare new corpus-based metrics against the current state of the art. The software is available at www.indiana.edu/~semantic/word2word/.

  5. Expression of P190 and P210 BCR/ABL1 in normal human CD34(+) cells induces similar gene expression profiles and results in a STAT5-dependent expansion of the erythroid lineage

    DEFF Research Database (Denmark)

    Järås, Marcus; Johnels, Petra; Agerstam, Helena

    2009-01-01

    OBJECTIVE: The P190 and P210 BCR/ABL1 fusion genes are mainly associated with different types of hematologic malignancies, but it is presently unclear whether they are functionally different following expression in primitive human hematopoietic cells. MATERIALS AND METHODS: We investigated...... and systematically compared the effects of retroviral P190 BCR/ABL1 and P210 BCR/ABL1 expression on cell proliferation, differentiation, and global gene expression in human CD34(+) cells from cord blood. RESULTS: Expression of either P190 BCR/ABL1 or P210 BCR/ABL1 resulted in expansion of erythroid cells...... and stimulated erythropoietin-independent burst-forming unit-erythroid colony formation. By using a lentiviral anti-signal transducer and activator of transcription 5 (STAT5) short-hairpin RNA, we found that both P190 BCR/ABL1- and P210 BCR/ABL1-induced erythroid cell expansion were STAT5-dependent. Under...

  6. Similarity measures for face recognition

    CERN Document Server

    Vezzetti, Enrico

    2015-01-01

    Face recognition has several applications, including security, such as (authentication and identification of device users and criminal suspects), and in medicine (corrective surgery and diagnosis). Facial recognition programs rely on algorithms that can compare and compute the similarity between two sets of images. This eBook explains some of the similarity measures used in facial recognition systems in a single volume. Readers will learn about various measures including Minkowski distances, Mahalanobis distances, Hansdorff distances, cosine-based distances, among other methods. The book also summarizes errors that may occur in face recognition methods. Computer scientists "facing face" and looking to select and test different methods of computing similarities will benefit from this book. The book is also useful tool for students undertaking computer vision courses.

  7. Identifying mechanistic similarities in drug responses

    KAUST Repository

    Zhao, C.

    2012-05-15

    Motivation: In early drug development, it would be beneficial to be able to identify those dynamic patterns of gene response that indicate that drugs targeting a particular gene will be likely or not to elicit the desired response. One approach would be to quantitate the degree of similarity between the responses that cells show when exposed to drugs, so that consistencies in the regulation of cellular response processes that produce success or failure can be more readily identified.Results: We track drug response using fluorescent proteins as transcription activity reporters. Our basic assumption is that drugs inducing very similar alteration in transcriptional regulation will produce similar temporal trajectories on many of the reporter proteins and hence be identified as having similarities in their mechanisms of action (MOA). The main body of this work is devoted to characterizing similarity in temporal trajectories/signals. To do so, we must first identify the key points that determine mechanistic similarity between two drug responses. Directly comparing points on the two signals is unrealistic, as it cannot handle delays and speed variations on the time axis. Hence, to capture the similarities between reporter responses, we develop an alignment algorithm that is robust to noise, time delays and is able to find all the contiguous parts of signals centered about a core alignment (reflecting a core mechanism in drug response). Applying the proposed algorithm to a range of real drug experiments shows that the result agrees well with the prior drug MOA knowledge. © The Author 2012. Published by Oxford University Press. All rights reserved.

  8. Characterization and application of UV detector spore films: the sensitivity curve of a new detector system provides good similarity to the action spectrum for UV-induced erythema in human skin.

    Science.gov (United States)

    Quintern, L E; Furusawa, Y; Fukutsu, K; Holtschmidt, H

    1997-01-01

    The UV action spectra of two different biologically weighting UV photofilms (spore films), produced with Bacillus subtilis spores (wild-type and DNA repair-deficient strains), were determined at the Okasaki large spectrograph (OLS) within the level of wavelength range 254-400 nm. The action spectrum of the mutant strain film was modified with a cut-off filter, yielding a sensitivity curve similar to the action spectrum for erythemal induction in human skin. The detector system was tested in a field study and in a study using lamps with different UV spectral compositions. The system demonstrated its applicability over the spectral region lambda = 290 nm to the visible light. The system could be calibrated to give the minimal erythemal dose.

  9. Kolmogorov's Lagrangian similarity law revisited

    Science.gov (United States)

    Barjona, Manuel; da Silva, Carlos B.

    2017-10-01

    Kolmogorov's similarity turbulence theory in a Lagrangian frame is assessed with new direct numerical simulations of isotropic turbulence with and without hyperviscosity, which attain higher Reynolds numbers than previously available. It is demonstrated that hyperviscous simulations can be used to accurately predict the second order Lagrangian velocity structure function (LVSF-2) in the inertial range, by using an original new procedure. The results strongly support Kolmogorov's Lagrangian similarity assumption and allow the universal constant of LVSF-2 to be computed with a new level of confidence with C0=7.4 ±0.2 .

  10. Inhalation of Aspergillus fumigatus spores induces airway inflammation in mice in a similar manner as observed in Recurrent Airway Obstruction in horses Inhalación de esporas de Aspergillus fumigatus induce en ratones una inflamación de las vías aéreas similar a la observada en equinos con Obstrucción Recurrente de las Vías Aéreas

    OpenAIRE

    G Morán; G Ojeda; K Diedrichs; A Ortloff; M Barria; H Folch

    2011-01-01

    The aim of this study was to determine if mice exposed to Aspergillus (A.) fumigatus spores develop airway inflammation in a similar manner to Recurrent Airway Obstruction (RAO) in horses. Different groups of 2-, 5-, 6- and 8-month-old Rockefeller (RK) mice were used throughout the experiment. The mice were maintained in the animal house for 16 days and kept in cages containing hay contaminated with A. fumigatus. After 16 days of mold exposure, the mice were bled and sacrificed to obtain bron...

  11. Antigen-specific CD4 T cells are induced after intravesical BCG-instillation therapy in patients with bladder cancer and show similar cytokine profiles as in active tuberculosis.

    Directory of Open Access Journals (Sweden)

    Julia Elsäßer

    Full Text Available Specific T cell immunity in patients with active tuberculosis is associated with a decrease in multifunctionality. However, it is unknown whether cytokine profiles differ in patients with primary infection and those with prior contact. We therefore used intravesical immunotherapy with attenuated live Bacille Calmette-Guérin (BCG in patients with urothelial carcinoma as a model to characterise the induction of systemic immunity towards purified protein derivate (PPD and to study whether cytokine profiles differ depending on pre-existing immunity. Eighteen patients with non-muscle invasive bladder cancer were recruited during the BCG-induction course. Fifty-four healthy individuals served as controls. Interferon (IFN-γ and interleukin (IL-2 producing PPD-specific CD4 T cells were analysed longitudinally before each instillation using a rapid flow-cytometric whole blood immunoassay. Baseline levels of IFN-γ producing PPD-specific T cells were comparable to controls. T cells showed a 5-fold increase to 0.23% by week 2/3, and further increased 8-fold by week 4/5 (to 0.42%, p=0.0007. Systemic immunity was induced in all patients, although the increase was less pronounced in patients with pre-existing immunity. As in active TB, cytokine profiling during therapy revealed a lower percentage of multifunctional IFN-γ/IL-2 double-positive T cells compared to controls (60.2% vs. 71.9%, p=0.0003. Of note, when comparing patients with and without pre-existing immunity, cytokine profiles in patients with primary immunity were shifted towards IL-2 single producing T cells (p=0.02, whereas those in patients with pre-existing immunity were shifted towards IFN-γ single-positivity (p=0.01. In conclusion, systemic T cell responses were induced after BCG-therapy, and their kinetics and cytokine profile depended on pre-existing immunity. Decreased functionality is a typical feature of specific immunity in both patients with active tuberculosis and BCG

  12. Revisiting Inter-Genre Similarity

    DEFF Research Database (Denmark)

    Sturm, Bob L.; Gouyon, Fabien

    2013-01-01

    We revisit the idea of ``inter-genre similarity'' (IGS) for machine learning in general, and music genre recognition in particular. We show analytically that the probability of error for IGS is higher than naive Bayes classification with zero-one loss (NB). We show empirically that IGS does...

  13. PLK1 and HOTAIR Accelerate Proteasomal Degradation of SUZ12 and ZNF198 during Hepatitis B Virus-Induced Liver Carcinogenesis.

    Science.gov (United States)

    Zhang, Hao; Diab, Ahmed; Fan, Huitao; Mani, Saravana Kumar Kailasam; Hullinger, Ronald; Merle, Philippe; Andrisani, Ourania

    2015-06-01

    Elucidating mechanisms of hepatitis B virus (HBV)-mediated hepatocarcinogenesis is needed to gain insights into the etiology and treatment of liver cancer. Cells where HBV is replicating exhibit increased expression of Plk1 kinase and reduced levels of two transcription repression factors, SUZ12 and ZNF198. SUZ12 is an essential subunit of the transcription repressive complex PRC2. ZNF198 stabilizes the transcription repressive complex composed of LSD1, Co-REST, and HDAC1. These two transcription repressive complexes are held together by binding the long noncoding RNA HOTAIR. In this study, we linked these regulatory events mechanistically by showing that Plk1 induces proteasomal degradation of SUZ12 and ZNF198 by site-specific phosphorylation. Plk1-dependent ubiquitination of SUZ12 and ZNF198 was enhanced by expression of HOTAIR, significantly reducing SUZ12 and ZNF198 stability. In cells expressing the HBV X protein (HBx), downregulation of SUZ12 and ZNF198 mediated global changes in histone modifications. In turn, HBx-expressing cells propagated an altered chromatin landscape after cell division, as exemplified by changes in histone modifications of the EpCAM promoter, a target of PRC2 and LSD1/Co-REST/HDAC1 complexes. Notably, liver tumors from X/c-myc bitransgenic mice exhibited downregulation of SUZ12 and ZNF198 along with elevated expression of Plk1, HOTAIR, and EpCAM. Clinically, similar effects were documented in a set of HBV-related liver tumors consistent with the likelihood that downregulation of SUZ12 and ZNF198 leads to epigenetic reprogramming of infected hepatocytes. Because both Plk1 and HOTAIR are elevated in many human cancers, we propose that their combined effects are involved in epigenetic reprogramming associated broadly with oncogenic transformation. ©2015 American Association for Cancer Research.

  14. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

    2009-01-01

    a synthetic example from molecular dynamics simulations. We then apply the algorithms to revisit the problem of ensemble averaging during structure determination of proteins, and find that an ensemble refinement method is able to recover the correct distribution of conformations better than standard single....... However, instead of examining individual conformations it is in many cases more relevant to analyse ensembles of conformations that have been obtained either through experiments or from methods such as molecular dynamics simulations. We here present three approaches that can be used to compare......Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformations...

  15. Alaska, Gulf spills share similarities

    Energy Technology Data Exchange (ETDEWEB)

    Usher, D. (Marine Pollution Control Co., Detroit, MI (United States))

    The accidental Exxon Valdez oil spill in Alaska and the deliberate dumping of crude oil into the Persian Gulf as a tactic of war contain both glaring differences and surprising similarities. Public reaction and public response was much greater to the Exxon Valdez spill in pristine Prince William Sound than to the war-related tragedy in the Persian Gulf. More than 12,000 workers helped in the Alaskan cleanup; only 350 have been involved in Kuwait. But in both instances, environmental damages appear to be less than anticipated. Natures highly effective self-cleansing action is primarily responsible for minimizing the damages. One positive action growing out of the two incidents is increased international cooperation and participation in oil-spill clean-up efforts. In 1990, in the aftermath of the Exxon Valdez spill, 94 nations signed an international accord on cooperation in future spills. The spills can be historic environmental landmarks leading to creation of more sophisticated response systems worldwide.

  16. Inducing a measure of phonetic similarity from pronunciation variation

    NARCIS (Netherlands)

    Wieling, Martijn; Margaretha, Eliza; Nerbonne, John

    Structuralists famously observed that language is "un systeme oil tout se tient" (Meillet, 1903, p.407), insisting that the system of relations of linguistic units was more important than their concrete content. This study attempts to derive content from relations, in particular phonetic (acoustic)

  17. Upregulation of DARS2 by HBV promotes hepatocarcinogenesis through the miR-30e-5p/MAPK/NFAT5 pathway.

    Science.gov (United States)

    Qin, Xian; Li, Changsheng; Guo, Tao; Chen, Jing; Wang, Hai-Tao; Wang, Yi-Tao; Xiao, Yu-Sha; Li, Jun; Liu, Pengpeng; Liu, Zhi-Su; Liu, Quan-Yan

    2017-10-19

    Infection with the hepatitis B virus (HBV) is closely associated with the development of hepatocellular carcinoma (HCC). The osmoregulatory transcription factor nuclear factor of activated T-cells 5 (NFAT5) has been shown to play an important role in the development of many types of human cancers. The role of NFAT5 in HBV-associated HCC has never previously been investigated. We compared expression profiles of NFAT5, DARS2 and miR-30e-5p in HCC samples, adjacent nontumor tissues and different hepatoma cell lines by quantitative real-time polymerase chain reaction and /or Western blot. Clinical data of HCC patients for up to 80 months were analyzed. The regulatory mechanisms upstream and convergent downstream pathways of NFAT5 in HBV-associated HCC were investigated by ChIP-seq, MSP, luciferase report assay and bioinformation anaylsis. We first found that higher levels of NFAT5 expression predict a good prognosis, suggesting that NFAT5 is a potential tumor-suppressing gene, and verified that NFAT5 promotes hepatoma cell apoptosis and inhibits cell growth in vitro. Second, our results showed that HBV could suppress NFAT5 expression by inducing hypermethylation of the AP1-binding site in the NFAT5 promoter in hepatoma cells. In addition, HBV also inhibited NFAT5 through miR-30e-5p targeted MAP4K4, and miR-30e-5p in turn inhibited HBV replication. Finally, we demonstrated that NFAT5 suppressed DARS2 by directly binding to its promoter. DARS2 was identified as an HCC oncogene that promotes HCC cell cycle progression and inhibits HCC cell apoptosis. HBV suppresses NFAT5 through the miR-30e-5p/mitogen-activated protein kinase (MAPK) signaling pathway upstream of NFAT5 and inhibits the NFAT5 to enhance HCC tumorigenesis via the downstream target genes of DARS2.

  18. RBP-J-interacting and tubulin-associated protein induces apoptosis and cell cycle arrest in human hepatocellular carcinoma by activating the p53–Fbxw7 pathway

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Haihe [The Key Laboratory of Molecular Diagnosis in Laboratory Medicine, Department of Pathogenobiology, Daqing Branch of Harbin Medical University, Daqing 163319 (China); Yang, Zhanchun [Department of General Surgery of Fifth Clinical Hospital of Harbin Medical University, Daqing 163319 (China); Liu, Chunbo; Huang, Shishun; Wang, Hongzhi; Chen, Yingli [The Key Laboratory of Molecular Diagnosis in Laboratory Medicine, Department of Pathogenobiology, Daqing Branch of Harbin Medical University, Daqing 163319 (China); Chen, Guofu, E-mail: zhangyanjie3@aliyun.com [Department of General Surgery of Fifth Clinical Hospital of Harbin Medical University, Daqing 163319 (China)

    2014-11-07

    Highlights: • RITA overexpression increased protein expression of p53 and Fbxw7 and downregulated the expression of cyclin D1, cyclin E, CDK2, Hes-1 and NF-κB p65. • RITA can significantly inhibit the in vitro growth of SMMC7721 and HepG2 cells. • RITA exerts tumor-suppressive effects in hepatocarcinogenesis through induction of G0/G1 cell cycle arrest and apoptosis and suggest a therapeutic application of RITA in HCC. - Abstract: Aberrant Notch signaling is observed in human hepatocellular carcinoma (HCC) and has been associated with the modulation of cell growth. However, the role of Notch signaling in HCC and its underlying mechanism remain elusive. RBP-J-interacting and tubulin-associated (RITA) mediates the nuclear export of RBP-J to tubulin fibers and downregulates Notch-mediated transcription. In this study, we found that RITA overexpression increased protein expression of p53 and Fbxw7 and downregulated the expression of cyclin D1, cyclin E, CDK2, Hes-1 and NF-κB p65. These changes led to growth inhibition and induced G0/G1 cell cycle arrest and apoptosis in SMMC7721 and HepG2 cells. Our findings indicate that RITA exerts tumor-suppressive effects in hepatocarcinogenesis through induction of G0/G1 cell cycle arrest and apoptosis and suggest a therapeutic application of RITA in HCC.

  19. Asthma and COPD: Differences and Similarities

    Science.gov (United States)

    ... and COPD: differences and similarities Share | Asthma and COPD: Differences and Similarities This article has been reviewed ... or you could have Chronic Obstructive Pulmonary Disease (COPD) , such as emphysema or chronic bronchitis. Because asthma ...

  20. 7 CFR 51.1997 - Similar type.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar type. 51.1997 Section 51.1997 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Filberts in the Shell 1 Definitions § 51.1997 Similar type. Similar type means that...

  1. Molecular quantum similarity using conceptual DFT descriptors

    Indian Academy of Sciences (India)

    This paper reports a Molecular Quantum Similarity study for a set of congeneric steroid molecules, using as basic similarity descriptors electron density ρ (r), shape function (r), the Fukui functions +(r) and -(r) and local softness +(r) and -(r). Correlations are investigated between similarity indices for each couple of ...

  2. The function of TAK1 in hepatocarcinogenesis

    OpenAIRE

    Bettermann, Kira

    2011-01-01

    The MAP3-kinase TGF-beta-activated kinase 1 (TAK1) is activated in response to cytokines like TNF-alpha, TGF-beta as well as by the bacterial endotoxin lipopolysaccharide (LPS). TAK1 is involved in controlling the activation of p38MAPK, JNK, and NF-kappaB in various cellular systems thereby critically modulating innate and adaptive immune responses and connecting cytokine stimulation with activation of inflammatory signalling pathways. After activation of the TNF signalling cascade, TAK1 and ...

  3. Role of Methionine Adenosyltransferase Genes in Hepatocarcinogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Ramani, Komal [Division of Gastroenterology and Liver Diseases, USC Research Center for Liver Diseases, Southern California Research Center for Alcoholic Liver and Pancreatic Diseases & Cirrhosis, Keck School of Medicine USC, Los Angeles, California 90033 (United States); Mato, José M. [CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (Ciberehd), Technology, Park of Bizkaia, 48160 Derio, Bizkaia (Spain); Lu, Shelly C., E-mail: shellylu@usc.edu [Division of Gastroenterology and Liver Diseases, USC Research Center for Liver Diseases, Southern California Research Center for Alcoholic Liver and Pancreatic Diseases & Cirrhosis, Keck School of Medicine USC, Los Angeles, California 90033 (United States)

    2011-03-24

    Hepatocellular carcinoma (HCC) is the most common primary malignant tumor of the liver. Detection of HCC can be difficult, as most of the patients who develop this tumor have no symptoms other than those related to their longstanding liver disease. There is an urgent need to understand the molecular mechanisms that are responsible for the development of this disease so that appropriate therapies can be designed. Methionine adenosyltransferase (MAT) is an essential enzyme required for the biosynthesis of S-adenosylmethionine (AdoMet), an important methyl donor in the cell. Alterations in the expression of MAT genes and a decline in AdoMet biosynthesis are known to be associated with liver injury, cirrhosis and HCC. This review focuses on the role of MAT genes in HCC development and the scope for therapeutic strategies using these genes.

  4. Sodium Valproate Induces Cell Senescence in Human Hepatocarcinoma Cells

    Directory of Open Access Journals (Sweden)

    Hong-Mei An

    2013-12-01

    Full Text Available Hepatocarcinogenesis is associated with epigenetic changes, including histone deacetylases (HDACs. Epigenetic modulation by HDAC inhibition is a potentially valuable approach for hepatocellular carcinoma treatment. In present study, we evaluated the anticancer effects of sodium valproate (SVP, a known HDAC inhibitor, in human hepatocarcinoma cells. The results showed SVP inhibited the proliferation of Bel-7402 cells in a dose-dependent manner. Low dose SVP treatment caused a large and flat morphology change, positive SA-β-gal staining, and G0/G1 phase cell cycle arrest in human hepatocarcinoma cells. Low dose SVP treatment also increased acetylation of histone H3 and H4 on p21 promoter, accompanied by up-regulation of p21 and down-regulation of RB phosphorylation. These observations suggested that a low dose of SVP could induce cell senescence in hepatocarcinoma cells, which might correlate with hyperacetylation of histone H3 and H4, up-regulation of p21, and inhibition of RB phosphorylation. Since the effective concentration inducing cell senescence in hepatocarcinoma cells is clinically available, whether a clinical dose of SVP could induce cell senescence in clinical hepatocarcinoma is worthy of further study.

  5. Cognitive consequences of motivational orientation: perceived similarity between objects.

    Science.gov (United States)

    Nussinson, Ravit; Seibt, Beate; Häfner, Michael; Strack, Fritz

    2011-09-01

    Recent findings suggest that the unconscious activation of the motivational orientations of approach and avoidance is accompanied by the adoption of a more global and a more local processing style, respectively. A global processing style, in turn, is assumed to instigate a focus on similarities whereas a local processing style is assumed to instigate a focus on differences. Integrating these two ideas, the present research examines the hypothesis that participants under approach perceive objects as more similar to each other than participants under avoidance. To test this assumption, we induced the two motivational orientations and elicited judgments of similarities (Experiments 1 and 2) and differences (Experiment 2) for pairs of pictures. Results confirmed the hypothesis. We propose that the relative attunement to similarities/differences under approach/avoidance is functional because it allows for a flexible conceptualization of the environment/an ability to discern slight deviations from what is expected. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji

    2016-07-14

    Self-similar processes have been widely used in modeling real-world phenomena occurring in environmetrics, network traffic, image processing, and stock pricing, to name but a few. The estimation of the degree of self-similarity has been studied extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi-self-similarity for a random field indexed in higher dimensions. If self-similarity is not rejected, our test provides a set of estimated self-similarity indexes. The key is to test stationarity of the inverse Lamperti transformations of the process. The inverse Lamperti transformation of a self-similar process is a strongly stationary process, revealing a theoretical connection between the two processes. To demonstrate the capability of our test, we test self-similarity of fractional Brownian motions and sheets, their time deformations and mixtures with Gaussian white noise, and the generalized Cauchy family. We also apply the self-similarity test to real data: annual minimum water levels of the Nile River, network traffic records, and surface heights of food wrappings. © 2016, International Biometric Society.

  7. Bridging Database Applications and Declarative Similarity Matching

    OpenAIRE

    Andrade Ribeiro, Leonardo; Schneider, Natália Cristina; de Souza Inácio, Andrei; Wagner, Harley Michel; von Wangenheim, Aldo

    2017-01-01

    Effective manipulation of string data is of fundamental importance to modern database applications. Very often, textual inconsistencies render equality comparisons meaningless and strings have to be matched in terms of their similarity. Previous work has proposed techniques to express similarity operations using declarative SQL statements. However, the non-trivial issue of embedding similarity support into object-oriented applications has received little attention. Particularly, declarative s...

  8. Integrating Triangle and Jaccard similarities for recommendation

    Science.gov (United States)

    Sun, Shuang-Bo; Zhang, Zhi-Heng; Dong, Xin-Ling; Zhang, Heng-Ru; Li, Tong-Jun; Zhang, Lin

    2017-01-01

    This paper proposes a new measure for recommendation through integrating Triangle and Jaccard similarities. The Triangle similarity considers both the length and the angle of rating vectors between them, while the Jaccard similarity considers non co-rating users. We compare the new similarity measure with eight state-of-the-art ones on four popular datasets under the leave-one-out scenario. Results show that the new measure outperforms all the counterparts in terms of the mean absolute error and the root mean square error. PMID:28817692

  9. Learning deep similarity in fundus photography

    Science.gov (United States)

    Chudzik, Piotr; Al-Diri, Bashir; Caliva, Francesco; Ometto, Giovanni; Hunter, Andrew

    2017-02-01

    Similarity learning is one of the most fundamental tasks in image analysis. The ability to extract similar images in the medical domain as part of content-based image retrieval (CBIR) systems has been researched for many years. The vast majority of methods used in CBIR systems are based on hand-crafted feature descriptors. The approximation of a similarity mapping for medical images is difficult due to the big variety of pixel-level structures of interest. In fundus photography (FP) analysis, a subtle difference in e.g. lesions and vessels shape and size can result in a different diagnosis. In this work, we demonstrated how to learn a similarity function for image patches derived directly from FP image data without the need of manually designed feature descriptors. We used a convolutional neural network (CNN) with a novel architecture adapted for similarity learning to accomplish this task. Furthermore, we explored and studied multiple CNN architectures. We show that our method can approximate the similarity between FP patches more efficiently and accurately than the state-of- the-art feature descriptors, including SIFT and SURF using a publicly available dataset. Finally, we observe that our approach, which is purely data-driven, learns that features such as vessels calibre and orientation are important discriminative factors, which resembles the way how humans reason about similarity. To the best of authors knowledge, this is the first attempt to approximate a visual similarity mapping in FP.

  10. Mining Diagnostic Assessment Data for Concept Similarity

    Science.gov (United States)

    Madhyastha, Tara; Hunt, Earl

    2009-01-01

    This paper introduces a method for mining multiple-choice assessment data for similarity of the concepts represented by the multiple choice responses. The resulting similarity matrix can be used to visualize the distance between concepts in a lower-dimensional space. This gives an instructor a visualization of the relative difficulty of concepts…

  11. Similarity Structure of Wave-Collapse

    DEFF Research Database (Denmark)

    Rypdal, Kristoffer; Juul Rasmussen, Jens; Thomsen, Kenneth

    1985-01-01

    Similarity transformations of the cubic Schrödinger equation (CSE) are investigated. The transformations are used to remove the explicit time variation in the CSE and reduce it to differential equations in the spatial variables only. Two different methods for similarity reduction are employed and...

  12. Similarity indices I: what do they measure.

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, J.W.

    1976-11-01

    A method for estimating the effects of environmental effusions on ecosystems is described. The characteristics of 25 similarity indices used in studies of ecological communities were investigated. The type of data structure, to which these indices are frequently applied, was described as consisting of vectors of measurements on attributes (species) observed in a set of samples. A general similarity index was characterized as the result of a two-step process defined on a pair of vectors. In the first step an attribute similarity score is obtained for each attribute by comparing the attribute values observed in the pair of vectors. The result is a vector of attribute similarity scores. These are combined in the second step to arrive at the similarity index. The operation in the first step was characterized as a function, g, defined on pairs of attribute values. The second operation was characterized as a function, F, defined on the vector of attribute similarity scores from the first step. Usually, F was a simple sum or weighted sum of the attribute similarity scores. It is concluded that similarity indices should not be used as the test statistic to discriminate between two ecological communities.

  13. Outsourced similarity search on metric data assets

    DEFF Research Database (Denmark)

    Yiu, Man Lung; Assent, Ira; Jensen, Christian Søndergaard

    2012-01-01

    This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example...

  14. Some Effects of Similarity Self-Disclosure

    Science.gov (United States)

    Murphy, Kevin C.; Strong, Stanley R.

    1972-01-01

    College males were interviewed about how college had altered their friendships, values, and plans. The interviewers diclosed experiences and feelings similar to those revealed by the students. Results support Byrne's Law of Similarity in generating interpersonal attraction in the interview and suggest that the timing of self-disclosures is…

  15. Correlation between social proximity and mobility similarity.

    Science.gov (United States)

    Fan, Chao; Liu, Yiding; Huang, Junming; Rong, Zhihai; Zhou, Tao

    2017-09-20

    Human behaviors exhibit ubiquitous correlations in many aspects, such as individual and collective levels, temporal and spatial dimensions, content, social and geographical layers. With rich Internet data of online behaviors becoming available, it attracts academic interests to explore human mobility similarity from the perspective of social network proximity. Existent analysis shows a strong correlation between online social proximity and offline mobility similarity, namely, mobile records between friends are significantly more similar than between strangers, and those between friends with common neighbors are even more similar. We argue the importance of the number and diversity of common friends, with a counter intuitive finding that the number of common friends has no positive impact on mobility similarity while the diversity plays a key role, disagreeing with previous studies. Our analysis provides a novel view for better understanding the coupling between human online and offline behaviors, and will help model and predict human behaviors based on social proximity.

  16. Similarity and a Duality for Fullerenes

    Directory of Open Access Journals (Sweden)

    Jennifer J. Edmond

    2015-11-01

    Full Text Available Fullerenes are molecules of carbon that are modeled by trivalent plane graphs with only pentagonal and hexagonal faces. Scaling up a fullerene gives a notion of similarity, and fullerenes are partitioned into similarity classes. In this expository article, we illustrate how the values of two important fullerene parameters can be deduced for all fullerenes in a similarity class by computing the values of these parameters for just the three smallest representatives of that class. In addition, it turns out that there is a natural duality theory for similarity classes of fullerenes based on one of the most important fullerene construction techniques: leapfrog construction. The literature on fullerenes is very extensive, and since this is a general interest journal, we will summarize and illustrate the fundamental results that we will need to develop similarity and this duality.

  17. The influence of phonological similarity neighborhoods on speech production.

    Science.gov (United States)

    Vitevitch, Michael S

    2002-07-01

    The influence of phonological similarity neighborhoods on the speed and accuracy of speech production was investigated with speech-error elicitation and picture-naming tasks. The results from 2 speech-error elicitation techniques-the spoonerisms of laboratory induced predisposition technique (B. J. Baars, 1992; B. J. Baars & M. T. Motley, 1974; M. T. Motley & B. J. Baars, 1976) and tongue twisters-showed that more errors were elicited for words with few similar sounding words (i.e., a sparse neighborhood) than for words with many similar sounding words (i.e., a dense neighborhood). The results from 3 picture-naming tasks showed that words with sparse neighborhoods were also named more slowly than words with dense neighborhoods. These findings demonstrate that multiple word forms are activated simultaneously and influence the speed and accuracy of speech production. The implications of these findings for current models of speech production are discussed.

  18. Notions of similarity for computational biology models

    KAUST Repository

    Waltemath, Dagmar

    2016-03-21

    Computational models used in biology are rapidly increasing in complexity, size, and numbers. To build such large models, researchers need to rely on software tools for model retrieval, model combination, and version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of similarity may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here, we introduce a general notion of quantitative model similarities, survey the use of existing model comparison methods in model building and management, and discuss potential applications of model comparison. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on different model aspects. Potentially relevant aspects of a model comprise its references to biological entities, network structure, mathematical equations and parameters, and dynamic behaviour. Future similarity measures could combine these model aspects in flexible, problem-specific ways in order to mimic users\\' intuition about model similarity, and to support complex model searches in databases.

  19. Two perspectives on similarity between words

    Science.gov (United States)

    Frisch, Stefan A.

    2003-10-01

    This presentation examines the similarity between words from both bottom up (phonetic) and top down (phonological/psycholinguistic) perspectives. From the phonological perspective, the influence of structure on similarity is explored using metalinguistic acceptability judgments for multisyllabic nonwords. Results from an experiment suggest that subjects try to align novel words with known words in order to maximize similarities while minimizing dissimilarities. This finding parallels results from psychology on similarity judgments for visual scenes. From the phonetic perspective, the influence of similar gestures on speech error rates is examined using ultrasound measurement of tongue position. In a pilot experiment, subjects, produced tongue twisters containing words where onset and vowel phonemes had similar gestures (e.g., tip, comb) and where the onset and vowel had dissimilar gestures (e.g., tube, keep). Preliminary results suggest that misarticulations are more frequent in the context of dissimilar gestures (e.g., in the tongue twister tip cape keep tape, error rates are higher for /k/ than /t/). These errors appear to be gestural interactions rather than errors at the phonemic or featural level of phonological spellout. Together, these two experiments indicate that similarity relations between words are found at multiple levels, any which are potentially relevant to the structure of phonological systems.

  20. Electrostatic Similarity Determination Using Multiresolution Analysis.

    Science.gov (United States)

    Hakkoymaz, Huseyin; Kieslich, Chris A; Jr, Ronald D Gorham; Gunopulos, Dimitrios; Morikis, Dimitrios

    2011-08-01

    Molecular similarity is an important tool in protein and drug design for analyzing the quantitative relationships between physicochemical properties of two molecules. We present a family of similarity measures which exploits the ability of wavelet transformation to analyze the spectral components of physicochemical properties and suggests a sensitive way for measuring similarities of biological molecules. In order to investigate how effective wavelet-based similarity measures were against conventional measures, we defined several patterns which involve scalar or topological changes in the distribution of electrostatic properties. The wavelet-based measures were more successful in discriminating these patterns in contrast to the current state-of-art similarity measures. We also present the validity of wavelet-based similarity measures through the hierarchical clustering of two protein datasets consisting of families of homologous domains and alanine scan mutants. This type of similarity analysis is useful for protein structure-function studies and protein design. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Measure of Node Similarity in Multilayer Networks.

    Directory of Open Access Journals (Sweden)

    Anders Mollgaard

    Full Text Available The weight of links in a network is often related to the similarity of the nodes. Here, we introduce a simple tunable measure for analysing the similarity of nodes across different link weights. In particular, we use the measure to analyze homophily in a group of 659 freshman students at a large university. Our analysis is based on data obtained using smartphones equipped with custom data collection software, complemented by questionnaire-based data. The network of social contacts is represented as a weighted multilayer network constructed from different channels of telecommunication as well as data on face-to-face contacts. We find that even strongly connected individuals are not more similar with respect to basic personality traits than randomly chosen pairs of individuals. In contrast, several socio-demographics variables have a significant degree of similarity. We further observe that similarity might be present in one layer of the multilayer network and simultaneously be absent in the other layers. For a variable such as gender, our measure reveals a transition from similarity between nodes connected with links of relatively low weight to dis-similarity for the nodes connected by the strongest links. We finally analyze the overlap between layers in the network for different levels of acquaintanceships.

