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Sample records for causality chemically induced

  1. Causality

    NASA Astrophysics Data System (ADS)

    Pearl, Judea

    2000-03-01

    Written by one of the pre-eminent researchers in the field, this book provides a comprehensive exposition of modern analysis of causation. It shows how causality has grown from a nebulous concept into a mathematical theory with significant applications in the fields of statistics, artificial intelligence, philosophy, cognitive science, and the health and social sciences. Pearl presents a unified account of the probabilistic, manipulative, counterfactual and structural approaches to causation, and devises simple mathematical tools for analyzing the relationships between causal connections, statistical associations, actions and observations. The book will open the way for including causal analysis in the standard curriculum of statistics, artifical intelligence, business, epidemiology, social science and economics. Students in these areas will find natural models, simple identification procedures, and precise mathematical definitions of causal concepts that traditional texts have tended to evade or make unduly complicated. This book will be of interest to professionals and students in a wide variety of fields. Anyone who wishes to elucidate meaningful relationships from data, predict effects of actions and policies, assess explanations of reported events, or form theories of causal understanding and causal speech will find this book stimulating and invaluable.

  2. Advances in forensic toxicology for establishing causality between Great Lakes epizootics and specific persistent toxic chemicals

    SciTech Connect

    Gilbertson, M.

    1997-09-01

    Populations of fish, wildlife, and humans in the Great Lakes basin have been injured during this century by exposures to organochlorine pollutants such as PCBs and dioxin. The evidence presented by scientists working on these outbreaks of chemically induced disease has been received with skepticism among officials, who have expressed a desire for a proven cause and effect before further costly regulatory and remedial action is taken. Scientists have adapted epidemiological criteria to infer causal relationships between the injury and exposures to specific chemicals. These forensic statements are different from traditional toxicological statements about potential effects. There is a priority need to institutionalize this methodology within governments to complement established risk assessment techniques.

  3. Drug and herb induced liver injury: Council for International Organizations of Medical Sciences scale for causality assessment.

    PubMed

    Teschke, Rolf; Wolff, Albrecht; Frenzel, Christian; Schwarzenboeck, Alexander; Schulze, Johannes; Eickhoff, Axel

    2014-01-27

    Causality assessment of suspected drug induced liver injury (DILI) and herb induced liver injury (HILI) is hampered by the lack of a standardized approach to be used by attending physicians and at various subsequent evaluating levels. The aim of this review was to analyze the suitability of the liver specific Council for International Organizations of Medical Sciences (CIOMS) scale as a standard tool for causality assessment in DILI and HILI cases. PubMed database was searched for the following terms: drug induced liver injury; herb induced liver injury; DILI causality assessment; and HILI causality assessment. The strength of the CIOMS lies in its potential as a standardized scale for DILI and HILI causality assessment. Other advantages include its liver specificity and its validation for hepatotoxicity with excellent sensitivity, specificity and predictive validity, based on cases with a positive reexposure test. This scale allows prospective collection of all relevant data required for a valid causality assessment. It does not require expert knowledge in hepatotoxicity and its results may subsequently be refined. Weaknesses of the CIOMS scale include the limited exclusion of alternative causes and qualitatively graded risk factors. In conclusion, CIOMS appears to be suitable as a standard scale for attending physicians, regulatory agencies, expert panels and other scientists to provide a standardized, reproducible causality assessment in suspected DILI and HILI cases, applicable primarily at all assessing levels involved.

  4. A causal role for posterior medial frontal cortex in choice-induced preference change.

    PubMed

    Izuma, Keise; Akula, Shyam; Murayama, Kou; Wu, Daw-An; Iacoboni, Marco; Adolphs, Ralph

    2015-02-25

    After a person chooses between two items, preference for the chosen item will increase and preference for the unchosen item will decrease because of the choice made. In other words, we tend to justify or rationalize our past behavior by changing our attitude. This phenomenon of choice-induced preference change has been traditionally explained by cognitive dissonance theory. Choosing something that is disliked or not choosing something that is liked are both cognitively inconsistent and, to reduce this inconsistency, people tend to change their subsequently stated preference in accordance with their past choices. Previously, human neuroimaging studies identified posterior medial frontal cortex (pMFC) as a key brain region involved in cognitive dissonance. However, it remains unknown whether the pMFC plays a causal role in inducing preference change after cognitive dissonance. Here, we demonstrate that 25 min, 1 Hz repetitive transcranial magnetic stimulation applied over the pMFC significantly reduces choice-induced preference change compared with sham stimulation or control stimulation over a different brain region, demonstrating a causal role for the pMFC.

  5. Causal Correlation Functions and Fourier Transforms: Application in Calculating Pressure Induced Shifts

    NASA Astrophysics Data System (ADS)

    Ma, Q.; Tipping, R. H.; Lavrentieva, N. N.

    2012-06-01

    By adopting a concept from signal processing, instead of starting from the correlation functions which are even, one considers the causal correlation functions whose Fourier transforms become complex. Their real and imaginary parts multiplied by 2 are the Fourier transforms of the original correlations and the subsequent Hilbert transforms, respectively. Thus, by taking this step one can complete the two previously needed transforms. However, to obviate performing the Cauchy principal integrations required in the Hilbert transforms is the greatest advantage. Meanwhile, because the causal correlations are well-bounded within the time domain and band limited in the frequency domain, one can replace their Fourier transforms by the discrete Fourier transforms and the latter can be carried out with the FFT algorithm. This replacement is justified by sampling theory because the Fourier transforms can be derived from the discrete Fourier transforms with the Nyquis rate without any distortions. We apply this method in calculating pressure induced shifts of H_2O lines and obtain more reliable values. By comparing the calculated shifts with those in HITRAN 2008 and by screening both of them with the pair identity and the smooth variation rules, one can conclude many of shift values in HITRAN are not correct. Q. Ma, R. H. Tipping, and N. N. Lavrentieva, JQSRT dio:10.1016/j.jqsrt.2012.02.012 (2012).

  6. Causal Correlation Functions and Fourier Transforms: Application in Calculating Pressure Induced Shifts

    NASA Technical Reports Server (NTRS)

    Ma, Q.; Tipping, R. H.; Lavrentieva, N. N.

    2012-01-01

    By adopting a concept from signal processing, instead of starting from the correlation functions which are even, one considers the causal correlation functions whose Fourier transforms become complex. Their real and imaginary parts multiplied by 2 are the Fourier transforms of the original correlations and the subsequent Hilbert transforms, respectively. Thus, by taking this step one can complete the two previously needed transforms. However, to obviate performing the Cauchy principal integrations required in the Hilbert transforms is the greatest advantage. Meanwhile, because the causal correlations are well-bounded within the time domain and band limited in the frequency domain, one can replace their Fourier transforms by the discrete Fourier transforms and the latter can be carried out with the FFT algorithm. This replacement is justified by sampling theory because the Fourier transforms can be derived from the discrete Fourier transforms with the Nyquis rate without any distortions. We apply this method in calculating pressure induced shifts of H2O lines and obtain more reliable values. By comparing the calculated shifts with those in HITRAN 2008 and by screening both of them with the pair identity and the smooth variation rules, one can conclude many of shift values in HITRAN are not correct.

  7. Antibiotic-induced liver toxicity: mechanisms, clinical features and causality assessment.

    PubMed

    Robles, Mercedes; Toscano, Elena; Cotta, Judith; Lucena, Maria Isabel; Andrade, Raúl J

    2010-07-01

    Antibiotics are the therapeutic agents most often associated with hepatotoxicity. However, this is mainly due to the widespread prescription of these drugs. The relative risk of antibiotic-related hepatotoxicity is low. Causality assessment of suspected drug-induced liver injury (DILI) related to antibiotics can be difficult, particularly because some cases occur long after the drug has been stopped. Among the penicillins, amoxicillin clavulanate is the most associated with hepatotoxicity and is the most frequent cause of DILI-related hospitalisations. Flucloxacillin ranks as the second highest cause of DILI in many countries. The severity of antibiotic-induced DILI varies widely, with the hepatitis-like (hepatocellular) damage tending to be more severe that than cholestatic/mixed type. The pattern is strongly influenced by age. Recently telithromycin (a new generation macrolide) has been linked with DILI, with a typical pattern, which includes abrupt commencement of fever, abdominal pain, jaundice and, in some cases, ascites. Antibiotic-induced DILI appears, in most instances, to be idiosyncratic. Genetic-association studies have recently identified genotypes related to flucloxacillin and possibly to amoxicillin-clavulanate hepatotoxicity.

  8. Bimatoprost-induced chemical blepharoplasty.

    PubMed

    Sarnoff, Deborah S; Gotkin, Robert H

    2015-05-01

    We report significant changes in the appearance of the periorbital area, beyond eyelash enhancement, induced by the topical application of bimatoprost ophthalmic solution, 0.03% (Latisse®, Allergan, Inc., Irvine, CA). To our knowledge, this is the first report in the dermatology or plastic surgery literature describing the rejuvenating effect and overall improvement in the appearance of the periorbital area resulting from applying Latisse to the upper eyelid margins. To date, reports in the literature discuss side-effects and potential complications of topical bimatoprost therapy causing a constellation of findings known as PAP (prostaglandin-associated periorbitopathy). While periorbitopathy implies pathology or a state of disease, we report changes that can be perceived as an improvement in the overall appearance of the periorbital area. We, therefore, propose a name change from PAP to PAPS - prostaglandin- associated periorbital syndrome. This better describes the beneficial, as well as the possible negative effects of topical bimatoprost. Although there is a risk for periorbital disfigurement, when used bilaterally, in properly selected candidates and titrated appropriately, bimatoprost can be beneficial. The striking improvement in the appearance of some individuals warrants further research into the potential use of topical bimatoprost to achieve a "chemical blepharoplasty."

  9. Time causal operational estimation of electric fields induced in the Earth's lithosphere during magnetic storms

    NASA Astrophysics Data System (ADS)

    Love, Jeffrey J.; Swidinsky, Andrei

    2014-04-01

    In support of projects for monitoring geomagnetic hazards for electric power grids, we develop a simple mathematical formalism, consistent with the time causality of deterministic physics, for estimating electric fields that are induced in the Earth's lithosphere during magnetic storms. For an idealized model of the lithosphere, an infinite half-space having uniform electrical conductivity properties described by a galvanic tensor, we work in the Laplace-transformed frequency domain to obtain a transfer function which, when convolved with measured magnetic field time series, gives an estimated electric field time series. Using data collected at the Kakioka, Japan observatory, we optimize lithospheric conductivity parameters by minimizing the discrepancy between model-estimated electric field variation and that actually measured. With our simple model, we can estimate 87% of the variance in storm time Kakioka electric field data; a more complicated model of lithospheric conductivity would be required to estimate the remaining 13% of the variance. We discuss how our estimation formalism might be implemented for geographically coordinated real-time monitoring of geoelectric fields.

  10. A new method for identifying causal genes of schizophrenia and anti-tuberculosis drug-induced hepatotoxicity

    PubMed Central

    Huang, Tao; Liu, Cheng-Lin; Li, Lin-Lin; Cai, Mei-Hong; Chen, Wen-Zhong; Xu, Yi-Feng; O’Reilly, Paul F.; Cai, Lei; He, Lin

    2016-01-01

    Schizophrenia (SCZ) may cause tuberculosis, the treatments for which can induce anti-tuberculosis drug-induced hepatotoxicity (ATDH) and SCZ-like disorders. To date, the causal genes of both SCZ and ATDH are unknown. To identify them, we proposed a new network-based method by integrating network random walk with restart algorithm, gene set enrichment analysis, and hypergeometric test; using this method, we identified 500 common causal genes. For gene validation, we created a regularly updated online database ATDH-SCZgenes and conducted a systematic meta-analysis of the association of each gene with either disease. Till now, only GSTM1 and GSTT1 have been well studied with respect to both diseases; and a total of 23 high-quality association studies were collected for the current meta-analysis validation. Finally, the GSTM1 present genotype was confirmed to be significantly associated with both ATDH [Odds Ratio (OR): 0.71, 95% confidence interval (CI): 0.56–0.90, P = 0.005] and SCZ (OR: 0.78, 95% CI: 0.66–0.92, P = 0.004) according to the random-effect model. Furthermore, these significant results were supported by “moderate” evidence according to the Venice criteria. Our findings indicate that GSTM1 may be a causal gene of both ATDH and SCZ, although further validation pertaining to other genes, such as CYP2E1 or DRD2, is necessary. PMID:27580934

  11. A new method for identifying causal genes of schizophrenia and anti-tuberculosis drug-induced hepatotoxicity.

    PubMed

    Huang, Tao; Liu, Cheng-Lin; Li, Lin-Lin; Cai, Mei-Hong; Chen, Wen-Zhong; Xu, Yi-Feng; O'Reilly, Paul F; Cai, Lei; He, Lin