  2. Trajectory similarity join in spatial networks

    KAUST Repository

    Shang, Shuo

    2017-09-07

    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider the case of trajectory similarity join (TS-Join), where the objects are trajectories of vehicles moving in road networks. Thus, given two sets of trajectories and a threshold θ, the TS-Join returns all pairs of trajectories from the two sets with similarity above θ. This join targets applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide a purposeful definition of similarity. To enable efficient TS-Join processing on large sets of trajectories, we develop search space pruning techniques and take into account the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer algorithm. For each trajectory, the algorithm first finds similar trajectories. Then it merges the results to achieve a final result. The algorithm exploits an upper bound on the spatiotemporal similarity and a heuristic scheduling strategy for search space pruning. The algorithm\\'s per-trajectory searches are independent of each other and can be performed in parallel, and the merging has constant cost. An empirical study with real data offers insight in the performance of the algorithm and demonstrates that is capable of outperforming a well-designed baseline algorithm by an order of magnitude.

  3. Similarity and Decay Laws of Momentumless Wakes.

    Science.gov (United States)

    1977-05-26

    Naval Sea Systems Command , Code NSEA—03133. -‘ F 9 —2— 26 May 1977 SN : j ep SIMILARITY AND DECAY LAWS OF MOMENTUI’ILESS WAKE S by Samuel Ilassid...and this neg lect will have to be justified a posteriori. Now, one seeks self-similar solutions of the type: k = Xh(ri) c = Ee(n) Ud = UDf (n) ~ = where...0 9x r 3r L6 c Again, seeking self-similar solutions of the type: k = Kh(ti) c = Ee(ri) Ud = UDf (n) r~ = (6.4) and letting 2 2 = 1 (6.5)E L one

  4. Similarity-based pattern analysis and recognition

    CERN Document Server

    Pelillo, Marcello

    2013-01-01

    This accessible text/reference presents a coherent overview of the emerging field of non-Euclidean similarity learning. The book presents a broad range of perspectives on similarity-based pattern analysis and recognition methods, from purely theoretical challenges to practical, real-world applications. The coverage includes both supervised and unsupervised learning paradigms, as well as generative and discriminative models. Topics and features: explores the origination and causes of non-Euclidean (dis)similarity measures, and how they influence the performance of traditional classification alg

  5. A Similarity Search Using Molecular Topological Graphs

    Directory of Open Access Journals (Sweden)

    Yoshifumi Fukunishi

    2009-01-01

    Full Text Available A molecular similarity measure has been developed using molecular topological graphs and atomic partial charges. Two kinds of topological graphs were used. One is the ordinary adjacency matrix and the other is a matrix which represents the minimum path length between two atoms of the molecule. The ordinary adjacency matrix is suitable to compare the local structures of molecules such as functional groups, and the other matrix is suitable to compare the global structures of molecules. The combination of these two matrices gave a similarity measure. This method was applied to in silico drug screening, and the results showed that it was effective as a similarity measure.

  6. Outsourced similarity search on metric data assets

    KAUST Repository

    Yiu, Man Lung

    2012-02-01

    This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example. Outsourcing offers the data owner scalability and a low-initial investment. The need for privacy may be due to the data being sensitive (e.g., in medicine), valuable (e.g., in astronomy), or otherwise confidential. Given this setting, the paper presents techniques that transform the data prior to supplying it to the service provider for similarity queries on the transformed data. Our techniques provide interesting trade-offs between query cost and accuracy. They are then further extended to offer an intuitive privacy guarantee. Empirical studies with real data demonstrate that the techniques are capable of offering privacy while enabling efficient and accurate processing of similarity queries.

  7. Distances and similarities in intuitionistic fuzzy sets

    CERN Document Server

    Szmidt, Eulalia

    2014-01-01

    This book presents the state-of-the-art in theory and practice regarding similarity and distance measures for intuitionistic fuzzy sets. Quantifying similarity and distances is crucial for many applications, e.g. data mining, machine learning, decision making, and control. The work provides readers with a comprehensive set of theoretical concepts and practical tools for both defining and determining similarity between intuitionistic fuzzy sets. It describes an automatic algorithm for deriving intuitionistic fuzzy sets from data, which can aid in the analysis of information in large databases. The book also discusses other important applications, e.g. the use of similarity measures to evaluate the extent of agreement between experts in the context of decision making.

  8. Comparing methods for single paragraph similarity analysis.

    Science.gov (United States)

    Stone, Benjamin; Dennis, Simon; Kwantes, Peter J

    2011-01-01

    The focus of this paper is two-fold. First, similarities generated from six semantic models were compared to human ratings of paragraph similarity on two datasets-23 World Entertainment News Network paragraphs and 50 ABC newswire paragraphs. Contrary to findings on smaller textual units such as word associations (Griffiths, Tenenbaum, & Steyvers, 2007), our results suggest that when single paragraphs are compared, simple nonreductive models (word overlap and vector space) can provide better similarity estimates than more complex models (LSA, Topic Model, SpNMF, and CSM). Second, various methods of corpus creation were explored to facilitate the semantic models' similarity estimates. Removing numeric and single characters, and also truncating document length improved performance. Automated construction of smaller Wikipedia-based corpora proved to be very effective, even improving upon the performance of corpora that had been chosen for the domain. Model performance was further improved by augmenting corpora with dataset paragraphs. Copyright © 2010 Cognitive Science Society, Inc.

  9. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Parrado-Hernandez, Emilio; Meng, Anders

    Automatic methods for music navigation and music recommendation exploit the structure in the music to carry out a meaningful exploration of the “song space”. To get a satisfactory performance from such systems, one should incorporate as much information about songs similarity as possible; however...... semantics”, in such a way that all observed similarities can be satisfactorily explained using the latent semantics. Therefore, one can think of these semantics as the real structure in music, in the sense that they can explain the observed similarities among songs. The suitability of the PLSA model...... for representing music structure is studied in a simplified scenario consisting of 4412 songs and two similarity measures among them. The results suggest that the PLSA model is a useful framework to combine different sources of information, and provides a reasonable space for song representation....

  10. Abundance estimation of spectrally similar minerals

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2009-07-01

    Full Text Available This paper evaluates a spectral unmixing method for estimating the partial abundance of spectrally similar minerals in complex mixtures. The method requires formulation of a linear function of individual spectra of individual minerals. The first...

  11. Privacy-preserving matching of similar patients.

    Science.gov (United States)

    Vatsalan, Dinusha; Christen, Peter

    2016-02-01

    The identification of similar entities represented by records in different databases has drawn considerable attention in many application areas, including in the health domain. One important type of entity matching application that is vital for quality healthcare analytics is the identification of similar patients, known as similar patient matching. A key component of identifying similar records is the calculation of similarity of the values in attributes (fields) between these records. Due to increasing privacy and confidentiality concerns, using the actual attribute values of patient records to identify similar records across different organizations is becoming non-trivial because the attributes in such records often contain highly sensitive information such as personal and medical details of patients. Therefore, the matching needs to be based on masked (encoded) values while being effective and efficient to allow matching of large databases. Bloom filter encoding has widely been used as an efficient masking technique for privacy-preserving matching of string and categorical values. However, no work on Bloom filter-based masking of numerical data, such as integer (e.g. age), floating point (e.g. body mass index), and modulus (numbers wrap around upon reaching a certain value, e.g. date and time), which are commonly required in the health domain, has been presented in the literature. We propose a framework with novel methods for masking numerical data using Bloom filters, thereby facilitating the calculation of similarities between records. We conduct an empirical study on publicly available real-world datasets which shows that our framework provides efficient masking and achieves similar matching accuracy compared to the matching of actual unencoded patient records. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Similarity search processing. Paralelization and indexing technologies.

    Directory of Open Access Journals (Sweden)

    Eder Dos Santos

    2015-08-01

    The next Scientific-Technical Report addresses the similarity search and the implementation of metric structures on parallel environments. It also presents the state of the art related to similarity search on metric structures and parallelism technologies. Comparative analysis are also proposed, seeking to identify the behavior of a set of metric spaces and metric structures over processing platforms multicore-based and GPU-based.

  13. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    Chang Chih-Hung

    2007-08-01

    Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

  14. Anthocyanin-rich black currant (Ribes nigrum L.) extract affords chemoprevention against diethylnitrosamine-induced hepatocellular carcinogenesis in rats.

    Science.gov (United States)

    Bishayee, Anupam; Mbimba, Thomas; Thoppil, Roslin J; Háznagy-Radnai, Erzsébet; Sipos, Péter; Darvesh, Altaf S; Folkesson, Hans G; Hohmann, Judit

    2011-11-01

    Anthocyanins are known to possess potent anticarcinogenic properties against several cancers thus demonstrating potential for cancer prevention. Black currant (Ribes nigrum L., Grossulariaceae) fruits have a high anthocyanin content. This "superfruit" is known to possess various pharmacological effects including alleviation of chronic oxidative stress and inflammation. In contrast to a large volume of literature on the health benefits of black currant, limited evidence on antitumor effects of black currant exists with virtually no data on the prevention of experimental carcinogenesis. In the current study, we have investigated the chemopreventive effects of an anthocyanin-rich black currant skin extract (BCSE) utilizing our well-characterized model of rat liver carcinogenesis. Initiation of hepatocarcinogenesis was done by intraperitoneal injection of diethylnitrosamine (DENA) followed by promotion with phenobarbital. The rats were exposed to dietary BCSE for 4 weeks prior to initiation, and the treatment was continued for 22 consecutive weeks. BCSE dose-dependently decreased the incidence, total number, multiplicity, size and volume of preneoplastic hepatic nodules. The antihepatocarcinogenic effect of BCSE was confirmed by histopathological examination of liver sections. Immunohistochemical analysis of proliferating cell nuclear antigen and DNA fragmentation revealed BCSE-mediated inhibition of abnormal cell proliferation and induction of apoptosis in DENA-induced rat liver tumorigenesis respectively. Mechanistic studies revealed that BCSE-mediated proapototic signal during experimental hepatocarcinogenesis may be propagated via the up-regulation of Bax and down-regulation of Bcl-2 expression at the translational level. These results along with a safety profile of BCSE encourage the development of black currant bioactive constituents as chemopreventive agents for human liver cancer. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. Similarity Search for Continuous Seismic Data

    Science.gov (United States)

    OReilly, O. J.; Yoon, C. E.; Beroza, G. C.

    2013-12-01

    Cross-correlation of seismic data streams with a priori known waveform templates has emerged as an effective tool to identify the occurrence of similar seismic signals; yet, this approach is difficult if the form of the templates is unknown. This challenge has been partially met by constructing waveform templates using reoccurring seismic signals sharing similar waveforms. This waveform similarity arises because the Earth's structure is essentially time invariant at the temporal scales considered in seismology. The problem of finding similar waveforms without known templates has been approached previously by segmenting incoming seismic data streams into multiple overlapping windows, each with a fixed length and lag, followed by matched filtering using each window as a template. An immediate shortcoming of this strategy is that it is computationally expensive; it scales quadratically with the number of lags needed, which limits the analysis to time series of short duration. The principal concept behind our approach, which enables scalable similarity search is to use a hierarchical approach to investigate only a small, near-constant sized subset of all possible waveform pairs for each query. In computer science and related fields, there are efficient techniques to solve this problem, which appears in numerous applications. Here, we bring these techniques into detection seismology. As a first step, we present a prototype database application that relies on a fingerprinting scheme that produces numerous high-dimensional sparse binary data representations of the windowed data streams (each fingerprint is significantly compressed compared to the actual window). These fingerprints encode key features of the actual window, enabling comparison among fingerprints rather than cross-correlating windows for comparison. Further dimensionality reduction is then applied to each fingerprint and similar fingerprints are grouped together using locality-sensitive hashing. Developing

  16. Semantic similarity between ontologies at different scales

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qingpeng; Haglin, David J.

    2016-04-01

    In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

  17. Earthquake detection through computationally efficient similarity search.

    Science.gov (United States)

    Yoon, Clara E; O'Reilly, Ossian; Bergen, Karianne J; Beroza, Gregory C

    2015-12-01

    Seismology is experiencing rapid growth in the quantity of data, which has outpaced the development of processing algorithms. Earthquake detection-identification of seismic events in continuous data-is a fundamental operation for observational seismology. We developed an efficient method to detect earthquakes using waveform similarity that overcomes the disadvantages of existing detection methods. Our method, called Fingerprint And Similarity Thresholding (FAST), can analyze a week of continuous seismic waveform data in less than 2 hours, or 140 times faster than autocorrelation. FAST adapts a data mining algorithm, originally designed to identify similar audio clips within large databases; it first creates compact "fingerprints" of waveforms by extracting key discriminative features, then groups similar fingerprints together within a database to facilitate fast, scalable search for similar fingerprint pairs, and finally generates a list of earthquake detections. FAST detected most (21 of 24) cataloged earthquakes and 68 uncataloged earthquakes in 1 week of continuous data from a station located near the Calaveras Fault in central California, achieving detection performance comparable to that of autocorrelation, with some additional false detections. FAST is expected to realize its full potential when applied to extremely long duration data sets over a distributed network of seismic stations. The widespread application of FAST has the potential to aid in the discovery of unexpected seismic signals, improve seismic monitoring, and promote a greater understanding of a variety of earthquake processes.

  18. Geometrical and frequential watermarking scheme using similarities

    Science.gov (United States)

    Bas, Patrick; Chassery, Jean-Marc; Davoine, Franck

    1999-04-01

    Watermarking schemes are more and more robust to classical degradations. The NEC system developed by Cox, using both original and marked images, can detect the mark with a JPEG compression ratio of 30. Nevertheless a very simple geometric attack done by the program Stirmark can remove the watermark. Most of the present watermarking schemes only map a mark on the image without geometric reference and therefore are not robust to geometric transformation. We present a scheme based on the modification of a collage map (issued from a fractal code used in fractal compression). We add a mark introducing similarities in the image. The embedding of the mark is done by selection of points of interest supporting blocks on which similarities are hided. This selection is done by the Stephens-Harris detector. The similarity is embedded locally to be robust to cropping. Contrary to many schemes, the reference mark used for the detection comes from the marked image and thus undergoes geometrical distortions. The detection of the mark is done by searching interest blocks and their similarities. It does not use the original image and the robustness is guaranteed by a key. Our first results show that the similarities-based watermarking is quite robust to geometric transformation such as translations, rotations and cropping.

  19. Affinity Propagation Clustering Using Path Based Similarity

    Directory of Open Access Journals (Sweden)

    Yuan Jiang

    2016-07-01

    Full Text Available Clustering is a fundamental task in data mining. Affinity propagation clustering (APC is an effective and efficient clustering technique that has been applied in various domains. APC iteratively propagates information between affinity samples, updates the responsibility matrix and availability matrix, and employs these matrices to choose cluster centers (or exemplars of respective clusters. However, since it mainly uses negative Euclidean distance between exemplars and samples as the similarity between them, it is difficult to identify clusters with complex structure. Therefore, the performance of APC deteriorates on samples distributed with complex structure. To mitigate this problem, we propose an improved APC based on a path-based similarity (APC-PS. APC-PS firstly utilizes negative Euclidean distance to find exemplars of clusters. Then, it employs the path-based similarity to measure the similarity between exemplars and samples, and to explore the underlying structure of clusters. Next, it assigns non-exemplar samples to their respective clusters via that similarity. Our empirical study on synthetic and UCI datasets shows that the proposed APC-PS significantly outperforms original APC and other related approaches.

  20. Percolation in Self-Similar Networks

    Science.gov (United States)

    Serrano, M. Ángeles; Krioukov, Dmitri; Boguñá, Marián

    2011-01-01

    We provide a simple proof that graphs in a general class of self-similar networks have zero percolation threshold. The considered self-similar networks include random scale-free graphs with given expected node degrees and zero clustering, scale-free graphs with finite clustering and metric structure, growing scale-free networks, and many real networks. The proof and the derivation of the giant component size do not require the assumption that networks are treelike. Our results rely only on the observation that self-similar networks possess a hierarchy of nested subgraphs whose average degree grows with their depth in the hierarchy. We conjecture that this property is pivotal for percolation in networks.

  1. Biosequence Similarity Search on the Mercury System

    Science.gov (United States)

    Krishnamurthy, Praveen; Buhler, Jeremy; Chamberlain, Roger; Franklin, Mark; Gyang, Kwame; Jacob, Arpith; Lancaster, Joseph

    2007-01-01

    Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described. PMID:18846267

  2. Measure of Node Similarity in Multilayer Networks

    DEFF Research Database (Denmark)

    Møllgaard, Anders; Zettler, Ingo; Dammeyer, Jesper

    2016-01-01

    university.Our analysis is based on data obtained using smartphones equipped with customdata collection software, complemented by questionnaire-based data. The networkof social contacts is represented as a weighted multilayer network constructedfrom different channels of telecommunication as well as data......The weight of links in a network is often related to the similarity of thenodes. Here, we introduce a simple tunable measure for analysing the similarityof nodes across different link weights. In particular, we use the measure toanalyze homophily in a group of 659 freshman students at a large...... might bepresent in one layer of the multilayer network and simultaneously be absent inthe other layers. For a variable such as gender, our measure reveals atransition from similarity between nodes connected with links of relatively lowweight to dis-similarity for the nodes connected by the strongest...

  3. Fast similarity search for learned metrics.

    Science.gov (United States)

    Kulis, Brian; Jain, Prateek; Grauman, Kristen

    2009-12-01

    We introduce a method that enables scalable similarity search for learned metrics. Given pairwise similarity and dissimilarity constraints between some examples, we learn a Mahalanobis distance function that captures the examples' underlying relationships well. To allow sublinear time similarity search under the learned metric, we show how to encode the learned metric parameterization into randomized locality-sensitive hash functions. We further formulate an indirect solution that enables metric learning and hashing for vector spaces whose high dimensionality makes it infeasible to learn an explicit transformation over the feature dimensions. We demonstrate the approach applied to a variety of image data sets, as well as a systems data set. The learned metrics improve accuracy relative to commonly used metric baselines, while our hashing construction enables efficient indexing with learned distances and very large databases.

  4. Large margin classification with indefinite similarities

    KAUST Repository

    Alabdulmohsin, Ibrahim

    2016-01-07

    Classification with indefinite similarities has attracted attention in the machine learning community. This is partly due to the fact that many similarity functions that arise in practice are not symmetric positive semidefinite, i.e. the Mercer condition is not satisfied, or the Mercer condition is difficult to verify. Examples of such indefinite similarities in machine learning applications are ample including, for instance, the BLAST similarity score between protein sequences, human-judged similarities between concepts and words, and the tangent distance or the shape matching distance in computer vision. Nevertheless, previous works on classification with indefinite similarities are not fully satisfactory. They have either introduced sources of inconsistency in handling past and future examples using kernel approximation, settled for local-minimum solutions using non-convex optimization, or produced non-sparse solutions by learning in Krein spaces. Despite the large volume of research devoted to this subject lately, we demonstrate in this paper how an old idea, namely the 1-norm support vector machine (SVM) proposed more than 15 years ago, has several advantages over more recent work. In particular, the 1-norm SVM method is conceptually simpler, which makes it easier to implement and maintain. It is competitive, if not superior to, all other methods in terms of predictive accuracy. Moreover, it produces solutions that are often sparser than more recent methods by several orders of magnitude. In addition, we provide various theoretical justifications by relating 1-norm SVM to well-established learning algorithms such as neural networks, SVM, and nearest neighbor classifiers. Finally, we conduct a thorough experimental evaluation, which reveals that the evidence in favor of 1-norm SVM is statistically significant.

  5. Inferring Trust Based on Similarity with TILLIT

    Science.gov (United States)

    Tavakolifard, Mozhgan; Herrmann, Peter; Knapskog, Svein J.

    A network of people having established trust relations and a model for propagation of related trust scores are fundamental building blocks in many of today’s most successful e-commerce and recommendation systems. However, the web of trust is often too sparse to predict trust values between non-familiar people with high accuracy. Trust inferences are transitive associations among users in the context of an underlying social network and may provide additional information to alleviate the consequences of the sparsity and possible cold-start problems. Such approaches are helpful, provided that a complete trust path exists between the two users. An alternative approach to the problem is advocated in this paper. Based on collaborative filtering one can exploit the like-mindedness resp. similarity of individuals to infer trust to yet unknown parties which increases the trust relations in the web. For instance, if one knows that with respect to a specific property, two parties are trusted alike by a large number of different trusters, one can assume that they are similar. Thus, if one has a certain degree of trust to the one party, one can safely assume a very similar trustworthiness of the other one. In an attempt to provide high quality recommendations and proper initial trust values even when no complete trust propagation path or user profile exists, we propose TILLIT — a model based on combination of trust inferences and user similarity. The similarity is derived from the structure of the trust graph and users’ trust behavior as opposed to other collaborative-filtering based approaches which use ratings of items or user’s profile. We describe an algorithm realizing the approach based on a combination of trust inferences and user similarity, and validate the algorithm using a real large-scale data-set.

  6. Temporal similarity measures for querying clinical workflows.

    Science.gov (United States)

    Combi, Carlo; Gozzi, Matteo; Oliboni, Barbara; Juarez, Jose M; Marin, Roque

    2009-05-01

    In this paper, we extend a preliminary proposal and discuss in a deeper and more formal way an approach to evaluate temporal similarity between clinical workflow cases (i.e., executions of clinical processes). More precisely, we focus on (i) the representation of clinical processes by using a temporal conceptual workflow model; (ii) the definition of ad hoc temporal constraint networks to formally represent clinical workflow cases; (iii) the definition of temporal similarity for clinical workflow cases based on the comparison of temporal constraint networks; (iv) the management of the similarity of clinical processes related to the Italian guideline for stroke prevention and management (SPREAD). Clinical processes are composed by clinical activities to be done by given actors in a given order satisfying given temporal constraints. This description means that clinical processes can be seen as organizational processes, and modeled by workflow schemata. When a workflow schema represents a clinical process, its cases represent different instances derived from dealing with different patients in different situations. With respect to all the cases related to a workflow schema, each clinical case can be different with respect to its structure and to its temporal aspects. Clinical cases can be stored in clinical databases and information retrieval can be done evaluating the similarity between workflow cases. We first describe a possible approach to the conceptual modeling of a clinical process, by using a temporally extended workflow model. Then, we define how a workflow case can be represented as a set of activities, and show how to express them through temporal constraint networks. Once we have built temporal constraint networks related to the cases to compare, we propose a similarity function able to evaluate the differences between the considered cases with respect to the order and duration of corresponding activities, and with respect to the presence/absence of some

  7. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

    , how to do so is not obvious. In this paper, we build on the ideas of the Probabilistic Latent Semantic Analysis (PLSA) that have been successfully used in the document retrieval community. Under this probabilistic framework, any song will be projected into a relatively low dimensional space of “latent...... semantics”, in such a way that all observed similarities can be satisfactorily explained using the latent semantics. Therefore, one can think of these semantics as the real structure in music, in the sense that they can explain the observed similarities among songs. The suitability of the PLSA model...

  8. Unveiling Music Structure Via PLSA Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Meng, Anders; Petersen, Kaare Brandt

    2007-01-01

    Nowadays there is an increasing interest in developing methods for building music recommendation systems. In order to get a satisfactory performance from such a system, one needs to incorporate as much information about songs similarity as possible; however, how to do so is not obvious...... observed similarities can be satisfactorily explained using the latent semantics. Additionally, this approach significantly simplifies the song retrieval phase, leading to a more practical system implementation. The suitability of the PLSA model for representing music structure is studied in a simplified...

  9. Earth Similarity Index with two free parameters

    OpenAIRE

    Chandra, Suresh; Nepal, Subas; Sharma, Mohit K

    2015-01-01

    We have derived Earth Similarity Index (ESI) with two free parameters m and T. These free parameters are optimized with the consideration that the planet Mars is almost similar to the Earth. For the optimized values of free parameters, the interior-ESI, surface-ESI and ESI for some planets are calculated. The results for m = 0.8 and T = 0.8 are compared with the values obtained by Schulze-Makuch {\\it et al.} (2011). We have found that the exoplanet 55 Cnc f is within 10% away from the thresho...

  10. PubChem3D: Similar conformers

    Directory of Open Access Journals (Sweden)

    Bolton Evan E

    2011-05-01

    Full Text Available Abstract Background PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features. Results The first two diverse 3-D conformers of 26.1 million PubChem Compound records were compared to each other, using a shape Tanimoto (ST of 0.8 or greater and a color Tanimoto (CT of 0.5 or greater, yielding 8.16 billion conformer neighbor pairs and 6.62 billion compound neighbor pairs, with an average of 253 "Similar Conformers" compound neighbors per compound. Comparing the 3-D neighboring relationship to the corresponding 2-D neighboring relationship ("Similar Compounds" for molecules such as caffeine, aspirin, and morphine, one finds unique sets of related chemical structures, providing additional significant biological annotation. The PubChem 3-D neighboring relationship is also shown to be able to group a set of non-steroidal anti-inflammatory drugs (NSAIDs, despite limited PubChem 2-D similarity. In a study of 4,218 chemical structures of biomedical interest, consisting of many known drugs, using more diverse conformers per compound results in more 3-D compound neighbors per compound; however, the overlap of the compound neighbor lists per conformer also increasingly resemble each other, being 38% identical at three conformers and 68% at ten conformers. Perhaps surprising is that the average

  11. Nuclear markers reveal that inter-lake cichlids' similar morphologies do not reflect similar genealogy.

    Science.gov (United States)

    Kassam, Daud; Seki, Shingo; Horic, Michio; Yamaoka, Kosaku

    2006-08-01

    The apparent inter-lake morphological similarity among East African Great Lakes' cichlid species/genera has left evolutionary biologists asking whether such similarity is due to sharing of common ancestor or mere convergent evolution. In order to answer such question, we first used Geometric Morphometrics, GM, to quantify morphological similarity and then subsequently used Amplified Fragment Length Polymorphism, AFLP, to determine if similar morphologies imply shared ancestry or convergent evolution. GM revealed that not all presumed morphological similar pairs were indeed similar, and the dendrogram generated from AFLP data indicated distinct clusters corresponding to each lake and not inter-lake morphological similar pairs. Such results imply that the morphological similarity is due to convergent evolution and not shared ancestry. The congruency of GM and AFLP generated dendrograms imply that GM is capable of picking up phylogenetic signal, and thus GM can be potential tool in phylogenetic systematics.

  12. Predicting spatial similarity of freshwater fish biodiversity.

    Science.gov (United States)

    Azaele, Sandro; Muneepeerakul, Rachata; Maritan, Amos; Rinaldo, Andrea; Rodriguez-Iturbe, Ignacio

    2009-04-28

    A major issue in modern ecology is to understand how ecological complexity at broad scales is regulated by mechanisms operating at the organismic level. What specific underlying processes are essential for a macroecological pattern to emerge? Here, we analyze the analytical predictions of a general model suitable for describing the spatial biodiversity similarity in river ecosystems, and benchmark them against the empirical occurrence data of freshwater fish species collected in the Mississippi-Missouri river system. Encapsulating immigration, emigration, and stochastic noise, and without resorting to species abundance data, the model is able to reproduce the observed probability distribution of the Jaccard similarity index at any given distance. In addition to providing an excellent agreement with the empirical data, this approach accounts for heterogeneities of different subbasins, suggesting a strong dependence of biodiversity similarity on their respective climates. Strikingly, the model can also predict the actual probability distribution of the Jaccard similarity index for any distance when considering just a relatively small sample. The proposed framework supports the notion that simplified macroecological models are capable of predicting fundamental patterns-a theme at the heart of modern community ecology.

  13. Houses and Apartments: Similar Assets, Different Financials

    National Research Council Canada - National Science Library

    Peter Chinloy; Prashant K Das; Jonathan A Wiley

    2014-01-01

    ....) Apartments and houses are highly substitutable in production and consumption. With similar materials and production costs, any differences in the markets for these two assets should have origins in financial contracts. The lessons available from this comparison have greater urgency given evidence that investment in new housing dominates the business cyc...

  14. Cross-kingdom similarities in microbiome functions

    NARCIS (Netherlands)

    Mendes, R.; Raaijmakers, J.M.

    2015-01-01

    Recent advances in medical research have revealed how humans rely on their microbiome for diverse traits and functions. Similarly, microbiomes of other higher organisms play key roles in disease, health, growth and development of their host. Exploring microbiome functions across kingdoms holds

  15. Efficient Similarity Retrieval in Music Databases

    DEFF Research Database (Denmark)

    Ruxanda, Maria Magdalena; Jensen, Christian Søndergaard

    2006-01-01

    Audio music is increasingly becoming available in digital form, and the digital music collections of individuals continue to grow. Addressing the need for effective means of retrieving music from such collections, this paper proposes new techniques for content-based similarity search. Each music...

  16. The triangle inequality constraint in similarity judgments.

    Science.gov (United States)

    Yearsley, James M; Barque-Duran, Albert; Scerrati, Elisa; Hampton, James A; Pothos, Emmanuel M

    2017-11-01

    Since Tversky's (1977) seminal investigation, the triangle inequality, along with symmetry and minimality, have had a central role in investigations of the fundamental constraints on human similarity judgments. The meaning of minimality and symmetry in similarity judgments has been straightforward, but this is not the case for the triangle inequality. Expressed in terms of dissimilarities, and assuming a simple, linear function between dissimilarities and distances, the triangle inequality constraint implies that human behaviour should be consistent with Dissimilarity (A,B) + Dissimilarity (B,C) ≥ Dissimilarity (A,C), where A, B, and C are any three stimuli. We show how we can translate this constraint into one for similarities, using Shepard's (1987) generalization law, and so derive the multiplicative triangle inequality for similarities, Sim(A,C)≥Sim(A,B)⋅Sim(B,C) where 0≤Sim(x,y)≤1. Can humans violate the multiplicative triangle inequality? An empirical demonstration shows that they can. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Anthropogenic and impact spherules: Morphological similarity and ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Earth System Science; Volume 120; Issue 6. Anthropogenic and impact spherules: Morphological similarity and chemical distinction – A case study from India and its implications. Ambalika Niyogi Jayanta K Pati Suresh C Patel Dipak Panda Shiv K Patil. Volume 120 Issue 6 December 2011 pp ...

  18. Great Apes' Capacities to Recognize Relational Similarity

    Science.gov (United States)

    Haun, Daniel B. M.; Call, Josep

    2009-01-01

    Recognizing relational similarity relies on the ability to understand that defining object properties might not lie in the objects individually, but in the relations of the properties of various object to each other. This aptitude is highly relevant for many important human skills such as language, reasoning, categorization and understanding…

  19. Partial order similarity based on mutual information

    CERN Document Server

    Tibély, Gergely; Palla, Gergely

    2016-01-01

    Comparing the ranking of candidates by different voters is an important topic in social and information science with a high relevance from the point of view of practical applications. In general, ties and pairs of incomparable candidates may occur, thus, the alternative rankings are described by partial orders. Various distance measures between partial orders have already been introduced, where zero distance is corresponding to a perfect match between a pair of partial orders, and larger values signal greater differences. Here we take a different approach and propose a similarity measure based on adjusted mutual information. In general, the similarity value of unity is corresponding to exactly matching partial orders, while a low similarity is associated to a pair of independent partial orders. The time complexity of the computation of this similarity measure is $\\mathcal{O}(\\left|{\\mathcal C}\\right|^3)$ in the worst case, and $\\mathcal{O}(\\left|{\\mathcal C}\\right|^2\\ln \\left|{\\mathcal C}\\right|)$ in the typi...

  20. Measurement of Similarity in Academic Contexts

    Directory of Open Access Journals (Sweden)

    Omid Mahian

    2017-06-01

    Full Text Available We propose some reflections, comments and suggestions about the measurement of similar and matched content in scientific papers and documents, and the need to develop appropriate tools and standards for an ethically fair and equitable treatment of authors.

  1. Music Retrieval based on Melodic Similarity

    NARCIS (Netherlands)

    Typke, R.

    2007-01-01

    This thesis introduces a method for measuring melodic similarity for notated music such as MIDI files. This music search algorithm views music as sets of notes that are represented as weighted points in the two-dimensional space of time and pitch. Two point sets can be compared by calculating how

  2. Contextual Factors for Finding Similar Experts

    DEFF Research Database (Denmark)

    Hofmann, Katja; Balog, Krisztian; Bogers, Toine

    2010-01-01

    -seeking models, are rarely taken into account. In this article, we extend content-based expert-finding approaches with contextual factors that have been found to influence human expert finding. We focus on a task of science communicators in a knowledge-intensive environment, the task of finding similar experts...

  3. UMLS-Interface and UMLS-Similarity : Open Source Software for Measuring Paths and Semantic Similarity

    OpenAIRE

    McInnes, Bridget T.; Pedersen, Ted; Pakhomov, Serguei V.S.

    2009-01-01

    A number of computational measures for determining semantic similarity between pairs of biomedical concepts have been developed using various standards and programming platforms. In this paper, we introduce two new open-source frameworks based on the Unified Medical Language System (UMLS). These frameworks consist of the UMLS-Similarity and UMLS-Interface packages. UMLS-Interface provides path information about UMLS concepts. UMLS-Similarity calculates the semantic similarity between UMLS con...

  4. Extending the Similarity-Attraction Effect : The effects of When-Similarity in mediated communication

    NARCIS (Netherlands)

    Kaptein, M.C.; Castaneda, D.; Fernandez, N.; Nass, C.

    2014-01-01

    The feeling of connectedness experienced in computer-mediated relationships can be explained by the similarity-attraction effect (SAE). Though SAE is well established in psychology, the effects of some types of similarity have not yet been explored. In 2 studies, we demonstrate similarity-attraction

  5. New similarity search based glioma grading

    Energy Technology Data Exchange (ETDEWEB)

    Haegler, Katrin; Brueckmann, Hartmut; Linn, Jennifer [Ludwig-Maximilians-University of Munich, Department of Neuroradiology, Munich (Germany); Wiesmann, Martin; Freiherr, Jessica [RWTH Aachen University, Department of Neuroradiology, Aachen (Germany); Boehm, Christian [Ludwig-Maximilians-University of Munich, Department of Computer Science, Munich (Germany); Schnell, Oliver; Tonn, Joerg-Christian [Ludwig-Maximilians-University of Munich, Department of Neurosurgery, Munich (Germany)

    2012-08-15

    MR-based differentiation between low- and high-grade gliomas is predominately based on contrast-enhanced T1-weighted images (CE-T1w). However, functional MR sequences as perfusion- and diffusion-weighted sequences can provide additional information on tumor grade. Here, we tested the potential of a recently developed similarity search based method that integrates information of CE-T1w and perfusion maps for non-invasive MR-based glioma grading. We prospectively included 37 untreated glioma patients (23 grade I/II, 14 grade III gliomas), in whom 3T MRI with FLAIR, pre- and post-contrast T1-weighted, and perfusion sequences was performed. Cerebral blood volume, cerebral blood flow, and mean transit time maps as well as CE-T1w images were used as input for the similarity search. Data sets were preprocessed and converted to four-dimensional Gaussian Mixture Models that considered correlations between the different MR sequences. For each patient, a so-called tumor feature vector (= probability-based classifier) was defined and used for grading. Biopsy was used as gold standard, and similarity based grading was compared to grading solely based on CE-T1w. Accuracy, sensitivity, and specificity of pure CE-T1w based glioma grading were 64.9%, 78.6%, and 56.5%, respectively. Similarity search based tumor grading allowed differentiation between low-grade (I or II) and high-grade (III) gliomas with an accuracy, sensitivity, and specificity of 83.8%, 78.6%, and 87.0%. Our findings indicate that integration of perfusion parameters and CE-T1w information in a semi-automatic similarity search based analysis improves the potential of MR-based glioma grading compared to CE-T1w data alone. (orig.)

  6. Why is the magnetic force similar to a Coriolis force?

    OpenAIRE

    Royer, Antoine

    2011-01-01

    It is pointed out that the underlying reason why the magnetic force is similar to a Coriolis force is that it is caused by Thomas rotations, induced by successions of non-collinear Lorentz boosts. The magnetic force may even be viewed as a kind of Coriolis force (making perhaps more acceptable the apparent non-existence of magnetic monopoles). We also show that under a change of inertial frames, Faraday lines of force Lorentz contract as if 'etched' in space, while 'Coriolis' terms get added on.

  7. Self-similar radiation from numerical Rosenau Hyman compactons

    Science.gov (United States)

    Rus, Francisco; Villatoro, Francisco R.

    2007-11-01

    The numerical simulation of compactons, solitary waves with compact support, is characterized by the presence of spurious phenomena, as numerically induced radiation, which is illustrated here using four numerical methods applied to the Rosenau-Hyman K( p, p) equation. Both forward and backward radiations are emitted from the compacton presenting a self-similar shape which has been illustrated graphically by the proper scaling. A grid refinement study shows that the amplitude of the radiations decreases as the grid size does, confirming its numerical origin. The front velocity and the amplitude of both radiations have been studied as a function of both the compacton and the numerical parameters. The amplitude of the radiations decreases exponentially in time, being characterized by a nearly constant scaling exponent. An ansatz for both the backward and forward radiations corresponding to a self-similar function characterized by the scaling exponent is suggested by the present numerical results.

  8. Picosecond laser welding of similar and dissimilar materials.

    Science.gov (United States)

    Carter, Richard M; Chen, Jianyong; Shephard, Jonathan D; Thomson, Robert R; Hand, Duncan P

    2014-07-01

    We report picosecond laser welding of similar and dissimilar materials based on plasma formation induced by a tightly focused beam from a 1030 nm, 10 ps, 400 kHz laser system. Specifically, we demonstrate the welding of fused silica, borosilicate, and sapphire to a range of materials including borosilicate, fused silica, silicon, copper, aluminum, and stainless steel. Dissimilar material welding of glass to aluminum and stainless steel has not been previously reported. Analysis of the borosilicate-to-borosilicate weld strength compares well to those obtained using similar welding systems based on femtosecond lasers. There is, however, a strong requirement to prepare surfaces to a high (10-60 nm Ra) flatness to ensure a successful weld.

  9. Measuring Source Code Similarity Using Reference Vectors

    Science.gov (United States)

    Ohno, Asako; Murao, Hajime

    In this paper, we propose a novel method to measure similarity between program source codes. Different to others, our method doues not compare two source codes directly but compares two reference vectors, where a reference vector is calculated from one source code and a set of reference source codes. This means that our method requires no original source code when considering an application open to public such as a search engine for the program source code on the internet. We have built a simple search system and have evaluated with Java source codes made in the university course of basic programming. Results show that the system can achieve quite high average precision rate in very short time which means the proposed method can measure correct similarity very fast.

  10. Cultural similarity and adjustment of expatriate academics

    DEFF Research Database (Denmark)

    Selmer, Jan; Lauring, Jakob

    2009-01-01

    The findings of a number of recent empirical studies of business expatriates, using different samples and methodologies, seem to support the counter-intuitive proposition that cultural similarity may be as difficult to adjust to as cultural dissimilarity. However, it is not obvious that these res......The findings of a number of recent empirical studies of business expatriates, using different samples and methodologies, seem to support the counter-intuitive proposition that cultural similarity may be as difficult to adjust to as cultural dissimilarity. However, it is not obvious...... that these results also are applicable to other groups of expatriates. To explore this eventuality, an electronic survey was directed towards expatriate academics in 34 universities in five European countries. For the purpose of this study, they were sorted into two groups, expatriate academics from EU countries...

  11. Similarity Arguments in the Genetic Modification Debate

    DEFF Research Database (Denmark)

    Christiansen, Andreas

    2017-01-01

    In the ethical debate on genetic modification (GM), it is common to encounter the claim that some anti-GM argument would also apply an established, ethically accepted technology, and that the anti-GM argument is therefore unsuccessful. The paper discusses whether this argumentative strategy....... Finally, the paper discusses what conclusions we can draw from the fact that genetic modification and established technologies are similar for the ethical status of genetic modification....... transferability of reasons from one case to another; and (iii) it runs the risk of equivocations, especially in cases where the anti-genetic-modification argument relies on gradable features. The paper then shows how these issues play out in three specific Similarity Arguments that can be found in the literature...

  12. Hashing for Similarity Search: A Survey

    OpenAIRE

    Wang, Jingdong; Shen, Heng Tao; Song, Jingkuan; Ji, Jianqiu

    2014-01-01

    Similarity search (nearest neighbor search) is a problem of pursuing the data items whose distances to a query item are the smallest from a large database. Various methods have been developed to address this problem, and recently a lot of efforts have been devoted to approximate search. In this paper, we present a survey on one of the main solutions, hashing, which has been widely studied since the pioneering work locality sensitive hashing. We divide the hashing algorithms two main categorie...

  13. Similarity-based Polymorphic Shellcode Detection

    Directory of Open Access Journals (Sweden)

    Denis Yurievich Gamayunov

    2013-02-01

    Full Text Available In the work the method for polymorphic shellcode dedection based on the set of known shellcodes is proposed. The method’s main idea is in sequential applying of deobfuscating transformations to a data analyzed and then recognizing similarity with malware samples. The method has been tested on the sets of shellcodes generated using Metasploit Framework v.4.1.0 and PELock Obfuscator and shows 87 % precision with zero false positives rate.

  14. Multidimensional Scaling Visualization Using Parametric Similarity Indices

    OpenAIRE

    Tenreiro Machado, J. A.; António M Lopes; Galhano, Alexandra M.

    2015-01-01

    In this paper, we apply multidimensional scaling (MDS) and parametric similarity indices (PSI) in the analysis of complex systems (CS). Each CS is viewed as a dynamical system, exhibiting an output time-series to be interpreted as a manifestation of its behavior. We start by adopting a sliding window to sample the original data into several consecutive time periods. Second, we define a given PSI for tracking pieces of data. We then compare the windows for different values of the parameter, an...

  15. Discovering Music Structure via Similarity Fusion

    OpenAIRE

    Meng, Anders

    2007-01-01

    Automatic methods for music navigation and music recommendation exploit the structure in the music to carry out a meaningful exploration of the “song space”. To get a satisfactory performance from such systems, one should incorporate as much information about songs similarity as possible; however, how to do so is not obvious. In this paper, we build on the ideas of the Probabilistic Latent Semantic Analysis (PLSA) that have been successfully used in the document retrieval community. Under thi...

  16. Privacy preserving similarity detection for data analysis

    OpenAIRE

    Leontiadis, Iraklis; Önen, Melek; Molva, Refik; Chorley, M.J.; Colombo, G.B.

    2013-01-01

    International audience; Current applications tend to use personal sensitive information to achieve better quality with respect to their services. Since the third parties are not trusted the data must be protected such that individual data privacy is not compromised but at the same time operations on it would be compatible. A wide range of data analysis operations entails a similarity detection algorithm between user data. For instance clustering on big data groups together objects based on th...

  17. Spectral clustering based on learning similarity matrix.

    Science.gov (United States)

    Park, Seyoung; Zhao, Hongyu; Birol, Inanc

    2018-02-08

    Single-cell RNA-sequencing (scRNA-seq) technology can generate genome-wide expression data at the single-cell levels. One important objective in scRNA-seq analysis is to cluster cells where each cluster consists of cells belonging to the same cell type based on gene expression patterns. We introduce a novel spectral clustering framework that imposes sparse structures on a target matrix. Specifically, we utilize multiple doubly stochastic similarity matrices to learn a similarity matrix, motivated by the observation that each similarity matrix can be a different informative representation of the data. We impose a sparse structure on the target matrix followed by shrinking pairwise differences of the rows in the target matrix, motivated by the fact that the target matrix should have these structures in the ideal case. We solve the proposed non-convex problem iteratively using the ADMM algorithm and show the convergence of the algorithm. We evaluate the performance of the proposed clustering method on various simulated as well as real scRNA-seq data, and show that it can identify clusters accurately and robustly. The algorithm is implemented in MATLAB. The source code can be downloaded at https://github.com/ishspsy/project/tree/master/MPSSC. seyoung.park@yale.edu. Supplementary data are available at Bioinformatics online.

  18. Similarities between rivers and submarine channels

    Science.gov (United States)

    Balcerak, Ernie

    2013-02-01

    Scientists have long known that the width and depth of rivers follows a power law relationship with discharge. They have also noticed that submarine channels appear to be similar to terrestrial rivers, but there have not been many systematic comparisons of the relationships between submarine channel morphology and discharge. Konsoer et al. compared the width, depth, and slope of 177 submarine channels to those of 231 river cross sections. They found that submarine channels are up to an order of magnitude wider and deeper than the largest terrestrial rivers, but they exhibit a similar power law relationship between width and depth. For submarine channels that were similar in size to rivers, the authors found that submarine channels tend to be 1 to 2 orders of magnitude steeper than rivers. The authors also inferred values for sediment concentration in the turbidity currents in the channels and combined this with estimated mean flow velocities to look for a relationship between discharge and morphology in the channels. They found that like rivers, the width and depth of the submarine channels follow a power law scaling with discharge. (Journal of Geophysical Research-Earth Surface, doi:10.1029/2012JF002422, 2013)

  19. Effects of similarity on environmental context cueing.

    Science.gov (United States)

    Smith, Steven M; Handy, Justin D; Angello, Genna; Manzano, Isabel

    2014-01-01

    Three experiments examined the prediction that context cues which are similar to study contexts can facilitate episodic recall, even if those cues are never seen before the recall test. Environmental context cueing effects have typically produced such small effect sizes that influences of moderating factors, such as the similarity between encoding and retrieval contexts, would be difficult to observe experimentally. Videos of environmental contexts, however, can be used to produce powerful context-dependent memory effects, particularly when only one memory target is associated with each video context, intentional item-context encoding is encouraged, and free recall tests are used. Experiment 1 showed that a not previously viewed video of the study context provided an effective recall cue, although it was not as effective as the originally viewed video context. Experiments 2 and 3 showed that videos of environments that were conceptually similar to encoding contexts (e.g., both were videos of ball field games) also cued recall, but not as well if the encoding contexts were given specific labels (e.g., "home run") incompatible with test contexts (e.g., a soccer scene). A fourth experiment that used incidental item-context encoding showed that video context reinstatement has a robust effect on paired associate memory, indicating that the video context reinstatement effect does not depend on interactive item-context encoding or free recall testing.

  20. From sample similarity to ensemble similarity: probabilistic distance measures in reproducing kernel Hilbert space.

    Science.gov (United States)

    Zhou, Shaohua Kevin; Chellappa, Rama

    2006-06-01

    This paper addresses the problem of characterizing ensemble similarity from sample similarity in a principled manner. Using reproducing kernel as a characterization of sample similarity, we suggest a probabilistic distance measure in the reproducing kernel Hilbert space (RKHS) as the ensemble similarity. Assuming normality in the RKHS, we derive analytic expressions for probabilistic distance measures that are commonly used in many applications, such as Chernoff distance (or the Bhattacharyya distance as its special case), Kullback-Leibler divergence, etc. Since the reproducing kernel implicitly embeds a nonlinear mapping, our approach presents a new way to study these distances whose feasibility and efficiency is demonstrated using experiments with synthetic and real examples. Further, we extend the ensemble similarity to the reproducing kernel for ensemble and study the ensemble similarity for more general data representations.

  1. CULTURAL SIMILARITIES AND DIFFERENCES IN CONSUMER BEHAVIOUR

    OpenAIRE

    Tunkkari, Siobhan

    2017-01-01

    The purpose of this thesis was to research the influence of culture on consumer behaviour and to determine if there are similarities and/or differences in consumer behaviour between cultures. For marketers all around the world, it is extremely important to understand the needs and behaviours of individuals in order to get a deeper insight to how they choose to purchase products and services. The influence of culture on consumer behaviour is vital to get to terms with. Culture can be defined a...

  2. Structural similarity and category-specificity

    DEFF Research Database (Denmark)

    Gerlach, Christian; Law, Ian; Paulson, Olaf B

    2004-01-01

    It has been suggested that category-specific recognition disorders for natural objects may reflect that natural objects are more structurally (visually) similar than artefacts and therefore more difficult to recognize following brain damage. On this account one might expect a positive relationship...... range of candidate integral units will be activated and compete for selection, thus explaining the higher error rate associated with animals. We evaluate the model based on previous evidence from both normal subjects and patients with category-specific disorders and argue that this model can help...

  3. Modeling Timbre Similarity of Short Music Clips.

    Science.gov (United States)

    Siedenburg, Kai; Müllensiefen, Daniel

    2017-01-01

    There is evidence from a number of recent studies that most listeners are able to extract information related to song identity, emotion, or genre from music excerpts with durations in the range of tenths of seconds. Because of these very short durations, timbre as a multifaceted auditory attribute appears as a plausible candidate for the type of features that listeners make use of when processing short music excerpts. However, the importance of timbre in listening tasks that involve short excerpts has not yet been demonstrated empirically. Hence, the goal of this study was to develop a method that allows to explore to what degree similarity judgments of short music clips can be modeled with low-level acoustic features related to timbre. We utilized the similarity data from two large samples of participants: Sample I was obtained via an online survey, used 16 clips of 400 ms length, and contained responses of 137,339 participants. Sample II was collected in a lab environment, used 16 clips of 800 ms length, and contained responses from 648 participants. Our model used two sets of audio features which included commonly used timbre descriptors and the well-known Mel-frequency cepstral coefficients as well as their temporal derivates. In order to predict pairwise similarities, the resulting distances between clips in terms of their audio features were used as predictor variables with partial least-squares regression. We found that a sparse selection of three to seven features from both descriptor sets-mainly encoding the coarse shape of the spectrum as well as spectrotemporal variability-best predicted similarities across the two sets of sounds. Notably, the inclusion of non-acoustic predictors of musical genre and record release date allowed much better generalization performance and explained up to 50% of shared variance (R(2)) between observations and model predictions. Overall, the results of this study empirically demonstrate that both acoustic features related to

  4. Measure of Node Similarity in Multilayer Networks

    DEFF Research Database (Denmark)

    Møllgaard, Anders; Zettler, Ingo; Dammeyer, Jesper

    2016-01-01

    The weight of links in a network is often related to the similarity of thenodes. Here, we introduce a simple tunable measure for analysing the similarityof nodes across different link weights. In particular, we use the measure toanalyze homophily in a group of 659 freshman students at a large...... university.Our analysis is based on data obtained using smartphones equipped with customdata collection software, complemented by questionnaire-based data. The networkof social contacts is represented as a weighted multilayer network constructedfrom different channels of telecommunication as well as data...

  5. Oxidative stress, a trigger of hepatitis C and B virus-induced liver carcinogenesis

    Science.gov (United States)

    Ivanov, Alexander V.; Valuev-Elliston, Vladimir T.; Tyurina, Daria A.; Ivanova, Olga N.; Kochetkov, Sergey N.; Bartosch, Birke; Isaguliants, Maria G.

    2017-01-01

    Virally induced liver cancer usually evolves over long periods of time in the context of a strongly oxidative microenvironment, characterized by chronic liver inflammation and regeneration processes. They ultimately lead to oncogenic mutations in many cellular signaling cascades that drive cell growth and proliferation. Oxidative stress, induced by hepatitis viruses, therefore is one of the factors that drives the neoplastic transformation process in the liver. This review summarizes current knowledge on oxidative stress and oxidative stress responses induced by human hepatitis B and C viruses. It focuses on the molecular mechanisms by which these viruses activate cellular enzymes/systems that generate or scavenge reactive oxygen species (ROS) and control cellular redox homeostasis. The impact of an altered cellular redox homeostasis on the initiation and establishment of chronic viral infection, as well as on the course and outcome of liver fibrosis and hepatocarcinogenesis will be discussed The review neither discusses reactive nitrogen species, although their metabolism is interferes with that of ROS, nor antioxidants as potential therapeutic remedies against viral infections, both subjects meriting an independent review. PMID:27965466

  6. Exploiting Data Similarity to Reduce Memory Footprints

    Energy Technology Data Exchange (ETDEWEB)

    Biswas, S; de Supinski, B R; Schulz, M; Franklin, D; Sherwood, T; Chong, F T

    2011-01-28

    Memory size has long limited large-scale applications on high-performance computing (HPC) systems. Since compute nodes frequently do not have swap space, physical memory often limits problem sizes. Increasing core counts per chip and power density constraints, which limit the number of DIMMs per node, have exacerbated this problem. Further, DRAM constitutes a significant portion of overall HPC system cost. Therefore, instead of adding more DRAM to the nodes, mechanisms to manage memory usage more efficiently - preferably transparently - could increase effective DRAM capacity and thus the benefit of multicore nodes for HPC systems. MPI application processes often exhibit significant data similarity. These data regions occupy multiple physical locations across the individual rank processes within a multicore node and thus offer a potential savings in memory capacity. These regions, primarily residing in heap, are dynamic, which makes them difficult to manage statically. Our novel memory allocation library, SBLLmalloc, automatically identifies identical memory blocks and merges them into a single copy. SBLLmalloc does not require application or OS changes since we implement it as a user-level library. Overall, we demonstrate that SBLLmalloc reduces the memory footprint of a range of MPI applications by 32.03% on average and up to 60.87%. Further, SBLLmalloc supports problem sizes for IRS over 21.36% larger than using standard memory management techniques, thus significantly increasing effective system size. Similarly, SBLLmalloc requires 43.75% fewer nodes than standard memory management techniques to solve an AMG problem.

  7. Parasite community similarity between four Irish lakes.

    Science.gov (United States)

    Byrne, C J; Grey, C; Holland, C; Poole, R

    2000-12-01

    A total of 140 trout were examined from four lakes in north west Ireland, Loughs Craghy, Waskel, Meela and Owennamarve. Eleven species of metazoan parasite were recorded, ten of which were of freshwater origin and Anisakissp. was the only marine species. No acanthocephalan species were found. Diphyllobothrium ditremum, D. dendriticum and Anisakissp. were the only allogenic species. Lough Owennamarve had the largest component community with nine species recorded. Lough Meela, the only brackish water lake had the smallest component community with six species recorded. Lough Waskel and Craghy had intermediate component community values. Lough Meela showed the lowest levels of similarity to any of the other lakes. Values for the Shannon-Wiener diversity index were highest for Lough Owennamarve and lowest for Lough Meela and intermediate for the other two lakes. Lough Meela had the highest values for the Simpson's dominance index and the Berger-Parker index. Lough Owennamarve had the highest Brillouin's index and Lough Meela had the lowest. The use of multiple regression techniques to control for the potentially confounding effect of geographical distance as a predictor of community similarity was discussed. No parasite species found could be considered as regionally and locally abundant and therefore described as a core species. The helminth community appears to have some degree of predictability, but chance colonization events are also important.

  8. Pharmacophore-based similarity scoring for DOCK.

    Science.gov (United States)

    Jiang, Lingling; Rizzo, Robert C

    2015-01-22

    Pharmacophore modeling incorporates geometric and chemical features of known inhibitors and/or targeted binding sites to rationally identify and design new drug leads. In this study, we have encoded a three-dimensional pharmacophore matching similarity (FMS) scoring function into the structure-based design program DOCK. Validation and characterization of the method are presented through pose reproduction, crossdocking, and enrichment studies. When used alone, FMS scoring dramatically improves pose reproduction success to 93.5% (∼20% increase) and reduces sampling failures to 3.7% (∼6% drop) compared to the standard energy score (SGE) across 1043 protein-ligand complexes. The combined FMS+SGE function further improves success to 98.3%. Crossdocking experiments using FMS and FMS+SGE scoring, for six diverse protein families, similarly showed improvements in success, provided proper pharmacophore references are employed. For enrichment, incorporating pharmacophores during sampling and scoring, in most cases, also yield improved outcomes when docking and rank-ordering libraries of known actives and decoys to 15 systems. Retrospective analyses of virtual screenings to three clinical drug targets (EGFR, IGF-1R, and HIVgp41) using X-ray structures of known inhibitors as pharmacophore references are also reported, including a customized FMS scoring protocol to bias on selected regions in the reference. Overall, the results and fundamental insights gained from this study should benefit the docking community in general, particularly researchers using the new FMS method to guide computational drug discovery with DOCK.

  9. Creating Birds of Similar Feathers: Leveraging Similarity to Improve Teacher-Student Relationships and Academic Achievement

    Science.gov (United States)

    Gehlbach, Hunter; Brinkworth, Maureen E.; King, Aaron M.; Hsu, Laura M.; McIntyre, Joseph; Rogers, Todd

    2016-01-01

    When people perceive themselves as similar to others, greater liking and closer relationships typically result. In the first randomized field experiment that leverages actual similarities to improve real-world relationships, we examined the affiliations between 315 9th grade students and their 25 teachers. Students in the treatment condition…

  10. Similar or different?: the importance of similarities and differences for support between siblings

    NARCIS (Netherlands)

    Voorpostel, M.; van der Lippe, T.; Dykstra, P.A.; Flap, H.

    2007-01-01

    Using a large-scale Dutch national sample (N = 7,126), the authors examine the importance of similarities and differences in the sibling dyad for the provision of support. Similarities are assumed to enhance attraction and empathy; differences are assumed to be related to different possibilities for

  11. Similar or Different? The Importance of Similarities and Differences for Support Between Siblings

    NARCIS (Netherlands)

    Voorpostel, Marieke; Lippe, Tanja van der; Dykstra, Pearl A.; Flap, Henk

    2007-01-01

    Using a large-scale Dutch national sample (N = 7,126), the authors examine the importance of similarities and differences in the sibling dyad for the provision of support. Similarities are assumed to enhance attraction and empathy; differences are assumed to be related to different possibilities for

  12. UMLS-Interface and UMLS-Similarity : open source software for measuring paths and semantic similarity.

    Science.gov (United States)

    McInnes, Bridget T; Pedersen, Ted; Pakhomov, Serguei V S

    2009-11-14

    A number of computational measures for determining semantic similarity between pairs of biomedical concepts have been developed using various standards and programming platforms. In this paper, we introduce two new open-source frameworks based on the Unified Medical Language System (UMLS). These frameworks consist of the UMLS-Similarity and UMLS-Interface packages. UMLS-Interface provides path information about UMLS concepts. UMLS-Similarity calculates the semantic similarity between UMLS concepts using several previously developed measures and can be extended to include new measures. We validate the functionality of these frameworks by reproducing the results from previous work. Our frameworks constitute a significant contribution to the field of biomedical Natural Language Processing by providing a common development and testing platform for semantic similarity measures based on the UMLS.

  13. A ligand's view of target similarity

    DEFF Research Database (Denmark)

    Garland, Stephen L; Gloriam, David E

    2011-01-01

    shows with several examples how focusing on the binding site(s) has a clear advantage when it comes to establishing sequence-correlated pharmacological profiles. By organizing and comparing sequence and structural data it is possible to "borrow" SAR from similar targets to increase the speed of lead......-finding and, potentially, to produce ligands for previously intractable receptors. Sequence motifs correlated with ligands can be applied in the design of target-specific focused libraries that are both efficient and cost-effective and should provide increased hit-rates over diversity screening. Furthermore......, in the optimization phase, the binding motif approach offers the possibility to identify quickly the most likely off-target candidates to be chosen for selectivity screening, as well as potentially characterizing those pockets which may best be exploited for improved selectivity....

  14. Social Values as Arguments: Similar is Convincing

    Directory of Open Access Journals (Sweden)

    Gregory R Maio

    2014-08-01

    Full Text Available Politicians, philosophers, and rhetors engage in co-value argumentation: appealing to one value in order to support another value (e.g., equality leads to freedom. Across four experiments in the United Kingdom and India, we found that the psychological relatedness of values affects the persuasiveness of the arguments that bind them. Experiment 1 found that participants were more persuaded by arguments citing values that fulfilled similar motives than by arguments citing opposing values. Experiments 2 and 3 replicated this result using a wider variety of values, while finding that the effect is stronger among people higher in need for cognition and that the effect is mediated by the greater plausibility of co-value arguments that link motivationally compatible values. Experiment 4 extended the effect to real-world arguments taken from political propaganda and replicated the mediating effect of argument plausibility. The findings highlight the importance of value relatedness in argument persuasiveness.

  15. [Generics: similarities, bioequivalence but no conformity].

    Science.gov (United States)

    Even-Adin, D; De Muylder, J A; Sternon, J

    2002-01-01

    The using of generic forms (GF) is presented as a potential source of budgetary "saving of money" in the field of pharmaceutical expenses. Not frequently prescribed in Belgium, they win a new interest thanks to the recent making use of the "reference repayment". Sale's authorization of GF is controlled by european rules, but some questions about their identity to original medications remain. Do similarities based only upon qualitative and quantitative composition in active molecules, pharmaceutical forms and biodisponibility give us all requested guaranties? Several cases of discordances can appear; the major elements of non conformity are the nature of excipients, notice's contents and the value of biodisponibility studies. However, in term of economy, in the drug market, development of GF appears to constitute an unavoidable phenomenon.

  16. [Generics: essentially similar, bioequivalent but not identical].

    Science.gov (United States)

    Even-Adin, D; De Muylder, J A; Sternon, J

    2001-12-01

    The using of generic forms (GF) is presented as a potential source of budgetary "saving of money" in the field of pharmaceutical expenses. Not frequently prescribed in Belgium, they win a new interest thanks to the recent making use of the "reference repayment". Sale's authorization of GF is controlled by european rules, but some questions about their identity to original medications remain. Do similarities based only upon qualitative and quantitative composition in active molecules, pharmaceutical forms and biodisponibility give us all requested guarantees? Several cases of discordances can appear: the major elements of non conformity are the nature of excipients, notice's contents and the value of biodisponibility studies. However, in term of economy, in the drug market, development of GF appears to constitute an unavoidable phenomenon.

  17. Retrieving Similar Styles to Parse Clothing.

    Science.gov (United States)

    Yamaguchi, Kota; Kiapour, M Hadi; Ortiz, Luis E; Berg, Tamara L

    2015-05-01

    Clothing recognition is a societally and commercially important yet extremely challenging problem due to large variations in clothing appearance, layering, style, and body shape and pose. In this paper, we tackle the clothing parsing problem using a retrieval-based approach. For a query image, we find similar styles from a large database of tagged fashion images and use these examples to recognize clothing items in the query. Our approach combines parsing from: pre-trained global clothing models, local clothing models learned on the fly from retrieved examples, and transferred parse-masks (Paper Doll item transfer) from retrieved examples. We evaluate our approach extensively and show significant improvements over previous state-of-the-art for both localization (clothing parsing given weak supervision in the form of tags) and detection (general clothing parsing). Our experimental results also indicate that the general pose estimation problem can benefit from clothing parsing.

  18. Similarity, trust in institutions, affect, and populism

    DEFF Research Database (Denmark)

    Scholderer, Joachim; Finucane, Melissa L.

    Following up on ideas originally proposed by Niklas Luhmann, recent research has suggested that individuals may trust institutions and political actors only to the degree that they assume them to share their own value orientations. Two studies were conducted to test this proposition. Study 1 was ...... the suspicion that this particular mechanism may be responsible for the success of populist politics. Understanding the role of affect is key to reducing polarization in debates about the value of new technologies....... on affect is a quicker, easier, and a more efficient way of navigating in a complex and uncertain world. Hence, many theorists give affect a direct and primary role in motivating behavior. Taken together, the results provide uncannily strong support for the value-similarity hypothesis, strengthening...

  19. Ubiquitin-binding proteins: similar, but different

    DEFF Research Database (Denmark)

    Andersen, Katrine M; Hofmann, Kay; Hartmann-Petersen, Rasmus

    2005-01-01

    described. UBA (ubiquitin-associated) domain-containing proteins is the largest family and includes members involved in different cell processes. The smaller groups of UIM (ubiquitin-interacting motif), GAT [GGA (Golgi-associated gamma-adaptin homologous) and Tom1 (target of Myb 1)], CUE (coupling......Covalent modification of proteins with ubiquitin is a common regulatory mechanism in eukaryotic cells. Typically, ubiquitinated proteins are targeted for degradation by the 26 S proteasome. However, more recently the ubiquitin signal has also been connected with many other cell processes, including...... endocytosis, vesicle fusion, DNA repair and transcriptional silencing. Hence ubiquitination may be comparable with phosphorylation in its importance as an intracellular switch, controlling various signal-transduction pathways. Similar to the regulation of the extent of phosphorylation by kinases...

  20. Social values as arguments: similar is convincing

    Science.gov (United States)

    Maio, Gregory R.; Hahn, Ulrike; Frost, John-Mark; Kuppens, Toon; Rehman, Nadia; Kamble, Shanmukh

    2014-01-01

    Politicians, philosophers, and rhetors engage in co-value argumentation: appealing to one value in order to support another value (e.g., “equality leads to freedom”). Across four experiments in the United Kingdom and India, we found that the psychological relatedness of values affects the persuasiveness of the arguments that bind them. Experiment 1 found that participants were more persuaded by arguments citing values that fulfilled similar motives than by arguments citing opposing values. Experiments 2 and 3 replicated this result using a wider variety of values, while finding that the effect is stronger among people higher in need for cognition and that the effect is mediated by the greater plausibility of co-value arguments that link motivationally compatible values. Experiment 4 extended the effect to real-world arguments taken from political propaganda and replicated the mediating effect of argument plausibility. The findings highlight the importance of value relatedness in argument persuasiveness. PMID:25147529

  1. Generalized Entropies and the Similarity of Texts

    CERN Document Server

    Altmann, Eduardo G; Gerlach, Martin

    2016-01-01

    We show how generalized Gibbs-Shannon entropies can provide new insights on the statistical properties of texts. The universal distribution of word frequencies (Zipf's law) implies that the generalized entropies, computed at the word level, are dominated by words in a specific range of frequencies. Here we show that this is the case not only for the generalized entropies but also for the generalized (Jensen-Shannon) divergences, used to compute the similarity between different texts. This finding allows us to identify the contribution of specific words (and word frequencies) for the different generalized entropies and also to estimate the size of the databases needed to obtain a reliable estimation of the divergences. We test our results in large databases of books (from the Google n-gram database) and scientific papers (indexed by Web of Science).

  2. A Lithium Vapor Box Divertor Similarity Experiment

    Science.gov (United States)

    Cohen, Robert A.; Emdee, Eric D.; Goldston, Robert J.; Jaworski, Michael A.; Schwartz, Jacob A.

    2017-10-01

    A lithium vapor box divertor offers an alternate means of managing the extreme power density of divertor plasmas by leveraging gaseous lithium to volumetrically extract power. The vapor box divertor is a baffled slot with liquid lithium coated walls held at temperatures which increase toward the divertor floor. The resulting vapor pressure differential drives gaseous lithium from hotter chambers into cooler ones, where the lithium condenses and returns. A similarity experiment was devised to investigate the advantages offered by a vapor box divertor design. We discuss the design, construction, and early findings of the vapor box divertor experiment including vapor can construction, power transfer calculations, joint integrity tests, and thermocouple data logging. Heat redistribution of an incident plasma-based heat flux from a typical linear plasma device is also presented. This work supported by DOE Contract No. DE-AC02-09CH11466 and The Princeton Environmental Institute.