    2016-01-01

    Schizophrenia (SCZ) may cause tuberculosis, the treatments for which can induce anti-tuberculosis drug-induced hepatotoxicity (ATDH) and SCZ-like disorders. To date, the causal genes of both SCZ and ATDH are unknown. To identify them, we proposed a new network-based method by integrating network random walk with restart algorithm, gene set enrichment analysis, and hypergeometric test; using this method, we identified 500 common causal genes. For gene validation, we created a regularly updated online database ATDH-SCZgenes and conducted a systematic meta-analysis of the association of each gene with either disease. Till now, only GSTM1 and GSTT1 have been well studied with respect to both diseases; and a total of 23 high-quality association studies were collected for the current meta-analysis validation. Finally, the GSTM1 present genotype was confirmed to be significantly associated with both ATDH [Odds Ratio (OR): 0.71, 95% confidence interval (CI): 0.56-0.90, P = 0.005] and SCZ (OR: 0.78, 95% CI: 0.66-0.92, P = 0.004) according to the random-effect model. Furthermore, these significant results were supported by "moderate" evidence according to the Venice criteria. Our findings indicate that GSTM1 may be a causal gene of both ATDH and SCZ, although further validation pertaining to other genes, such as CYP2E1 or DRD2, is necessary. PMID:27580934

  12. Causal and causally separable processes

    NASA Astrophysics Data System (ADS)

    Oreshkov, Ognyan; Giarmatzi, Christina

    2016-09-01

    The idea that events are equipped with a partial causal order is central to our understanding of physics in the tested regimes: given two pointlike events A and B, either A is in the causal past of B, B is in the causal past of A, or A and B are space-like separated. Operationally, the meaning of these order relations corresponds to constraints on the possible correlations between experiments performed in the vicinities of the respective events: if A is in the causal past of B, an experimenter at A could signal to an experimenter at B but not the other way around, while if A and B are space-like separated, no signaling is possible in either direction. In the context of a concrete physical theory, the correlations compatible with a given causal configuration may obey further constraints. For instance, space-like correlations in quantum mechanics arise from local measurements on joint quantum states, while time-like correlations are established via quantum channels. Similarly to other variables, however, the causal order of a set of events could be random, and little is understood about the constraints that causality implies in this case. A main difficulty concerns the fact that the order of events can now generally depend on the operations performed at the locations of these events, since, for instance, an operation at A could influence the order in which B and C occur in A’s future. So far, no formal theory of causality compatible with such dynamical causal order has been developed. Apart from being of fundamental interest in the context of inferring causal relations, such a theory is imperative for understanding recent suggestions that the causal order of events in quantum mechanics can be indefinite. Here, we develop such a theory in the general multipartite case. Starting from a background-independent definition of causality, we derive an iteratively formulated canonical decomposition of multipartite causal correlations. For a fixed number of settings and

  13. Laser Induced Chemical Liquid Phase Deposition (LCLD)

    SciTech Connect

    Nanai, Laszlo; Balint, Agneta M.

    2012-08-17

    Laser induced chemical deposition (LCLD) of metals onto different substrates attracts growing attention during the last decade. Deposition of metals onto the surface of dielectrics and semiconductors with help of laser beam allows the creation of conducting metal of very complex architecture even in 3D. In the processes examined the deposition occurs from solutions containing metal ions and reducing agents. The deposition happens in the region of surface irradiated by laser beam (micro reactors). Physics -chemical reactions driven by laser beam will be discussed for different metal-substrate systems. The electrical, optical, mechanical properties of created interfaces will be demonstrated also including some practical-industrial applications.

  14. Study of chemical and radiation induced carcinogenesis

    SciTech Connect

    Chmura, A.

    1995-11-01

    The study of chemical and radiation induced carcinogenesis has up to now based many of its results on the detection of genetic aberrations using the fluorescent in situ hybridization (FISH) technique. FISH is time consuming and this tends to hinder its use for looking at large numbers of samples. We are currently developing new technological advances which will increase the speed, clarity and functionality of the FISH technique. These advances include multi-labeled probes, amplification techniques, and separation techniques.

  15. Epidemiological causality.

    PubMed

    Morabia, Alfredo

    2005-01-01

    Epidemiological methods, which combine population thinking and group comparisons, can primarily identify causes of disease in populations. There is therefore a tension between our intuitive notion of a cause, which we want to be deterministic and invariant at the individual level, and the epidemiological notion of causes, which are invariant only at the population level. Epidemiologists have given heretofore a pragmatic solution to this tension. Causal inference in epidemiology consists in checking the logical coherence of a causality statement and determining whether what has been found grossly contradicts what we think we already know: how strong is the association? Is there a dose-response relationship? Does the cause precede the effect? Is the effect biologically plausible? Etc. This approach to causal inference can be traced back to the English philosophers David Hume and John Stuart Mill. On the other hand, the mode of establishing causality, devised by Jakob Henle and Robert Koch, which has been fruitful in bacteriology, requires that in every instance the effect invariably follows the cause (e.g., inoculation of Koch bacillus and tuberculosis). This is incompatible with epidemiological causality which has to deal with probabilistic effects (e.g., smoking and lung cancer), and is therefore invariant only for the population.

  16. Does methylmercury-induced hypercholesterolemia play a causal role in its neurotoxicity and cardiovascular disease?

    PubMed

    Moreira, Eduardo Luiz; de Oliveira, Jade; Dutra, Márcio Ferreira; Santos, Danúbia Bonfanti; Gonçalves, Carlos Alberto; Goldfeder, Eliane Maria; de Bem, Andreza Fabro; Prediger, Rui Daniel; Aschner, Michael; Farina, Marcelo

    2012-12-01

    Methylmercury (MeHg) is an environmental pollutant that biomagnifies throughout the aquatic food chain, thus representing a toxicological concern for humans subsiding on fish for their dietary intake. Although the developing brain is considered the critical target organ of MeHg toxicity, recent evidence indicates that the cardiovascular system may be the most sensitive in adults. However, data on the mechanisms mediating MeHg-induced cardiovascular toxicity are scarce. Based on the close relationship between cardiovascular disease and dyslipidemia, this study was designed to investigate the effects of long-term MeHg exposure on plasma lipid levels in mice, as well as their underlying mechanisms and potential relationships to MeHg-induced neurotoxicity. Our major finding was that long-term MeHg exposure induced dyslipidemia in rodents. Specifically, Swiss and C57BL/6 mice treated for 21 days with a drinking solution of MeHg (40 mg/l, ad libitum) diluted in tap water showed increased total and non-HDL plasma cholesterol levels. MeHg-induced hypercholesterolemia was also observed in low-density lipoprotein receptor knockout (LDLr⁻/⁻) mice, indicating that this effect was not related to decreased LDLr-mediated cholesterol transport from blood to other tissues. Although the hepatic synthesis of cholesterol was unchanged, significant signs of nephrotoxicity (glomerular shrinkage, tubular vacuolization, and changed urea levels) were observed in MeHg-exposed mice, indicating that the involvement of nephropathy in MeHg-induced lipid dyshomeostasis may not be ruled out. Notably, Probucol (a lipid-lowering drug) prevented the development of hypercholesterolemia when coadministered with MeHg. Finally, hypercholesterolemic LDLr⁻/⁻ mice were more susceptible to MeHg-induced cerebellar glial activation, suggesting that hypercholesterolemia in itself may pose a risk factor in MeHg-induced neurotoxicity. Overall, based on the strong and graded positive association between

  17. Is contrast medium osmolality a causal factor for contrast-induced nephropathy?

    PubMed

    Bucher, Andreas M; De Cecco, Carlo N; Schoepf, U Joseph; Meinel, Felix G; Krazinski, Aleksander W; Spearman, James V; McQuiston, Andrew D; Wang, Rui; Bucher, Judith; Vogl, Thomas J; Katzberg, Richard W

    2014-01-01

    The exact pathophysiology of contrast-induced nephropathy (CIN) is not fully clarified, yet the osmotic characteristics of contrast media (CM) have been a significant focus in many investigations of CIN. Osmotic effects of CM specific to the kidney include transient decreases in blood flow, filtration fraction, and glomerular filtration rate. Potentially significant secondary effects include an osmotically induced diuresis with a concomitant dehydrating effect. Clinical experiences that have compared the occurrence of CIN between the various classes of CM based on osmolality have suggested a much less than anticipated advantage, if any, with a lower osmolality. Recent animal experiments actually suggest that induction of a mild osmotic diuresis in association with iso-osmolar agents tends to offset potentially deleterious renal effects of high viscosity-mediated intratubular CM stagnation.

  18. Evidence chain-based causality identification in herb-induced liver injury: exemplification of a well-known liver-restorative herb Polygonum multiflorum.

    PubMed

    Wang, Jiabo; Ma, Zhijie; Niu, Ming; Zhu, Yun; Liang, Qingsheng; Zhao, Yanling; Song, Jingyuan; Bai, Zhaofang; Zhang, Yaming; Zhang, Ping; Li, Na; Meng, Yakun; Li, Qi; Qin, Lushan; Teng, Guangju; Cao, Junling; Li, Baosen; Chen, Shilin; Li, Yonggang; Zou, Zhengsheng; Zhou, Honghao; Xiao, Xiaohe

    2015-12-01

    Herbal medicines have recently been recognized as the second most common cause of drug-induced liver injury (DILI) in the United States. However, reliable methods to identify the DILI causality of some herbs, such as Heshouwu (dried root of Polygonum multiflorum), remain lacking. In this study, a total of 12 307 inpatients with liver dysfunction and 147 literature-reported cases of Heshouwu DILI were screened. A general algorithm indicated that only 22.5% (9/40) and 30.6% (45/147) of all hospitalization and literature case reports, respectively, demonstrate the high probability of DILI causality of Heshouwu. By contrast, 95% (19/20) of all cases prospectively investigated by pharmacognosy, phytochemistry, and metabolomic tests exhibited highly probable causality, including a patient who was previously incorrectly attributed and a case that was excluded from Heshouwu causality by pharmacognostic evidence. Toxin (heavy metals, pesticides, and mycotoxins) contamination was also excluded from Heshouwu DILI causality. The objectivity of these screening methods for Heshouwu DILI diagnosis addresses safety concerns regarding stilbene-containing herbal medicines and dietary supplements.

  19. Evidence chain-based causality identification in herb-induced liver injury: exemplification of a well-known liver-restorative herb Polygonum multiflorum.

    PubMed

    Wang, Jiabo; Ma, Zhijie; Niu, Ming; Zhu, Yun; Liang, Qingsheng; Zhao, Yanling; Song, Jingyuan; Bai, Zhaofang; Zhang, Yaming; Zhang, Ping; Li, Na; Meng, Yakun; Li, Qi; Qin, Lushan; Teng, Guangju; Cao, Junling; Li, Baosen; Chen, Shilin; Li, Yonggang; Zou, Zhengsheng; Zhou, Honghao; Xiao, Xiaohe

    2015-12-01

    Herbal medicines have recently been recognized as the second most common cause of drug-induced liver injury (DILI) in the United States. However, reliable methods to identify the DILI causality of some herbs, such as Heshouwu (dried root of Polygonum multiflorum), remain lacking. In this study, a total of 12 307 inpatients with liver dysfunction and 147 literature-reported cases of Heshouwu DILI were screened. A general algorithm indicated that only 22.5% (9/40) and 30.6% (45/147) of all hospitalization and literature case reports, respectively, demonstrate the high probability of DILI causality of Heshouwu. By contrast, 95% (19/20) of all cases prospectively investigated by pharmacognosy, phytochemistry, and metabolomic tests exhibited highly probable causality, including a patient who was previously incorrectly attributed and a case that was excluded from Heshouwu causality by pharmacognostic evidence. Toxin (heavy metals, pesticides, and mycotoxins) contamination was also excluded from Heshouwu DILI causality. The objectivity of these screening methods for Heshouwu DILI diagnosis addresses safety concerns regarding stilbene-containing herbal medicines and dietary supplements. PMID:26459430

  20. Theory-Based Causal Induction

    ERIC Educational Resources Information Center

    Griffiths, Thomas L.; Tenenbaum, Joshua B.

    2009-01-01

    Inducing causal relationships from observations is a classic problem in scientific inference, statistics, and machine learning. It is also a central part of human learning, and a task that people perform remarkably well given its notorious difficulties. People can learn causal structure in various settings, from diverse forms of data: observations…

  1. Oralair(®): a causal treatment for grass pollen-induced allergic rhinoconjunctivitis.

    PubMed

    Köberlein, Juliane; Mösges, Ralph

    2013-01-01

    Grass pollen-induced allergic rhinoconjunctivitis is a common disease, comprising more than just the classic symptoms of nasal obstruction, sneezing, rhinorrhea and itchy, watery eyes. Sufferers deal with severe impairments in daily life. Allergic rhinoconjunctivitis is also considered an important risk factor in the development of asthma. Allergen avoidance, medication for symptomatic treatment and allergen-specific immunotherapy are cornerstones in therapeutic management, but immunotherapy is the only available treatment that is able to affect the natural course of allergy. In recent decades, clinical trials have investigated the efficacy and safety of subcutaneous immunotherapy. To date, efforts have been made to develop more convenient routes of administration. Substantial improvement may be achieved through the application of sublingual tablets. This article discusses the development process of immunotherapy and the clinical background of the Oralair(®) (Stallergènes, Hauts-de-Seine, France) five-grass pollen tablet. Furthermore, it outlines this tablet's efficacy and safety properties. PMID:23256794

  2. Drug-Induced Liver Injury Network Causality Assessment: Criteria and Experience in the United States

    PubMed Central

    Hayashi, Paul H.