  3. Self-Similar Dynamics of SNe Ejecta

    Science.gov (United States)

    Wang, Lile

    2012-01-01

    With proper physical mechanisms of energy and momentum input from around the centre of a self-gravitating polytropic gas sphere, a central spherical "void" or "cavity" or "bubble" of very much less mass contents may emerge and then dynamically expand into a variety of surrounding more massive gas envelopes with or without shocks. We explore self-similar evolution of a self-gravitating polytropic hydrodynamic flow of spherical symmetry with such an expanding "void" embedded around the center. The void boundary supporting a massive envelope represents a pressure-balanced contact discontinuity where drastic changes in mass density and temperature occur. We obtain numerical void solutions that can cross the sonic critical surface either smoothly or by shocks. Using the conventional polytropic equation of state, we construct global void solutions with shocks travelling into various envelopes including static polytropic sphere, outflow, inflow, breeze and contraction types. In the context of supernovae, we discuss the possible scenario of separating a central collapsing compact object from an outgoing gas envelope with a powerful void in dynamic expansion. Initially, a central bubble is carved out by an extremely powerful neutrinosphere. After the escape of neutrinos during the decoupling, the strong electromagnetic radiation field and/or electron-positron pair plasma continue to drive the cavity expansion. In a self-similar dynamic evolution, the pressure across the contact discontinuity decreases with time to a negligible level for a sufficiently long lapse and eventually, the gas envelope continues to expand by inertia. We describe model cases of polytropic index γ=4/3-ɛ with ɛ>0 and discuss pertinent requirements to justify our proposed scenario.

  4. Optimal neighborhood indexing for protein similarity search.

    Science.gov (United States)

    Peterlongo, Pierre; Noé, Laurent; Lavenier, Dominique; Nguyen, Van Hoa; Kucherov, Gregory; Giraud, Mathieu

    2008-12-16

    Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website http://bioinfo.lifl.fr/reblosum. We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.

  5. State and Mafia, Differences and Similarities

    Directory of Open Access Journals (Sweden)

    Alfano Vincenzo

    2015-02-01

    Full Text Available The purpose of this article is to investigate about the differences and, if any, the similarities among the modern State and the mafia criminal organizations. In particular, starting from their definitions, I will try to find the differences between State and mafia, to then focus on the operational aspects of the functioning of these two organizations, with specific reference to the effect/impact that both these human constructs have on citizens’ existences, and especially on citizen’s economic lives. All this in order to understand whether it is possible to identify an objective difference – beside morals – between taxation by the modern State and extortion by criminal organizations. With this of course I do not want to argue that the mafia is in any way justifiable or absolvable, nor that it is better than the State. However, I want to investigate whether there is a real, logical reason why the State should be considered by the citizens more desirable than the criminal organizations oppressing Southern Italy, from a strictly logical point of view and not from the point of view of ethics and morality.

  6. Reading network in dyslexia: Similar, yet different.

    Science.gov (United States)

    Waldie, Karen E; Wilson, Anna J; Roberts, Reece P; Moreau, David

    2017-11-01

    Dyslexia is a developmental disorder characterized by reading and phonological difficulties, yet important questions remain regarding its underlying neural correlates. In this study, we used partial least squares (PLS), a multivariate analytic technique, to investigate the neural networks used by dyslexics while performing a word-rhyming task. Although the overall reading network was largely similar in dyslexics and typical readers, it did not correlate with behavior in the same way in the two groups. In particular, there was a positive association between reading performance and both right superior temporal gyrus and bilateral insula activation in dyslexic readers but a negative correlation in typical readers. Together with differences in lateralization unique to dyslexics, this suggests that the combination of poor reading performance with high insula activity and atypical laterality is a consistent marker of dyslexia. These findings emphasize the importance of understanding right-hemisphere activation in dyslexia and provide promising directions for the remediation of reading disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Multidimensional Scaling Visualization Using Parametric Similarity Indices

    Directory of Open Access Journals (Sweden)

    J. A. Tenreiro Machado

    2015-03-01

    Full Text Available In this paper, we apply multidimensional scaling (MDS and parametric similarity indices (PSI in the analysis of complex systems (CS. Each CS is viewed as a dynamical system, exhibiting an output time-series to be interpreted as a manifestation of its behavior. We start by adopting a sliding window to sample the original data into several consecutive time periods. Second, we define a given PSI for tracking pieces of data. We then compare the windows for different values of the parameter, and we generate the corresponding MDS maps of ‘points’. Third, we use Procrustes analysis to linearly transform the MDS charts for maximum superposition and to build a globalMDS map of “shapes”. This final plot captures the time evolution of the phenomena and is sensitive to the PSI adopted. The generalized correlation, theMinkowski distance and four entropy-based indices are tested. The proposed approach is applied to the Dow Jones Industrial Average stock market index and the Europe Brent Spot Price FOB time-series.

  8. Mining patents using molecular similarity search.

    Science.gov (United States)

    Rhodes, James; Boyer, Stephen; Kreulen, Jeffrey; Chen, Ying; Ordonez, Patricia

    2007-01-01

    Text analytics is becoming an increasingly important tool used in biomedical research. While advances continue to be made in the core algorithms for entity identification and relation extraction, a need for practical applications of these technologies arises. We developed a system that allows users to explore the US Patent corpus using molecular information. The core of our system contains three main technologies: A high performing chemical annotator which identifies chemical terms and converts them to structures, a similarity search engine based on the emerging IUPAC International Chemical Identifier (InChI) standard, and a set of on demand data mining tools. By leveraging this technology we were able to rapidly identify and index 3,623,248 unique chemical structures from 4,375,036 US Patents and Patent Applications. Using this system a user may go to a web page, draw a molecule, search for related Intellectual Property (IP) and analyze the results. Our results prove that this is a far more effective way for identifying IP than traditional keyword based approaches.

  9. Similarities and differences in conceptualizing critical thinking

    Directory of Open Access Journals (Sweden)

    Pešić Jelena

    2011-01-01

    Full Text Available In this paper we explore the core similarities and differences in conceptualizing critical thinking. The framework of analysis refers to conceptions of leading critical thinking theorists: Ennis, Siegel, Paul, McPeck and Lipman. Two key questions are in the focus of consideration: which are the defining characteristics of critical thinking, distinguishing it from other types of thinking, and what are its constituents. The nature of identified differences has lead to a dilemma whether critical thinking skills are generalized or domain specific, as well as to the question regarding the role of noncognitive critical thinking dispositions. We also discuss the relation between the dominant approach founded in informal logic and epistemological conceptions that expanded the meaning of critical thinking by elaborating its reflective, dialectical and dialogical dimensions. The prevailing view that emphasizes the pragmatic purpose of critical thinking is contrasted with the competing Endeavour to base and justify its purpose in the concept of emancipatory rationality. The analysis outcomes suggest that, in spite of the lack of a consistent theoretical framework, competing conceptions do share some core principles, especially with respect to the distinctive features of critical thinking. However, there are deep and intrinsic differences regarding the nature of critical thinking standards and constituents, which can probably be attributed to complex and multidiscoursive nature of the concept itself. .

  10. Voxel similarity measures for automated image registration

    Science.gov (United States)

    Hill, Derek L.; Studholme, Colin; Hawkes, David J.

    1994-09-01

    We present the concept of the feature space sequence: 2D distributions of voxel features of two images generated at registration and a sequence of misregistrations. We provide an explanation of the structure seen in these images. Feature space sequences have been generated for a pair of MR image volumes identical apart from the addition of Gaussian noise to one, MR image volumes with and without Gadolinium enhancement, MR and PET-FDG image volumes and MR and CT image volumes, all of the head. The structure seen in the feature space sequences was used to devise two new measures of similarity which in turn were used to produce plots of cost versus misregistration for the 6 degrees of freedom of rigid body motion. One of these, the third order moment of the feature space histogram, was used to register the MR image volumes with and without Gadolinium enhancement. These techniques have the potential for registration accuracy to within a small fraction of a voxel or resolution element and therefore interpolation errors in image transformation can be the dominant source of error in subtracted images. We present a method for removing these errors using sinc interpolation and show how interpolation errors can be reduced by over two orders of magnitude.

  11. Different-but-Similar Judgments by Bumblebees

    Directory of Open Access Journals (Sweden)

    Vicki Xu

    2016-08-01

    Full Text Available This study examines picture perception in an invertebrate. Two questions regarding possible picture-object correspondence are addressed for bumblebees (Bombus impatiens: (1 Do bees perceive the difference between an object and its corresponding picture even when they have not been trained to do so? (2 Do they also perceive the similarity? Twenty bees from each of four colonies underwent discrimination training of stimuli placed in a radial maze. Bees were trained to discriminate between two objects (artificial flowers in one group and between photos of those objects in another. Subsequent testing on unrewarding stimuli revealed, for both groups, a significant discrimination between the object and its photo: discrimination training was not necessary for bees to detect a difference between corresponding objects and pictures. We obtained not only object-to-picture transfer, as in previous research, but also the reverse: picture-to-object transfer. In the absence of the rewarding object, its photo, though never seen before by the bees, was accepted as a substitute. The reverse was also true. Bumblebees treated pictures as “different-but-similar” without having been trained to do so, which is in turn useful in floral categorization.

  12. Extended Self Similarity in Solar Wind Turbulence

    Science.gov (United States)

    Rowlands, G.; Chapman, S. C.; Hnat, B.

    2005-12-01

    The solar wind provides a natural laboratory for observations of MHD turbulence over extended temporal scales. A hallmark of turbulence is scaling- and scaling in the Probability Density Functions (PDF) of fluctuations in certain solar wind in- situ bulk plasma parameters has been established from WIND and ACE observations on `short' timescales up to a few hours. On longer timescales there is a crossover in scaling to uncorrelated behaviour. The intermittency of the system is expressed in these parameters through the non-Gaussian nature of the fluctuations PDF up to this timescale. Here we apply a generic approach to turbulence- that of Extended Self Similarity (ESS)- to the analysis of solar wind observations. We find that ESS can extend the range of scaling and for some parameters reveals two distinct scaling regions for the `short' and long timescales, whereas for others, a single scaling encompasses the behaviour over the full range of timescales. That certain parameters, and conditions, can be distinguished via ESS may provide physical insight into the turbulent solar wind.

  13. Effects of categorical labels on similarity judgments: A critical analysis of similarity-based approaches

    OpenAIRE

    Noles, Nicholaus S.; Gelman, Susan A.

    2011-01-01

    The goal of the present study was to evaluate the claim that category labels affect children’s judgments of visual similarity. We presented preschool children with discriminable and identical sets of animal pictures and asked them to make perceptual judgments in the presence or absence of labels. Our findings indicate that children who are asked to make perceptual judgments about identical items judge discriminable items less accurately when making subsequent similarity judgments. Thus, label...

  14. Similarly shaped letters evoke similar colors in grapheme-color synesthesia.

    Science.gov (United States)

    Brang, David; Rouw, Romke; Ramachandran, V S; Coulson, Seana

    2011-04-01

    Grapheme-color synesthesia is a neurological condition in which viewing numbers or letters (graphemes) results in the concurrent sensation of color. While the anatomical substrates underlying this experience are well understood, little research to date has investigated factors influencing the particular colors associated with particular graphemes or how synesthesia occurs developmentally. A recent suggestion of such an interaction has been proposed in the cascaded cross-tuning (CCT) model of synesthesia, which posits that in synesthetes connections between grapheme regions and color area V4 participate in a competitive activation process, with synesthetic colors arising during the component-stage of grapheme processing. This model more directly suggests that graphemes sharing similar component features (lines, curves, etc.) should accordingly activate more similar synesthetic colors. To test this proposal, we created and regressed synesthetic color-similarity matrices for each of 52 synesthetes against a letter-confusability matrix, an unbiased measure of visual similarity among graphemes. Results of synesthetes' grapheme-color correspondences indeed revealed that more similarly shaped graphemes corresponded with more similar synesthetic colors, with stronger effects observed in individuals with more intense synesthetic experiences (projector synesthetes). These results support the CCT model of synesthesia, implicate early perceptual mechanisms as driving factors in the elicitation of synesthetic hues, and further highlight the relationship between conceptual and perceptual factors in this phenomenon. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. Similarity and assumed similarity in personality reports of well-acquainted persons.

    Science.gov (United States)

    Lee, Kibeom; Ashton, Michael C; Pozzebon, Julie A; Visser, Beth A; Bourdage, Joshua S; Ogunfowora, Babatunde

    2009-02-01

    The authors obtained self- and observer reports of personality from pairs of well-acquainted college students. Consistent with previous findings, results of Study 1 showed strong cross-source agreement for all 6 HEXACO personality factors (rs approximately .55). In addition, the authors found modest levels of similarity (r approximately .25) between dyad members' self-reports on each of 2 dimensions, Honesty-Humility and Openness to Experience. For these same 2 factors, dyad members' self-reports were correlated with their observer reports of the other dyad member (r approximately .40), thus indicating moderately high assumed similarity. In Study 2, Honesty-Humility and Openness to Experience were the 2 personality factors most strongly associated with the 2 major dimensions of personal values, which also showed substantial assumed similarity. In Study 3, assumed similarity was considerably stronger for close friends than for nonfriend acquaintances. Results suggest that assumed similarity for Honesty-Humility and Openness to Experience reflects a tendency to overestimate one's similarity to persons with whom one has a close relationship, but only on those personality characteristics whose relevance to values gives them central importance to one's identity.

  16. A toolbox for representational similarity analysis.

    Directory of Open Access Journals (Sweden)

    Hamed Nili

    2014-04-01

    Full Text Available Neuronal population codes are increasingly being investigated with multivariate pattern-information analyses. A key challenge is to use measured brain-activity patterns to test computational models of brain information processing. One approach to this problem is representational similarity analysis (RSA, which characterizes a representation in a brain or computational model by the distance matrix of the response patterns elicited by a set of stimuli. The representational distance matrix encapsulates what distinctions between stimuli are emphasized and what distinctions are de-emphasized in the representation. A model is tested by comparing the representational distance matrix it predicts to that of a measured brain region. RSA also enables us to compare representations between stages of processing within a given brain or model, between brain and behavioral data, and between individuals and species. Here, we introduce a Matlab toolbox for RSA. The toolbox supports an analysis approach that is simultaneously data- and hypothesis-driven. It is designed to help integrate a wide range of computational models into the analysis of multichannel brain-activity measurements as provided by modern functional imaging and neuronal recording techniques. Tools for visualization and inference enable the user to relate sets of models to sets of brain regions and to statistically test and compare the models using nonparametric inference methods. The toolbox supports searchlight-based RSA, to continuously map a measured brain volume in search of a neuronal population code with a specific geometry. Finally, we introduce the linear-discriminant t value as a measure of representational discriminability that bridges the gap between linear decoding analyses and RSA. In order to demonstrate the capabilities of the toolbox, we apply it to both simulated and real fMRI data. The key functions are equally applicable to other modalities of brain-activity measurement. The

  17. Expanding the boundaries of local similarity analysis.

    Science.gov (United States)

    Durno, W Evan; Hanson, Niels W; Konwar, Kishori M; Hallam, Steven J

    2013-01-01

    Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic identifies the existence of local and lagged relationships, but determining significance through a p-value has been algorithmically cumbersome due to an intensive permutation test, shuffling rows and columns and repeatedly calculating the statistic. Furthermore, this p-value is calculated with the assumption of normality -- a statistical luxury dissociated from most real world datasets. To improve the performance of LSA on big datasets, an asymptotic upper bound on the p-value calculation was derived without the assumption of normality. This change in the bound calculation markedly improved computational speed from O(pm²n) to O(m²n), where p is the number of permutations in a permutation test, m is the number of time series, and n is the length of each time series. The bounding process is implemented as a computationally efficient software package, FASTLSA, written in C and optimized for threading on multi-core computers, improving its practical computation time. We computationally compare our approach to previous implementations of LSA, demonstrate broad applicability by analyzing time series data from public health, microbial ecology, and social media, and visualize resulting networks using the Cytoscape software. The FASTLSA software package expands the boundaries of LSA allowing analysis on datasets with millions of co-varying time series. Mapping metadata onto force-directed graphs derived from FASTLSA allows investigators to view correlated cliques and explore previously unrecognized network relationships. The software is freely available for download at: http://www.cmde.science.ubc.ca/hallam/fastLSA/.

  18. Similar Symmetries: The Role of Wallpaper Groups in Perceptual Texture Similarity

    Directory of Open Access Journals (Sweden)

    Fraser Halley

    2011-05-01

    Full Text Available Periodic patterns and symmetries are striking visual properties that have been used decoratively around the world throughout human history. Periodic patterns can be mathematically classified into one of 17 different Wallpaper groups, and while computational models have been developed which can extract an image's symmetry group, very little work has been done on how humans perceive these patterns. This study presents the results from a grouping experiment using stimuli from the different wallpaper groups. We find that while different images from the same wallpaper group are perceived as similar to one another, not all groups have the same degree of self-similarity. The similarity relationships between wallpaper groups appear to be dominated by rotations.

  19. Similarity, agreement, and assumed similarity in proxy end-of-life decision making.

    Science.gov (United States)

    McDade-Montez, Elizabeth; Watson, David; Beer, Andrew

    2013-12-01

    Medical decisions near the end of life are often made by proxies who can be inaccurate in their judgments of patient preferences. Given that accuracy in surrogate decision making is an important goal in end-of-life decision making, and in light of that previously seen levels of accuracy reflect substantial disagreement, error, or both, this study examined both relationship and individual factors that potentially affect surrogate accuracy. Specifically, this study examined similarity, agreement, and assumed similarity-a process whereby raters use their own traits and preferences to rate another person-in spousal ratings of end-of-life treatment. This study expands on previous research by examining the potential influence of relationship factors and assumed similarity on end-of-life decision making among a sample of newlyweds. Newly married couples (n = 197) completed self and spouse measures of hypothetical end-of-life preferences and scales assessing marital satisfaction, personality, and attitudes. Results indicate a moderate level of similarity on husband and wife self-rated end-of-life treatment preferences (rs = .18-.29) and a moderate level of agreement between self and proxy ratings (rs = .17-.41). The largest correlations were seen between self ratings and proxy ratings (e.g., husband self ratings and husband proxy ratings of wife preferences, rs = .46-.69), reflecting strong assumed similarity in proxy ratings. For wives, similarity with husbands on a few attitudinal variables (i.e., spirituality, moral strictness, and conservatism) influenced proxy accuracy. Recognizing the potential impact of personal preferences on proxy ratings, as well as the potential influence of relationship factors, may help improve proxy accuracy and end-of-life care for patients and families.

  20. Perceptual similarity co-existing with lexical dissimilarity

    Science.gov (United States)

    Weber, Andrea; Cutler, Anne

    2003-10-01

    The extreme case of perceptual similarity is indiscriminability, as when two second-language phonemes map to a single native category. An example is the English had-head vowel contrast for Dutch listeners; Dutch has just one such central vowel, transcribed [E]. We examine whether the failure to discriminate in phonetic categorization implies indiscriminability in other-e.g., lexical-processing. Eyetracking experiments show that Dutch-native listeners instructed in English to ``click on the panda'' look (significantly more than native listeners) at a pictured pencil, suggesting that pan- activates their lexical representation of pencil. The reverse, however, is not the case: ``click on the pencil'' does not induce looks to a panda, suggesting that pen- does not activate panda in the lexicon. Thus prelexically undiscriminated second-language distinctions can nevertheless be maintained in stored lexical representations. The problem of mapping a resulting unitary input to two distinct categories in lexical representations is solved by allowing input to activate only one second-language category. For Dutch listeners to English, this is English [E], as a result of which no vowels in the signal ever map to words containing [ae]. We suggest that the choice of category is here motivated by a more abstract, phonemic, metric of similarity.

  1. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.

    Science.gov (United States)

    Seyler, Sean L; Kumar, Avishek; Thorpe, M F; Beckstein, Oliver

    2015-10-01

    Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational geometry) to quantify the degree of similarity between piecewise-linear curves. It thus completely avoids relying on projections into low dimensional spaces, as used in traditional approaches. To elucidate the principles of PSA, we quantified the effect of path roughness induced by thermal fluctuations using a toy model system. Using, as an example, the closed-to-open transitions of the enzyme adenylate kinase (AdK) in its substrate-free form, we compared a range of protein transition path-generating algorithms. Molecular dynamics-based dynamic importance sampling (DIMS) MD and targeted MD (TMD) and the purely geometric FRODA (Framework Rigidity Optimized Dynamics Algorithm) were tested along with seven other methods publicly available on servers, including several based on the popular elastic network model (ENM). PSA with clustering revealed that paths produced by a given method are more similar to each other than to those from another method and, for instance, that the ENM-based methods produced relatively similar paths. PSA applied to ensembles of DIMS MD and FRODA trajectories of the conformational transition of diphtheria toxin, a particularly challenging example, showed that

  2. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.

    Directory of Open Access Journals (Sweden)

    Sean L Seyler

    2015-10-01

    Full Text Available Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational geometry to quantify the degree of similarity between piecewise-linear curves. It thus completely avoids relying on projections into low dimensional spaces, as used in traditional approaches. To elucidate the principles of PSA, we quantified the effect of path roughness induced by thermal fluctuations using a toy model system. Using, as an example, the closed-to-open transitions of the enzyme adenylate kinase (AdK in its substrate-free form, we compared a range of protein transition path-generating algorithms. Molecular dynamics-based dynamic importance sampling (DIMS MD and targeted MD (TMD and the purely geometric FRODA (Framework Rigidity Optimized Dynamics Algorithm were tested along with seven other methods publicly available on servers, including several based on the popular elastic network model (ENM. PSA with clustering revealed that paths produced by a given method are more similar to each other than to those from another method and, for instance, that the ENM-based methods produced relatively similar paths. PSA applied to ensembles of DIMS MD and FRODA trajectories of the conformational transition of diphtheria toxin, a particularly challenging example

  3. Effects of Categorical Labels on Similarity Judgments: A Critical Analysis of Similarity-Based Approaches

    Science.gov (United States)

    Noles, Nicholaus S.; Gelman, Susan A.

    2012-01-01

    Our goal in the present study was to evaluate the claim that category labels affect children's judgments of visual similarity. We presented preschool children with discriminable and identical sets of animal pictures and asked them to make perceptual judgments in the presence or absence of labels. Our findings indicate that children who are asked…

  4. Sexual Preference Similarity, Attitude Similarity, and Perceived Counselor Credibility and Attractiveness.

    Science.gov (United States)

    Atkinson, Donald R.; And Others

    1981-01-01

    Examined the effect of membership group and attitudinal similarity on perceived counselor credibility and attractiveness. Homosexual men (N=84) rated the counselor's credibility and attractiveness after listening to a recorded counseling interview. The counselor was rated more expert, trustworthy, and attractive when he stated a sexual preference…

  5. Systematic revelation of the protective effect and mechanism of Cordycep sinensis on diethylnitrosamine-induced rat hepatocellular carcinoma with proteomics.

    Science.gov (United States)

    Wang, Pei-Wen; Hung, Yu-Chiang; Li, Wen-Tai; Yeh, Chau-Ting; Pan, Tai-Long

    2016-09-13

    Cordyceps sinensis (C. sinensis) has been reported to treat liver diseases. Here, we investigated the inhibitory effect of C. sinensis on hepatocarcinoma in a diethylnitrosamine (DEN)-induced rat model with functional proteome tools.In the DEN-exposed group, levels of serum alanine aminotransferase and aspartate aminotransferase were increased while C. sinensis application remarkably inhibited the activities of these enzymes. Histopathological analysis also indicated that C. sinensis could substantially restore hypertrophic hepatocytes caused by DEN, suggesting that C. sinensis is effective in preventing DEN-induced hepatocarcinogenesis.We therefore comprehensively delineated the global protein alterations using a proteome platform. The most meaningful changes were found among proteins involved in oxidative stress and detoxification. Meanwhile, C. sinensis application could attenuate the carbonylation level of several enzymes as well as chaperone proteins. Network analysis implied that C. sinensis could obviously alleviate hepatocarcinoma via modulating redox imbalance, protein ubiquitination and tumor growth-associated transcription factors.Our findings provide new insight into the potential effects of C. sinensis in preventing carcinogenesis and might help in developing novel therapeutic strategies against chemical-induced hepatocarcinoma.

  6. Similar or different? The role of the ventrolateral prefrontal cortex in similarity detection.

    Directory of Open Access Journals (Sweden)

    Béatrice Garcin

    Full Text Available Patients with frontal lobe syndrome can exhibit two types of abnormal behaviour when asked to place a banana and an orange in a single category: some patients categorize them at a concrete level (e.g., "both have peel", while others continue to look for differences between these objects (e.g., "one is yellow, the other is orange". These observations raise the question of whether abstraction and similarity detection are distinct processes involved in abstract categorization, and that depend on separate areas of the prefrontal cortex (PFC. We designed an original experimental paradigm for a functional magnetic resonance imaging (fMRI study involving healthy subjects, confirming the existence of two distinct processes relying on different prefrontal areas, and thus explaining the behavioural dissociation in frontal lesion patients. We showed that: 1 Similarity detection involves the anterior ventrolateral PFC bilaterally with a right-left asymmetry: the right anterior ventrolateral PFC is only engaged in detecting physical similarities; 2 Abstraction per se activates the left dorsolateral PFC.

  7. Psychosocial interventions for bipolar disorder and coping style modification: similar clinical outcomes, similar mechanisms?

    Science.gov (United States)

    Parikh, Sagar V; Hawke, Lisa D; Zaretsky, Ari; Beaulieu, Serge; Patelis-Siotis, Irene; Macqueen, Glenda; Young, L Trevor; Yatham, Lakshmi; Velyvis, Vytas; Bélanger, Claude; Poirier, Nancy; Enright, Jean; Cervantes, Pablo

    2013-08-01

    To investigate changes in the use of coping styles in response to early symptoms of mania in cognitive-behavioural therapy (CBT), compared with psychoeducation, for bipolar disorder. Data were drawn from a randomized controlled trial comparing CBT and psychoeducation. A subsample of 119 participants completed the Coping Inventory for the Prodromes of Mania and symptom assessments before treatment and 72 weeks later. Both CBT and psychoeducation were associated with similar improvements in symptom burden. Both treatments also produced equivalent improvements in stimulation reduction and problem-directed coping styles, but no statistically significant change on the endorsement of help-seeking behaviours. A treatment interaction showed that a reduction in denial and blame was present only in the CBT treatment condition. CBT and psychoeducation have similar impacts on coping styles for the prodromes of mania. The exception to this is denial and blame, which is positively impacted only by CBT but which does not translate into improved outcome. Given the similar change in coping styles and mood burden, teaching patients about how to cope in adaptive ways with the symptoms of mania may be a shared mechanism of change for CBT and psychoeducation. NCT00188838.

  8. Perception of timbre and rhythm similarity in electronic dance music

    NARCIS (Netherlands)

    Honingh, A.; Panteli, M.; Brockmeier, T.; López Mejía, D.I.; Sadakata, M.

    2015-01-01

    Music similarity is known to be a multi-dimensional concept, depending among others on rhythm similarity and timbre similarity. The present study aims to investigate whether such sub-dimensions of similarity can be assessed independently and how they relate to general similarity. To this end, we

  9. Perception of Timbre and Rhythm Similarity in Electronic Dance Music

    NARCIS (Netherlands)

    Honingh, A.; Panteli, M.; Brockmeier, T.; López Mejía, D.I.; Sadakata, M.

    2015-01-01

    Music similarity is known to be a multi-dimensional concept, depending among others on rhythm similarity and timbre similarity. The present study aims to investigate whether such sub-dimensions of similarity can be assessed independently and how they relate to general similarity. To this end, we

  10. Similarities in the Metabolic Reprogramming of Immune System and Endothelium

    Directory of Open Access Journals (Sweden)

    Chu-Yik Tang

    2017-07-01

    Full Text Available Cellular metabolism has been known for its role in bioenergetics. In recent years, much light has been shed on the reprogrammable cellular metabolism underlying many vital cellular processes, such as cell activation, proliferation, and differentiation. Metabolic reprogramming in immune and endothelial cells (ECs is being studied extensively. These cell compartments are implicated in inflammation and pathogenesis of many diseases but their similarities in metabolic reprogramming have not been analyzed in detail. One of the most notable metabolic reprogramming is the Warburg-like effect, famously described as one of the hallmarks of cancer cells. Immune cells and ECs can display this phenotype that is characterized by a metabolic switch favoring glycolysis over oxidative phosphorylation (OXPHOS in aerobic conditions. Though energy-inefficient, aerobic glycolysis confers many benefits to the respiring cells ranging from higher rate of adenosine triphosphate production to maintaining redox homeostasis. Chemical and biological regulators either promote or perturb this effect. In this review, nitric oxide, hypoxia-inducible factor, and adenosine monophosphate-activated protein kinase have been discussed for their common involvement in metabolic reprogramming of both systems. From in vitro and animal studies, various discrepancies exist regarding the effects of those regulators on metabolic switch. However, it is generally accepted that glycolysis favors inflammatory reactions while OXPHOS favors anti-inflammatory processes. The reasons for such observation are currently subject of intense studies and not completely understood. Finally, metabolic reprogramming in immune cells and ECs does not limit to the physiological state in health but can also be observed in pathological states, such as atherosclerosis and cancer. These new insights provide us with a better understanding of the similarities in metabolic reprogramming across a number of cell types

  11. Similarities in the Metabolic Reprogramming of Immune System and Endothelium.

    Science.gov (United States)

    Tang, Chu-Yik; Mauro, Claudio

    2017-01-01

    Cellular metabolism has been known for its role in bioenergetics. In recent years, much light has been shed on the reprogrammable cellular metabolism underlying many vital cellular processes, such as cell activation, proliferation, and differentiation. Metabolic reprogramming in immune and endothelial cells (ECs) is being studied extensively. These cell compartments are implicated in inflammation and pathogenesis of many diseases but their similarities in metabolic reprogramming have not been analyzed in detail. One of the most notable metabolic reprogramming is the Warburg-like effect, famously described as one of the hallmarks of cancer cells. Immune cells and ECs can display this phenotype that is characterized by a metabolic switch favoring glycolysis over oxidative phosphorylation (OXPHOS) in aerobic conditions. Though energy-inefficient, aerobic glycolysis confers many benefits to the respiring cells ranging from higher rate of adenosine triphosphate production to maintaining redox homeostasis. Chemical and biological regulators either promote or perturb this effect. In this review, nitric oxide, hypoxia-inducible factor, and adenosine monophosphate-activated protein kinase have been discussed for their common involvement in metabolic reprogramming of both systems. From in vitro and animal studies, various discrepancies exist regarding the effects of those regulators on metabolic switch. However, it is generally accepted that glycolysis favors inflammatory reactions while OXPHOS favors anti-inflammatory processes. The reasons for such observation are currently subject of intense studies and not completely understood. Finally, metabolic reprogramming in immune cells and ECs does not limit to the physiological state in health but can also be observed in pathological states, such as atherosclerosis and cancer. These new insights provide us with a better understanding of the similarities in metabolic reprogramming across a number of cell types, which could pave

  12. Pollinators show flower colour preferences but flowers with similar colours do not attract similar pollinators.

    Science.gov (United States)

    Reverté, Sara; Retana, Javier; Gómez, José M; Bosch, Jordi

    2016-08-01

    Colour is one of the main floral traits used by pollinators to locate flowers. Although pollinators show innate colour preferences, the view that the colour of a flower may be considered an important predictor of its main pollinators is highly controversial because flower choice is highly context-dependent, and initial innate preferences may be overridden by subsequent associative learning. Our objective is to establish whether there is a relationship between flower colour and pollinator composition in natural communities. We measured the flower reflectance spectrum and pollinator composition in four plant communities (85 plant species represented by 109 populations, and 32 305 plant-pollinator interactions in total). Pollinators were divided into six taxonomic groups: bees, ants, wasps, coleopterans, dipterans and lepidopterans. We found consistent associations between pollinator groups and certain colours. These associations matched innate preferences experimentally established for several pollinators and predictions of the pollination syndrome theory. However, flowers with similar colours did not attract similar pollinator assemblages. The explanation for this paradoxical result is that most flower species are pollination generalists. We conclude that although pollinator colour preferences seem to condition plant-pollinator interactions, the selective force behind these preferences has not been strong enough to mediate the appearance and maintenance of tight colour-based plant-pollinator associations. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. Phenobarbital induces alterations in the proteome of hepatocytes and mesenchymal cells of rat livers.

    Directory of Open Access Journals (Sweden)

    Philip Klepeisz

    Full Text Available Preceding studies on the mode of action of non-genotoxic hepatocarcinogens (NGCs have concentrated on alterations induced in hepatocytes (HCs. A potential role of non-parenchymal liver cells (NPCs in NGC-driven hepatocarcinogenesis has been largely neglected so far. The aim of this study is to characterize NGC-induced alterations in the proteome profiles of HCs as well as NPCs. We chose the prototypic NGC phenobarbital (PB which was applied to male rats for a period of 14 days. The livers of PB-treated rats were perfused by collagenase and the cell suspensions obtained were subjected to density gradient centrifugation to separate HCs from NPCs. In addition, HCs and NPC isolated from untreated animals were treated with PB in vitro. Proteome profiling was done by CHIP-HPLC and ion trap mass spectrometry. Proteome analyses of the in vivo experiments showed many of the PB effects previously described in HCs by other methods, e.g. induction of phase I and phase II drug metabolising enzymes. In NPCs proteins related to inflammation and immune regulation such as PAI-1 and S100-A10, ADP-ribosyl cyclase 1 and to cell migration such as kinesin-1 heavy chain, myosin regulatory light chain RLC-A and dihydropyrimidinase-related protein 1 were found to be induced, indicating major PB effects on these cells. Remarkably, in vitro treatment of HCs and NPCs with PB hardly reproduced the proteome alterations observed in vivo, indicating differences of NGC induced responses of cells at culture conditions compared to the intact organism. To conclude, the present study clearly demonstrated that PB induces proteome alterations not only in HCs but also in NPCs. Thus, any profound molecular understanding on the mode of action of NGCs has to consider effects on cells of the hepatic mesenchyme.