    2016-01-01

    Hepatotoxicity due to drugs, herbal or dietary supplements remains largely a clinical diagnosis based on meticulous history taking and exclusion of other causes of liver injury. In 2004, the U.S. Drug-Induced Liver Injury Network (DILIN) was created under the auspices of the U.S. National Institute of Diabetes and Digestive and Kidney Diseases with the aims of establishing a large registry of cases for clinical, epidemiological and mechanistic study. From inception, the DILIN has used an expert opinion process that incorporates consensus amongst three different DILIN hepatologists assigned to each case. It is the most well-established, well-described and vigorous expert opinion process for DILI to date, and yet it is an imperfect standard. This review will discuss the DILIN expert opinion process, its strengths and weaknesses, psychometric performance and future. PMID:26861284

  3. Sativex-induced neurobehavioral effects: causal or concausal? A practical advice!

    PubMed

    Russo, Margherita; Rifici, Carmela; Sessa, Edoardo; D'Aleo, Giangaetano; Bramanti, Placido; Calabrò, Rocco Salvatore

    2015-01-01

    Nabiximols (Sativex) is an oromucosal spray, containing delta-9 tetrahydrocannabinol (THC) and cannabidiol (CBD), used as treatment for unresponsive spasticity in multiple sclerosis (MS) patients. Sativex is thought to not affect cognition or induce any psychiatric problem at the doses generally used. Nonetheless, it is known that the concomitant use of more than one muscle-relaxant drugs can result in additive neuropsychiatric effects. Herein we describe a case of a woman affected by MS and treated with baclofen and methylprednisolone, who developed important behavioral changes, including suicidal ideation, after 4 weeks of Sativex administration. We are not completely able to state if Sativex alone was responsible for our patient's psychiatric symptoms, in reason of the concomitant use of the other drugs.In conclusion, physicians should pay more attention when prescribing drugs to MS patients affected by spasticity, including Sativex, since neurobehavioral side effects may emerge especially in predisposed individuals. PMID:25881038

  4. Causality between expansion of seismic cloud and maximum magnitude of induced seismicity in geothermal field

    NASA Astrophysics Data System (ADS)

    Mukuhira, Yusuke; Asanuma, Hiroshi; Ito, Takatoshi; Häring, Markus

    2016-04-01

    Occurrence of induced seismicity with large magnitude is critical environmental issues associated with fluid injection for shale gas/oil extraction, waste water disposal, carbon capture and storage, and engineered geothermal systems (EGS). Studies for prediction of the hazardous seismicity and risk assessment of induced seismicity has been activated recently. Many of these studies are based on the seismological statistics and these models use the information of the occurrence time and event magnitude. We have originally developed physics based model named "possible seismic moment model" to evaluate seismic activity and assess seismic moment which can be ready to release. This model is totally based on microseismic information of occurrence time, hypocenter location and magnitude (seismic moment). This model assumes existence of representative parameter having physical meaning that release-able seismic moment per rock volume (seismic moment density) at given field. Seismic moment density is to be estimated from microseismic distribution and their seismic moment. In addition to this, stimulated rock volume is also inferred by progress of microseismic cloud at given time and this quantity can be interpreted as the rock volume which can release seismic energy due to weakening effect of normal stress by injected fluid. Product of these two parameters (equation (1)) provide possible seismic moment which can be released from current stimulated zone as a model output. Difference between output of this model and observed cumulative seismic moment corresponds the seismic moment which will be released in future, based on current stimulation conditions. This value can be translated into possible maximum magnitude of induced seismicity in future. As this way, possible seismic moment can be used to have feedback to hydraulic stimulation operation in real time as an index which can be interpreted easily and intuitively. Possible seismic moment is defined as equation (1), where D

  5. Particle-induced pulmonary acute phase response may be the causal link between particle inhalation and cardiovascular disease

    PubMed Central

    Saber, Anne T; Jacobsen, Nicklas R; Jackson, Petra; Poulsen, Sarah Søs; Kyjovska, Zdenka O; Halappanavar, Sabina; Yauk, Carole L; Wallin, Håkan; Vogel, Ulla

    2014-01-01

    Inhalation of ambient and workplace particulate air pollution is associated with increased risk of cardiovascular disease. One proposed mechanism for this association is that pulmonary inflammation induces a hepatic acute phase response, which increases risk of cardiovascular disease. Induction of the acute phase response is intimately linked to risk of cardiovascular disease as shown in both epidemiological and animal studies. Indeed, blood levels of acute phase proteins, such as C-reactive protein and serum amyloid A, are independent predictors of risk of cardiovascular disease in prospective epidemiological studies. In this review, we present and review emerging evidence that inhalation of particles (e.g., air diesel exhaust particles and nanoparticles) induces a pulmonary acute phase response, and propose that this induction constitutes the causal link between particle inhalation and risk of cardiovascular disease. Increased levels of acute phase mRNA and proteins in lung tissues, bronchoalveolar lavage fluid and plasma clearly indicate pulmonary acute phase response following pulmonary deposition of different kinds of particles including diesel exhaust particles, nanoparticles, and carbon nanotubes. The pulmonary acute phase response is dose-dependent and long lasting. Conversely, the hepatic acute phase response is reduced relative to lung or entirely absent. We also provide evidence that pulmonary inflammation, as measured by neutrophil influx, is a predictor of the acute phase response and that the total surface area of deposited particles correlates with the pulmonary acute phase response. We discuss the implications of these findings in relation to occupational exposure to nanoparticles. How to cite this article: WIREs Nanomed Nanobiotechnol 2014, 6:517–531. doi: 10.1002/wnan.1279 PMID:24920450

  6. Chemically induced compaction bands in geomaterials

    NASA Astrophysics Data System (ADS)

    Stefanou, Ioannis; Sulem, Jean

    2013-04-01

    Compaction bands play an important role in oil production and may provide useful information on various geological processes. Various mechanisms can be involved at different scales: the micro scale (e.g. the grain scale), the meso scale (e.g. the Representative Element Volume) and the macro scale (e.g. the structure). Moreover, hydro-chemo-mechanical couplings might play an important role in triggering instabilities in the form of compaction bands. Compaction bands can be seen as an instability of the underneath mathematical problem leading to localization of deformation [1,2,3]. Here we explore the conditions of compaction banding in quartz-based geomaterials by considering the effect of chemical dissolution and precipitation [4,5]. In due course of the loading process grain crushing affects the residual strength, the porosity and the permeability of the material. Moreover, at the micro-level, grain crushing results in an increase of the grain specific surface, which accelerates the dissolution [6]. Consequently, the silica is removed more rapidly from the grain skeleton and the overall mechanical properties are degraded due to chemical factors. The proposed model accounts for these phenomena. In particular, the diffusion of the diluted in the water silica is considered through the mass balance equation of the porous medium. The reduction of the mechanical strength of the material is described through a macroscopic failure criterion with chemical softening. The grain size reduction is related to the total energy input [7]. A grain size and porosity dependent permeability law is adopted. These degradation mechanisms are coupled with the dissolution/precipitation reaction kinetics. The obtained hydro-chemo-mechanical model is used to investigate the conditions, the material parameters and the chemical factors inducing compaction bands formation. References [1] J.W. Rudnicki, and J.R. Rice. "Conditions for the Localization of Deformation in Pressure

  7. AOP: An R Package For Sufficient Causal Analysis in Pathway-based Screening of Drugs and Chemicals for Adversity

    EPA Science Inventory

    Summary: How can I quickly find the key events in a pathway that I need to monitor to predict that a/an beneficial/adverse event/outcome will occur? This is a key question when using signaling pathways for drug/chemical screening in pharma-cology, toxicology and risk assessment. ...

  8. Causality in epidemiology.

    PubMed

    Kamangar, Farin

    2012-10-01

    This article provides an introduction to the meaning of causality in epidemiology and methods that epidemiologists use to distinguish causal associations from non-causal ones. Alternatives to causal association are discussed in detail. Hill's guidelines, set forth approximately 50 years ago, and more recent developments are reviewed. The role of religious and philosophic views in our understanding of causality is briefly discussed.

  9. Chemically induced intestinal damage models in zebrafish larvae.

    PubMed

    Oehlers, Stefan H; Flores, Maria Vega; Hall, Christopher J; Okuda, Kazuhide S; Sison, John Oliver; Crosier, Kathryn E; Crosier, Philip S

    2013-06-01

    Several intestinal damage models have been developed using zebrafish, with the aim of recapitulating aspects of human inflammatory bowel disease (IBD). These experimentally induced inflammation models have utilized immersion exposure to an array of colitogenic agents (including live bacteria, bacterial products, and chemicals) to induce varying severity of inflammation. This technical report describes methods used to generate two chemically induced intestinal damage models using either dextran sodium sulfate (DSS) or trinitrobenzene sulfonic acid (TNBS). Methods to monitor intestinal damage and inflammatory processes, and chemical-genetic methods to manipulate the host response to injury are also described.

  10. Chemical inducers of systemic immunity in plants.

    PubMed

    Gao, Qing-Ming; Kachroo, Aardra; Kachroo, Pradeep

    2014-04-01

    Systemic acquired resistance (SAR) is a highly desirable form of resistance that protects against a broad-spectrum of related or unrelated pathogens. SAR involves the generation of multiple signals at the site of primary infection, which arms distal portions against subsequent secondary infections. The last decade has witnessed considerable progress, and a number of chemical signals contributing to SAR have been isolated and characterized. The diverse chemical nature of these chemicals had led to the growing belief that SAR might involve interplay of multiple diverse and independent signals. However, recent results suggest that coordinated signalling from diverse signalling components facilitates SAR in plants. This review mainly discusses organized signalling by two such chemicals, glycerol-3-phoshphate and azelaic acid, and the role of basal salicylic acid levels in G3P-conferred SAR.

  11. Mechanisms of chemical-induced porphyrinopathies

    SciTech Connect

    Silbergeld, E.K. Fowler, B.A.

    1987-01-01

    This book contains 45 selections. Some of the titles are: Genetic Regulation of the Heme Pathway; Porphyrins in Urine as an Indication of Exposure to Chlorinated Hydrocarbons; Mechanisms of PCB-induced Porphyria and Yusho Disease; and Lead-Induced Abnormalities of Porphyrin Metabolism: The Relationship with Iron Deficiency.

  12. Circular causality.

    PubMed

    Thomas, R

    2006-07-01

    The problem of disentangling complex dynamic systems is addressed, especially with a view to identifying those variables that take part in the essential qualitative behaviour of systems. The author presents a series of reflections about the methods of formalisation together with the principles that govern the global operation of systems. In particular, a section on circuits, nuclei, and circular causality and a rather detailed description of the analytic use of the generalised asynchronous logical description, together with a brief description of its synthetic use (OreverseO logic). Some basic rules are recalled, such as the fact that a positive circuit is a necessary condition of multistationarity. Also, the interest of considering as a model, rather than a well-defined set of differential equations, a variety of systems that differ from each other only by the values of constant terms is emphasised. All these systems have a common Jacobian matrix and for all of them phase space has exactly the same structure. It means that all can be partitioned in the same way as regards the signs of the eigenvalues and thus as regards the precise nature of any steady states that might be present. Which steady states are actually present, depends on the values of terms of order zero in the ordinary differential equations (ODEs), and it is easy to find for which values of these terms a given point in phase space is steady. Models can be synthesised first at the level of the circuits involved in the Jacobian matrix (that determines which types and numbers of steady states are consistent with the model), then only at the level of terms of order zero in the ODE's (that determines which of the steady states actually exist), hence the title 'Circular casuality'.

  13. Quantum causal modelling

    NASA Astrophysics Data System (ADS)

    Costa, Fabio; Shrapnel, Sally

    2016-06-01

    Causal modelling provides a powerful set of tools for identifying causal structure from observed correlations. It is well known that such techniques fail for quantum systems, unless one introduces ‘spooky’ hidden mechanisms. Whether one can produce a genuinely quantum framework in order to discover causal structure remains an open question. Here we introduce a new framework for quantum causal modelling that allows for the discovery of causal structure. We define quantum analogues for core features of classical causal modelling techniques, including the causal Markov condition and faithfulness. Based on the process matrix formalism, this framework naturally extends to generalised structures with indefinite causal order.

  14. Causal reasoning with forces

    PubMed Central

    Wolff, Phillip; Barbey, Aron K.

    2015-01-01

    Causal composition allows people to generate new causal relations by combining existing causal knowledge. We introduce a new computational model of such reasoning, the force theory, which holds that people compose causal relations by simulating the processes that join forces in the world, and compare this theory with the mental model theory (Khemlani et al., 2014) and the causal model theory (Sloman et al., 2009), which explain causal composition on the basis of mental models and structural equations, respectively. In one experiment, the force theory was uniquely able to account for people's ability to compose causal relationships from complex animations of real-world events. In three additional experiments, the force theory did as well as or better than the other two theories in explaining the causal compositions people generated from linguistically presented causal relations. Implications for causal learning and the hierarchical structure of causal knowledge are discussed. PMID:25653611

  15. Causally nonseparable processes admitting a causal model

    NASA Astrophysics Data System (ADS)

    Feix, Adrien; Araújo, Mateus; Brukner, Časlav

    2016-08-01

    A recent framework of quantum theory with no global causal order predicts the existence of ‘causally nonseparable’ processes. Some of these processes produce correlations incompatible with any causal order (they violate so-called ‘causal inequalities’ analogous to Bell inequalities) while others do not (they admit a ‘causal model’ analogous to a local model). Here we show for the first time that bipartite causally nonseparable processes with a causal model exist, and give evidence that they have no clear physical interpretation. We also provide an algorithm to generate processes of this kind and show that they have nonzero measure in the set of all processes. We demonstrate the existence of processes which stop violating causal inequalities but are still causally nonseparable when mixed with a certain amount of ‘white noise’. This is reminiscent of the behavior of Werner states in the context of entanglement and nonlocality. Finally, we provide numerical evidence for the existence of causally nonseparable processes which have a causal model even when extended with an entangled state shared among the parties.