  14. Centrifugal fans: Similarity, scaling laws, and fan performance

    Science.gov (United States)

    Sardar, Asad Mohammad

    Centrifugal fans are rotodynamic machines used for moving air continuously against moderate pressures through ventilation and air conditioning systems. There are five major topics presented in this thesis: (1) analysis of the fan scaling laws and consequences of dynamic similarity on modelling; (2) detailed flow visualization studies (in water) covering the flow path starting at the fan blade exit to the evaporator core of an actual HVAC fan scroll-diffuser module; (3) mean velocity and turbulence intensity measurements (flow field studies) at the inlet and outlet of large scale blower; (4) fan installation effects on overall fan performance and evaluation of fan testing methods; (5) two point coherence and spectral measurements conducted on an actual HVAC fan module for flow structure identification of possible aeroacoustic noise sources. A major objective of the study was to identity flow structures within the HVAC module that are responsible for noise and in particular "rumble noise" generation. Possible mechanisms for the generation of flow induced noise in the automotive HVAC fan module are also investigated. It is demonstrated that different modes of HVAC operation represent very different internal flow characteristics. This has implications on both fan HVAC airflow performance and noise characteristics. It is demonstrated from principles of complete dynamic similarity that fan scaling laws require that Reynolds, number matching is a necessary condition for developing scale model fans or fan test facilities. The physical basis for the fan scaling laws derived was established from both pure dimensional analysis and also from the fundamental equations of fluid motion. Fan performance was measured in a three times scale model (large scale blower) in air of an actual forward curved automotive HVAC blower. Different fan testing methods (based on AMCA fan test codes) were compared on the basis of static pressure measurements. Also, the flow through an actual HVAC

  15. Role of Oxidative Stress in Hepatitis C Virus Induced Hepatocellular Carcinoma.

    Science.gov (United States)

    Fu, Na; Yao, Hui; Nan, Yuemin; Qiao, Liang

    2017-01-01

    Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. Hepatitis C virus (HCV) infection is the predominant cause of chronic liver diseases and HCC, particularly in Western countries. Multiple molecular mechanisms are involved in the development and progression of HCV-related HCC, of which oxidative stress plays a pivotal role. HCV infection induces overproduction of reactive oxygen species (ROS) and impairs the function of endogenous antioxidants. Excessive amount of ROS directly damages DNA, lipids and proteins. Meanwhile, ROS indirectly activates a series of signaling cascades, and modulates the activity of many transcription factors, resulting in altered expression of genes that control cell survival, proliferation, angiogenesis, invasion and metastasis. In this review, we aim to summarize the possible molecular mechanisms underlying the link between the oxidative stress and hepatocarcinogenesis in HCV-infected individuals, in order to facilitate discovery of possible approaches or interventional targets for HCV-related HCC. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  16. Activated Hepatic Stellate Cells Induce Tumor Progression of Neoplastic Hepatocytes in a TGF-β Dependent Fashion

    Science.gov (United States)

    MIKULA, M.; PROELL, V.; FISCHER, A.N.M.; MIKULITS, W.

    2010-01-01

    The development of hepatocellular carcinomas from malignant hepatocytes is frequently associated with intra- and peritumoral accumulation of connective tissue arising from activated hepatic stellate cells. For both tumorigenesis and hepatic fibrogenesis, transforming growth factor (TGF)-β signaling executes key roles and therefore is considered as a hallmark of these pathological events. By employing cellular transplantation we show that the interaction of neoplastic MIM-R hepatocytes with the tumor microenvironment, containing either activated hepatic stellate cells (M1-4HSCs) or myofibroblasts derived thereof (M-HTs), induces progression in malignancy. Cotransplantation of MIM-R hepatocytes with M-HTs yielded strongest MIM-R generated tumor formation accompanied by nuclear localization of Smad2/3 as well as of β-catenin. Genetic interference with TGF-β signaling by gain of antagonistic Smad7 in MIM-R hepatocytes diminished epithelial dedifferentiation and tumor progression upon interaction with M1-4HSCs or M-HTs. Further analysis showed that tumors harboring disrupted Smad signaling are devoid of nuclear β-catenin accumulation, indicating a crosstalk between TGF-β and β-catenin signaling. Together, these data demonstrate that activated HSCs and myofibroblasts directly govern hepatocarcinogenesis in a TGF-β dependent fashion by inducing autocrine TGF-β signaling and nuclear β-catenin accumulation in neoplastic hepatocytes. These results indicate that intervention with TGF-β signaling is highly promising in liver cancer therapy. PMID:16883581

  17. Prediction of maize hybrid performance using similarity in state and similarity by descent information.

    Science.gov (United States)

    Ferreira, D V; Von Pinho, R G; Balestre, M; Oliveira, R L

    2010-12-14

    We evaluated the efficiency of the best linear unbiased predictor (BLUP) and the influence of the use of similarity in state (SIS) and similarity by descent (SBD) in the prediction of untested maize hybrids. Nine inbred lines of maize were crossed using a randomized complete diallel method. These materials were genotyped with 48 microsatellite markers (SSR) associated with the QTL regions for grain yield. Estimates of four coefficients of SIS and four coefficients of SBD were used to construct the additive genetic and dominance matrices, which were later used in combination with the BLUP for predicting genotypic values and specific combining ability (SCA) in unanalyzed hybrids under simulated unbalance. The values of correlations between the genotypic values predicted and the means observed, depending on the degree of unbalance, ranged from 0.48 to 0.99 for SIS and 0.40 to 0.99 using information from SBD. The results obtained for the SCA ranged from 0.26 to 0.98 using the SIS and 0.001 to 0.990 using the SBD information. It was also observed that the predictions using SBD showed less biased than SIS predictions demonstrating that the predictions obtained by these coefficients (SBD) were closer to the observed value, but were less efficient in the ranking of genotypes. Although the SIS showed a bias due to overestimation of relatedness, this type of coefficient may be used where low values are detected in the SBD in the group of parents because of its greater efficiency in ranking the candidates hybrids.

  18. Evolution of Nuclear Many-Body Forces with the Similarity Renormalization Group

    OpenAIRE

    Jurgenson, E. D.; Navratil, P.; Furnstahl, R. J.

    2009-01-01

    The first practical method to evolve many-body nuclear forces to softened form using the Similarity Renormalization Group (SRG) in a harmonic oscillator basis is demonstrated. When applied to He4 calculations, the two- and three-body oscillator matrix elements yield rapid convergence of the ground-state energy with a small net contribution of the induced four-body force.

  19. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  20. An inducible krasV12 transgenic zebrafish model for liver tumorigenesis and chemical drug screening

    Directory of Open Access Journals (Sweden)

    Anh Tuan Nguyen

    2012-01-01

    Because Ras signaling is frequently activated by major hepatocellular carcinoma etiological factors, a transgenic zebrafish constitutively expressing the krasV12 oncogene in the liver was previously generated by our laboratory. Although this model depicted and uncovered the conservation between zebrafish and human liver tumorigenesis, the low tumor incidence and early mortality limit its use for further studies of tumor progression and inhibition. Here, we employed a mifepristone-inducible transgenic system to achieve inducible krasV12 expression in the liver. The system consisted of two transgenic lines: the liver-driver line had a liver-specific fabp10 promoter to produce the LexPR chimeric transactivator, and the Ras-effector line contained a LexA-binding site to control EGFP-krasV12 expression. In double-transgenic zebrafish (driver-effector embryos and adults, we demonstrated mifepristone-inducible EGFP-krasV12 expression in the liver. Robust and homogeneous liver tumors developed in 100% of double-transgenic fish after 1 month of induction and the tumors progressed from hyperplasia by 1 week post-treatment (wpt to carcinoma by 4 wpt. Strikingly, liver tumorigenesis was found to be ‘addicted’ to Ras signaling for tumor maintenance, because mifepristone withdrawal led to tumor regression via cell death in transgenic fish. We further demonstrated the potential use of the transparent EGFP-krasV12 larvae in inhibitor treatments to suppress Ras-driven liver tumorigenesis by targeting its downstream effectors, including the Raf-MEK-ERK and PI3K-AKT-mTOR pathways. Collectively, this mifepristone-inducible and reversible krasV12 transgenic system offers a novel model for understanding hepatocarcinogenesis and a high-throughput screening platform for anti-cancer drugs.

  1. Interferon-α and cyclooxygenase-2 inhibitor cooperatively mediates TRAIL-induced apoptosis in hepatocellular carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Zuo, Chaohui, E-mail: zuochaohui@vip.sina.com [Department of Gastroduodenal and Pancreatic Surgery, Translation Medicine Research Center of Liver Cancer, Hunan Province Tumor Hospital & Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan Province (China); Department of Pathology, Immunology and Laboratory Medicine and Shands Cancer Center, University of Florida, Gainesville, FL (United States); Qiu, Xiaoxin [Department of Gastroduodenal and Pancreatic Surgery, Translation Medicine Research Center of Liver Cancer, Hunan Province Tumor Hospital & Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan Province (China); Cancer Research Institute, University of South China, Hengyang, Hunan Province (China); Liu, Nianli; Yang, Darong [Cancer Research Institute, University of South China, Hengyang, Hunan Province (China); Xia, Man [Department of Gastroduodenal and Pancreatic Surgery, Translation Medicine Research Center of Liver Cancer, Hunan Province Tumor Hospital & Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan Province (China); Department of Pathology, Immunology and Laboratory Medicine and Shands Cancer Center, University of Florida, Gainesville, FL (United States); Liu, Jingshi [Department of Gastroduodenal and Pancreatic Surgery, Translation Medicine Research Center of Liver Cancer, Hunan Province Tumor Hospital & Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan Province (China); Wang, Xiaohong [Cancer Research Institute, University of South China, Hengyang, Hunan Province (China); and others

    2015-05-01

    Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. Interferon-alpha (IFN-α) has recently been recognized to harbor therapeutic potential in the prevention and treatment of HCC, but it remains controversial as to whether IFN-α exerts direct cytotoxicity against HCC. Cyclooxygenase-2 (COX-2) is overexpressed in HCC and is considered to play a role in hepatocarcinogenesis. Therefore, we aimed to elucidate the combined effect of a COX-2 inhibitor, celecoxib, and IFN-α on in vitro growth suppression of HCC using the hepatoma cell line HLCZ01 and the in vivo nude mouse xenotransplantation model using HLCZ01 cells. Treatment with celecoxib and IFN-α synergistically inhibited cell proliferation in a dose- and time-dependent manner. Apoptosis was identified by 4',6-diamidino-2-phenylindole dihydrochloride and fluorescent staining. IFN-α upregulated the expression of TRAIL, while celecoxib increased the expression of TRAIL receptors. The combined regimen with celecoxib and IFN-α reduced the growth of xenotransplanted HCCs in nude mice. The regulation of IFN-α- and COX-2 inhibitor-induced cell death is impaired in a subset of TRAIL-resistant cells. The molecular mechanisms of HCC cells resistant to TRAIL-induced apoptosis were explored using molecular biological and immunological methods. Interferon-α and the COX-2 inhibitor celecoxib synergistically increased TRAIL-induced apoptosis in hepatocellular carcinoma. These data suggest that IFN-α and celecoxib may offer a novel role with important implications in designing new therapeutics for TRAIL-resistant tumors. - Highlights: ●The cytotoxic effect of TRAIL on a developed HCC HLCZ01 cells infected with HBV. ●IFN-α and celecoxib induced apoptosis in HLCZ01 cells infected with HBV. ●The combined regime reduced the growth of xenotransplanted HCCs in nude mice model.

  2. Scaling for stress similarity and distorted-shape similarity in bending and torsion under maximal muscle forces concurs with geometric similarity among different-sized animals.

    Science.gov (United States)

    Norberg, R Ake; Aldrin, Björn S Wetterholm

    2010-08-15

    When geometric similarity, or isometry, prevails among animals of different sizes their form and proportions are similar. Weight increases as the cube of the length dimension, while cross-sectional areas increase as its square, so in load-bearing structural elements the stress, caused by the body weight, increases in direct proportion to the length dimension, both for pure axial loads and for transverse bending and torsional loads. On this account, large body sizes would be expected to set up compensatory selection on the proportions of supporting structures, making them disproportionately thicker as required to maintain similar, size-independent safety factors against breakage. Most previous scaling theories have assumed that the strength of support elements has evolved with respect to loads due to the body weight. But then, from the arguments above, a scaling principle different from the geometric similarity rule would be required in order for safety factors to remain similar among different-sized animals. Still, most comparable animals of 'similar kind' scale in accordance with the geometric similarity rule. Here, we instead argue that muscle forces cause much larger loads on structural support elements during maximum performance events (such as during prey capture or escape from predators) than do loads dictated by the body weight (such as during cruising locomotion), and that structural strength therefore might evolve with respect to maximal muscle forces rather than to the body weight. We explore how the transverse and longitudinal lengths of structural support elements must scale to one another, and to muscle transverse length, in order to satisfy each of the following, functionally based, similarity principles for support elements placed in bending, or in torsion, by maximal muscle forces during locomotion: (1) similarity in axial stress, or (2) in torsional shear stress, and (3) similarity in bent shape, or (4) in twisted shape. A dimensional relationship

  3. Triplet correlations among similarly tuned cells impact population coding

    Directory of Open Access Journals (Sweden)

    Natasha Alexandra Cayco Gajic

    2015-05-01

    Full Text Available Which statistical features of spiking activity matter for how stimuli are encoded in neural populations? A vast body of work has explored how firing rates in individual cells and correlations in the spikes of cell pairs impact coding. Recent experiments have shown evidence for the existence of higher-order spiking correlations, which describe simultaneous firing in triplets and larger ensembles of cells; however, little is known about their impact on encoded stimulus information. Here, we take a first step toward closing this gap. We vary triplet correlations in small (approximately 10 cell neural populations while keeping single cell and pairwise statistics fixed at typically reported values. This connection with empirically observed lower-order statistics important, as it places strong constraints on the level of triplet correlations that can occur. For each value of triplet correlations, we estimate the performance of the neural population on a two-stimulus discrimination task. We find that the allowed changes in the level of triplet correlations can significantly enhance coding, in particular if triplet correlations differ for the two stimuli. In this scenario, triplet correlations must be included in order to accurately quantify the functionality of neural populations. When both stimuli elicit similar triplet correlations, however, pairwise models provide relatively accurate descriptions of coding accuracy. We explain our findings geometrically via the skew that triplet correlations induce in population-wide distributions of neural responses. Finally, we calculate how many samples are necessary to accurately measure spiking correlations of this type, providing an estimate of the necessary recording times in future experiments.

  4. Priming of plant innate immunity by rhizobacteria and β-aminobutyric acid: differences and similarities in regulation

    NARCIS (Netherlands)

    Ent, S. van der; Hulten, M.H.A. van; Pozo, Maria J.; Czechowski, Tomasz; Udvardi, Michael K.; Pieterse, C.M.J.; Ton, J.

    Pseudomonas fluorescens WCS417r bacteria and β-aminobutyric acid can induce disease resistance in Arabidopsis, which is based on priming of defence. In this study, we examined the differences and similarities of WCS417r- and β-aminobutyric acid-induced priming. Both WCS417r and β-aminobutyric acid

  5. Cognitive Complexity and the Similarity-Attraction Paradigm

    Science.gov (United States)

    Leonard, Russell L., Jr.

    1976-01-01

    Tested the hypothesis that cognitively complex judges will be more attracted to similar others than to dissimilar others, while cognitively simple judges will not be differentially attracted to similar and dissimilar others. (Author/RK)

  6. Compression-based Modelling of Musical Similarity Perception

    OpenAIRE

    Pearce, Marcus; Müllensiefen, Daniel

    2017-01-01

    Similarity is an important concept in music cognition research since the similarity between (parts of) musical pieces determines perception of stylistic categories and structural relationships between parts of musical works. The purpose of the present research is to develop and test models of musical similarity perception inspired by a transformational approach which conceives of similarity between two perceptual objects in terms of the complexity of the cognitive operations required to trans...

  7. Towards Modelling Variation in Music as Foundation for Similarity

    NARCIS (Netherlands)

    Volk, A.; de Haas, W.B.; van Kranenburg, P.; Cambouropoulos, E.; Tsougras, C.; Mavromatis, P.; Pastiadis, K.

    2012-01-01

    This paper investigates the concept of variation in music from the perspective of music similarity. Music similarity is a central concept in Music Information Retrieval (MIR), however there exists no comprehensive approach to music similarity yet. As a consequence, MIR faces the challenge on how to

  8. 50 CFR 17.52 - Permits-similarity of appearance.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 2 2010-10-01 2010-10-01 false Permits-similarity of appearance. 17.52... WILDLIFE AND PLANTS (CONTINUED) ENDANGERED AND THREATENED WILDLIFE AND PLANTS Similarity of Appearance § 17.52 Permits—similarity of appearance. Upon receipt of a complete application and unless otherwise...

  9. Systems chemistry : using thermodynamically controlled networks to assess molecular similarity

    NARCIS (Netherlands)

    Saggiomo, Vittorio; Hristova, Yana R.; Ludlow, R. Frederick; Otto, Sijbren

    2013-01-01

    Background: The assessment of mol. similarity is a key step in the drug discovery process that has thus far relied almost exclusively on computational approaches. We now report an exptl. method for similarity assessment based on dynamic combinatorial chem. Results: In order to assess mol. similarity

  10. Genetics similarity among four breeds of goat in Saudi Arabia ...

    African Journals Online (AJOL)

    user

    2012-02-28

    Feb 28, 2012 ... share about 73.5% genetic similarity, while Habsi and Masri goat breeds were closer to each other more than the previous two breeds, where they share about 82.5% of genetic similarity. Key words: Goats, breeds, RAPD, genetic similarity. INTRODUCTION. Goats were among the first farm animals to be.

  11. Articulation of Phonologically Similar Items Disrupts Free Recall of Nonwords

    Science.gov (United States)

    Nishiyama, Ryoji; Ukita, Jun

    2013-01-01

    The present study sought to clarify whether phonological similarity of encoded information impairs free recall performance (the phonological similarity effect: PSE) for nonwords. Five experiments examined the influence of the encoding process on the PSE in a step-by-step fashion, by using lists that consisted of phonologically similar (decoy)…

  12. 7 CFR 51.3202 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.3202 Section 51.3202 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... Similar varietal characteristics. Similar varietal characteristics means that the onions in any container...

  13. 7 CFR 51.2081 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.2081 Section 51.2081 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the almonds are similar in shape, and are reasonably...

  14. 7 CFR 51.632 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.632 Section 51.632 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards..., and Arizona) Definitions § 51.632 Similar varietal characteristics. Similar varietal characteristics...

  15. 7 CFR 51.694 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.694 Section 51.694 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards..., and Arizona) Definitions § 51.694 Similar varietal characteristics. Similar varietal characteristics...

  16. 7 CFR 51.763 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.763 Section 51.763 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the fruits in any container are similar in color and...

  17. 7 CFR 51.2650 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.2650 Section 51.2650 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the cherries in any container are similar in color...

  18. 7 CFR 51.2116 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.2116 Section 51.2116 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the kernels are similar in shape and appearance. For...

  19. 7 CFR 51.567 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.567 Section 51... STANDARDS) United States Standards for Celery Definitions § 51.567 Similar varietal characteristics. Similar varietal characteristics means that the stalks in any package have the same general appearance and...

  20. 7 CFR 51.3057 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.3057 Section 51.3057 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the avocados in any container are similar in shape...

  1. Processes of Overall Similarity Sorting in Free Classification

    Science.gov (United States)

    Milton, Fraser; Longmore, Christopher A.; Wills, A. J.

    2008-01-01

    The processes of overall similarity sorting were investigated in 5 free classification experiments. Experiments 1 and 2 demonstrated that increasing time pressure can reduce the likelihood of overall similarity categorization. Experiment 3 showed that a concurrent load also reduced overall similarity sorting. These findings suggest that overall…

  2. Induced Abortion

    Science.gov (United States)

    ... Education & Events Advocacy For Patients About ACOG Induced Abortion Home For Patients Search FAQs Induced Abortion Page ... Induced Abortion FAQ043, May 2015 PDF Format Induced Abortion Special Procedures What is an induced abortion? What ...

  3. Hepatitis B virus X protein induces EpCAM expression via active DNA demethylation directed by RelA in complex with EZH2 and TET2.

    Science.gov (United States)

    Fan, H; Zhang, H; Pascuzzi, P E; Andrisani, O

    2016-02-11

    Chronic hepatitis B virus (HBV) infection is a major risk factor for developing hepatocellular carcinoma (HCC), and HBV X protein (HBx) acts as cofactor in hepatocarcinogenesis. In liver tumors from animals modeling HBx- and HBV-mediated hepatocarcinogenesis, downregulation of chromatin regulating proteins SUZ12 and ZNF198 induces expression of several genes, including epithelial cell adhesion molecule (EpCAM). EpCAM upregulation occurs in HBV-mediated HCCs and hepatic cancer stem cells, by a mechanism not understood. Herein we demonstrate HBx induces EpCAM expression via active DNA demethylation. In hepatocytes, EpCAM is silenced by polycomb repressive complex 2 (PRC2) and ZNF198/LSD1/Co-REST/HDAC1 chromatin-modifying complexes. Cells with stable knockdown of SUZ12, an essential PRC2 subunit, upon HBx expression demethylate a CpG dinucleotide located adjacent to NF-κB/RelA half-site. This NF-κB/RelA site is in a CpG island downstream from EpCAM transcriptional start site (TSS). Chromatin immunoprecipitation (ChIP) assays demonstrate HBx-dependent RelA occupancy of NF-κB half-site, whereas RelA knockdown suppresses CpG demethylation and EpCAM expression. Tumor necrosis factor-α activates RelA, propagating demethylation to nearby CpG sites, shown by sodium bisulfite sequencing. RelA-dependent demethylation occurring upon HBx expression requires methyltrasferase EZH2, TET2 a key factor in cytosine demethylation and inactive DNMT3L, shown by knockdown assays and sodium bisulfite sequencing. Co-immunoprecipitations and sequential ChIP assays demonstrate that RelA in the presence of HBx forms a complex with EZH2, TET2 and DNMT3L, although the role of DNMT3L remains to be understood. Interestingly, the human EpCAM gene also has a CpG island downstream from its TSS, and a NF-κB-binding site flanked by CpGs. HepG2 cells derived from human HCC exhibit demethylation of these NF-κB-flanking CpG sites, and HBV replication propagates demethylation to nearby CpG sites. DLK

  4. Interpersonal Similarity and Knowledge Sharing within Multinational Organizations

    DEFF Research Database (Denmark)

    Mäkelä, Kristiina; Andersson, Ulf; Seppälä, Tomi

    2012-01-01

    defined and observable faultlines, often coinciding with unit boundaries. We further argue that it may not be similarity as such that matters but rather its positive impact on different dimensions of social capital, which mediate the relationship between similarity and knowledge sharing......Previous research has established that interpersonal similarity can influence knowledge sharing in such a way that similar people are more likely to share knowledge than those who are dissimilar. We contribute to the literature by showing that in the MNC context, cultural and functional similarity....... These microfoundations of inter-unit knowledge exchange point to important theoretical and practical implications for international management....

  5. TBI-Induced Formation of Toxic Tau and Its Biochemical Similarities to Tau in AD Brains

    Science.gov (United States)

    2016-10-01

    During the last year we have worked on the first point of the hypothesis. We have found that administration of tau purified from shockwave-exposed mice...accomplished under these goals? We have found that administration of tau purified from shockwave-exposed mice onto wild-type mice markedly reduces 1...DeKosky, S.T., M.D. Ikonomovic, and S. Gandy, Traumatic brain injury-- football , warfare, and long-term effects. N Engl J Med, 2010. 363(14): p. 1293-6. 2

  6. Do continuous and intermittent exercises sets induce similar cardiovascular responses in the elderly women?

    Directory of Open Access Journals (Sweden)

    Veloso Úrsula

    2003-01-01

    Full Text Available There is a lack of information about elderly acute cardiovascular responses in the elderly during exercise involving different muscle groups and strategies of load/repetition interaction (LRI in continuous and intermittent sets. The purpose of this study was to compare heart rate (HR, systolic blood pressure (SBP, rate-pressure product (RPP and quality of exercise performance (QEx of upper and lower body exercises (arms abduction and hip flexion in different situations of LRI. Twelve healthy women aged 65 to 85 years old volunteered to this study. The subjects performed both exercises at 12 maximal repetitions workload, continuously (2 sets of 12 reps and alternately (4 sets of 6 reps. HR was measured with a cardiotachometer and SBP through auscultation technique at the end of the last repetition of each set. The exercises were recorded in video to evaluate QEx. At least for the selected exercises, LRI did not influence QEx. However, SBP and RPP values for the intermittent sets were significantly higher than for continuous situations (p < 0.05. The authors concluded that continuous sets seem to be associated to greater cardiovascular stress in elder subjects, mainly because of SBP responses during the exercise.

  7. Use of waveform similarity to define planes of mining-induced seismic events

    CSIR Research Space (South Africa)

    Spottiswoode, SM

    1998-04-15

    Full Text Available ; Deichmann and Garcia- Fernandez, 1992). Groups of doublets can be called multiplets (Fremont and Malone, 1987; Moriya et al., 1996). In this paper we extend the doublet relative location procedure and introduce multiplet relocation using arrival... planes in- ferred from an aftershock sequence. Fehler et al. (1987) proposed the ?three-point method? to infer the planes of events locations. This method assumes that the earthquakes occur over pre-existing planes (fault planes) and defines each plane...

  8. Monetary, Food, and Social Rewards Induce Similar Pavlovian-to-Instrumental Transfer Effects.

    Science.gov (United States)

    Lehner, Rea; Balsters, Joshua H; Herger, Andreas; Hare, Todd A; Wenderoth, Nicole

    2016-01-01

    Multiple types of reward, such as money, food or social approval, are capable of driving behavior. However, most previous investigations have only focused on one of these reward classes in isolation, as such it is not clear whether different reward classes have a unique influence on instrumental responding or whether the subjective value of the reward, rather than the reward type per se, is most important in driving behavior. Here, we investigate behavior using a well-established reward paradigm, Pavlovian-to-instrumental transfer (PIT), and three different reward types: monetary, food and social rewards. The subjective value of each reward type was matched using a modified Becker-DeGroot-Marschak (BDM) auction where subjective reward value was expressed through physical effort using a bimanual grip force task. We measured the influence of reward-associated stimuli on how participants distributed forces between hands when reaching a target effort range on the screen bimanually and on how much time participants spent in this target range. Participants spent significantly more time in the target range (15% ± 2% maximal voluntary contraction) when a stimulus was presented that was associated with a reward used during instrumental conditioning or Pavlovian conditioning compared to a stimulus associated with a neutral outcome (i.e., general PIT). The strength of the PIT effect was modulated by subjective value (i.e., individuals who showed a stronger PIT effect rated the value of rewards more highly), but not by reward type, demonstrating that stimuli of all reward types were able to act as appetitive reinforcers and influenced instrumental responding, when matched to the same subjective reward value. This is the first demonstration that individually matched monetary, food and social rewards are equally effective as appetitive reinforcers in PIT. These findings strengthen the hypotheses that the subjective value is crucial for how much reward-associated stimuli influence behavior.

  9. Two opposite extremes of adiposity similarly reduce inflammatory response of antigen-induced acute joint inflammation

    NARCIS (Netherlands)

    Oliveira, M.C.; Silveira, A.L.; Tavares, L.P.; Rodrigues, D.F.; Loo, F.A.J. van de; Sousa, L.P.; Teixeira, M.M.; Amaral, F.A.; Ferreira, A.V.

    2017-01-01

    OBJECTIVE: Acute inflammation is a normal response of tissue to an injury. During this process, inflammatory mediators are produced and metabolic alterations occur. Adipose tissue is metabolically activated, and upon food consumption, it disrupts the inflammatory response. However, little is known

  10. Low-load bench press and push-up induce similar muscle hypertrophy and strength gain

    National Research Council Canada - National Science Library

    Naoki Kikuchi; Koichi Nakazato

    2017-01-01

    ...) bench press on muscle hypertrophy and strength gain in men. Methods: Eighteen male participants (age, 20.2 ± 0.73 years, range: 19−22 years, height: 169.8 ± 4.4 cm, weight: 64.5 ± 4.7 kg...

  11. Plant defenses against parasitic plants show similarities to those induced by herbivores and pathogens

    Science.gov (United States)

    Justin B. Runyon; Mark C. Mescher; Consuelo M. De Moraes

    2010-01-01

    Herbivores and pathogens come quickly to mind when one thinks of the biotic challenges faced by plants. Important but less appreciated enemies are parasitic plants, which can have important consequences for the fitness and survival of their hosts. Our knowledge of plant perception, signaling and response to herbivores and pathogens has expanded rapidly in recent years...

  12. Similarities between exercise-induced hypoalgesia and conditioned pain modulation in humans

    DEFF Research Database (Denmark)

    Vægter, Henrik Bjarke; Handberg, Gitte; Graven-Nielsen, Thomas

    2014-01-01

    -65 years participated in this randomized repeated-measures crossover trial with data collection on two different days. CPM was assessed by two different cold pressor tests (hand,foot). EIH was assessed through two intensities of aerobic bicycling exercises and two intensities of isometric muscle...... contraction exercises (arm,leg). Pressure pain thresholds (PPTs) were recorded before, during, after, and 15 min after conditioning/exercise, at sites local and remote to the extremity used for cold pressor stimulation and exercise. PPTs increased at local as well as remote sites during both cold pressor...... compared with non-exercising body parts for all exercise conditions. High intensity exercise produced larger EIH response compared with low intensity exercise. The change in PPTs during cold pressor test and the change in PPTs after exercises were not correlated. The CPM response was not dominated by local...

  13. Depletion of the AP-1 repressor JDP2 induces cell death similar to apoptosis

    DEFF Research Database (Denmark)

    Lerdrup, Mads; Holmberg, Christian Henrik; Dietrich, Nikolaj

    2005-01-01

    JDP2 is a ubiquitously expressed nuclear protein that efficiently represses the activity of the transcription factor AP-1. Thus far, all studies of JDP2 function have relied on the ectopic expression of the protein. In this study, we use a different approach: depletion of JDP2 from cells. Specific...... following UV-irradiation, as reported earlier, but also under normal culture conditions. Thus, our data support that JDP2 is a cellular survival protein whose presence is necessary for normal cellular function....

  14. Extending the Similarity-Attraction Effect: The Effects of When-Similarity in Computer-Mediated Communication

    NARCIS (Netherlands)

    Kaptein, M.C.; Castaneda, D.; Fernandez, N.; Nass, C.

    2014-01-01

    The feeling of connectedness experienced in computer-mediated relationships can be explained by the similarity-attraction effect (SAE). Though SAE is well established in psychology, the effects of some types of similarity have not yet been explored. In 2 studies, we demonstrate similarity-attraction

  15. Effect of pioglitazone, quercetin, and hydroxy citric acid on vascular endothelial growth factor messenger RNA (VEGF mRNA) expression in experimentally induced nonalcoholic steatohepatitis (NASH).

    Science.gov (United States)

    Surapaneni, Krishna Mohan; Vishnu Priya, Veeraraghavan; Mallika, Jainu

    2015-01-01

    Vascular endothelial growth factor (VEGF) is associated with various ischemic and inflammatory diseases, and plays an important role in the development of liver fibrosis and hepatocarcinogenesis in nonalcoholic steatohepatitis (NASH). In this study, the comparative effect of pioglitazone, quercetin, and hydroxy citric acid on VEGF mRNA in experimentally induced NASH was investigated. The experimental protocol consisted of five groups: control, NASH, NASH + pioglitazone, NASH + quercetin, and NASH + hydroxy citric acid. The VEGF mRNA expression was evaluated by reverse transcription polymerase chain reaction (RT- PCR) analysis for all experimental groups, and the levels of VEGF mRNA were quantitatively measured by densitometry. A higher expression of VEGF mRNA was found in the hepatic cells of rats with experimentally induced NASH compared to the control group. A very mild increase in VEGF mRNA expression was observed in the rats treated with quercetin. In contrast, a mild increase in the expression of VEGF mRNA was observed in the rats treated with pioglitazone and hydroxy citric acid. Quercetin exhibited an effective inhibition of VEGF mRNA expression, while a lower inhibition of the VEGF mRNA level was observed in the hydroxy citric acid- and the pioglitazone-treated rats.

  16. Free-classification of perceptually similar speakers with dysarthria.

    Science.gov (United States)

    Lansford, Kaitlin L; Liss, Julie M; Norton, Rebecca E

    2014-12-01

    In this investigation, the construct of perceptual similarity was explored in the dysarthrias. Specifically, we employed an auditory free-classification task to determine whether listeners could cluster speakers by perceptual similarity, whether the clusters mapped to acoustic metrics, and whether the clusters were constrained by dysarthria subtype diagnosis. Twenty-three listeners blinded to speakers' medical and dysarthria subtype diagnoses participated. The task was to group together (drag and drop) the icons corresponding to 33 speakers with dysarthria on the basis of how similar they sounded. Cluster analysis and multidimensional scaling (MDS) modeled the perceptual dimensions underlying similarity. Acoustic metrics and perceptual judgments were used in correlation analyses to facilitate interpretation of the derived dimensions. Six clusters of similar-sounding speakers and 3 perceptual dimensions underlying similarity were revealed. The clusters of similar-sounding speakers were not constrained by dysarthria subtype diagnosis. The 3 perceptual dimensions revealed by MDS were correlated with metrics for articulation rate, intelligibility, and vocal quality, respectively. This study shows (a) feasibility of a free-classification approach for studying perceptual similarity in dysarthria, (b) correspondence between acoustic and perceptual metrics to clusters of similar-sounding speakers, and (c) similarity judgments transcended dysarthria subtype diagnosis.

  17. Similarity analysis between chromosomes of Homo sapiens and monkeys with correlation coefficient, rank correlation coefficient and cosine similarity measures.

    Science.gov (United States)

    Someswara Rao, Chinta; Viswanadha Raju, S

    2016-03-01

    In this paper, we consider correlation coefficient, rank correlation coefficient and cosine similarity measures for evaluating similarity between Homo sapiens and monkeys. We used DNA chromosomes of genome wide genes to determine the correlation between the chromosomal content and evolutionary relationship. The similarity among the H. sapiens and monkeys is measured for a total of 210 chromosomes related to 10 species. The similarity measures of these different species show the relationship between the H. sapiens and monkey. This similarity will be helpful at theft identification, maternity identification, disease identification, etc.

  18. Magmatic versus sedimentary volcanism: similarities of two different geological phenomena

    Science.gov (United States)

    Mazzini, Adriano

    2015-04-01

    Sedimentary volcanoes (or more commonly called mud volcanoes) are geological phenomena that are present in sedimentary basins of passive and active margins. At these localities gas and water related to hydrocarbon diagenetic and catagenetic production generate overpressure facilitating the rise of mobile and ductily deformable materials that breach through the denser overlying rocks. The results are surface powerful manifestations of mud eruptions that strikingly resemble to those of magmatic volcanoes. Magmatic and sedimentary volcanoes share many other similarities. Initially both systems are essentially gas driven and the subsurface plumbing systems are characterized by intrusions and a complex system of fractures and conduits that bifurcate from a central feeder channel that manifest in the surface as numerous satellite seeps and vents. In both cases are inferred secondary shallower chambers where reactions take place. Comparable structural morphologies (e.g. conical, elongated, pie-shaped, multicrater, swap-like, caldera collapse, subsiding flanks, plateau-like) and/or alteration of the original shape are in both cases related to e.g. density and viscosity of the erupted solids, to the gas content, to the frequency of the eruptions, and to the action of meteoric factors (e.g. strong erosion by rain, wind, temperature changes etc. etc.). Like for magmatic volcanoes, the periodicity of the eruptive activity is related to the time required to charge the system and create new overpressure, as well as how the structure seals during periods of dormancy. Earthquakes are documented to be a powerful trigger capable to activate faults (often hosting magmatic and sedimentary volcanoes) and/or facilitating the breaching of the upper layers, and allowing the rise of deeper charged fluids. Finally, both systems significantly contribute as active source for CH4 (sedimentary) and CO2 (magmatic) resulting of great importance for global budget estimates of sensitive gasses. The

  19. Specific aspects of evaluation of control systems similarity

    Science.gov (United States)

    Evtushenko, V. F.; Burkov, V. N.; Myshlyaev, L. P.; Makarov, G. V.

    2017-09-01

    The paper discusses the problem of estimating the similarity of two or more control systems. In accordance with the statements made earlier it is indicated that such management systems should be characterized by a strict or approximate equality of the values of targeted indicators (criteria) of control effectiveness. Two main variants of procedures for estimating the control systems similarity are proposed. The first is based on the direct evaluation of the targeted indicators of control performance, the second - on the use of the so-called similarity relations, describing the conditions the fulfillment of which is valid for such systems. The procedures for evaluating the control systems similarity with the help of special similarity relations are associated with considerably less expenses. However, they are formed for a relatively narrow class of automatic control systems and are basically special cases of similarity, which requires further research in this direction.

  20. Perceptions of Ideal and Former Partners’ Personality and Similarity

    Directory of Open Access Journals (Sweden)

    Pieternel Dijkstra

    2010-12-01

    Full Text Available The present study aimed to test predictions based on both the ‗similarity-attraction‘ hypothesis and the ‗attraction-similarity‘ hypothesis, by studying perceptions of ideal and former partners. Based on the ‗similarity-attraction‘ hypothesis, we expected individuals to desire ideal partners who are similar to the self in personality. In addition, based on the ‗attraction-similarity hypothesis‘, we expected individuals to perceive former partners as dissimilar to them in terms of personality. Findings showed that, whereas the ideal partner was seen as similar to and more positive than the self, the former partner was seen as dissimilar to and more negative than the self. In addition, our study showed that individuals did not rate similarity in personality as very important when seeking a mate. Our findings may help understand why so many relationships end in divorce due to mismatches in personality.

  1. A Minimum Spanning Tree Representation of Anime Similarities

    OpenAIRE

    Wibowo, Canggih Puspo

    2016-01-01

    In this work, a new way to represent Japanese animation (anime) is presented. We applied a minimum spanning tree to show the relation between anime. The distance between anime is calculated through three similarity measurements, namely crew, score histogram, and topic similarities. Finally, the centralities are also computed to reveal the most significance anime. The result shows that the minimum spanning tree can be used to determine the similarity anime. Furthermore, by using centralities c...

  2. Similarity grouping and repetition blindness are both influenced by attention

    Directory of Open Access Journals (Sweden)

    Bianca De Haan

    2010-03-01

    Full Text Available Previous studies have reported seemingly conflicting results regarding how the amount of stimulus similarity between two simultaneously presented target stimuli impacts perceptual performance. There are many reports of ‘repetition blindness’, where individuals do worse when shown two similar stimuli relative to two different stimuli. On the other hand, there are reports of ‘similarity grouping’, where participants perform better when identifying two similar objects relative to two different objects. This manuscript posits that repetition blindness and similarity grouping coexist and can be elicited in the same subjects in a single task. This not only explains the previous opposite effects of stimulus similarity on task performance, but also provides a unique opportunity to directly compare these opposite effects of stimulus similarity with respect to susceptibility to a modulating factor. Since previous studies have provided inconclusive results on whether attentional relevance can modulate the effect of stimulus similarity on task performance, the current manuscript aims to compare repetition blindness and similarity grouping with respect to their susceptibility to attentional relevance. The results of the first experiment confirmed that both repetition blindness and similarity grouping can be elicited in the same experiment, suggesting that repetition blindness and similarity grouping coexist. The results of the second experiment suggest that both repetition blindness and similarity grouping can be modulated by attentional relevance. These results support the explanation of repetition blindness as a token individuation failure. Furthermore, these results suggest that supposedly pre-attentional grouping mechanisms might not operate as independently from top-down attentional modulations as traditionally thought.

  3. A New Trajectory Similarity Measure for GPS Data

    KAUST Repository

    Ismail, Anas

    2016-08-08

    We present a new algorithm for measuring the similarity between trajectories, and in particular between GPS traces. We call this new similarity measure the Merge Distance (MD). Our approach is robust against subsampling and supersampling. We perform experiments to compare this new similarity measure with the two main approaches that have been used so far: Dynamic Time Warping (DTW) and the Euclidean distance. © 2015 ACM.

  4. The Influence of Contour on Similarity Perception of Star Glyphs.

    Science.gov (United States)

    Fuchs, Johannes; Isenberg, Petra; Bezerianos, Anastasia; Fischer, Fabian; Bertini, Enrico

    2014-12-01

    We conducted three experiments to investigate the effects of contours on the detection of data similarity with star glyph variations. A star glyph is a small, compact, data graphic that represents a multi-dimensional data point. Star glyphs are often used in small-multiple settings, to represent data points in tables, on maps, or as overlays on other types of data graphics. In these settings, an important task is the visual comparison of the data points encoded in the star glyph, for example to find other similar data points or outliers. We hypothesized that for data comparisons, the overall shape of a star glyph--enhanced through contour lines--would aid the viewer in making accurate similarity judgments. To test this hypothesis, we conducted three experiments. In our first experiment, we explored how the use of contours influenced how visualization experts and trained novices chose glyphs with similar data values. Our results showed that glyphs without contours make the detection of data similarity easier. Given these results, we conducted a second study to understand intuitive notions of similarity. Star glyphs without contours most intuitively supported the detection of data similarity. In a third experiment, we tested the effect of star glyph reference structures (i.e., tickmarks and gridlines) on the detection of similarity. Surprisingly, our results show that adding reference structures does improve the correctness of similarity judgments for star glyphs with contours, but not for the standard star glyph. As a result of these experiments, we conclude that the simple star glyph without contours performs best under several criteria, reinforcing its practice and popularity in the literature. Contours seem to enhance the detection of other types of similarity, e. g., shape similarity and are distracting when data similarity has to be judged. Based on these findings we provide design considerations regarding the use of contours and reference structures on star

  5. Similarities/Differences in Combat/Peacetime Leadership

    Science.gov (United States)

    1992-04-15

    similarities and differences in the way a leader must lead. This paper is a study of peacetime and combat leadership in today’s Army using Operations Desert...and safety; family support; and transition from peace to combat. The author concludes that leadership in peacetime and combat is very similar in 20... SIMILARITIES /DIFFERENCES IN COMBAT/PEACETIME LEADERSHIP AN INDIVIDUAL STUDY PROJECT by Lieutenant Colonel Kenneth R. Knight, FA Accesion For NTIS CR&I J TiC TAB

  6. A Survey of Binary Similarity and Distance Measures

    Directory of Open Access Journals (Sweden)

    Seung-Seok Choi

    2010-02-01

    Full Text Available The binary feature vector is one of the most common representations of patterns and measuring similarity and distance measures play a critical role in many problems such as clustering, classification, etc. Ever since Jaccard proposed a similarity measure to classify ecological species in 1901, numerous binary similarity and distance measures have been proposed in various fields. Applying appropriate measures results in more accurate data analysis. Notwithstanding, few comprehensive surveys on binary measures have been conducted. Hence we collected 76 binary similarity and distance measures used over the last century and reveal their correlations through the hierarchical clustering technique.

  7. Application of the principle of similarity fluid mechanics

    Science.gov (United States)

    Hendricks, R. C.; Sengers, J. V.

    1979-01-01

    Possible applications of the principle of similarity to fluid mechanics is described and illustrated. In correlating thermophysical properties of fluids, the similarity principle transcends the traditional corresponding states principle. In fluid mechanics the similarity principle is useful in correlating flow processes that can be modeled adequately with one independent variable (i.e., one-dimensional flows). In this paper we explore the concept of transforming the conservation equations by combining similarity principles for thermophysical properties with those for fluid flow. We illustrate the usefulness of the procedure by applying such a transformation to calculate two phase critical mass flow through a nozzle.

  8. Similarities and Differences in Group and Family Therapy.

    Science.gov (United States)

    Hines, Max

    1988-01-01

    Examines contextual and process similarities and differences in group and family therapy, with emphasis on Yalom's group therapy and structural, strategic, and symbolic-experiential family therapy. (Author)

  9. Phonological similarity effects in simple and complex span tasks.

    Science.gov (United States)

    Macnamara, Brooke N; Moore, Adam B; Conway, Andrew R A

    2011-10-01

    Three experiments were conducted to examine the effect of phonological similarity in simple and complex memory span tasks. In Experiment 1, participants performed either a simple or a complex span task, and the memoranda within lists were either phonologically similar or distinct. Phonologically similar lists consisted of words that rhymed.The simple span task was word span. There were two complex span tasks; one was the original reading span task, and the other was a variant of reading span in which all the sentences within a list were contextually related. The classic phonological similarity decrement was observed in word span. In contrast, phonological similarity facilitation was observed in both versions of reading span. This facilitation effect was further investigated in Experiment 2 using two new versions of reading span. In Experiment 2, the sentences in reading span were either short or long, and the memoranda were presented separately from, and were unrelated to, the sentences. Again, words within phonologically similar lists rhymed, and again, facilitation was observed. In Experiment 3, phonological similarity was operationalized in terms of feature overlap, rather than rhyme. The classic phonological similarity decrement was still observed in word span, but facilitation was not observed in complex span. The results suggest that phonological similarity, when operationalized using words that rhyme, serves as a list retrieval cue and that complex span tasks are more dependent on cue-driven memory retrieval mechanisms than are simple span tasks.

  10. Common neighbour structure and similarity intensity in complex networks

    Science.gov (United States)

    Hou, Lei; Liu, Kecheng

    2017-10-01

    Complex systems as networks always exhibit strong regularities, implying underlying mechanisms governing their evolution. In addition to the degree preference, the similarity has been argued to be another driver for networks. Assuming a network is randomly organised without similarity preference, the present paper studies the expected number of common neighbours between vertices. A symmetrical similarity index is accordingly developed by removing such expected number from the observed common neighbours. The developed index can not only describe the similarities between vertices, but also the dissimilarities. We further apply the proposed index to measure of the influence of similarity on the wring patterns of networks. Fifteen empirical networks as well as artificial networks are examined in terms of similarity intensity and degree heterogeneity. Results on real networks indicate that, social networks are strongly governed by the similarity as well as the degree preference, while the biological networks and infrastructure networks show no apparent similarity governance. Particularly, classical network models, such as the Barabási-Albert model, the Erdös-Rényi model and the Ring Lattice, cannot well describe the social networks in terms of the degree heterogeneity and similarity intensity. The findings may shed some light on the modelling and link prediction of different classes of networks.

  11. A Guaranteed Similarity Metric Learning Framework for Biological Sequence Comparison.

    Science.gov (United States)

    Hua, Keru; Yu, Qin; Zhang, Ruiming

    2016-01-01

    Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. The distance and similarity between two sequence are very important and widely studied. During the last decades, Similarity(distance) metric learning is one of the hottest topics of machine learning/data mining as well as their applications in the bioinformatics field. It is feasible to introduce machine learning technology to learn similarity metric from biological data. In this paper, we propose a novel framework of guaranteed similarity metric learning (GMSL) to perform alignment of biology sequences in any feature vector space. It introduces the (ϵ, γ, τ)-goodness similarity theory to Mahalanobis metric learning. As a theoretical guaranteed similarity metric learning approach, GMSL guarantees that the learned similarity function performs well in classification and clustering. Our experiments on the most used datasets demonstrate that our approach outperforms the state-of-the-art biological sequences alignment methods and other similarity metric learning algorithms in both accuracy and stability.

  12. Semantic similarity: normative ratings for 185 Spanish noun triplets.

    Science.gov (United States)

    Moldovan, Cornelia D; Ferré, Pilar; Demestre, Josep; Sánchez-Casas, Rosa

    2015-09-01

    The present study introduces the first Spanish database with normative ratings of semantic similarity for 185 word triplets. Each word triplet is constituted by a target word (e.g., guisante [pea]) and two semantically related and nonassociatively related words: a word highly related in meaning to the target (e.g., judía [bean]), and a word less related in meaning to the target (e.g., patata [potato]). The degree of meaning similarity was assessed by 332 participants by using a semantic similarity rating task on a 9-point scale. Pairs having a value of semantic similarity ranging from 5 to 9 were classified as being more semantically related, whereas those with values ranging from 2 to 4.99 were considered as being less semantically related. The relative distance between the two pairs for the same target ranged from 0.48 to 5.07 points. Mean comparisons revealed that participants rated the more similar words as being significantly more similar in meaning to the target word than were the less similar words. In addition to the semantic similarity norms, values of concreteness and familiarity of each word in a triplet are provided. The present database can be a very useful tool for scientists interested in designing experiments to examine the role of semantics in language processing. Since the variable of semantic similarity includes a wide range of values, it can be used as either a continuous or a dichotomous variable. The full database is available in the supplementary materials.

  13. A Framework for Analysis of Music Similarity Measures

    DEFF Research Database (Denmark)

    Jensen, Jesper Højvang; Christensen, Mads G.; Jensen, Søren Holdt

    2007-01-01

    To analyze specific properties of music similarity measures that the commonly used genre classification evaluation procedure does not reveal, we introduce a MIDI based test framework for music similarity measures. We introduce the framework by example and thus outline an experiment to analyze...... the dependency of a music similarity measure on the instrumentation of a song compared to the melody, and to analyze its sensitivity to transpositions. Using the outlined experiment, we analyze music similarity measures from three software packages, namely Marsyas, MA toolbox and Intelligent Sound Processing...

  14. Similarity Solutions for Flow and Heat Transfer of Non-Newtonian Fluid over a Stretching Surface

    OpenAIRE

    Atta Sojoudi; Ali Mazloomi; Saha, Suvash C.; Gu, Y. T.

    2014-01-01

    Similarity solutions are carried out for flow of power law non-Newtonian fluid film on unsteady stretching surface subjected to constant heat flux. Free convection heat transfer induces thermal boundary layer within a semi-infinite layer of Boussinesq fluid. The nonlinear coupled partial differential equations (PDE) governing the flow and the boundary conditions are converted to a system of ordinary differential equations (ODE) using two-parameter groups. This technique reduces the number of ...

  15. Effects of promoters on N-butyl-N-(4-hydroxybutyl)nitrosamine-induced urinary bladder carcinogenesis in the rat.

    Science.gov (United States)

    Ito, N; Fukushima, S; Shirai, T; Nakanishi, K

    1983-01-01

    It has been shown that the occurrence of the preneoplastic lesion, papillary or nodular hyperplasia (PN hyperplasia) in rat urinary bladder induced by carcinogens is correlated with that of cancer. Therefore, the promoting effects of chemicals in two-stage bladder carcinogenesis were judged by measuring their ability to induce PN hyperplasia in rats. Male rats were given N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) for 4 weeks and then one of 16 test chemicals for 32 to 34 weeks. Saccharin, ascorbate, DL-tryptophan, allopurinol, and diphenyl promoted development of PN hyperplasia. The dose-response of the promoters were examined in both sexes of rats by administration of saccharin at doses of 0.04, 0.2, 1.0 and 5.0% for 32 weeks after BBN treatment. The occurrence of PN hyperplasia was significantly increased in the group given 5% saccharin. Dose-response curves showed enhanced hyperplastic responses in both sexes given 0.2 to 5% saccharin. The organ specificities of promoters were studied in rats initiated with BBN or 2-acetylamino-fluorene (2-AAF) followed by phenobarbital or saccharin for 32 weeks. Phenobarbital greatly enhanced hepatocarcinogenesis. Saccharin significantly enhanced the occurrence of both BBN-induced and 2-AAF-induced PN hyperplasia. However, there was no effect of phenobarbital on the urinary bladder or of saccharin on the liver. The rats showed a strain difference in susceptibility of the urinary bladder to saccharin; ACI rats were most susceptible and Sprague Dawley rats were most resistant to saccharin. The membrane potential of superficial epithelial cells in the urinary bladder of rats treated with saccharin was measured with an intracellular microelectrode and found to be higher than that of controls. PMID:6873032

  16. Relationship between genetic similarity and some productive traits ...

    African Journals Online (AJOL)

    Random amplified polymorphic DNA (RAPD) technique was applied to detect genetic similarity between five local chicken strains that have been selected for eggs and meat production in Egypt. Based on six oligonucleotide primers, the genetic similarity between the egg-producing strains (Anshas, Silver Montazah and ...

  17. Self-similar solution for coupled thermal electromagnetic model ...

    African Journals Online (AJOL)

    An investigation into the existence and uniqueness solution of self-similar solution for the coupled Maxwell and Pennes Bio-heat equations have been done. Criteria for existence and uniqueness of self-similar solution are revealed in the consequent theorems. Journal of the Nigerian Association of Mathematical Physics ...

  18. Calculating critical orientations of polyhedra for similarity measure evaluation

    NARCIS (Netherlands)

    Bekker, Henk; Roerdink, Jos B.T.M.

    1999-01-01

    This paper studies a problem related to the computation of similarity measures for two convex polyhedra based on Minkowski sums and mixed volumes. To compute the similarity measure a function has to be evaluated over a number so-called critical relative orientations of these polyhedra. An open

  19. Semantic similarity measure in biomedical domain leverage web search engine.

    Science.gov (United States)

    Chen, Chi-Huang; Hsieh, Sheau-Ling; Weng, Yung-Ching; Chang, Wen-Yung; Lai, Feipei

    2010-01-01

    Semantic similarity measure plays an essential role in Information Retrieval and Natural Language Processing. In this paper we propose a page-count-based semantic similarity measure and apply it in biomedical domains. Previous researches in semantic web related applications have deployed various semantic similarity measures. Despite the usefulness of the measurements in those applications, measuring semantic similarity between two terms remains a challenge task. The proposed method exploits page counts returned by the Web Search Engine. We define various similarity scores for two given terms P and Q, using the page counts for querying P, Q and P AND Q. Moreover, we propose a novel approach to compute semantic similarity using lexico-syntactic patterns with page counts. These different similarity scores are integrated adapting support vector machines, to leverage the robustness of semantic similarity measures. Experimental results on two datasets achieve correlation coefficients of 0.798 on the dataset provided by A. Hliaoutakis, 0.705 on the dataset provide by T. Pedersen with physician scores and 0.496 on the dataset provided by T. Pedersen et al. with expert scores.

  20. The semantics of similarity in geographic information retrieval

    Directory of Open Access Journals (Sweden)

    Krzysztof Janowicz

    2011-05-01

    Full Text Available Similarity measures have a long tradition in fields such as information retrieval, artificial intelligence, and cognitive science. Within the last years, these measures have been extended and reused to measure semantic similarity; i.e., for comparing meanings rather than syntactic differences. Various measures for spatial applications have been developed, but a solid foundation for answering what they measure; how they are best applied in information retrieval; which role contextual information plays; and how similarity values or rankings should be interpreted is still missing. It is therefore difficult to decide which measure should be used for a particular application or to compare results from different similarity theories. Based on a review of existing similarity measures, we introduce a framework to specify the semantics of similarity. We discuss similarity-based information retrieval paradigms as well as their implementation in web-based user interfaces for geographic information retrieval to demonstrate the applicability of the framework. Finally, we formulate open challenges for similarity research.

  1. 38 CFR 17.150 - Prosthetic and similar appliances.

    Science.gov (United States)

    2010-07-01

    ... appliances. 17.150 Section 17.150 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Prosthetic, Sensory, and Rehabilitative Aids § 17.150 Prosthetic and similar appliances. Artificial limbs, braces, orthopedic shoes, hearing aids, wheelchairs, medical accessories, similar...

  2. Similarities in functional attributes and nutritional effects of magadi ...

    African Journals Online (AJOL)

    Similarities in functional attributes and nutritional effects of magadi soda and bean debris-ash used in cooking African traditional dishes. ... profile, alkalinity, decreased cooking time and lowered mineral uptake by magadi soda and bean debris-ash explain similar functionality in foods they are added to during cooking.

  3. Visual reconciliation of alternative similarity spaces in climate modeling

    Science.gov (United States)

    J Poco; A Dasgupta; Y Wei; William Hargrove; C.R. Schwalm; D.N. Huntzinger; R Cook; E Bertini; C.T. Silva

    2015-01-01

    Visual data analysis often requires grouping of data objects based on their similarity. In many application domains researchers use algorithms and techniques like clustering and multidimensional scaling to extract groupings from data. While extracting these groups using a single similarity criteria is relatively straightforward, comparing alternative criteria poses...

  4. Multicriteria decision-making method based on a cosine similarity ...

    African Journals Online (AJOL)

    the cosine similarity measure is often used in information retrieval, citation analysis, and automatic classification. However, it scarcely deals with trapezoidal fuzzy information and multicriteria decision-making problems. For this purpose, a cosine similarity measure between trapezoidal fuzzy numbers is proposed based on ...

  5. Similarities Derived from 3-D Nonlinear Psychophysics: Variance Distributions.

    Science.gov (United States)

    Gregson, Robert A. M.

    1994-01-01

    The derivation of the variance of similarity judgments is made from the 3-D process in nonlinear psychophysics. The idea of separability of dimensions in metric space theories of similarity is replaced by one parameter that represents the degree of a form of interdimensional cross-sampling. (SLD)

  6. A Remark on the Similarity and Perturbation Problems

    DEFF Research Database (Denmark)

    Cameron, J.; Christensen, Erik; Sinclair, A. M.

    2013-01-01

    In this note we show that Kadison's similarity problem for C*-algebras is equivalent to a problem in perturbation theory: must close C*-algebras have close commutants?......In this note we show that Kadison's similarity problem for C*-algebras is equivalent to a problem in perturbation theory: must close C*-algebras have close commutants?...

  7. The Gestalt principle of similarity benefits visual working memory.

    Science.gov (United States)

    Peterson, Dwight J; Berryhill, Marian E

    2013-12-01

    Visual working memory (VWM) is essential for many cognitive processes, yet it is notably limited in capacity. Visual perception processing is facilitated by Gestalt principles of grouping, such as connectedness, similarity, and proximity. This introduces the question, do these perceptual benefits extend to VWM? If so, can this be an approach to enhance VWM function by optimizing the processing of information? Previous findings have demonstrated that several Gestalt principles (connectedness, common region, and spatial proximity) do facilitate VWM performance in change detection tasks (Jiang, Olson, & Chun, 2000; Woodman, Vecera, & Luck, 2003; Xu, 2002, 2006; Xu & Chun, 2007). However, one prevalent Gestalt principle, similarity, has not been examined with regard to facilitating VWM. Here, we investigated whether grouping by similarity benefits VWM. Experiment 1 established the basic finding that VWM performance could benefit from grouping. Experiment 2 replicated and extended this finding by showing that similarity was only effective when the similar stimuli were proximal. In short, the VWM performance benefit derived from similarity was constrained by spatial proximity, such that similar items need to be near each other. Thus, the Gestalt principle of similarity benefits visual perception, but it can provide benefits to VWM as well.

  8. Representing Documents Using an Explicit Model of Their Similarities.

    Science.gov (United States)

    Bartell, Brian T.; And Others

    1995-01-01

    Discussion of the failure of individual keywords to identify conceptual content of documents in retrieval systems highlights Metric Similarity Modeling, a method for creating vector space representation of documents based on modeling target interdocument similarity values. Semantic relatedness, latent semantic indexing, an indexing and retrieval…

  9. Mixed-List Phonological Similarity Effects in Delayed Serial Recall

    Science.gov (United States)

    Farrell, Simon

    2006-01-01

    Recent experiments have shown that placing dissimilar items on lists of phonologically similar items enhances accuracy of ordered recall of the dissimilar items [Farrell, S., & Lewandowsky, S. (2003). Dissimilar items benefit from phonological similarity in serial recall. "Journal of Experimental Psychology: Learning, Memory, and Cognition," 29,…

  10. Phonological Similarity in Serial Recall: Constraints on Theories of Memory

    Science.gov (United States)

    Lewandowsky, Stephan; Farrell, Simon

    2008-01-01

    In short-term serial recall, similar-sounding items are remembered more poorly than items that do not sound alike. When lists mix similar and dissimilar items, performance on the dissimilar items is of considerable theoretical interest. Farrell and Lewandowsky [Farrell, S., & Lewandowsky, S. (2003). Dissimilar items benefit from phonological…

  11. COMPLEMENTARITY AND SIMILARITY OF PARTNERS IN INTERNATIONAL MERGERS

    NARCIS (Netherlands)

    Van Oudenhoven, J.P.; Boer, Th

    1995-01-01

    The effects of degree of cultural and strategic similarity on the preference for a potential merger candidate were investigated. The main objective of the study was to test predictions based on the similarity-attraction hypothesis, Bryne and Clore's (1970) reinforcement-affect model, and social

  12. Exploring the Effects of Similarity on Mapping Spatial Relations

    Science.gov (United States)

    Vasilyeva, Marina; Bowers, Edmond

    2010-01-01

    Solving a map task requires transferring information acquired in one spatial context to another context, an ability that marks an important step in cognitive development. This study investigated how preschoolers' mapping performance was affected by the extent of similarity between spaces. Whereas prior work examined effects of similarity in tasks…

  13. Love Attitudes: Similarities between Parents and between Parents and Children.

    Science.gov (United States)

    Inman-Amos, Jill; And Others

    1994-01-01

    Describes investigation exploring parent-child love attitude similarity among young adult children and parents by assessing demographics, love attitudes, parent-child relationship quality, children's self-disclosure, and parental relationship satisfaction. Results indicate considerable love attitude similarity between marital partners but not…

  14. 7 CFR 51.603 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.603 Section 51.603 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the stalks in any container have the same character...

  15. 7 CFR 51.1864 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.1864 Section 51.1864 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the tomatoes are alike as to firmness of flesh and...

  16. 7 CFR 51.1154 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.1154 Section 51.1154 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... varietal characteristics. Similar varietal characteristics means that the fruits in any container are...

  17. 7 CFR 51.1550 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.1550 Section 51.1550 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the potatoes in any lot have the same general shape...

  18. 7 CFR 51.2714 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.2714 Section 51.2714 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the peanut kernels in the lot are not of distinctly...

  19. 7 CFR 51.2756 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.2756 Section 51.2756 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the peanut kernels in the lot are not of distinctly...

  20. 7 CFR 51.1906 - Similar varietal characteristics.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar varietal characteristics. 51.1906 Section 51.1906 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... characteristics. Similar varietal characteristics means that the tomatoes are alike as to color, i.e., bright red...

  1. Similarity Predicts Liking in 3-Year-Old Children

    Science.gov (United States)

    Fawcett, Christine A.; Markson, Lori

    2010-01-01

    Two studies examined the influence of similarity on 3-year-old children's initial liking of their peers. Children were presented with pairs of childlike puppets who were either similar or dissimilar to them on a specified dimension and then were asked to choose one of the puppets to play with as a measure of liking. Children selected the puppet…

  2. VOS: A New Method for Visualizing Similarities between Objects

    NARCIS (Netherlands)

    N.J.P. van Eck (Nees Jan); L. Waltman (Ludo)

    2006-01-01

    textabstractWe present a new method for visualizing similarities between objects. The method is called VOS, which is an abbreviation for visualization of similarities. The aim of VOS is to provide a low-dimensional visualization in which objects are located in such a way that the distance between

  3. Functional analysis techniques to improve similarity matrices in discrimination problems

    NARCIS (Netherlands)

    Gonzalez, Javier; Munoz, Alberto

    In classification problems an appropriate choice of the data similarity measure is a key step to guarantee the success of discrimination procedures. In this work, we propose a general methodology to transform the available data similarity S, incorporating the data labels, to improve the performance

  4. Comparative mapping reveals similar linkage of functional genes to ...

    Indian Academy of Sciences (India)

    ... B. napus homologues were located in similar yield-related QTL between species. Our results indicate that homologous genes between O. sativa and B. napus may have consistent function and control similar traits, which may be helpful for agronomic gene characterization in B. napus based on what is known in O. sativa.

  5. Epistemic Similarities between Students' Scientific and Supernatural Beliefs

    Science.gov (United States)

    Shtulman, Andrew

    2013-01-01

    The evidential support for scientific claims is quantitatively and qualitatively superior to that for supernatural claims, yet students may not appreciate this difference in light of the fact that both types of claims are learned in similar ways (through testimony rather than firsthand observation) and perform similar functions (explaining…

  6. Alcohol consumption, Wnt/ß-catenin cignaling, and hepatocarcinogenesis

    Science.gov (United States)

    Alcohol is a well-established risk factor for hepatocellular carcinoma, and the mechanisms by which alcohol liver cancer is complex. It has been suggested that ethanol (EtOH) metabolism may enhance tumor progression by increasing hepatocyte proliferation. To test this hypothesis, ethanol (EtOH) feed...

  7. Exact Score Distribution Computation for Similarity Searches in Ontologies

    Science.gov (United States)

    Schulz, Marcel H.; Köhler, Sebastian; Bauer, Sebastian; Vingron, Martin; Robinson, Peter N.

    Semantic similarity searches in ontologies are an important component of many bioinformatic algorithms, e.g., protein function prediction with the Gene Ontology. In this paper we consider the exact computation of score distributions for similarity searches in ontologies, and introduce a simple null hypothesis which can be used to compute a P-value for the statistical significance of similarity scores. We concentrate on measures based on Resnik’s definition of ontological similarity. A new algorithm is proposed that collapses subgraphs of the ontology graph and thereby allows fast score distribution computation. The new algorithm is several orders of magnitude faster than the naive approach, as we demonstrate by computing score distributions for similarity searches in the Human Phenotype Ontology.

  8. Improved collaborative filtering recommendation algorithm of similarity measure

    Science.gov (United States)

    Zhang, Baofu; Yuan, Baoping

    2017-05-01

    The Collaborative filtering recommendation algorithm is one of the most widely used recommendation algorithm in personalized recommender systems. The key is to find the nearest neighbor set of the active user by using similarity measure. However, the methods of traditional similarity measure mainly focus on the similarity of user common rating items, but ignore the relationship between the user common rating items and all items the user rates. And because rating matrix is very sparse, traditional collaborative filtering recommendation algorithm is not high efficiency. In order to obtain better accuracy, based on the consideration of common preference between users, the difference of rating scale and score of common items, this paper presents an improved similarity measure method, and based on this method, a collaborative filtering recommendation algorithm based on similarity improvement is proposed. Experimental results show that the algorithm can effectively improve the quality of recommendation, thus alleviate the impact of data sparseness.

  9. Quantifying similarity of pore-geometry in nanoporous materials

    Science.gov (United States)

    Lee, Yongjin; Barthel, Senja D.; Dłotko, Paweł; Moosavi, S. Mohamad; Hess, Kathryn; Smit, Berend

    2017-05-01

    In most applications of nanoporous materials the pore structure is as important as the chemical composition as a determinant of performance. For example, one can alter performance in applications like carbon capture or methane storage by orders of magnitude by only modifying the pore structure. For these applications it is therefore important to identify the optimal pore geometry and use this information to find similar materials. However, the mathematical language and tools to identify materials with similar pore structures, but different composition, has been lacking. We develop a pore recognition approach to quantify similarity of pore structures and classify them using topological data analysis. This allows us to identify materials with similar pore geometries, and to screen for materials that are similar to given top-performing structures. Using methane storage as a case study, we also show that materials can be divided into topologically distinct classes requiring different optimization strategies.