  16. Simulating Chemical-Induced Injury Using Virtual Hepatic Tissues

    EPA Science Inventory

    Chemical-induced liver injury involves a dynamic sequence of events that span multiple levels of biological organization. Current methods for testing the toxicity of a single chemical can cost millions of dollars, take up to two years and sacrifice thousands of animals. It is dif...

  17. Cryogenic electron beam induced chemical etching.

    PubMed

    Martin, Aiden A; Toth, Milos

    2014-11-12

    Cryogenic cooling is used to enable efficient, gas-mediated electron beam induced etching (EBIE) in cases where the etch rate is negligible at room and elevated substrate temperatures. The process is demonstrated using nitrogen trifluoride (NF3) as the etch precursor, and Si, SiO2, SiC, and Si3N4 as the materials volatilized by an electron beam. Cryogenic cooling broadens the range of precursors that can be used for EBIE, and enables high-resolution, deterministic etching of materials that are volatilized spontaneously by conventional etch precursors as demonstrated here by NF3 and XeF2 EBIE of silicon. PMID:25333843

  18. Chemically Induced Surface Evolutions with Level Sets

    2006-11-17

    ChISELS is used for the theoretical modeling of detailed surface chemistry and consomitant surface evolutions occurring during microsystem fabrication processes conducted at low pressures. Examples include physical vapor deposition (PVD), low pressure chemical vapor deposition (PECVD), and plasma etching. Evolving interfaces are represented using the level-set method and the evolution equations time integrated using a Semi-Lagrangian approach. A Ballistic transport model is employed to solve for the fluxes incident on each of the surface elements.more » Surface chemistry leading to etching or deposition is computed by either coupling to Surface Chemkin (a commercially available code) or by providing user defined subroutines. The computational meshes used are quad-trees (2-D) and oct-trees (3-D), constructed such that grid refinement is localized to regions near the surface interfaces. As the interface evolves, the mesh is dynamically reconstructed as needed for the grid to remain fine only around the interface. For parallel computation, a domain decomposition scheme with dynamic load balancing is used to distribute the computational work across processors.« less

  19. Chemical Detection Based on Adsorption-Induced and Photo-Induced Stresses in MEMS Devices

    SciTech Connect

    Datskos, P.G.

    1999-04-05

    Recently there has been an increasing demand to perform real-time in-situ chemical detection of hazardous materials, contraband chemicals, and explosive chemicals. Currently, real-time chemical detection requires rather large analytical instrumentation that are expensive and complicated to use. The advent of inexpensive mass produced MEMS (micro-electromechanical systems) devices opened-up new possibilities for chemical detection. For example, microcantilevers were found to respond to chemical stimuli by undergoing changes in their bending and resonance frequency even when a small number of molecules adsorb on their surface. In our present studies, we extended this concept by studying changes in both the adsorption-induced stress and photo-induced stress as target chemicals adsorb on the surface of microcantilevers. For example, microcantilevers that have adsorbed molecules will undergo photo-induced bending that depends on the number of absorbed molecules on the surface. However, microcantilevers that have undergone photo-induced bending will adsorb molecules on their surfaces in a distinctly different way. Depending on the photon wavelength and microcantilever material, the microcantilever can be made to bend by expanding or contracting the irradiated surface. This is important in cases where the photo-induced stresses can be used to counter any adsorption-induced stresses and increase the dynamic range. Coating the surface of the microstructure with a different material can provide chemical specificity for the target chemicals. However, by selecting appropriate photon wavelengths we can change the chemical selectivity due to the introduction of new surface states in the MEMS device. We will present and discuss our results on the use of adsorption-induced and photo-induced bending of microcantilevers for chemical detection.

  20. Causality and persistence in ecological systems: a nonparametric spectral granger causality approach.

    PubMed

    Detto, Matteo; Molini, Annalisa; Katul, Gabriel; Stoy, Paul; Palmroth, Sari; Baldocchi, Dennis

    2012-04-01

    Abstract Directionality in coupling, defined as the linkage relating causes to their effects at a later time, can be used to explain the core dynamics of ecological systems by untangling direct and feedback relationships between the different components of the systems. Inferring causality from measured ecological variables sampled through time remains a formidable challenge further made difficult by the action of periodic drivers overlapping the natural dynamics of the system. Periodicity in the drivers can often mask the self-sustained oscillations originating from the autonomous dynamics. While linear and direct causal relationships are commonly addressed in the time domain, using the well-established machinery of Granger causality (G-causality), the presence of periodic forcing requires frequency-based statistics (e.g., the Fourier transform), able to distinguish coupling induced by oscillations in external drivers from genuine endogenous interactions. Recent nonparametric spectral extensions of G-causality to the frequency domain pave the way for the scale-by-scale decomposition of causality, which can improve our ability to link oscillatory behaviors of ecological networks to causal mechanisms. The performance of both spectral G-causality and its conditional extension for multivariate systems is explored in quantifying causal interactions within ecological networks. Through two case studies involving synthetic and actual time series, it is demonstrated that conditional G-causality outperforms standard G-causality in identifying causal links and their concomitant timescales.

  1. Chemical changes induced by ultrasound in iron

    NASA Astrophysics Data System (ADS)

    Albertini, G.; Calbucci, V.; Cardone, F.; Petrucci, A.; Ridolfi, F.

    2014-03-01

    The focus of this work is a careful chemical investigation of structural damage produced by the exposure of an iron bar to pressure waves generated using an ultrasound machine (called the R-1-S reactor). In addition to the emission of neutron bursts, the ultrasound treatment caused the appearance of zones of macroscopic damage (˜1 mm in size) on the exterior of the bar. Reflected-light optical and environmental scanning electron microscopy (ESEM) has shown that these external damage zones are characterized by microcraters and are covered by a thin layer of cracked amorphous material. Under back scattered electron (BSE) observation, this material shows a lower brightness than the intact ferrite surface. In addition, a zone with a high density of deformed cavities (˜1300 per mm2) with irregular walls and a maximum size of 10 μm was found inside the bar. These deformed microcavities are partially filled with a material composed of a chaotic assemblage of submicron-sized (most likely amorphous) particles. A careful compositional investigation of the chaotic material inside the microcavities using the semi-quantitative data obtained with the ESEM X-ray Energy Dispersive System (EDS) has shown that it is primarily composed of carbon, manganese and chromium. These elements are also found in lower amounts within the intact ferrite matrix. In contrast, the damaged surface surrounding the craters is characterized by elements not found in the ferrite at all (i.e., O, Cl, K, Cu); elements the presence of which cannot be attributed to the occurrence of non-metallic inclusions or to contamination during fabrication. These results are also difficult to explain using the generally accepted laws of physics; however, they do appear to agree with a recent theory predicting the deformation of the local spacetime and the violation of the Local Lorentz Invariance. Such a violation should occur following the collapse of micron-sized discontinuities internal to the materials

  2. The Virtual Liver: Modeling Chemical-Induced Liver Toxicity

    EPA Science Inventory

    The US EPA Virtual Liver (v-Liver) project is aimed at modeling chemical-induced processes in hepatotoxicity and simulating their dose-dependent perturbations. The v-Liver embodies an emerging field of research in computational tissue modeling that integrates molecular and cellul...

  3. Extensin network formation in Vitis vinifera callus cells is an essential and causal event in rapid and H2O2-induced reduction in primary cell wall hydration

    PubMed Central

    2011-01-01

    Background Extensin deposition is considered important for the correct assembly and biophysical properties of primary cell walls, with consequences to plant resistance to pathogens, tissue morphology, cell adhesion and extension growth. However, evidence for a direct and causal role for the extensin network formation in changes to cell wall properties has been lacking. Results Hydrogen peroxide treatment of grapevine (Vitis vinifera cv. Touriga) callus cell walls was seen to induce a marked reduction in their hydration and thickness. An analysis of matrix proteins demonstrated this occurs with the insolubilisation of an abundant protein, GvP1, which displays a primary structure and post-translational modifications typical of dicotyledon extensins. The hydration of callus cell walls free from saline-soluble proteins did not change in response to H2O2, but fully regained this capacity after addition of extensin-rich saline extracts. To assay the specific contribution of GvP1 cross-linking and other wall matrix proteins to the reduction in hydration, GvP1 levels in cell walls were manipulated in vitro by binding selected fractions of extracellular proteins and their effect on wall hydration during H2O2 incubation assayed. Conclusions This approach allowed us to conclude that a peroxidase-mediated formation of a covalently linked network of GvP1 is essential and causal in the reduction of grapevine callus wall hydration in response to H2O2. Importantly, this approach also indicated that extensin network effects on hydration was only partially irreversible and remained sensitive to changes in matrix charge. We discuss this mechanism and the importance of these changes to primary wall properties in the light of extensin distribution in dicotyledons. PMID:21672244

  4. Post-transcriptional silencing of the SGE1 gene induced by a dsRNA hairpin in Fusarium oxysporum f. sp cubense, the causal agent of Panama disease.

    PubMed

    Fernandes, J S; Angelo, P C S; Cruz, J C; Santos, J M M; Sousa, N R; Silva, G F

    2016-01-01

    Fusarium oxysporum f. sp cubense (Foc), the causal agent of Panama disease, is responsible for economic losses in banana crops worldwide. The identification of genes that effectively act on pathogenicity and/or virulence may contribute to the development of different strategies for disease control and the production of resistant plants. The objective of the current study was to analyze the importance of SGE1 gene expression in Foc virulence through post-transcriptional silencing using a double-stranded RNA hairpin. Thirteen transformants were selected based on different morphological characteristics, and sporulation in these transformants was significantly reduced by approximately 95% (P < 0.05) compared to that of the wild-type strain. The relative SGE1 expression levels in the transformant strains were reduced by 27 to 47% compared to those in the wild-type strain. A pathogenicity analysis revealed that the transformants were able to reach the rhizomes and pseudostems of the inoculated banana plants. However, the transformants induced initial disease symptoms in the banana plants approximately 10 days later than that by the wild-type Foc, and initial disease symptoms persisted even at 45 days after inoculation. These results indicate that the SGE1 gene is directly involved in the virulence of Foc. Therefore, SGE1 may be a potential candidate for host-induced gene silencing in banana plants. PMID:27173186

  5. Effect of chemical chaperones on glucose-induced lysozyme modifications.

    PubMed

    Bathaie, S Zahra; Nobakht, B B Fateme; Mirmiranpour, Hossein; Jafarnejad, Akbar; Moosavi-Nejad, S Zahra

    2011-10-01

    Nonenzymatic glycation of biomacromolecules occurs due to the diabetes mellitus and ageing. A number of small molecules, known as chemical chaperones, stabilize protein conformation against thermal and chemically induced denaturation. These compounds are including: polyamines (e.g. spermine and spermidine), amino acids (e.g. lysine) and polyols (e.g. glycerol). In this study the effect of spermidine (Spd), spermine (Spm), and glycerol on glycation, structure and function of lysozyme (LZ), as an extra-cellular protein, by different techniques is investigated. LZ is incubated with or without glucose (50 or 100 mM) in the absence or presence of Spd/Spm/glycerol at 37 °C up to 16 weeks. All the observed changes of glycated-LZ in comparison with the native protein, including: increased fluorescence emission, alteration in the secondary and tertiary structure, and reduced electrophoretic mobility- indicate its structural changes that are accompanied with its reduced activity. Glucose in the presence or absence of Spd induces the protein dimerization, but glucose plus Spm induces its trimmerization. In contrast, glycerol inhibits the LZ glycation and prevents the large changes on its structure and function. Glucose binds lysine residues, decreases the protein positive charges and induces some alterations in its structure and activity. Polyamines also directly bind to LZ, increase its positive charges and hence induce more glycation; more conformational changes, oligomerization and its inactivation in the presence of glucose, but glycerol affect the protein environment and preserve protein from these harmful effects.