  10. Modeling Tanimoto Similarity Value Distributions and Predicting Search Results.

    Science.gov (United States)

    Vogt, Martin; Bajorath, Jürgen

    2017-07-01

    Similarity searching using molecular fingerprints has a long history in chemoinformatics and continues to be a popular approach for virtual screening. Typically, known active reference molecules are used to search databases for new active compounds. However, this search has black box character because similarity value distributions are dependent on fingerprints and compound classes. Consequently, no generally applicable similarity threshold values are available as reliable indicators of activity relationships between reference and database compounds. Therefore, it is generally uncertain where new active compounds might appear in database rankings, if at all. In this contribution, methods are discussed for modeling similarity value distributions of fingerprint search calculations using Tanimoto coefficients and estimating rank positions of active compounds. To our knowledge, these are the first approaches for predicting the results of fingerprint-based similarity searching. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Similar words analysis based on POS-CBOW language model

    Directory of Open Access Journals (Sweden)

    Dongru RUAN

    2015-10-01

    Full Text Available Similar words analysis is one of the important aspects in the field of natural language processing, and it has important research and application values in text classification, machine translation and information recommendation. Focusing on the features of Sina Weibo's short text, this paper presents a language model named as POS-CBOW, which is a kind of continuous bag-of-words language model with the filtering layer and part-of-speech tagging layer. The proposed approach can adjust the word vectors' similarity according to the cosine similarity and the word vectors' part-of-speech metrics. It can also filter those similar words set on the base of the statistical analysis model. The experimental result shows that the similar words analysis algorithm based on the proposed POS-CBOW language model is better than that based on the traditional CBOW language model.

  12. A Model-Based Approach to Constructing Music Similarity Functions

    Science.gov (United States)

    West, Kris; Lamere, Paul

    2006-12-01

    Several authors have presented systems that estimate the audio similarity of two pieces of music through the calculation of a distance metric, such as the Euclidean distance, between spectral features calculated from the audio, related to the timbre or pitch of the signal. These features can be augmented with other, temporally or rhythmically based features such as zero-crossing rates, beat histograms, or fluctuation patterns to form a more well-rounded music similarity function. It is our contention that perceptual or cultural labels, such as the genre, style, or emotion of the music, are also very important features in the perception of music. These labels help to define complex regions of similarity within the available feature spaces. We demonstrate a machine-learning-based approach to the construction of a similarity metric, which uses this contextual information to project the calculated features into an intermediate space where a music similarity function that incorporates some of the cultural information may be calculated.

  13. Average is Boring: How Similarity Kills a Meme's Success

    Science.gov (United States)

    Coscia, Michele

    2014-09-01

    Every day we are exposed to different ideas, or memes, competing with each other for our attention. Previous research explained popularity and persistence heterogeneity of memes by assuming them in competition for limited attention resources, distributed in a heterogeneous social network. Little has been said about what characteristics make a specific meme more likely to be successful. We propose a similarity-based explanation: memes with higher similarity to other memes have a significant disadvantage in their potential popularity. We employ a meme similarity measure based on semantic text analysis and computer vision to prove that a meme is more likely to be successful and to thrive if its characteristics make it unique. Our results show that indeed successful memes are located in the periphery of the meme similarity space and that our similarity measure is a promising predictor of a meme success.

  14. Imaging phonological similarity effects on verbal working memory.

    Science.gov (United States)

    Sweet, Lawrence H; Paskavitz, James F; Haley, Andreana P; Gunstad, John J; Mulligan, Richard C; Nyalakanti, Prashanth K; Cohen, Ronald A

    2008-03-07

    Studies of verbal working memory (VWM) report that performance declines as the phonemic similarity of stimuli increases. To determine how phonological similarity affects brain function during VWM, "standard" and "similarity" versions of the 2-Back task were presented to 34 healthy participants during functional magnetic resonance imaging (FMRI). Letter consonants presented during similarity blocks rhymed, while consonants did not rhyme during standard blocks. Empirical ROIs were identified from significant 2-Back-related activity observed during either condition. A priori ROIs were selected from functional neuroimaging literature on phonological processing. Although VWM-related activity was not modulated by similarity in any of four regions recruited (dorsolateral prefrontal, posterior parietal, anterior insular, and supplementary motor cortices), four of five regions of deactivation exhibited significantly greater deactivation during the similarity compared to the standard condition (posterior cingulate, paracentral lobule, posterior insula, and parahippocampal gyrus). In a priori phonological processing-related ROIs, similarity did not affect observed increases in activity (supplementary motor area, Broca's area, and cerebellum), while two of the three regions exhibiting decreased activity (near Wernicke's area and Heschel's Gyrus) also exhibited more deactivation during similarity. Accuracy was lower during the similarity 2-Back, positively related to activity within recruited VWM-related ROIs, and inversely related to activity in regions of VWM-related deactivation. Based on known functions of these ROIs, we conclude that language, audition, and self-reflection processes may disengage during phonological interference, while activity levels are maintained in regions recruited during VWM processing. Similarity effects likely include suspension of attention to unrelated and distracting processes to improve concentration.

  15. Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key.

    Science.gov (United States)

    Haupt, V Joachim; Daminelli, Simone; Schroeder, Michael

    2013-01-01

    Drug repositioning applies established drugs to new disease indications with increasing success. A pre-requisite for drug repurposing is drug promiscuity (polypharmacology) - a drug's ability to bind to several targets. There is a long standing debate on the reasons for drug promiscuity. Based on large compound screens, hydrophobicity and molecular weight have been suggested as key reasons. However, the results are sometimes contradictory and leave space for further analysis. Protein structures offer a structural dimension to explain promiscuity: Can a drug bind multiple targets because the drug is flexible or because the targets are structurally similar or even share similar binding sites? We present a systematic study of drug promiscuity based on structural data of PDB target proteins with a set of 164 promiscuous drugs. We show that there is no correlation between the degree of promiscuity and ligand properties such as hydrophobicity or molecular weight but a weak correlation to conformational flexibility. However, we do find a correlation between promiscuity and structural similarity as well as binding site similarity of protein targets. In particular, 71% of the drugs have at least two targets with similar binding sites. In order to overcome issues in detection of remotely similar binding sites, we employed a score for binding site similarity: LigandRMSD measures the similarity of the aligned ligands and uncovers remote local similarities in proteins. It can be applied to arbitrary structural binding site alignments. Three representative examples, namely the anti-cancer drug methotrexate, the natural product quercetin and the anti-diabetic drug acarbose are discussed in detail. Our findings suggest that global structural and binding site similarity play a more important role to explain the observed drug promiscuity in the PDB than physicochemical drug properties like hydrophobicity or molecular weight. Additionally, we find ligand flexibility to have a minor

  16. Automatic classification of protein structures relying on similarities between alignments

    Directory of Open Access Journals (Sweden)

    Santini Guillaume

    2012-09-01

    Full Text Available Abstract Background Identification of protein structural cores requires isolation of sets of proteins all sharing a same subset of structural motifs. In the context of an ever growing number of available 3D protein structures, standard and automatic clustering algorithms require adaptations so as to allow for efficient identification of such sets of proteins. Results When considering a pair of 3D structures, they are stated as similar or not according to the local similarities of their matching substructures in a structural alignment. This binary relation can be represented in a graph of similarities where a node represents a 3D protein structure and an edge states that two 3D protein structures are similar. Therefore, classifying proteins into structural families can be viewed as a graph clustering task. Unfortunately, because such a graph encodes only pairwise similarity information, clustering algorithms may include in the same cluster a subset of 3D structures that do not share a common substructure. In order to overcome this drawback we first define a ternary similarity on a triple of 3D structures as a constraint to be satisfied by the graph of similarities. Such a ternary constraint takes into account similarities between pairwise alignments, so as to ensure that the three involved protein structures do have some common substructure. We propose hereunder a modification algorithm that eliminates edges from the original graph of similarities and gives a reduced graph in which no ternary constraints are violated. Our approach is then first to build a graph of similarities, then to reduce the graph according to the modification algorithm, and finally to apply to the reduced graph a standard graph clustering algorithm. Such method was used for classifying ASTRAL-40 non-redundant protein domains, identifying significant pairwise similarities with Yakusa, a program devised for rapid 3D structure alignments. Conclusions We show that filtering

  17. Representational Similarity of Body Parts in Human Occipitotemporal Cortex.

    Science.gov (United States)

    Bracci, Stefania; Caramazza, Alfonso; Peelen, Marius V

    2015-09-23

    Regions in human lateral and ventral occipitotemporal cortices (OTC) respond selectively to pictures of the human body and its parts. What are the organizational principles underlying body part responses in these regions? Here we used representational similarity analysis (RSA) of fMRI data to test multiple possible organizational principles: shape similarity, physical proximity, cortical homunculus proximity, and semantic similarity. Participants viewed pictures of whole persons, chairs, and eight body parts (hands, arms, legs, feet, chests, waists, upper faces, and lower faces). The similarity of multivoxel activity patterns for all body part pairs was established in whole person-selective OTC regions. The resulting neural similarity matrices were then compared with similarity matrices capturing the hypothesized organizational principles. Results showed that the semantic similarity model best captured the neural similarity of body parts in lateral and ventral OTC, which followed an organization in three clusters: (1) body parts used as action effectors (hands, feet, arms, and legs), (2) noneffector body parts (chests and waists), and (3) face parts (upper and lower faces). Whole-brain RSA revealed, in addition to OTC, regions in parietal and frontal cortex in which neural similarity was related to semantic similarity. In contrast, neural similarity in occipital cortex was best predicted by shape similarity models. We suggest that the semantic organization of body parts in high-level visual cortex relates to the different functions associated with the three body part clusters, reflecting the unique processing and connectivity demands associated with the different types of information (e.g., action, social) different body parts (e.g., limbs, faces) convey. Significance statement: While the organization of body part representations in motor and somatosensory cortices has been well characterized, the principles underlying body part representations in visual cortex

  18. Similarities in murine infection and immune response to Borrelia bissettii and Borrelia burgdorferi sensu stricto.

    Science.gov (United States)

    Leydet, Brian F; Liang, Fang Ting

    2015-12-01

    In 1982, Borrelia burgdorferi sensu stricto (ss) was identified as the aetiological agent of Lyme disease. Since then an increasing number of Borrelia burgdorferi sensu lato (sl) species have been isolated in the United States. To date, many of these species remain understudied despite mounting evidence associating them with human illness. Borrelia bissettii is a spirochaete closely related to B. burgdorferi that has been loosely associated with human illness. Using an experimental murine infection model, we compared the infectivity and humoral immune response with a North American isolate of B. bissettii and B. burgdorferi using culture, molecular and serological methods. The original B. bissettii cultures were unable to infect immunocompetent mice, but were confirmed to be infectious after adaptation in immunodeficient animals. B. bissettii infection resulted in spirochaete burdens similar to B. burgdorferi in skin, heart and bladder whereas significantly lower burdens were observed in the joint tissues. B. bissettii induced an antibody response similar to B. burgdorferi as measured by both immunoblotting and the C6 ELISA. Additionally, this isolate of B. bissettii was sequenced on the Ion Torrent PGM, which successfully identified many genes orthologous to mammalian virulence factors described in B. burgdorferi. Similarities seen between both infections in this well-characterized murine model contribute to our understanding of the potential pathogenic nature of B. bissettii. Infection dynamics of B. bissettii, and especially the induced humoral response, are similar to B. burgdorferi, suggesting this species may contribute to the epidemiology of human borreliosis.

  19. Generalized Framework for Similarity Measure of Time Series

    Directory of Open Access Journals (Sweden)

    Hongsheng Yin

    2014-01-01

    Full Text Available Currently, there is no definitive and uniform description for the similarity of time series, which results in difficulties for relevant research on this topic. In this paper, we propose a generalized framework to measure the similarity of time series. In this generalized framework, whether the time series is univariable or multivariable, and linear transformed or nonlinear transformed, the similarity of time series is uniformly defined using norms of vectors or matrices. The definitions of the similarity of time series in the original space and the transformed space are proved to be equivalent. Furthermore, we also extend the theory on similarity of univariable time series to multivariable time series. We present some experimental results on published time series datasets tested with the proposed similarity measure function of time series. Through the proofs and experiments, it can be claimed that the similarity measure functions of linear multivariable time series based on the norm distance of covariance matrix and nonlinear multivariable time series based on kernel function are reasonable and practical.

  20. ESG: extended similarity group method for automated protein function prediction.

    Science.gov (United States)

    Chitale, Meghana; Hawkins, Troy; Park, Changsoon; Kihara, Daisuke

    2009-07-15

    Importance of accurate automatic protein function prediction is ever increasing in the face of a large number of newly sequenced genomes and proteomics data that are awaiting biological interpretation. Conventional methods have focused on high sequence similarity-based annotation transfer which relies on the concept of homology. However, many cases have been reported that simple transfer of function from top hits of a homology search causes erroneous annotation. New methods are required to handle the sequence similarity in a more robust way to combine together signals from strongly and weakly similar proteins for effectively predicting function for unknown proteins with high reliability. We present the extended similarity group (ESG) method, which performs iterative sequence database searches and annotates a query sequence with Gene Ontology terms. Each annotation is assigned with probability based on its relative similarity score with the multiple-level neighbors in the protein similarity graph. We will depict how the statistical framework of ESG improves the prediction accuracy by iteratively taking into account the neighborhood of query protein in the sequence similarity space. ESG outperforms conventional PSI-BLAST and the protein function prediction (PFP) algorithm. It is found that the iterative search is effective in capturing multiple-domains in a query protein, enabling accurately predicting several functions which originate from different domains. ESG web server is available for automated protein function prediction at http://dragon.bio.purdue.edu/ESG/.

  1. Similarity in romantic couples' drinking motivations and drinking behaviors.

    Science.gov (United States)

    Kehayes, Ivy-Lee L; Mackinnon, Sean P; Sherry, Simon B; Leonard, Kenneth E; Stewart, Sherry H

    2017-01-01

    Research suggests that enhancement, conformity, social, coping-with-anxiety, and coping-with-depression drinking motives are linked to specific drinking outcomes in a theoretically expected manner. Social learning theory suggests that people who spend more time together emulate each other's behavior to acquire reinforcing outcomes. The present study sought to integrate drinking motives theory and social learning theory to investigate similarity in drinking behaviors and drinking motives in romantic couples. We hypothesized that couples would be more similar than chance in their drinking behaviors and motives. We also hypothesized that demographics reflecting time around and interactions with romantic partners (e.g., days spent drinking together) would positively correlate with similarity in drinking behaviors and motivations. The present study tested hypotheses in 203 romantic couples. Participants completed a Timeline Follow-Back measure and the Modified Drinking Motives Questionnaire-Revised to track their alcohol use and drinking motives. Similarity profiles were calculated using McCrae's (J Pers Assess. 2008;90:105-109) coefficient of profile agreement, rpa. Couples were more similar in their drinking behavioral and motivational profiles than could be explained by chance. Days spent drinking together and days with face-to-face contact predicted increased similarity in drinking behavior profiles, but not similarity in drinking motives profiles. Results are partially consistent with social learning theory and suggest that social influences within couples could be important intervention targets to prevent escalations in drinking.

  2. Similarity Measure and Entropy of Fuzzy Soft Sets

    Directory of Open Access Journals (Sweden)

    Zhicai Liu

    2014-01-01

    Full Text Available Soft set theory, proposed by Molodtsov, has been regarded as an effective mathematical tool to deal with uncertainties. Recently, uncertainty measures of soft sets and fuzzy soft sets have gained attentions from researchers. This paper is devoted to the study of uncertainty measures of fuzzy soft sets. The axioms for similarity measure and entropy are proposed. A new category of similarity measures and entropies is presented based on fuzzy equivalence. Our approach is general in the sense that by using different fuzzy equivalences one gets different similarity measures and entropies. The relationships among these measures and the other proposals in the literatures are analyzed.

  3. Identifying and Attributing Similar Traces with Greatest Common Factor Analysis

    Directory of Open Access Journals (Sweden)

    Fred Cohen

    2012-06-01

    Full Text Available This paper presents an algorithm for comparing large numbers of traces to each other and identifying and presenting groups of traces with similar features. It is applied to forensic analysis in which groups of similar traces are automatically identified and presented so that attribution and other related claims may be asserted, and independently confirmed or refuted. The approach of this paper is to identify an approximate algorithm that will find a large subset of greatest common factor similar groups of arbitrary factors in far less time and space than an exact algorithm using examiner-provided selection criteria for factor definition.

  4. Conceptual similarity promotes generalization of higher order fear learning

    Science.gov (United States)

    Dunsmoor, Joseph E.; White, Allison J.; LaBar, Kevin S.

    2011-01-01

    We tested the hypothesis that conceptual similarity promotes generalization of conditioned fear. Using a sensory preconditioning procedure, three groups of subjects learned an association between two cues that were conceptually similar, unrelated, or mismatched. Next, one of the cues was paired with a shock. The other cue was then reintroduced to test for fear generalization, as measured by the skin conductance response. Results showed enhanced fear generalization that correlated with trait anxiety levels in the group that learned an association between conceptually similar stimuli. These findings suggest that conceptual representations of conditional stimuli influence human fear learning processes. PMID:21330378

  5. Demonstration of Functional Similarity of Proposed Biosimilar ABP 501 to Adalimumab.

    Science.gov (United States)

    Velayudhan, Jyoti; Chen, Yuh-Feng; Rohrbach, Amanda; Pastula, Christina; Maher, Gwen; Thomas, Heather; Brown, Ryan; Born, Teresa L

    2016-08-01

    Due to the complex molecular structure and proprietary manufacturing processes of monoclonal antibodies (mAbs), differences in structure and function may be expected during development of biosimilar mAbs. Important regulatory requirements for approval of biosimilar products involve comprehensive assessments of any potential differences between proposed biosimilars and reference mAbs, including differences in all known mechanisms of action, using sensitive and relevant methods. Any identified structural differences should not result in differences in biofunctional or clinical activity. A comprehensive assessment comparing the Amgen biosimilar candidate ABP 501 with FDA-licensed adalimumab (adalimumab [US]) and EU-authorized adalimumab (adalimumab [EU]) was conducted to demonstrate similarity in biofunctional activity. The functional similarity assessment included testing of binding kinetics to soluble tumor necrosis factor α (TNFα) and relative binding to transmembrane TNFα. The neutralization of TNFα-induced caspase activation, TNFα- and lymphotoxin-α (LTα)-induced chemokine production, and cytotoxicity was also tested. Binding to Fc-gamma receptors FcγRIa, FcγRIIa (131H), FcγRIIIa (158V and 158F), and neonatal Fc receptor (FcRn) was compared with the reference mAbs, as was antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity. The data demonstrate that ABP 501 is similar to both adalimumab (US) and adalimumab (EU) with respect to evaluated biofunctional activities. Similarity in biofunctional activity is a critical component of the totality of evidence required for demonstration of biosimilarity. The functional similarity demonstrated for ABP 501 comprehensively assesses the known mechanisms of action of adalimumab, supporting the conclusion that ABP 501, adalimumab (US), and adalimumab (EU) are likely to be clinically similar.

  6. A Signal Processing Method to Explore Similarity in Protein Flexibility

    Directory of Open Access Journals (Sweden)

    Simina Vasilache

    2010-01-01

    Full Text Available Understanding mechanisms of protein flexibility is of great importance to structural biology. The ability to detect similarities between proteins and their patterns is vital in discovering new information about unknown protein functions. A Distance Constraint Model (DCM provides a means to generate a variety of flexibility measures based on a given protein structure. Although information about mechanical properties of flexibility is critical for understanding protein function for a given protein, the question of whether certain characteristics are shared across homologous proteins is difficult to assess. For a proper assessment, a quantified measure of similarity is necessary. This paper begins to explore image processing techniques to quantify similarities in signals and images that characterize protein flexibility. The dataset considered here consists of three different families of proteins, with three proteins in each family. The similarities and differences found within flexibility measures across homologous proteins do not align with sequence-based evolutionary methods.

  7. Aviation Safety: FAA and DOD Response to Similar Safety Concerns

    National Research Council Canada - National Science Library

    2002-01-01

    .... The Federal Aviation Administration (FAA) and the military services often face common safety issues as they oversee the operation of similar aircraft or even dissimilar aircraft that use common parts and materials...

  8. Scaling, Similarity, and the Fourth Paradigm for Hydrology

    Science.gov (United States)

    Peters-Lidard, Christa D.; Clark, Martyn; Samaniego, Luis; Verhoest, Niko E. C.; van Emmerik, Tim; Uijlenhoet, Remko; Achieng, Kevin; Franz, Trenton E.; Woods, Ross

    2017-01-01

    In this synthesis paper addressing hydrologic scaling and similarity, we posit that roadblocks in the search for universal laws of hydrology are hindered by our focus on computational simulation (the third paradigm), and assert that it is time for hydrology to embrace a fourth paradigm of data-intensive science. Advances in information-based hydrologic science, coupled with an explosion of hydrologic data and advances in parameter estimation and modelling, have laid the foundation for a data-driven framework for scrutinizing hydrological scaling and similarity hypotheses. We summarize important scaling and similarity concepts (hypotheses) that require testing, describe a mutual information framework for testing these hypotheses, describe boundary condition, state flux, and parameter data requirements across scales to support testing these hypotheses, and discuss some challenges to overcome while pursuing the fourth hydrological paradigm. We call upon the hydrologic sciences community to develop a focused effort towards adopting the fourth paradigm and apply this to outstanding challenges in scaling and similarity.

  9. Neutrosophic Cubic MCGDM Method Based on Similarity Measure

    Directory of Open Access Journals (Sweden)

    Surapati Pramanik

    2017-06-01

    Full Text Available The notion of neutrosophic cubic set is originated from the hybridization of the concept of neutrosophic set and interval valued neutrosophic set. We define similarity measure for neutrosophic cubic sets and prove some of its basic properties.

  10. Self-similarity properties in the multiplicity distributions

    Energy Technology Data Exchange (ETDEWEB)

    Calucci, G.; Treleani, D. [Trieste Univ. (Italy). Dipartimento di Fisica Teorica

    1999-03-01

    Some formal observations about the self similarity property of the negative binomial distribution are presented and the suggestion is made that the property can help in the individuation of the elementary sources in a complex production process. (orig.) 11 refs.

  11. Self-similarity properties in the multiplicity distributions

    Energy Technology Data Exchange (ETDEWEB)

    Calucci, G.; Treleani, D

    1999-03-01

    Some formal observations about the self similarity property of the negative binomial distribution are presented and the suggestion is made that the property can help in the individuation of the elementary sources in a complex production process.

  12. Interbehavioral psychology and radical behaviorism: Some similarities and differences

    Science.gov (United States)

    Morris, Edward K.

    1984-01-01

    Both J. R. Kantor's interbehavioral psychology and B. F. Skinner's radical behaviorism represent wellarticulated approaches to a natural science of behavior. As such, they share a number of similar features, yet they also differ on a number of dimensions. Some of these similarities and differences are examined by describing their emergence in the professional literature and by comparing the respective units of analysis of the two approaches—the interbehavioral field and the three-term contingency. An evaluation of the similarities and differences shows the similarities to be largely fundamental, and the differences largely ones of emphasis. Nonetheless, the two approaches do make unique contributions to a natural science of behavior, the integration of which can facilitate the development of that science and its acceptance among other sciences and within society at large. PMID:22478612

  13. Similarity-Based Interference and the Acquisition of Adjunct Control

    Directory of Open Access Journals (Sweden)

    Juliana Gerard

    2017-10-01

    Full Text Available Previous research on the acquisition of adjunct control has observed non-adultlike behavior for sentences like “John bumped Mary after tripping on the sidewalk.” While adults only allow a subject control interpretation for these sentences (that John tripped on the sidewalk, preschool-aged children have been reported to allow a much wider range of interpretations. A number of different tasks have been used with the aim of identifying a grammatical source of children’s errors. In this paper, we consider the role of extragrammatical factors. In two comprehension experiments, we demonstrate that error rates go up when the similarity increases between an antecedent and a linearly intervening noun phrase, first with similarity in gender, and next with similarity in number marking. This suggests that difficulties with adjunct control are to be explained (at least in part by the sentence processing mechanisms that underlie similarity-based interference in adults.

  14. Interference effects in learning similar sequences of discrete movements

    NARCIS (Netherlands)

    Koedijker, J.M.; Oudejans, R.R.D.; Beek, P.J.

    2010-01-01

    Three experiments were conducted to examine proactive and retroactive interference effects in learning two similar sequences of discrete movements. In each experiment, the participants in the experimental group practiced two movement sequences on consecutive days (1 on each day, order

  15. Scaling, similarity, and the fourth paradigm for hydrology

    Science.gov (United States)

    Peters-Lidard, Christa D.; Clark, Martyn; Samaniego, Luis; Verhoest, Niko E. C.; van Emmerik, Tim; Uijlenhoet, Remko; Achieng, Kevin; Franz, Trenton E.; Woods, Ross

    2017-07-01

    In this synthesis paper addressing hydrologic scaling and similarity, we posit that roadblocks in the search for universal laws of hydrology are hindered by our focus on computational simulation (the third paradigm) and assert that it is time for hydrology to embrace a fourth paradigm of data-intensive science. Advances in information-based hydrologic science, coupled with an explosion of hydrologic data and advances in parameter estimation and modeling, have laid the foundation for a data-driven framework for scrutinizing hydrological scaling and similarity hypotheses. We summarize important scaling and similarity concepts (hypotheses) that require testing; describe a mutual information framework for testing these hypotheses; describe boundary condition, state, flux, and parameter data requirements across scales to support testing these hypotheses; and discuss some challenges to overcome while pursuing the fourth hydrological paradigm. We call upon the hydrologic sciences community to develop a focused effort towards adopting the fourth paradigm and apply this to outstanding challenges in scaling and similarity.

  16. Self-concept and attraction for similar and dissimilar others.

    Science.gov (United States)

    Leonard, R L

    1975-05-01

    The present study investigated the role of self-concept as a moderator of the similarity-attraction relationship described by Byrne. Subjects conducted face-to-face interviews with confederates who played roles as job applicants. Similarity-dissimilarity was manipulated by the confederate roles as well as by the information given the subjects in accordance with the procedures described by Byrne. The hypothesis was tested and confirmed that persons with favorable self-concepts would be more attracted to others with similar attitudes than to others with dissimilar attitudes. Persons with negative self-concepts did not show a preference for similar others. It was suggested that earlier studies in this area suffered from methodological flaws and did not constitute an adequate test of the hypothesis. Suggestions for future work in the area were given.

  17. Multifocal motor neuropathy and progressive atrophy : Pathophysiological similarities and differences

    NARCIS (Netherlands)

    Vlam, L.

    2015-01-01

    Progressive muscular atrophy (PMA) and multifocal motor neuropathy (MMN) share many clinical similarities. They are both characterized by progressive asymmetric muscle weakness with atrophy and fasciculations. Tendon reflexes are normally low or absent, although in some patients with MMN normal

  18. Protein structure similarity from principle component correlation analysis

    Directory of Open Access Journals (Sweden)

    Chou James

    2006-01-01

    Full Text Available Abstract Background Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. Results We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. Conclusion The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum

  19. Earthquake Fingerprints: Representing Earthquake Waveforms for Similarity-Based Detection

    Science.gov (United States)

    Bergen, K.; Beroza, G. C.

    2016-12-01

    New earthquake detection methods, such as Fingerprint and Similarity Thresholding (FAST), use fast approximate similarity search to identify similar waveforms in long-duration data without templates (Yoon et al. 2015). These methods have two key components: fingerprint extraction and an efficient search algorithm. Fingerprint extraction converts waveforms into fingerprints, compact signatures that represent short-duration waveforms for identification and search. Earthquakes are detected using an efficient indexing and search scheme, such as locality-sensitive hashing, that identifies similar waveforms in a fingerprint database. The quality of the search results, and thus the earthquake detection results, is strongly dependent on the fingerprinting scheme. Fingerprint extraction should map similar earthquake waveforms to similar waveform fingerprints to ensure a high detection rate, even under additive noise and small distortions. Additionally, fingerprints corresponding to noise intervals should have mutually dissimilar fingerprints to minimize false detections. In this work, we compare the performance of multiple fingerprint extraction approaches for the earthquake waveform similarity search problem. We apply existing audio fingerprinting (used in content-based audio identification systems) and time series indexing techniques and present modified versions that are specifically adapted for seismic data. We also explore data-driven fingerprinting approaches that can take advantage of labeled or unlabeled waveform data. For each fingerprinting approach we measure its ability to identify similar waveforms in a low signal-to-noise setting, and quantify the trade-off between true and false detection rates in the presence of persistent noise sources. We compare the performance using known event waveforms from eight independent stations in the Northern California Seismic Network.

  20. A Semantics-Based Measure of Emoji Similarity

    OpenAIRE

    Wijeratne, Sanjaya; Balasuriya, Lakshika; Sheth, Amit; Doran, Derek

    2017-01-01

    Emoji have grown to become one of the most important forms of communication on the web. With its widespread use, measuring the similarity of emoji has become an important problem for contemporary text processing since it lies at the heart of sentiment analysis, search, and interface design tasks. This paper presents a comprehensive analysis of the semantic similarity of emoji through embedding models that are learned over machine-readable emoji meanings in the EmojiNet knowledge base. Using e...

  1. The Impact of Role Model Similarity on Women's Leadership Outcomes

    OpenAIRE

    Shah, Yashna Jitendra

    2015-01-01

    Role models can serve as a means to counteract the prevalent 'Think Leader, Think Male' stereotype. This study was designed to assess the impact of role model similarity on women's leadership self-efficacy, task performance and future leadership behavior, using two conceptualizations of similarity – match with leadership self-concept and attainability of the role model. Additionally, the process by which one's self-perceptions of leadership impact judgments of one's own behavior was also inve...

  2. Similarity law in spectral estimation of a time series. V.

    Science.gov (United States)

    Terebizh, V. Yu.

    1998-04-01

    A continuation of [V. Yu. Terebizh, Astrofizika, 40, 139, 273, 413 (1997); 41, 113 (1998)]. When following recommendations based on a similarity law, a least-squares estimate is justified. Ockham’s approach is free of assumptions, but more complicated; it leads to results close to those for the least-squares method in conjunction with a similarity law and the condition of nonnegativity of the solution. The theoretical conclusions are illustrated by calculations for an AR-1 process.

  3. Networks at their Limits: Software, Similarity, and Continuity in Vietnam

    OpenAIRE

    Nguyen, Lilly Uyen

    2013-01-01

    This dissertation explores the social worlds of pirated software discs and free/open source software in Vietnam to describe the practices of copying, evangelizing, and translation. This dissertation also reveals the cultural logics of similarity and continuity that sustain these social worlds. Taken together, this dissertation argues that the logics of similarity and continuity are expressions of Vietnam's distance from global networks. Vietnam is currently in a period of rapid economic trans...

  4. Inter Genre Similarity Modelling For Automatic Music Genre Classification

    OpenAIRE

    Bagci, Ulas; Erzin, Engin

    2009-01-01

    Music genre classification is an essential tool for music information retrieval systems and it has been finding critical applications in various media platforms. Two important problems of the automatic music genre classification are feature extraction and classifier design. This paper investigates inter-genre similarity modelling (IGS) to improve the performance of automatic music genre classification. Inter-genre similarity information is extracted over the mis-classified feature population....

  5. Plant injury due to air pollution - similar symptoms. Part I

    Energy Technology Data Exchange (ETDEWEB)

    Matsuoka, Y.

    1976-01-01

    Many plant diseases cause injuries to leaves which mimic the damage inflicted by air pollution. The relationship between air pollution injuries and those caused by meteorological conditions are discussed. Rice plants often contract akagare which causes reddish-brown spots on leaves similar to the symptoms caused by photochemical oxidants. Spider mites produce leaf damage in kidney beans which mimics the spotting caused by photochemical oxidants. Lace bugs produce minute white spots on azaleas similar to those caused by photochemical oxidants.

  6. Average is Boring: How Similarity Kills a Meme's Success

    OpenAIRE

    Coscia, Michele

    2014-01-01

    Every day we are exposed to different ideas, or memes, competing with each other for our attention. Previous research explained popularity and persistence heterogeneity of memes by assuming them in competition for limited attention resources, distributed in a heterogeneous social network. Little has been said about what characteristics make a specific meme more likely to be successful. We propose a similarity-based explanation: memes with higher similarity to other memes have a significant di...

  7. The Role of Familiarity, Priming and Perception in Similarity Judgments

    Science.gov (United States)

    2013-08-01

    Inprovements to industrial colour -difference evaluation (Tech. Rep. No. CIE 142-2001). Vienna: Com- mission Internationale de l’Eclairage. Glucksberg, S...Keysar, B. (1990). Understanding metaphorical comparisons: Beyond similarity. Psycholog - ical Review, 97, 3-18. Goldstone, R. L. (1994). Similarity...interactive activation, and mapping. Journal of Experimental Psychology : Learn- ing, Memory and Cognition, 20(3-28). Harrison, A. M., & Trafton, J. G

  8. Phishing Detection: Analysis of Visual Similarity Based Approaches

    Directory of Open Access Journals (Sweden)

    Ankit Kumar Jain

    2017-01-01

    Full Text Available Phishing is one of the major problems faced by cyber-world and leads to financial losses for both industries and individuals. Detection of phishing attack with high accuracy has always been a challenging issue. At present, visual similarities based techniques are very useful for detecting phishing websites efficiently. Phishing website looks very similar in appearance to its corresponding legitimate website to deceive users into believing that they are browsing the correct website. Visual similarity based phishing detection techniques utilise the feature set like text content, text format, HTML tags, Cascading Style Sheet (CSS, image, and so forth, to make the decision. These approaches compare the suspicious website with the corresponding legitimate website by using various features and if the similarity is greater than the predefined threshold value then it is declared phishing. This paper presents a comprehensive analysis of phishing attacks, their exploitation, some of the recent visual similarity based approaches for phishing detection, and its comparative study. Our survey provides a better understanding of the problem, current solution space, and scope of future research to deal with phishing attacks efficiently using visual similarity based approaches.