  6. Protective effect of silymarin against chemical-induced cardiotoxicity

    PubMed Central

    Razavi, Bibi Marjan; Karimi, Gholamreza

    2016-01-01

    Cardiac disorders remain one of the most important causes of death in the world. Oxidative stress has been suggested as one of the molecular mechanisms involved in drug-induced cardiac toxicity. Recently, several natural products have been utilized in different studies with the aim to protect the progression of oxidative stress-induced cardiac disorders. There is a large body of evidence that administration of antioxidants may be useful in ameliorating cardiac toxicity. Silymarin, a polyphenolic flavonoid has been shown to have utility in several cardiovascular disorders. In this review, various studies in scientific databases regarding the preventive effects of silymarin against cardiotoxicity induced by chemicals were introduced. Although there are many studies representing the valuable effects of silymarin in different diseases, the number of researches relating to the possible cardiac protective effects of silymarin against drugs induced toxicity is rather limited. Results of these studies show that silymarin has a broad spectrum of cardiac protective activity against toxicity induced by some chemicals including metals, environmental pollutants, oxidative agents and anticancer drugs. Further studies are needed to establish the utility of silymarin in protection against cardiac toxicity. PMID:27803777

  7. Mthfd1 is a modifier of chemically induced intestinal carcinogenesis

    PubMed Central

    MacFarlane, Amanda J.; Perry, Cheryll A.; McEntee, Michael F.; Lin, David M.; Stover, Patrick J.

    2011-01-01

    The causal metabolic pathways underlying associations between folate and risk for colorectal cancer (CRC) have yet to be established. Folate-mediated one-carbon metabolism is required for the de novo synthesis of purines, thymidylate and methionine. Methionine is converted to S-adenosylmethionine (AdoMet), the major one-carbon donor for cellular methylation reactions. Impairments in folate metabolism can modify DNA synthesis, genomic stability and gene expression, characteristics associated with tumorigenesis. The Mthfd1 gene product, C1-tetrahydrofolate synthase, is a trifunctional enzyme that generates one-carbon substituted tetrahydrofolate cofactors for one-carbon metabolism. In this study, we use Mthfd1gt/+ mice, which demonstrate a 50% reduction in C1-tetrahydrofolate synthase, to determine its influence on tumor development in two mouse models of intestinal cancer, crosses between Mthfd1gt/+ and Apcmin/+ mice and azoxymethane (AOM)-induced colon cancer in Mthfd1gt/+ mice. Mthfd1 hemizygosity did not affect colon tumor incidence, number or load in Apcmin/+ mice. However, Mthfd1 deficiency increased tumor incidence 2.5-fold, tumor number 3.5-fold and tumor load 2-fold in AOM-treated mice. DNA uracil content in the colon was lower in Mthfd1gt/+ mice, indicating that thymidylate biosynthesis capacity does not play a significant role in AOM-induced colon tumorigenesis. Mthfd1 deficiency-modified cellular methylation potential, as indicated by the AdoMet: S-adenosylhomocysteine ratio and gene expression profiles, suggesting that changes in the transcriptome and/or decreased de novo purine biosynthesis and associated mutability cause cellular transformation in the AOM CRC model. This study emphasizes the impact and complexity of gene–nutrient interactions with respect to the relationships among folate metabolism and colon cancer initiation and progression. PMID:21156972

  8. Chemically induced electric field: flat band potential engineering

    NASA Astrophysics Data System (ADS)

    Bak, T.; Guo, Z.; Li, W.; Atanacio, A. J.; Nowotny, J.

    2012-10-01

    The present work considers engineering of the flat band potential, FBP, of metal oxides in a controlled manner. The aim is to minimise the energy losses related to recombination. The related experimental approaches include imposition of a chemically-induced electric field using the phenomena of segregation, diffusion and the formation of multilayer systems. This paper considers several basic phenomena that allow the modification of the surface charge and the space charge at the gas/solid and solid/liquid interfaces.

  9. Granger causality revisited

    PubMed Central

    Friston, Karl J.; Bastos, André M.; Oswal, Ashwini; van Wijk, Bernadette; Richter, Craig; Litvak, Vladimir

    2014-01-01

    This technical paper offers a critical re-evaluation of (spectral) Granger causality measures in the analysis of biological timeseries. Using realistic (neural mass) models of coupled neuronal dynamics, we evaluate the robustness of parametric and nonparametric Granger causality. Starting from a broad class of generative (state-space) models of neuronal dynamics, we show how their Volterra kernels prescribe the second-order statistics of their response to random fluctuations; characterised in terms of cross-spectral density, cross-covariance, autoregressive coefficients and directed transfer functions. These quantities in turn specify Granger causality — providing a direct (analytic) link between the parameters of a generative model and the expected Granger causality. We use this link to show that Granger causality measures based upon autoregressive models can become unreliable when the underlying dynamics is dominated by slow (unstable) modes — as quantified by the principal Lyapunov exponent. However, nonparametric measures based on causal spectral factors are robust to dynamical instability. We then demonstrate how both parametric and nonparametric spectral causality measures can become unreliable in the presence of measurement noise. Finally, we show that this problem can be finessed by deriving spectral causality measures from Volterra kernels, estimated using dynamic causal modelling. PMID:25003817

  10. Granger causality revisited.

    PubMed

    Friston, Karl J; Bastos, André M; Oswal, Ashwini; van Wijk, Bernadette; Richter, Craig; Litvak, Vladimir

    2014-11-01

    This technical paper offers a critical re-evaluation of (spectral) Granger causality measures in the analysis of biological timeseries. Using realistic (neural mass) models of coupled neuronal dynamics, we evaluate the robustness of parametric and nonparametric Granger causality. Starting from a broad class of generative (state-space) models of neuronal dynamics, we show how their Volterra kernels prescribe the second-order statistics of their response to random fluctuations; characterised in terms of cross-spectral density, cross-covariance, autoregressive coefficients and directed transfer functions. These quantities in turn specify Granger causality - providing a direct (analytic) link between the parameters of a generative model and the expected Granger causality. We use this link to show that Granger causality measures based upon autoregressive models can become unreliable when the underlying dynamics is dominated by slow (unstable) modes - as quantified by the principal Lyapunov exponent. However, nonparametric measures based on causal spectral factors are robust to dynamical instability. We then demonstrate how both parametric and nonparametric spectral causality measures can become unreliable in the presence of measurement noise. Finally, we show that this problem can be finessed by deriving spectral causality measures from Volterra kernels, estimated using dynamic causal modelling.

  11. Embeddings of Causal Sets

    SciTech Connect

    Reid, David D.

    2009-07-06

    A key postulate of the causal set program is that this discrete partial order offers a sufficiently rich structure to make it a viable model of spacetime for quantum gravity. If the deep structure of spacetime is that of a causal set, then the correspondence principle (with the spacetimes of general relativity) must be obeyed. Therefore, one of the requirements of this program is to establish that the causal set structure is in fact, not just in principle, fully consistent with our macroscopic notion of spacetime as a Lorentzian manifold. An important component of any such 'manifold test' is the ability to find embeddings of causal sets into Lorentzian manifolds.

  12. Chemical inducers and transcriptional markers of oligodendrocyte differentiation.

    PubMed

    Joubert, Lara; Foucault, Isabelle; Sagot, Yves; Bernasconi, Lilia; Duval, François; Alliod, Chantal; Frossard, Marie-José; Pescini Gobert, Rosanna; Curchod, Marie-Laure; Salvat, Catherine; Nichols, Anthony; Pouly, Sandrine; Rommel, Christian; Roach, Arthur; Hooft van Huijsduijnen, Rob

    2010-09-01

    Oligodendrocytes generate and maintain myelin, which is essential for axonal function and protection of the mammalian central nervous system. To advance our molecular understanding of differentiation by these cells, we screened libraries of pharmacologically active compounds and identified inducers of differentiation of Oli-neu, a stable cell line of mouse oligodendrocyte precursors (OPCs). We identified four broad classes of inducers, namely, forskolin/cAMP (protein kinase A activators), steroids (glucocorticoids and retinoic acid), ErbB2 inhibitors, and nucleoside analogs, and confirmed the activity of these compounds on rat primary oligodendrocyte precursors and mixed cortical cultures. We also analyzed transcriptional responses in the chemically induced mouse and rat OPC differentiation processes and compared these with earlier studies. We confirm the view that ErbB2 is a natural signaling component that is required for OPC proliferation, whereas ErbB2 inhibition or genetic knockdown results in OPC differentiation.

  13. Granger causality for state-space models

    NASA Astrophysics Data System (ADS)

    Barnett, Lionel; Seth, Anil K.

    2015-04-01

    Granger causality has long been a prominent method for inferring causal interactions between stochastic variables for a broad range of complex physical systems. However, it has been recognized that a moving average (MA) component in the data presents a serious confound to Granger causal analysis, as routinely performed via autoregressive (AR) modeling. We solve this problem by demonstrating that Granger causality may be calculated simply and efficiently from the parameters of a state-space (SS) model. Since SS models are equivalent to autoregressive moving average models, Granger causality estimated in this fashion is not degraded by the presence of a MA component. This is of particular significance when the data has been filtered, downsampled, observed with noise, or is a subprocess of a higher dimensional process, since all of these operations—commonplace in application domains as diverse as climate science, econometrics, and the neurosciences—induce a MA component. We show how Granger causality, conditional and unconditional, in both time and frequency domains, may be calculated directly from SS model parameters via solution of a discrete algebraic Riccati equation. Numerical simulations demonstrate that Granger causality estimators thus derived have greater statistical power and smaller bias than AR estimators. We also discuss how the SS approach facilitates relaxation of the assumptions of linearity, stationarity, and homoscedasticity underlying current AR methods, thus opening up potentially significant new areas of research in Granger causal analysis.

  14. Chemical-induced atrial thrombosis in NTP rodent studies.

    PubMed

    Yoshizawa, Katsuhiko; Kissling, Grace E; Johnson, Jo Anne; Clayton, Natasha P; Flagler, Norris D; Nyska, Abraham

    2005-01-01

    Cardiac thrombosis, one of the causes of sudden death throughout the world, plays a principal role in several cardiovascular diseases, such as myocardial infarction and stroke in humans. Data from studies of induction of chemical thrombosis in rodents help to identify substances in our environment that may contribute to cardiac thrombosis. Results for more than 500 chemicals tested in rodents in 2-year bioassays have been published as Technical Reports of the National Toxicology Program (NTP) http://ntp-server.niehs.nih.gov/index. We evaluated atrial thrombosis induced by these chemical exposures and compared it to similarly induced lesions reported in the literature. Spontaneous rates of cardiac thrombosis were determined for control Fischer 344 rats and B6C3F1 mice: 0% in rats and mice in 90-day studies and, in 2-year studies, 0.7% in both genders of mice, 4% in male rats, and 1% in female rats. Incidences of atrial thrombosis were increased in high-dosed groups involving 13 compounds (incidence rate: 20-100%): 2-butoxyethanol, C.I. Direct Blue 15, bis(2-chloroethoxy)methane, diazoaminobenzene, diethanolamine, 3,3'-dimethoxybenzidine dihydrochloride, hexachloroethane, isobutene, methyleugenol, oxazepam, C.I. Pigment Red 23, C.I. Acid Red 114, and 4,4'-thiobis(6-t-butyl-m-cresol). The main localization of spontaneously occurring and chemically induced thromboses occurred in the left atrium. The literature survey suggested that chemical-induced atrial thrombosis might be closely related to myocardial injury, endothelial injury, circulatory stasis, hypercoagulability, and impaired atrial mechanical activity, such as atrial fibrillation, which could cause stasis of blood within the left atrial appendage, contributing to left atrial thrombosis. Supplementary data referenced in this paper are not printed in this issue of Toxicologic Pathology. They are available as downloadable files at http://taylorandfrancis.metapress.com/openurl.asp?genre=journal&issn=0192-6233. To

  15. Causal Learning Across Domains

    ERIC Educational Resources Information Center

    Schulz, Laura E.; Gopnik, Alison

    2004-01-01

    Five studies investigated (a) children's ability to use the dependent and independent probabilities of events to make causal inferences and (b) the interaction between such inferences and domain-specific knowledge. In Experiment 1, preschoolers used patterns of dependence and independence to make accurate causal inferences in the domains of…

  16. Causality in Classical Electrodynamics

    ERIC Educational Resources Information Center

    Savage, Craig

    2012-01-01

    Causality in electrodynamics is a subject of some confusion, especially regarding the application of Faraday's law and the Ampere-Maxwell law. This has led to the suggestion that we should not teach students that electric and magnetic fields can cause each other, but rather focus on charges and currents as the causal agents. In this paper I argue…

  17. Assessing Interactive Causal Influence

    ERIC Educational Resources Information Center

    Novick, Laura R.; Cheng, Patricia W.

    2004-01-01

    The discovery of conjunctive causes--factors that act in concert to produce or prevent an effect--has been explained by purely covariational theories. Such theories assume that concomitant variations in observable events directly license causal inferences, without postulating the existence of unobservable causal relations. This article discusses…

  18. Repeated Causal Decision Making

    ERIC Educational Resources Information Center

    Hagmayer, York; Meder, Bjorn

    2013-01-01

    Many of our decisions refer to actions that have a causal impact on the external environment. Such actions may not only allow for the mere learning of expected values or utilities but also for acquiring knowledge about the causal structure of our world. We used a repeated decision-making paradigm to examine what kind of knowledge people acquire in…

  19. Agency, time, and causality

    PubMed Central

    Widlok, Thomas

    2014-01-01

    Cognitive Scientists interested in causal cognition increasingly search for evidence from non-Western Educational Industrial Rich Democratic people but find only very few cross-cultural studies that specifically target causal cognition. This article suggests how information about causality can be retrieved from ethnographic monographs, specifically from ethnographies that discuss agency and concepts of time. Many apparent cultural differences with regard to causal cognition dissolve when cultural extensions of agency and personhood to non-humans are taken into account. At the same time considerable variability remains when we include notions of time, linearity and sequence. The article focuses on ethnographic case studies from Africa but provides a more general perspective on the role of ethnography in research on the diversity and universality of causal cognition. PMID:25414683

  20. Chemical consequences of laser-induced breakdown in molecular gases

    NASA Astrophysics Data System (ADS)

    Babánková, Dagmar; Civiš, Svatopluk; Juha, Libor

    This article gives an account of chemical reactions initiated by laser-induced dielectric breakdown (LIDB) in homogeneous molecular gases. The systematic part of the article describes the laser-plasma-chemical behavior of simple inorganic gases and their mixtures, metal carbonyls and organometallics, and organic molecular gases. Research on LIDB-initiated chemical reactions producing well-defined fine solid particles has been triggered again recently by the advent of nanotechnologies. Laser ignition of fuel mixtures is also a well researched branch of laser-plasma chemistry because of strong commercial and military interests. However, the strongest current impulses for studying laser-spark chemistry come from planetary sciences, where laser sparks have been used as a laboratory model of high-energy-density phenomena (e.g., impact of extraterrestrial bodies, lightning) in planetary atmospheres. A single pulse from a high-power laser system was used to develop an improved method for investigating this phenomenon. The particular processes responsible for the chemical action of a laser spark are identified and described in detail by the end of the article.

  1. A chemical chaperone induces inhomogeneous conformational changes in flexible proteins.

    PubMed

    Hamdane, Djemel; Velours, Christophe; Cornu, David; Nicaise, Magali; Lombard, Murielle; Fontecave, Marc

    2016-07-27

    Organic osmolytes also known as chemical chaperones are major cellular compounds that favor, by an unclear mechanism, protein's compaction and stabilization of the native state. Here, we have examined the chaperone effect of the naturally occurring trimethylamine N-oxide (TMAO) osmolyte on a loosely packed protein (LPP), known to be a highly flexible form, using an apoprotein mutant of the flavin-dependent RNA methyltransferase as a model. Thermal and chemical denaturation experiments showed that TMAO stabilizes the structural integrity of the apoprotein dramatically. The denaturation reaction is irreversible indicating that the stability of the apoprotein is under kinetic control. This result implies that the stabilization is due to a TMAO-induced reconfiguration of the flexible LPP state, which leads to conformational limitations of the apoprotein likely driven by favorable entropic contribution. Evidence for the conformational perturbation of the apoprotein had been obtained through several biophysical approaches notably analytical ultracentrifugation, circular dichroism, fluorescence spectroscopy, labelling experiments and proteolysis coupled to mass spectrometry. Unexpectedly, TMAO promotes an overall elongation or asymmetrical changes of the hydrodynamic shape of the apoprotein without alteration of the secondary structure. The modulation of the hydrodynamic properties of the protein is associated with diverse inhomogenous conformational changes: loss of the solvent accessible cavities resulting in a dried protein matrix; some side-chain residues initially buried become solvent exposed while some others become hidden. Consequently, the TMAO-induced protein state exhibits impaired capability in the flavin binding process. Our study suggests that the nature of protein conformational changes induced by the chemical chaperones may be specific to protein packing and plasticity. This could be an efficient mechanism by which the cell controls and finely tunes the

  2. Plasma membrane reorganization induced by chemical transformation in cultura

    SciTech Connect

    Packard, B.S.

    1984-04-01

    Induction of increased rigidity in the plasma membrane paralleling properties associated with a transformed state was suggested by two experiments. Fluorescence recovery after photobleaching (FRAP) indicated the induction of an environment in the plasma membrane where the synthetic fluorescent phospholipid collarein was immobile on the FRAP timescale. The other technique revealed the binding of epidermal growth factor (EGF) to a cryptic class of receptors which become accessible upon chemical transformation. These two lines of evidence are consistent with a reorganization of the plasma membrane induced by tumor promoters. 110 references, 38 figures, 4 tables.

  3. Chemically induced magnetism in atomically precise gold clusters.

    PubMed

    Krishna, Katla Sai; Tarakeshwar, Pilarisetty; Mujica, Vladimiro; Kumar, Challa S S R

    2014-03-12

    Comparative theoretical and experimental investigations are reported into chemically induced magnetism in atomically-precise, ligand-stabilized gold clusters Au25 , Au38 and Au55 . The results indicate that [Au25 (PPh3 )10 (SC12 H25 )5 Cl2 ](2+) and Au38 (SC12 H25 )24 are diamagnetic, Au25 (SC2 H4 Ph)18 is paramagnetic, and Au55 (PPh3 )12 Cl6 , is ferromagnetic at room temperature. Understanding the magnetic properties resulting from quantum size effects in such atomically precise gold clusters could lead to new fundamental discoveries and applications.

  4. Causal Networks or Causal Islands? The Representation of Mechanisms and the Transitivity of Causal Judgment

    ERIC Educational Resources Information Center

    Johnson, Samuel G. B.; Ahn, Woo-kyoung

    2015-01-01

    Knowledge of mechanisms is critical for causal reasoning. We contrasted two possible organizations of causal knowledge--an interconnected causal "network," where events are causally connected without any boundaries delineating discrete mechanisms; or a set of disparate mechanisms--causal "islands"--such that events in different…

  5. Warp drive and causality

    NASA Astrophysics Data System (ADS)

    Everett, Allen E.

    1996-06-01

    Alcubierre recently exhibited a spacetime which, within the framework of general relativity, allows travel at superluminal speeds if matter with a negative energy density can exist, and conjectured that it should be possible to use similar techniques to construct a theory containing closed causal loops and, thus, travel backwards in time. We verify this conjecture by exhibiting a simple modification of Alcubierre's model, requiring no additional assumptions, in which causal loops are possible. We also note that this mechanism for generating causal loops differs in essential ways from that discovered by Gott involving cosmic strings.

  6. Importance of plasma membrane dynamics in chemical-induced carcinogenesis.

    PubMed

    Tekpli, Xavier; Holme, Jørn A; Sergent, Odile; Lagadic-Gossmann, Dominique

    2011-09-01

    In the last decade, a lot of patents have been filled regarding molecular biology and functions of cellular membranes. The membrane bilayer model has evolved from a static, passive, homogeneous barrier to a highly dynamic, asymmetric, heterogeneous structure composed of distinct domains. Changes in membrane fluidity and composition of microdomains have been proven to be involved in the regulation of many important physiological signaling pathways. Recently, several xenobiotics, including various drugs and environmental pollutants, have been reported to change plasma membrane characteristics, thereby altering cell physiology. Interestingly, it has been suggested that a cross talk between chemical-induced cellular membrane effects and DNA damages may be important for the final mutation outcome of genotoxic chemicals. Thus, effects on plasma membrane remodeling may give additional mechanistic explanations to how certain chemicals exert their carcinogenic effect. With respect to such effects, recent patents suggest to focus on plasma membrane and its components like caveolin-1 for cancer screening and chemotherapy. Here, we review the effects of environmental toxicants on cellular plasma membrane structure and function, and further describe possible implication for health and disease.

  7. Chemical-gene interaction networks and causal reasoning for biological effects prediction and prioritization of contaminants for environmental monitoring and surveillance

    EPA Science Inventory

    Evaluating the potential human health and ecological risks associated with exposures to complex chemical mixtures in the environment is one of the main challenges of chemical safety assessment and environmental protection. There is a need for approaches that can help to integrat...

  8. Chemical-induced disease relation extraction with various linguistic features

    PubMed Central

    Gu, Jinghang; Qian, Longhua; Zhou, Guodong

    2016-01-01

    Understanding the relations between chemicals and diseases is crucial in various biomedical tasks such as new drug discoveries and new therapy developments. While manually mining these relations from the biomedical literature is costly and time-consuming, such a procedure is often difficult to keep up-to-date. To address these issues, the BioCreative-V community proposed a challenging task of automatic extraction of chemical-induced disease (CID) relations in order to benefit biocuration. This article describes our work on the CID relation extraction task on the BioCreative-V tasks. We built a machine learning based system that utilized simple yet effective linguistic features to extract relations with maximum entropy models. In addition to leveraging various features, the hypernym relations between entity concepts derived from the Medical Subject Headings (MeSH)-controlled vocabulary were also employed during both training and testing stages to obtain more accurate classification models and better extraction performance, respectively. We demoted relation extraction between entities in documents to relation extraction between entity mentions. In our system, pairs of chemical and disease mentions at both intra- and inter-sentence levels were first constructed as relation instances for training and testing, then two classification models at both levels were trained from the training examples and applied to the testing examples. Finally, we merged the classification results from mention level to document level to acquire final relations between chemicals and diseases. Our system achieved promising F-scores of 60.4% on the development dataset and 58.3% on the test dataset using gold-standard entity annotations, respectively. Database URL: https://github.com/JHnlp/BC5CIDTask PMID:27052618

  9. Chemical-induced disease relation extraction with various linguistic features.

    PubMed

    Gu, Jinghang; Qian, Longhua; Zhou, Guodong

    2016-01-01

    Understanding the relations between chemicals and diseases is crucial in various biomedical tasks such as new drug discoveries and new therapy developments. While manually mining these relations from the biomedical literature is costly and time-consuming, such a procedure is often difficult to keep up-to-date. To address these issues, the BioCreative-V community proposed a challenging task of automatic extraction of chemical-induced disease (CID) relations in order to benefit biocuration. This article describes our work on the CID relation extraction task on the BioCreative-V tasks. We built a machine learning based system that utilized simple yet effective linguistic features to extract relations with maximum entropy models. In addition to leveraging various features, the hypernym relations between entity concepts derived from the Medical Subject Headings (MeSH)-controlled vocabulary were also employed during both training and testing stages to obtain more accurate classification models and better extraction performance, respectively. We demoted relation extraction between entities in documents to relation extraction between entity mentions. In our system, pairs of chemical and disease mentions at both intra- and inter-sentence levels were first constructed as relation instances for training and testing, then two classification models at both levels were trained from the training examples and applied to the testing examples. Finally, we merged the classification results from mention level to document level to acquire final relations between chemicals and diseases. Our system achieved promisingF-scores of 60.4% on the development dataset and 58.3% on the test dataset using gold-standard entity annotations, respectively. Database URL:https://github.com/JHnlp/BC5CIDTask. PMID:27052618

  10. Cross-species malaria immunity induced by chemically attenuated parasites

    PubMed Central

    Good, Michael F.; Reiman, Jennifer M.; Rodriguez, I. Bibiana; Ito, Koichi; Yanow, Stephanie K.; El-Deeb, Ibrahim M.; Batzloff, Michael R.; Stanisic, Danielle I.; Engwerda, Christian; Spithill, Terry; Hoffman, Stephen L.; Lee, Moses; McPhun, Virginia

    2013-01-01

    Vaccine development for the blood stages of malaria has focused on the induction of antibodies to parasite surface antigens, most of which are highly polymorphic. An alternate strategy has evolved from observations that low-density infections can induce antibody-independent immunity to different strains. To test this strategy, we treated parasitized red blood cells from the rodent parasite Plasmodium chabaudi with seco-cyclopropyl pyrrolo indole analogs. These drugs irreversibly alkylate parasite DNA, blocking their ability to replicate. After administration in mice, DNA from the vaccine could be detected in the blood for over 110 days and a single vaccination induced profound immunity to different malaria parasite species. Immunity was mediated by CD4+ T cells and was dependent on the red blood cell membrane remaining intact. The human parasite, Plasmodium falciparum, could also be attenuated by treatment with seco-cyclopropyl pyrrolo indole analogs. These data demonstrate that vaccination with chemically attenuated parasites induces protective immunity and provide a compelling rationale for testing a blood-stage parasite-based vaccine targeting human Plasmodium species. PMID:23863622

  11. Light-induced chemical vapour deposition painting with titanium dioxide

    NASA Astrophysics Data System (ADS)

    Halary-Wagner, E.; Bret, T.; Hoffmann, P.

    2003-03-01

    Light-induced chemical vapour deposits of titanium dioxide are obtained from titanium tetra-isopropoxide (TTIP) in an oxygen and nitrogen atmosphere with a long pulse (250 ns) 308 nm XeCl excimer laser using a mask projection set-up. The demonstrated advantages of this technique are: (i) selective area deposition, (ii) precise control of the deposited thickness and (iii) low temperature deposition, enabling to use a wide range of substrates. A revolving mask system enables, in a single reactor load, to deposit shapes of controlled heights, which overlap to build up a complex pattern. Interferential multi-coloured deposits are achieved, and the process limitations (available colours and resolution) are discussed.

  12. Shock induced chemical reactions in energetic structural materials

    NASA Astrophysics Data System (ADS)

    Reding, Derek J.