  9. Protein-protein interaction based on pairwise similarity

    Directory of Open Access Journals (Sweden)

    Zaki Nazar

    2009-05-01

    Full Text Available Abstract Background Protein-protein interaction (PPI is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. Given that the association and dissociation of protein molecules is crucial, computational tools capable of effectively identifying PPI are desirable. In this paper, we propose a simple yet effective method to detect PPI based on pairwise similarity and using only the primary structure of the protein. The PPI based on Pairwise Similarity (PPI-PS method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences. Each coordinate of this vector is typically the E-value of the Smith-Waterman score. These vectors are then used to compute the kernel matrix which will be exploited in conjunction with support vector machines. Results To assess the ability of the proposed method to recognize the difference between "interacted" and "non-interacted" proteins pairs, we applied it on different datasets from the available yeast saccharomyces cerevisiae protein interaction. The proposed method achieved reasonable improvement over the existing state-of-the-art methods for PPI prediction. Conclusion Pairwise similarity score provides a relevant measure of similarity between protein sequences. This similarity incorporates biological knowledge about proteins and it is extremely powerful when combined with support vector machine to predict PPI.

  10. Limiting similarity of competitive species and demographic stochasticity.

    Science.gov (United States)

    Zheng, Xiu-Deng; Deng, Ling-Ling; Qiang, Wei-Ya; Cressman, Ross; Tao, Yi

    2017-04-01

    The limiting similarity of competitive species and its relationship with the competitive exclusion principle is still one of the most important concepts in ecology. In the 1970s, May [R. M. May, Stability and Complexity in Model Ecosystems (Princeton University, Princeton, NJ, 1973)] developed a concise theoretical framework to investigate the limiting similarity of competitive species. His theoretical results show that no limiting similarity threshold of competitive species can be identified in the deterministic model system whereby species more similar than this threshold never coexist. Theoretically, for competitive species coexisting in an unvarying environment, deterministic interspecific interactions and demographic stochasticity can be considered two sides of a coin. To investigate how the "tension" between these two forces affects the coexistence of competing species, a simple two-species competitive system based only on May's model system is transformed into an equivalent replicator equation. The effect of demographic stochasticity on the system stability is measured by the expected drift of the Lyapunov function. Our main results show that the limiting similarity of competitive species should not be considered to be an absolute measure. Specifically, very similar competitive species should be able to coexist in an environment with a high productivity level but big differences between competitive species should be necessary in an ecosystem with a low productivity level.

  11. Craniofacial similarity analysis through sparse principal component analysis.

    Directory of Open Access Journals (Sweden)

    Junli Zhao

    Full Text Available The computer-aided craniofacial reconstruction (CFR technique has been widely used in the fields of criminal investigation, archaeology, anthropology and cosmetic surgery. The evaluation of craniofacial reconstruction results is important for improving the effect of craniofacial reconstruction. Here, we used the sparse principal component analysis (SPCA method to evaluate the similarity between two sets of craniofacial data. Compared with principal component analysis (PCA, SPCA can effectively reduce the dimensionality and simultaneously produce sparse principal components with sparse loadings, thus making it easy to explain the results. The experimental results indicated that the evaluation results of PCA and SPCA are consistent to a large extent. To compare the inconsistent results, we performed a subjective test, which indicated that the result of SPCA is superior to that of PCA. Most importantly, SPCA can not only compare the similarity of two craniofacial datasets but also locate regions of high similarity, which is important for improving the craniofacial reconstruction effect. In addition, the areas or features that are important for craniofacial similarity measurements can be determined from a large amount of data. We conclude that the craniofacial contour is the most important factor in craniofacial similarity evaluation. This conclusion is consistent with the conclusions of psychological experiments on face recognition and our subjective test. The results may provide important guidance for three- or two-dimensional face similarity evaluation, analysis and face recognition.

  12. Learning-Based Video Superresolution Reconstruction Using Spatiotemporal Nonlocal Similarity

    Directory of Open Access Journals (Sweden)

    Meiyu Liang

    2015-01-01

    Full Text Available Aiming at improving the video visual resolution quality and details clarity, a novel learning-based video superresolution reconstruction algorithm using spatiotemporal nonlocal similarity is proposed in this paper. Objective high-resolution (HR estimations of low-resolution (LR video frames can be obtained by learning LR-HR correlation mapping and fusing spatiotemporal nonlocal similarities between video frames. With the objective of improving algorithm efficiency while guaranteeing superresolution quality, a novel visual saliency-based LR-HR correlation mapping strategy between LR and HR patches is proposed based on semicoupled dictionary learning. Moreover, aiming at improving performance and efficiency of spatiotemporal similarity matching and fusion, an improved spatiotemporal nonlocal fuzzy registration scheme is established using the similarity weighting strategy based on pseudo-Zernike moment feature similarity and structural similarity, and the self-adaptive regional correlation evaluation strategy. The proposed spatiotemporal fuzzy registration scheme does not rely on accurate estimation of subpixel motion, and therefore it can be adapted to complex motion patterns and is robust to noise and rotation. Experimental results demonstrate that the proposed algorithm achieves competitive superresolution quality compared to other state-of-the-art algorithms in terms of both subjective and objective evaluations.

  13. Phenotypic similarity in sympatric crow species: Evidence of social convergence?

    Science.gov (United States)

    Laiolo, Paola

    2017-04-01

    Crows, rooks, and ravens (Corvus spp.) display marked morphological and voice similarities that have been hypothesized to stem from competitive interactions, as a case of nonaposematic mimicry. Here, I test predictions of the mimicry hypothesis at the macrovolutionary scale, examining whether species morphological and acoustic traits covary with those of coexisting congeners, and whether phenotypic similarity has facilitated the coexistence of related species after secondary contact. Body size and the temporal patterns of the commonest call display high levels of similarity among sympatric species, even after controlling for the effect of shared climate and habitat, and phylogenetic constraints in the production of variation. When sister species differed in these acoustic and morphological traits, their transition to secondary sympatry was delayed relative to those with more similar traits. No similarity was found in the sexual call of crows, suggesting that convergence occurs only when function does not favour maintenance of species-specific traits. Crow similarities in morphological and acoustic features may therefore be associated with coevolving interactions with congeners, in line with a broad array of studies documenting convergence among species that interact aggressively or forage communally. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  14. Limiting similarity of competitive species and demographic stochasticity

    Science.gov (United States)

    Zheng, Xiu-Deng; Deng, Ling-Ling; Qiang, Wei-Ya; Cressman, Ross; Tao, Yi

    2017-04-01

    The limiting similarity of competitive species and its relationship with the competitive exclusion principle is still one of the most important concepts in ecology. In the 1970s, May [R. M. May, Stability and Complexity in Model Ecosystems (Princeton University, Princeton, NJ, 1973)] developed a concise theoretical framework to investigate the limiting similarity of competitive species. His theoretical results show that no limiting similarity threshold of competitive species can be identified in the deterministic model system whereby species more similar than this threshold never coexist. Theoretically, for competitive species coexisting in an unvarying environment, deterministic interspecific interactions and demographic stochasticity can be considered two sides of a coin. To investigate how the "tension" between these two forces affects the coexistence of competing species, a simple two-species competitive system based only on May's model system is transformed into an equivalent replicator equation. The effect of demographic stochasticity on the system stability is measured by the expected drift of the Lyapunov function. Our main results show that the limiting similarity of competitive species should not be considered to be an absolute measure. Specifically, very similar competitive species should be able to coexist in an environment with a high productivity level but big differences between competitive species should be necessary in an ecosystem with a low productivity level.

  15. Polo-like kinase 1 inhibition suppresses hepatitis B virus X protein-induced transformation in an in vitro model of liver cancer progression.

    Science.gov (United States)

    Studach, Leo L; Rakotomalala, Lova; Wang, Wen-Horng; Hullinger, Ronald L; Cairo, Stefano; Buendia, Marie-Annick; Andrisani, Ourania M

    2009-08-01

    Chronic hepatitis B virus (HBV) infection is linked to development of hepatocellular carcinoma (HCC). The HBV X protein (pX) is implicated in HCC pathogenesis acting as a weak oncogene or a cofactor in hepatocarcinogenesis. pX induces DNA re-replication, DNA damage, and partial polyploidy in a poorly differentiated, immortalized hepatocyte cell line. In this study we employed sorted, pX-induced polyploid cells to investigate their growth and oncogenic transformation potential over the course of 70 cell doublings. Immediately after live cell-sorting, nearly 40% of pX-induced polyploid cells undergo apoptosis, whereas the surviving cells exhibit proliferation sensitive to p53. After 40 cell generations the pX-expressing polyploid cultures exhibit loss of p53 function and become growth factor- and anchorage-independent, indicative of oncogenic transformation. The pX-induced polyploid cultures in the course of 70 cell generations undergo progressively increasing DNA damage, propagate damaged DNA to daughter cells, and display increased expression of a cluster of proliferation genes shown to be elevated in human HCC, including HBV-HCC. One of these genes is the mitotic kinase Polo-like kinase 1 (Plk1). Oncogenic transformation is suppressed in the absence of pX expression, and significantly, by inhibition of Plk1. These results identify Plk1 as crucial in pX-mediated oncogenic transformation. Partial polyploidy induced by pX is not immediately associated with oncogenic transformation. Continued DNA damage for 40 cell generations is reproducibly associated with loss of p53 function, enhanced expression of Plk1, and oncogenic transformation. Because Plk1 expression is also elevated in HBV-HCC tumors, this in vitro cellular model simulates liver cancer progression and pathogenesis in chronic HBV patients. Inhibition of Plk1 activity suppresses pX-mediated oncogenic transformation, identifying Plk1 as a promising therapeutic target for HBV-mediated HCC.

  16. Neuromuscular fatigue following isometric contractions with similar torque time integral.

    Science.gov (United States)

    Rozand, V; Cattagni, T; Theurel, J; Martin, A; Lepers, R

    2015-01-01

    Torque time integral (TTI) is the combination of intensity and duration of a contraction. The aim of this study was to compare neuromuscular alterations following different isometric sub-maximal contractions of the knee extensor muscles but with similar TTI. Sixteen participants performed 3 sustained contractions at different intensities (25%, 50%, and 75% of Maximal Voluntary Contraction (MVC) torque) with different durations (68.5±33.4 s, 35.1±16.8 s and 24.8±12.9 s, respectively) but similar TTI value. MVC torque, maximal voluntary activation level (VAL), M-wave characteristics and potentiated doublet amplitude were assessed before and immediately after the sustained contractions. EMG activity of the vastus lateralis (VL) and -rectus femoris (RF) muscles was recorded during the sustained contractions. MVC torque reduction was similar in the 3 conditions after the exercise (-23.4±2.7%). VAL decreased significantly in a similar extent (-3.1±1.3%) after the 3 sustained contractions. Potentiated doublet amplitude was similarly reduced in the 3 conditions (-19.7±1.5%), but VL and RF M-wave amplitudes remained unchanged. EMG activity of VL and RF muscles increased in the same extent during the 3 contractions (VL: 54.5±40.4%; RF: 53.1±48.7%). These results suggest that central and peripheral alterations accounting for muscle fatigue are similar following isometric contractions with similar TTI. TTI should be considered in the exploration of muscle fatigue during sustained isometric contractions. © Georg Thieme Verlag KG Stuttgart · New York.

  17. Anti-Tumor Action, Clinical Biochemistry Profile and Phytochemical Constituents of a Pharmacologically Active Fraction of S. crispus in NMU-Induced Rat Mammary Tumour Model.

    Directory of Open Access Journals (Sweden)

    Nik Soriani Yaacob

    Full Text Available Cancer patients seek alternative remedies such as traditional medicinal plants for safe and effective treatment and help overcome the side effects of conventional therapy. Current knowledge indicates that extracts of Strobilanthes crispus of the Acanthaceae family exhibit potent anticancer properties in vitro and are non-toxic in vivo. S. crispus was also reported to be protective against chemical hepatocarcinogenesis. We previously showed that a bioactive fraction of S. crispus leaves also synergized with tamoxifen to cause apoptosis of human breast cancer cell lines without damaging non-malignant epithelial cells. The present study aimed to evaluate the antitumor effect of S. crispus dichloromethane fraction (F3 using N-methyl-N-Nitrosourea (NMU-induced rat mammary tumor model. Tumor regression was observed in 75% of the rats following 8-week oral administration of F3 with no secondary tumour formation and no signs of anemia or infection. However, no improvement in the liver and renal function profiles was observed. Major constituents of F3 were identified as lutein, 131-hydroxy-132-oxo-pheophytin a, campesterol, stigmasterol, β-sitosterol, pheophytin a and 132-hydroxy-pheophytin a. These compounds however, may not significantly contribute to the antitumor effect of F3.

  18. Protein similarity from knot theory: geometric convolution and line weavings.

    Science.gov (United States)

    Erdmann, Michael A

    2005-01-01

    Shape similarity is one of the most elusive and intriguing questions of nature and mathematics. Proteins provide a rich domain in which to test theories of shape similarity. Proteins can match at different scales and in different arrangements. Sometimes the detection of common local structure is sufficient to infer global alignment of two proteins; at other times it provides false information. Proteins with very low sequence identity may share large substructures, or perhaps just a central core. There are even examples of proteins with nearly identical primary sequences in which alpha-helices have become beta-sheets. Shape similarity can be formulated (i) in terms of global metrics, such as RMSD or Hausdorff distance, (ii) in terms of subgraph isomorphisms, such as the detection of shared substructures with similar relative locations, or (iii) purely topologically, in terms of structure preserving transformations. Existing protein structure detection programs are built on the first two types of similarity. The third forms the foundations of knot theory. The thesis of this paper is this: Protein similarity detection leads naturally to algorithms operating at the metric, relational, and isotopic scales. The paper introduces a definition of similarity based on atomic motions that preserve local backbone topology without incurring significant distance errors. Such motions are motivated by the physical requirements for rearranging subsequences of a protein. Similarity detection then seeks rigid body motions able to overlay pairs of substructures, each related by a substructure-preserving motion, without necessarily requiring global structure preservation. This definition is general enough to span a wide range of questions: One can ask for full rearrangement of one protein into another while preserving global topology, as in drug design; or one can ask for rearrangements of sets of smaller substructures, preserving local but not global topology, as in protein evolution

  19. Efficient Set Similarity Joins Using Min-prefixes

    Science.gov (United States)

    Ribeiro, Leonardo A.; Härder, Theo

    Identification of all objects in a dataset whose similarity is not less than a specified threshold is of major importance for management, search, and analysis of data. Set similarity joins are commonly used to implement this operation; they scale to large datasets and are versatile to represent a variety of similarity notions. Most set similarity join methods proposed so far present two main phases at a high level of abstraction: candidate generation producing a set of candidate pairs and verification applying the actual similarity measure to the candidates and returning the correct answer. Previous work has primarily focused on the reduction of candidates, where candidate generation presented the major effort to obtain better pruning results. Here, we propose an opposite approach. We drastically decrease the computational cost of candidate generation by dynamically reducing the number of indexed objects at the expense of increasing the workload of the verification phase. Our experimental findings show that this trade-off is advantageous: we consistently achieve substantial speed-ups as compared to previous algorithms.

  20. Distance decay of ß-similarity: spatial or ecological barriers?

    Directory of Open Access Journals (Sweden)

    Duccio Rocchini

    2008-01-01

    Full Text Available ß-diversity is defined as the complementarity in species composition between pairs of sites and plays a crucial role in biodiversity management and conservation, since it allows to detect those environmental gradients that functionally act in determining the variation of species composition. From an ecological viewpoint, the decay of ß-similarity principally arises from: (i a decrease in environmental similarity with distance, which inevitably creates a competition among species with different physiological abilities (niche difference model; (ii a spatial configuration which creates spatial barriers and thus isolation among habitats, that influences species and gene movement across landscapes. To date, efforts were made to demonstrate the effect of distance on species similarity. However, few tests have been performed at local scale, i.e. at the community level. The aim of this study is to test the distance decay of ß-similarity hypothesis at local scale (10x10 m plots considering both (i spatial distance between pairs of sites; (ii the ecological distance between pairs of sites, measured as Euclidean distance in vector spaces defined by ecological variables (elevation, aspect, slope, assolation, spectral reflectance considering both the whole multispectral system of a Landsat ETM+ image and the Near Infrared Wavelength, band 4. ß-similarity decay rates at different thresholds (t have been quantified by means of quantile regressions based on exponential models, focusing on the main factors influencing their trends.

  1. Brand name confusion: Subjective and objective measures of orthographic similarity.

    Science.gov (United States)

    Burt, Jennifer S; McFarlane, Kimberley A; Kelly, Sarah J; Humphreys, Michael S; Weatherall, Kimberlee; Burrell, Robert G

    2017-09-01

    Determining brand name similarity is vital in areas of trademark registration and brand confusion. Students rated the orthographic (spelling) similarity of word pairs (Experiments 1, 2, and 4) and brand name pairs (Experiment 5). Similarity ratings were consistently higher when words shared beginnings rather than endings, whereas shared pronunciation of the stressed vowel had small and less consistent effects on ratings. In Experiment 3 a behavioral task confirmed the similarity of shared beginnings in lexical processing. Specifically, in a task requiring participants to decide whether 2 words presented in the clear (a probe and a later target) were the same or different, a masked prime word preceding the target shortened response latencies if it shared its initial 3 letters with the target. The ratings of students for word and brand name pairs were strongly predicted by metrics of orthographic similarity from the visual word identification literature based on the number of shared letters and their relative positions. The results indicate a potential use for orthographic metrics in brand name registration and trademark law. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  2. Anonymous indexing of health conditions for a similarity measure.

    Science.gov (United States)

    Song, Insu; Marsh, Nigel V

    2012-07-01

    A health social network is an online information service which facilitates information sharing between closely related members of a community with the same or a similar health condition. Over the years, many automated recommender systems have been developed for social networking in order to help users find their communities of interest. For health social networking, the ideal source of information for measuring similarities of patients is the medical information of the patients. However, it is not desirable that such sensitive and private information be shared over the Internet. This is also true for many other security sensitive domains. A new information-sharing scheme is developed where each patient is represented as a small number of (possibly disjoint) d-words (discriminant words) and the d-words are used to measure similarities between patients without revealing sensitive personal information. The d-words are simple words like "food,'' and thus do not contain identifiable personal information. This makes our method an effective one-way hashing of patient assessments for a similarity measure. The d-words can be easily shared on the Internet to find peers who might have similar health conditions.

  3. Effects of Spatial Frequency Similarity and Dissimilarity on Contour Integration.

    Directory of Open Access Journals (Sweden)

    Malte Persike

    Full Text Available We examined the effects of spatial frequency similarity and dissimilarity on human contour integration under various conditions of uncertainty. Participants performed a temporal 2AFC contour detection task. Spatial frequency jitter up to 3.0 octaves was applied either to background elements, or to contour and background elements, or to none of both. Results converge on four major findings. (1 Contours defined by spatial frequency similarity alone are only scarcely visible, suggesting the absence of specialized cortical routines for shape detection based on spatial frequency similarity. (2 When orientation collinearity and spatial frequency similarity are combined along a contour, performance amplifies far beyond probability summation when compared to the fully heterogenous condition but only to a margin compatible with probability summation when compared to the fully homogenous case. (3 Psychometric functions are steeper but not shifted for homogenous contours in heterogenous backgrounds indicating an advantageous signal-to-noise ratio. The additional similarity cue therefore not so much improves contour detection performance but primarily reduces observer uncertainty about whether a potential candidate is a contour or just a false positive. (4 Contour integration is a broadband mechanism which is only moderately impaired by spatial frequency dissimilarity.

  4. A Quantum-Based Similarity Method in Virtual Screening

    Directory of Open Access Journals (Sweden)

    Mohammed Mumtaz Al-Dabbagh

    2015-10-01

    Full Text Available One of the most widely-used techniques for ligand-based virtual screening is similarity searching. This study adopted the concepts of quantum mechanics to present as state-of-the-art similarity method of molecules inspired from quantum theory. The representation of molecular compounds in mathematical quantum space plays a vital role in the development of quantum-based similarity approach. One of the key concepts of quantum theory is the use of complex numbers. Hence, this study proposed three various techniques to embed and to re-represent the molecular compounds to correspond with complex numbers format. The quantum-based similarity method that developed in this study depending on complex pure Hilbert space of molecules called Standard Quantum-Based (SQB. The recall of retrieved active molecules were at top 1% and top 5%, and significant test is used to evaluate our proposed methods. The MDL drug data report (MDDR, maximum unbiased validation (MUV and Directory of Useful Decoys (DUD data sets were used for experiments and were represented by 2D fingerprints. Simulated virtual screening experiment show that the effectiveness of SQB method was significantly increased due to the role of representational power of molecular compounds in complex numbers forms compared to Tanimoto benchmark similarity measure.

  5. Discovery of Human-Similar Gene Fusions in Canine Cancers.

    Science.gov (United States)

    Ulvé, Ronan; Rault, Mélanie; Bahin, Mathieu; Lagoutte, Laetitia; Abadie, Jérôme; De Brito, Clotilde; Coindre, Jean-Michel; Botherel, Nadine; Rousseau, Audrey; Wucher, Valentin; Cadieu, Edouard; Thieblemont, Catherine; Hitte, Christophe; Cornevin, Laurence; Cabillic, Florian; Bachelot, Laura; Gilot, David; Hennuy, Benoit; Guillaudeux, Thierry; Le Goff, Arnaud; Derrien, Thomas; Hédan, Benoît; André, Catherine

    2017-11-01

    Canine cancers represent a tremendous natural resource due to their incidence and striking similarities to human cancers, sharing similar clinical and pathologic features as well as oncogenic events, including identical somatic mutations. Considering the importance of gene fusions as driver alterations, we explored their relevance in canine cancers. We focused on three distinct human-comparable canine cancers representing different tissues and embryonic origins. Through RNA-Seq, we discovered similar gene fusions as those found in their human counterparts: IGK-CCND3 in B-cell lymphoma, MPB-BRAF in glioma, and COL3A1-PDGFB in dermatofibrosarcoma protuberans-like. We showed not only similar partner genes but also identical breakpoints leading to oncogene overexpression. This study demonstrates similar gene fusion partners and mechanisms in human-dog corresponding tumors and allows for selection of targeted therapies in preclinical and clinical trials with pet dogs prior to human trials, within the framework of personalized medicine. Cancer Res; 77(21); 5721-7. ©2017 AACR. ©2017 American Association for Cancer Research.

  6. A Model-Based Approach to Constructing Music Similarity Functions

    Directory of Open Access Journals (Sweden)

    Lamere Paul

    2007-01-01

    Full Text Available Several authors have presented systems that estimate the audio similarity of two pieces of music through the calculation of a distance metric, such as the Euclidean distance, between spectral features calculated from the audio, related to the timbre or pitch of the signal. These features can be augmented with other, temporally or rhythmically based features such as zero-crossing rates, beat histograms, or fluctuation patterns to form a more well-rounded music similarity function. It is our contention that perceptual or cultural labels, such as the genre, style, or emotion of the music, are also very important features in the perception of music. These labels help to define complex regions of similarity within the available feature spaces. We demonstrate a machine-learning-based approach to the construction of a similarity metric, which uses this contextual information to project the calculated features into an intermediate space where a music similarity function that incorporates some of the cultural information may be calculated.

  7. A Measure of Similarity Between Trajectories of Vessels

    Directory of Open Access Journals (Sweden)

    Le QI

    2016-03-01

    Full Text Available The measurement of similarity between trajectories of vessels is one of the kernel problems that must be addressed to promote the development of maritime intelligent traffic system (ITS. In this study, a new model of trajectory similarity measurement was established to improve the data processing efficiency in dynamic application and to reflect actual sailing behaviors of vessels. In this model, a feature point detection algorithm was proposed to extract feature points, reduce data storage space and save computational resources. A new synthesized distance algorithm was also created to measure the similarity between trajectories by using the extracted feature points. An experiment was conducted to measure the similarity between the real trajectories of vessels. The growth of these trajectories required measurements to be conducted under different voyages. The results show that the similarity measurement between the vessel trajectories is efficient and correct. Comparison of the synthesized distance with the sailing behaviors of vessels proves that results are consistent with actual situations. The experiment results demonstrate the promising application of the proposed model in studying vessel traffic and in supplying reliable data for the development of maritime ITS.

  8. Similar cellular responses after treatment with either praziquantel or ...

    African Journals Online (AJOL)

    in immuno-modulation was observed post-treatment with elevated immune reactivity and cytokine production in ..... helminthic drugs kills adult schistosomes. Praziquantel acts quickly and kills worms by inducing ... immunomodulation of their responses resulting in cellular unresponsiveness that has been reported before.

  9. Self-similar processes in collective risk theory

    Directory of Open Access Journals (Sweden)

    Zbigniew Michna

    1998-01-01

    Full Text Available Collective risk theory is concerned with random fluctuations of the total assets and the risk reserve of an insurance company. In this paper we consider self-similar, continuous processes with stationary increments for the renewal model in risk theory. We construct a risk model which shows a mechanism of long range dependence of claims. We approximate the risk process by a self similar process with drift. The ruin probability within finite time is estimated for fractional Brownian motion with drift. A similar model is applicable in queueing systems, describing long range dependence in on/off processes and associated fluid models. The obtained results are useful in communication network models, as well as storage and inventory models.

  10. Self-similarity in explosive synchronization of complex networks

    Science.gov (United States)

    Koronovskii, Alexey A.; Kurovskaya, Maria K.; Moskalenko, Olga I.; Hramov, Alexander; Boccaletti, Stefano

    2017-12-01

    We report that explosive synchronization of networked oscillators (a process through which the transition to coherence occurs without intermediate stages but is rather characterized by a sudden and abrupt jump from the network's asynchronous to synchronous motion) is related to self-similarity of synchronous clusters of different size. Self-similarity is revealed by destructing the network synchronous state during the backward transition and observed with the decrease of the coupling strength between the nodes of the network. As illustrative examples, networks of Kuramoto oscillators with different topologies of links have been considered. For each one of such topologies, the destruction of the synchronous state goes step by step with self-similar configurations of interacting oscillators. At the critical point, the invariance of the phase distribution in the synchronized cluster with respect to the cluster size is reported.

  11. Fourteen-month-old infants learn similar sounding words

    Science.gov (United States)

    Yoshida, Katherine A.; Fennell, Christopher T.; Swingley, Daniel; Werker, Janet F.

    2010-01-01

    Can infants, in the very first stages of word learning, use their perceptual sensitivity to the phonetics of speech while learning words? Research to date suggests that infants of 14 months cannot learn two similar sounding words unless there is substantial contextual support. The current experiment advances our understanding of this failure by testing whether the source of infants’ difficulty lies in the learning or testing phase. Infants were taught to associate two similar sounding words with two different objects, and tested using a visual choice method rather than the standard Switch task. The results reveal that 14-month-olds are capable of learning and mapping two similar sounding labels; they can apply phonetic detail in new words. The findings are discussed in relation to infants’ concurrent failure, and the developmental transition to success, in the Switch task. PMID:19371365

  12. Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy

    CERN Document Server

    Jiang, J J; Jiang, Jay J.; Conrath, David W.

    1997-01-01

    This paper presents a new approach for measuring semantic similarity/distance between words and concepts. It combines a lexical taxonomy structure with corpus statistical information so that the semantic distance between nodes in the semantic space constructed by the taxonomy can be better quantified with the computational evidence derived from a distributional analysis of corpus data. Specifically, the proposed measure is a combined approach that inherits the edge-based approach of the edge counting scheme, which is then enhanced by the node-based approach of the information content calculation. When tested on a common data set of word pair similarity ratings, the proposed approach outperforms other computational models. It gives the highest correlation value (r = 0.828) with a benchmark based on human similarity judgements, whereas an upper bound (r = 0.885) is observed when human subjects replicate the same task.

  13. Target similarity effects: support for the parallel distributed processing assumptions.

    Science.gov (United States)

    Humphreys, M S; Tehan, G; O'Shea, A; Bolland, S W

    2000-07-01

    Recent research has begun to provide support for the assumptions that memories are stored as a composite and are accessed in parallel (Tehan & Humphreys, 1998). New predictions derived from these assumptions and from the Chappell and Humphreys (1994) implementation of these assumptions were tested. In three experiments, subjects studied relatively short lists of words. Some of the lists contained two similar targets (thief and theft) or two dissimilar targets (thief and steal) associated with the same cue (robbery). As predicted, target similarity affected performance in cued recall but not free association. Contrary to predictions, two spaced presentations of a target did not improve performance in free association. Two additional experiments confirmed and extended this finding. Several alternative explanations for the target similarity effect, which incorporate assumptions about separate representations and sequential search, are rejected. The importance of the finding that, in at least one implicit memory paradigm, repetition does not improve performance is also discussed.

  14. Density-based retrieval from high-similarity image databases

    DEFF Research Database (Denmark)

    Hansen, Michael Edberg; Carstensen, Jens Michael

    2004-01-01

    Many image classification problems can fruitfully be thought of as image retrieval in a "high similarity image database" (HSID) characterized by being tuned towards a specific application and having a high degree of visual similarity between entries that should be distinguished. We introduce...... a method for HSID retrieval using a similarity measure based on a linear combination of Jeffreys-Matusita distances between distributions of local (pixelwise) features estimated from a set of automatically and consistently defined image regions. The weight coefficients are estimated based on optimal...... retrieval performance. Experimental results on the difficult task of visually identifying clones of fungal colonies grown in a petri dish and categorization of pelts show a high retrieval accuracy of the method when combined with standardized sample preparation and image acquisition....

  15. Application of Similarity in Fault Diagnosis of Power Electronics Circuits

    Science.gov (United States)

    Rongjie, Wang; Yiju, Zhan; Meiqian, Chen; Haifeng, Zhou; Kewei, Guo

    A method of fault diagnosis was proposed for power electronics circuits based on S transforms similarity. At first, the standard module time-frequency matrixes of S transforms for all fault signals were constructed, then the similarity of fault signals' module time-frequency matrixes to standard module time-frequency matrixes were calculated, and according to the principle of maximum similarity, the faults were diagnosed. The simulation result of fault diagnosis of a thyristor in a three-phase full-bridge controlled rectifier shows that the method can accurately diagnose faults and locate the fault element for power electronics circuits, and it has excellent performance for noise robustness and calculation complexity, thus it also has good practical engineering value in the solution to the fault problems for power electronics circuits.

  16. The Hofmethode: Computing Semantic Similarities between E-Learning Products

    Directory of Open Access Journals (Sweden)

    Oliver Michel

    2009-11-01

    Full Text Available The key task in building useful e-learning repositories is to develop a system with an algorithm allowing users to retrieve information that corresponds to their specific requirements. To achieve this, products (or their verbal descriptions, i.e. presented in metadata need to be compared and structured according to the results of this comparison. Such structuring is crucial insofar as there are many search results that correspond to the entered keyword. The Hofmethode is an algorithm (based on psychological considerations to compute semantic similarities between texts and therefore offer a way to compare e-learning products. The computed similarity values are used to build semantic maps in which the products are visually arranged according to their similarities. The paper describes how the Hofmethode is implemented in the online database edulap, and how it contributes to help the user to explore the data in which he is interested.

  17. Event Shape Sorting: selecting events with similar evolution

    Directory of Open Access Journals (Sweden)

    Tomášik Boris

    2017-01-01

    Full Text Available We present novel method for the organisation of events. The method is based on comparing event-by-event histograms of a chosen quantity Q that is measured for each particle in every event. The events are organised in such a way that those with similar shape of the Q-histograms end-up placed close to each other. We apply the method on histograms of azimuthal angle of the produced hadrons in ultrarelativsitic nuclear collisions. By selecting events with similar azimuthal shape of their hadron distribution one chooses events which are likely that they underwent similar evolution from the initial state to the freeze-out. Such events can more easily be compared to theoretical simulations where all conditions can be controlled. We illustrate the method on data simulated by the AMPT model.

  18. Autoencoding beyond pixels using a learned similarity metric

    DEFF Research Database (Denmark)

    Larsen, Anders Boesen Lindbo; Sønderby, Søren Kaae; Larochelle, Hugo

    2016-01-01

    We present an autoencoder that leverages learned representations to better measure similarities in data space. By combining a variational autoencoder (VAE) with a generative adversarial network (GAN) we can use learned feature representations in the GAN discriminator as basis for the VAE reconstr......We present an autoencoder that leverages learned representations to better measure similarities in data space. By combining a variational autoencoder (VAE) with a generative adversarial network (GAN) we can use learned feature representations in the GAN discriminator as basis for the VAE...... reconstruction objective. Thereby, we replace element-wise errors with feature-wise errors to better capture the data distribution while offering invariance towards e.g. translation. We apply our method to images of faces and show that it outperforms VAEs with element-wise similarity measures in terms of visual...

  19. Enhancing Media Personalization by Extracting Similarity Knowledge from Metadata

    DEFF Research Database (Denmark)

    Butkus, Andrius

    with many interrelated parts – recommendation engines, content metadata, contextual information and user profiles. In the center of any type of recommendation lies the notion of similarity. The most popular way to approach similarity is to look for the feature overlaps. This results often in recommending......, especially when we talk about the contents of music. Therefore the main focus in the thesis is how to extract such emotional information from media, and how to use it to enhance media personalization. This dissertation proposes a novel method to extract emotional information from text (unstructured metadata......) using Latent Semantic Analysis (one of the unsupervised machine learning techniques). It presents three separate cases to illustrate the similarity knowledge extraction from the metadata, where the emotional components in each case represents different abstraction levels – genres, synopsis and lyrics...

  20. Similarity analysis of the streamer zone of Blue Jets

    CERN Document Server

    Popov, N A; Milikh, G M

    2016-01-01

    Multiple observations of Blue Jets (BJ)) show that BJ emits a fan of streamers similar to a laboratory leader. Moreover,in the exponential atmosphere those long streamers grow preferentially upward, producing a narrow coneconfined by the aperture angle. It was also noticed that BJ are similar to the streamer zone of a leader (streamer corona) and the modeling studies based on the streamers fractal structure were conducted. Objective of this paper is to study the fractal dimension of the bunch of streamer channels emitted by BJ, at different altitude and under the varying reduced electric field. This similarity analysis has been done in three steps: First we described the dendritic structure of streamers in corona discharge applying the fractal theory. Then using this model and the data from existing laboratory experiments we obtained the fractal dimension of the branching streamer channels. Finally the model was validated by the observations of BJ available from the literature.