    Energetic structural materials (ESMs) constitute a new class of materials that provide dual functions of strength and energetic characteristics. ESMs are typically composed of micron-scale or nano-scale intermetallic mixtures or mixtures of metals and metal oxides, polymer binders, and structural reinforcements. Voids are included to produce a composite with favorable chemical reaction characteristics. In this thesis, a continuum approach is used to simulate gas-gun or explosive loading experiments where a strong shock is induced in the ESM by an impacting plate. Algorithms are developed to obtain equations of state of mixtures. It is usually assumed that the shock loading increases the energy of the ESM and causes the ESM to reach the transition state. It is also assumed that the activation energy needed to reach the transition state is a function of the temperature of the mixture. In this thesis, it is proposed that the activation energy is a function of temperature and the stress state of the mixture. The incorporation of such an activation energy is selected in this thesis. Then, a multi-scale chemical reaction model for a heterogeneous mixture is introduced. This model incorporates reaction initiation, propagation, and extent of completed reaction in spatially heterogeneous distributions of reactants. A new model is proposed for the pore collapse of mixtures. This model is formulated by modifying the Carol, Holt, and Nesterenko spherically symmetric model to include mixtures and compressibility effects. Uncertainties in the model result from assumptions in formulating the models for continuum relationships and chemical reactions in mixtures that are distributed heterogeneously in space and in numerical integration of the resulting equations. It is important to quantify these uncertainties. In this thesis, such an uncertainty quantification is investigated by systematically identifying the physical processes that occur during shock compression of ESMs which are

  13. Charged impurity-induced scatterings in chemical vapor deposited graphene

    SciTech Connect

    Li, Ming-Yang; Tang, Chiu-Chun; Ling, D. C.; Li, L. J.; Chi, C. C.; Chen, Jeng-Chung

    2013-12-21

    We investigate the effects of defect scatterings on the electric transport properties of chemical vapor deposited (CVD) graphene by measuring the carrier density dependence of the magneto-conductivity. To clarify the dominant scattering mechanism, we perform extensive measurements on large-area samples with different mobility to exclude the edge effect. We analyze our data with the major scattering mechanisms such as short-range static scatters, short-range screened Coulomb disorders, and weak-localization (WL). We establish that the charged impurities are the predominant scatters because there is a strong correlation between the mobility and the charge impurity density. Near the charge neutral point (CNP), the electron-hole puddles that are induced by the charged impurities enhance the inter-valley scattering, which is favorable for WL observations. Away from the CNP, the charged-impurity-induced scattering is weak because of the effective screening by the charge carriers. As a result, the local static structural defects govern the charge transport. Our findings provide compelling evidence for understanding the scattering mechanisms in graphene and pave the way for the improvement of fabrication techniques to achieve high-quality CVD graphene.

  14. Causal conditionals and counterfactuals

    PubMed Central

    Frosch, Caren A.; Byrne, Ruth M.J.

    2012-01-01

    Causal counterfactuals e.g., ‘if the ignition key had been turned then the car would have started’ and causal conditionals e.g., ‘if the ignition key was turned then the car started’ are understood by thinking about multiple possibilities of different sorts, as shown in six experiments using converging evidence from three different types of measures. Experiments 1a and 1b showed that conditionals that comprise enabling causes, e.g., ‘if the ignition key was turned then the car started’ primed people to read quickly conjunctions referring to the possibility of the enabler occurring without the outcome, e.g., ‘the ignition key was turned and the car did not start’. Experiments 2a and 2b showed that people paraphrased causal conditionals by using causal or temporal connectives (because, when), whereas they paraphrased causal counterfactuals by using subjunctive constructions (had…would have). Experiments 3a and 3b showed that people made different inferences from counterfactuals presented with enabling conditions compared to none. The implications of the results for alternative theories of conditionals are discussed. PMID:22858874

  15. Causality discovery technology

    NASA Astrophysics Data System (ADS)

    Chen, M.; Ertl, T.; Jirotka, M.; Trefethen, A.; Schmidt, A.; Coecke, B.; Bañares-Alcántara, R.

    2012-11-01

    Causality is the fabric of our dynamic world. We all make frequent attempts to reason causation relationships of everyday events (e.g., what was the cause of my headache, or what has upset Alice?). We attempt to manage causality all the time through planning and scheduling. The greatest scientific discoveries are usually about causality (e.g., Newton found the cause for an apple to fall, and Darwin discovered natural selection). Meanwhile, we continue to seek a comprehensive understanding about the causes of numerous complex phenomena, such as social divisions, economic crisis, global warming, home-grown terrorism, etc. Humans analyse and reason causality based on observation, experimentation and acquired a priori knowledge. Today's technologies enable us to make observations and carry out experiments in an unprecedented scale that has created data mountains everywhere. Whereas there are exciting opportunities to discover new causation relationships, there are also unparalleled challenges to benefit from such data mountains. In this article, we present a case for developing a new piece of ICT, called Causality Discovery Technology. We reason about the necessity, feasibility and potential impact of such a technology.

  16. Causal networks or causal islands? The representation of mechanisms and the transitivity of causal judgment

    PubMed Central

    Johnson, Samuel G. B.; Ahn, Woo-kyoung

    2014-01-01

    Knowledge of mechanisms is critical for causal reasoning. We contrasted two possible organizations of causal knowledge—an interconnected causal network, where events are causally connected without any boundaries delineating discrete mechanisms; or a set of disparate mechanisms—causal islands—such that events in different mechanisms are not thought to be related even when they belong to the same causal chain. To distinguish these possibilities, we used causal transitivity—the inference given A causes B and B causes C that A causes C. Specifically, causal chains schematized as one chunk or mechanism in semantic memory (e.g., exercising, becoming thirsty, drinking water) led to transitive causal judgments. On the other hand, chains schematized as multiple chunks (e.g., having sex, becoming pregnant, becoming nauseous) led to intransitive judgments despite strong intermediate links (Experiments 1–3). Normative accounts of causal intransitivity could not explain these intransitive judgments (Experiments 4–5). PMID:25556901

  17. Causal premise semantics.

    PubMed

    Kaufmann, Stefan

    2013-08-01

    The rise of causality and the attendant graph-theoretic modeling tools in the study of counterfactual reasoning has had resounding effects in many areas of cognitive science, but it has thus far not permeated the mainstream in linguistic theory to a comparable degree. In this study I show that a version of the predominant framework for the formal semantic analysis of conditionals, Kratzer-style premise semantics, allows for a straightforward implementation of the crucial ideas and insights of Pearl-style causal networks. I spell out the details of such an implementation, focusing especially on the notions of intervention on a network and backtracking interpretations of counterfactuals.

  18. Water-borne cues induce chemical defense in a marine alga (Ascophyllum nodosum).

    PubMed

    Toth, G B; Pavia, H

    2000-12-19

    It is well known that herbivores can induce chemical defenses in terrestrial vascular plants, but few examples of inducible production of defense chemicals have been reported for aquatic macrophytes. Furthermore, it is well established that water-borne chemical cues from predators or predator-wounded conspecifics can induce defensive changes of aquatic prey animals, but no such communication between aquatic herbivores and seaweeds has been reported. Here we show that water-borne cues from actively feeding herbivorous gastropods, flat periwinkles (Littorina obtusata), can serve as external signals to induce production of defense chemicals (phlorotannins) in unharmed individuals of seaweeds, knotted wrack (Ascophyllum nodosum), and that the increased levels of defense chemicals deter further feeding by periwinkles. Because seaweeds have poorly developed internal-transport systems and may not be able to elicit systemic-induced chemical defenses through conveyance of internal signals, this mechanism ensures that seaweeds can anticipate future periwinkle attacks without receiving direct damage by herbivores. PMID:11106371

  19. Water-borne cues induce chemical defense in a marine alga (Ascophyllum nodosum)

    PubMed Central

    Toth, Gunilla B.; Pavia, Henrik

    2000-01-01

    It is well known that herbivores can induce chemical defenses in terrestrial vascular plants, but few examples of inducible production of defense chemicals have been reported for aquatic macrophytes. Furthermore, it is well established that water-borne chemical cues from predators or predator-wounded conspecifics can induce defensive changes of aquatic prey animals, but no such communication between aquatic herbivores and seaweeds has been reported. Here we show that water-borne cues from actively feeding herbivorous gastropods, flat periwinkles (Littorina obtusata), can serve as external signals to induce production of defense chemicals (phlorotannins) in unharmed individuals of seaweeds, knotted wrack (Ascophyllum nodosum), and that the increased levels of defense chemicals deter further feeding by periwinkles. Because seaweeds have poorly developed internal-transport systems and may not be able to elicit systemic-induced chemical defenses through conveyance of internal signals, this mechanism ensures that seaweeds can anticipate future periwinkle attacks without receiving direct damage by herbivores. PMID:11106371

  20. Evaluating Causal Models.

    ERIC Educational Resources Information Center

    Watt, James H., Jr.

    Pointing out that linear causal models can organize the interrelationships of a large number of variables, this paper contends that such models are particularly useful to mass communication research, which must by necessity deal with complex systems of variables. The paper first outlines briefly the philosophical requirements for establishing a…

  1. Causal Responsibility and Counterfactuals

    ERIC Educational Resources Information Center

    Lagnado, David A.; Gerstenberg, Tobias; Zultan, Ro'i

    2013-01-01

    How do people attribute responsibility in situations where the contributions of multiple agents combine to produce a joint outcome? The prevalence of over-determination in such cases makes this a difficult problem for counterfactual theories of causal responsibility. In this article, we explore a general framework for assigning responsibility in…

  2. Causal Premise Semantics

    ERIC Educational Resources Information Center

    Kaufmann, Stefan

    2013-01-01

    The rise of causality and the attendant graph-theoretic modeling tools in the study of counterfactual reasoning has had resounding effects in many areas of cognitive science, but it has thus far not permeated the mainstream in linguistic theory to a comparable degree. In this study I show that a version of the predominant framework for the formal…

  3. Causal essentialism in kinds.

    PubMed

    Ahn, Woo-kyoung; Taylor, Eric G; Kato, Daniel; Marsh, Jessecae K; Bloom, Paul

    2013-06-01

    The current study examines causal essentialism, derived from psychological essentialism of concepts. We examine whether people believe that members of a category share some underlying essence that is both necessary and sufficient for category membership and that also causes surface features. The main claim is that causal essentialism is restricted to categories that correspond to our intuitive notions of existing kinds and hence is more attenuated for categories that are based on arbitrary criteria. Experiments 1 and 3 found that people overtly endorse causal essences in nonarbitrary kinds but are less likely to do so for arbitrary categories. Experiments 2 and 4 found that people were more willing to generalize a member's known causal relations (or lack thereof) when dealing with a kind than when dealing with an arbitrary category. These differences between kinds and arbitrary categories were found across various domains-not only for categories of living things, but also for artefacts. These findings have certain real-world implications, including how people make sense of mental disorders that are treated as real kinds. PMID:23098315

  4. The Causal Asymmetry

    ERIC Educational Resources Information Center

    White, Peter A.

    2006-01-01

    It is hypothesized that there is a pervasive and fundamental bias in humans' understanding of physical causation: Once the roles of cause and effect are assigned to objects in interactions, people tend to overestimate the strength and importance of the causal object and underestimate that of the effect object in bringing about the outcome. This…

  5. Causality: Physics and Philosophy

    ERIC Educational Resources Information Center

    Chatterjee, Atanu

    2013-01-01

    Nature is a complex causal network exhibiting diverse forms and species. These forms or rather systems are physically open, structurally complex and naturally adaptive. They interact with the surrounding media by operating a positive-feedback loop through which, they adapt, organize and self-organize themselves in response to the ever-changing…

  6. Photo-induced chemical reaction of trans-resveratrol.

    PubMed

    Zhao, Yue; Shi, Meng; Ye, Jian-Hui; Zheng, Xin-Qiang; Lu, Jian-Liang; Liang, Yue-Rong

    2015-03-15

    Photo-induced chemical reaction of trans-resveratrol has been studied. UV B, liquid state and sufficient exposure time are essential conditions to the photochemical change of trans-resveratrol. Three principal compounds, cis-resveratrol, 2,4,6-phenanthrenetriol and 2-(4-hydroxyphenyl)-5,6-benzofurandione, were successively generated in the reaction solution of trans-resveratrol (0.25 mM, 100% ethanol) under 100 μW cm(-2) UV B radiation for 4h. cis-Resveratrol, originated from isomerization of trans-resveratrol, resulted in 2,4,6-phenanthrenetriol through photocyclisation reaction meanwhile loss of 2 H. 2,4,6-Phenanthrenetriol played a role of photosensitizer producing singlet oxygen in the reaction pathway. The singlet oxygen triggered [4+2] cycloaddition reaction of trans-resveratrol, and then resulted in the generation of 2-(4-hydroxyphenyl)-5,6-benzofurandione through photorearrangement and oxidation reaction. The singlet oxygen reaction was closely related to the substrate concentration of trans-resveratrol in solution.

  7. Epidemiological assessment of occupationally related, chemically induced sperm count suppression

    SciTech Connect

    Milby, T.H.; Whorton, D.

    1980-02-01

    Occupationally related, chemically induced sperm count suppression is a recently recognized problem, first brought to light in connection with the manufacture and formulation of dibromochloropropane (DBCP). The authors studied sperm count data from four occupational cohorts - two exposed to DBCP and two exposed to epichlorohydrin (ECH). In both DBCP cohorts there was a significant difference (alpha = 0.05) between sperm count distribution functions of the exposed group and of the non-exposed group. A much higher percentage of exposed men was oligospermic and the median sperm count for each exposed group was substantially lower than that for the respective non-exposed group. In the ECH cohorts there was no significant difference between sperm count data for the exposed group and for the non-exposed group. The authors concluded that exposure to DBCP, but not to ECH, was positively associated with detectable sperm count suppression. It is suggested that the key to identifying and assessing occupationally related sperm count suppression lies in the proper classification and interpretation of group sperm count data.

  8. Chemically induced skin carcinogenesis: Updates in experimental models (Review)

    PubMed Central

    NEAGU, MONICA; CARUNTU, CONSTANTIN; CONSTANTIN, CAROLINA; BODA, DANIEL; ZURAC, SABINA; SPANDIDOS, DEMETRIOS A.; TSATSAKIS, ARISTIDIS M.

    2016-01-01

    Skin cancer is one of the most common malignancies affecting humans worldwide, and its incidence is rapidly increasing. The study of skin carcinogenesis is of major interest for both scientific research and clinical practice and the use of in vivo systems may facilitate the investigation of early alterations in the skin and of the mechanisms involved, and may also lead to the development of novel therapeutic strategies for skin cancer. This review outlines several aspects regarding the skin toxicity testing domain in mouse models of chemically induced skin carcinogenesis. There are important strain differences in view of the histological type, development and clinical evolution of the skin tumor, differences reported decades ago and confirmed by our hands-on experience. Using mouse models in preclinical testing is important due to the fact that, at the molecular level, common mechanisms with human cutaneous tumorigenesis are depicted. These animal models resemble human skin cancer development, in that genetic changes caused by carcinogens and pro-inflammatory cytokines, and simultaneous inflammation sustained by pro-inflammatory cytokines and chemokines favor tumor progression. Drugs and environmental conditions can be tested using these animal models. keeping in mind the differences between human and rodent skin physiology. PMID:26986013

  9. Causal Discovery of Dynamic Systems

    ERIC Educational Resources Information Center

    Voortman, Mark

    2010-01-01

    Recently, several philosophical and computational approaches to causality have used an interventionist framework to clarify the concept of causality [Spirtes et al., 2000, Pearl, 2000, Woodward, 2005]. The characteristic feature of the interventionist approach is that causal models are potentially useful in predicting the effects of manipulations.…

  10. Context, causality, and appreciation.

    PubMed

    Ross, Stephanie

    2013-04-01

    I applaud and elaborate on the contextualism at the heart of Bullot & Reber's (B&R's) theory, challenge two aspects of the appreciative structure they posit (the causal reasoning that allegedly underlies the design stance and the segregation of the component stages), suggest that expert and novice appreciators operate differently, and question the degree to which B&R's final theory is open to empirical investigation. PMID:23507111

  11. Context, causality, and appreciation.

    PubMed

    Ross, Stephanie

    2013-04-01

    I applaud and elaborate on the contextualism at the heart of Bullot & Reber's (B&R's) theory, challenge two aspects of the appreciative structure they posit (the causal reasoning that allegedly underlies the design stance and the segregation of the component stages), suggest that expert and novice appreciators operate differently, and question the degree to which B&R's final theory is open to empirical investigation.

  12. Causal Responsibility and Counterfactuals

    PubMed Central

    Lagnado, David A; Gerstenberg, Tobias; Zultan, Ro'i

    2013-01-01

    How do people attribute responsibility in situations where the contributions of multiple agents combine to produce a joint outcome? The prevalence of over-determination in such cases makes this a difficult problem for counterfactual theories of causal responsibility. In this article, we explore a general framework for assigning responsibility in multiple agent contexts. We draw on the structural model account of actual causation (e.g., Halpern & Pearl, 2005) and its extension to responsibility judgments (Chockler & Halpern, 2004). We review the main theoretical and empirical issues that arise from this literature and propose a novel model of intuitive judgments of responsibility. This model is a function of both pivotality (whether an agent made a difference to the outcome) and criticality (how important the agent is perceived to be for the outcome, before any actions are taken). The model explains empirical results from previous studies and is supported by a new experiment that manipulates both pivotality and criticality. We also discuss possible extensions of this model to deal with a broader range of causal situations. Overall, our approach emphasizes the close interrelations between causality, counterfactuals, and responsibility attributions. PMID:23855451

  13. Laser-induced destination of hazardous chemicals: A preliminary analysis

    NASA Astrophysics Data System (ADS)

    Morrison, P. F.; Wolf, K. A.

    1982-10-01

    Technical methods that might prove effective in destroying dangerous chemicals before they leave the plant environment and become subject to regulation are studied. Laser infrared multiphoton dissociation, for decomposing deleterious chemical gases is evaluated. The chlorinated ethylenes and the chlorinated ethanes are emphasized. A detailed method for decomposing chlorinated chemicals in the workplace using a relatively inexpensive CO2 laser is discussed. Results show that CO2 laser photodegradation of vinyl chloride, a chlorinated ethylene, is promising.

  14. Positive affect increases secondary control among causally uncertain individuals.

    PubMed

    Tobin, Stephanie J; George, Melanie P

    2015-01-01

    Secondary control (acceptance of and adjustment to negative events) is thought to promote positive affect. We examined the opposite path: could positive affect increase secondary control, particularly among individuals high in causal uncertainty, who stand to benefit from it the most? In two studies, participants completed a causal uncertainty scale, thought about a problem while listening to affect-inducing music or no music, and then completed items that assessed secondary control. In Study 1, the music induced positive or negative affect. In Study 2, the music induced affect that was high or low in activation and positive or negative in valence. In both studies, we found that positive affect-inducing music increased secondary control among high causal uncertainty participants. Furthermore, trait affect did not account for the effects of causal uncertainty, and music did not influence primary control. These findings show that secondary control can fluctuate as a function of state affect.

  15. Competition induces allelopathy but suppresses growth and anti-herbivore defence in a chemically rich seaweed

    PubMed Central

    Rasher, Douglas B.; Hay, Mark E.

    2014-01-01

    Many seaweeds and terrestrial plants induce chemical defences in response to herbivory, but whether they induce chemical defences against competitors (allelopathy) remains poorly understood. We evaluated whether two tropical seaweeds induce allelopathy in response to competition with a reef-building coral. We also assessed the effects of competition on seaweed growth and seaweed chemical defence against herbivores. Following 8 days of competition with the coral Porites cylindrica, the chemically rich seaweed Galaxaura filamentosa induced increased allelochemicals and became nearly twice as damaging to the coral. However, it also experienced significantly reduced growth and increased palatability to herbivores (because of reduced chemical defences). Under the same conditions, the seaweed Sargassum polycystum did not induce allelopathy and did not experience a change in growth or palatability. This is the first demonstration of induced allelopathy in a seaweed, or of competitors reducing seaweed chemical defences against herbivores. Our results suggest that the chemical ecology of coral–seaweed–herbivore interactions can be complex and nuanced, highlighting the need to incorporate greater ecological complexity into the study of chemical defence. PMID:24403332

  16. Competition induces allelopathy but suppresses growth and anti-herbivore defence in a chemically rich seaweed.

    PubMed

    Rasher, Douglas B; Hay, Mark E

    2014-02-22

    Many seaweeds and terrestrial plants induce chemical defences in response to herbivory, but whether they induce chemical defences against competitors (allelopathy) remains poorly understood. We evaluated whether two tropical seaweeds induce allelopathy in response to competition with a reef-building coral. We also assessed the effects of competition on seaweed growth and seaweed chemical defence against herbivores. Following 8 days of competition with the coral Porites cylindrica, the chemically rich seaweed Galaxaura filamentosa induced increased allelochemicals and became nearly twice as damaging to the coral. However, it also experienced significantly reduced growth and increased palatability to herbivores (because of reduced chemical defences). Under the same conditions, the seaweed Sargassum polycystum did not induce allelopathy and did not experience a change in growth or palatability. This is the first demonstration of induced allelopathy in a seaweed, or of competitors reducing seaweed chemical defences against herbivores. Our results suggest that the chemical ecology of coral-seaweed-herbivore interactions can be complex and nuanced, highlighting the need to incorporate greater ecological complexity into the study of chemical defence. PMID:24403332

  17. Causal Entropic Forces

    NASA Astrophysics Data System (ADS)

    Wissner-Gross, A. D.; Freer, C. E.

    2013-04-01

    Recent advances in fields ranging from cosmology to computer science have hinted at a possible deep connection between intelligence and entropy maximization, but no formal physical relationship between them has yet been established. Here, we explicitly propose a first step toward such a relationship in the form of a causal generalization of entropic forces that we find can cause two defining behaviors of the human “cognitive niche”—tool use and social cooperation—to spontaneously emerge in simple physical systems. Our results suggest a potentially general thermodynamic model of adaptive behavior as a nonequilibrium process in open systems.

  18. Quantum information causality.

    PubMed

    Pitalúa-García, Damián

    2013-05-24

    How much information can a transmitted physical system fundamentally communicate? We introduce the principle of quantum information causality, which states the maximum amount of quantum information that a quantum system can communicate as a function of its dimension, independently of any previously shared quantum physical resources. We present a new quantum information task, whose success probability is upper bounded by the new principle, and show that an optimal strategy to perform it combines the quantum teleportation and superdense coding protocols with a task that has classical inputs. PMID:23745844

  19. Fast causal multicast

    NASA Technical Reports Server (NTRS)

    Birman, Kenneth P.; Schiper, Andre; Stephenson, Pat

    1990-01-01

    A new protocol is presented that efficiently implements a reliable, causally ordered multicast primitive and is easily extended into a totally ordered one. Intended for use in the ISIS toolkit, it offers a way to bypass the most costly aspects of ISIS while benefiting from virtual synchrony. The facility scales with bounded overhead. Measured speedups of more than an order of magnitude were obtained when the protocol was implemented within ISIS. One conclusion is that systems such as ISIS can achieve performance competitive with the best existing multicast facilities - a finding contradicting the widespread concern that fault-tolerance may be unacceptably costly.

  20. CD-REST: a system for extracting chemical-induced disease relation in literature.

    PubMed

    Xu, Jun; Wu, Yonghui; Zhang, Yaoyun; Wang, Jingqi; Lee, Hee-Jin; Xu, Hua

    2016-01-01

    Mining chemical-induced disease relations embedded in the vast biomedical literature could facilitate a wide range of computational biomedical applications, such as pharmacovigilance. The BioCreative V organized a Chemical Disease Relation (CDR) Track regarding chemical-induced disease relation extraction from biomedical literature in 2015. We participated in all subtasks of this challenge. In this article, we present our participation system Chemical Disease Relation Extraction SysTem (CD-REST), an end-to-end system for extracting chemical-induced disease relations in biomedical literature. CD-REST consists of two main components: (1) a chemical and disease named entity recognition and normalization module, which employs the Conditional Random Fields algorithm for entity recognition and a Vector Space Model-based approach for normalization; and (2) a relation extraction module that classifies both sentence-level and document-level candidate drug-disease pairs by support vector machines. Our system achieved the best performance on the chemical-induced disease relation extraction subtask in the BioCreative V CDR Track, demonstrating the effectiveness of our proposed machine learning-based approaches for automatic extraction of chemical-induced disease relations in biomedical literature. The CD-REST system provides web services using HTTP POST request. The web services can be accessed fromhttp://clinicalnlptool.com/cdr The online CD-REST demonstration system is available athttp://clinicalnlptool.com/cdr/cdr.html. Database URL:http://clinicalnlptool.com/cdr;http://clinicalnlptool.com/cdr/cdr.html.

  1. Learning a theory of causality.

    PubMed

    Goodman, Noah D; Ullman, Tomer D; Tenenbaum, Joshua B

    2011-01-01

    The very early appearance of abstract knowledge is often taken as evidence for innateness. We explore the relative learning speeds of abstract and specific knowledge within a Bayesian framework and the role for innate structure. We focus on knowledge about causality, seen as a domain-general intuitive theory, and ask whether this knowledge can be learned from co-occurrence of events. We begin by phrasing the causal Bayes nets theory of causality and a range of alternatives in a logical language for relational theories. This allows us to explore simultaneous inductive learning of an abstract theory of causality and a causal model for each of several causal systems. We find that the correct theory of causality can be learned relatively quickly, often becoming available before specific causal theories have been learned--an effect we term the blessing of abstraction. We then explore the effect of providing a variety of auxiliary evidence and find that a collection of simple perceptual input analyzers can help to bootstrap abstract knowledge. Together, these results suggest that the most efficient route to causal knowledge may be to build in not an abstract notion of causality but a powerful inductive learning mechanism and a variety of perceptual supports. While these results are purely computational, they have implications for cognitive development, which we explore in the conclusion.

  2. Oncogene activation in spontaneous and chemically induced rodent tumors: implications for risk analysis

    SciTech Connect

    Reynolds, S.H.; Stowers, S.J.; Patterson, R.M.; Maronpot, R.R.; Anderson, M.W.

    1988-06-01

    The validity of rodent tumor end points in assessing the potential hazards of chemical exposure to humans is a somewhat controversial but very important issue since most chemicals are classified as potentially hazardous to humans on the basis of long-term carcinogenesis studies in rodents. The ability to distinguish between genotoxic, cytotoxic, or receptor-mediated promotion effects of chemical treatment would aid in the interpretation of rodent carcinogenesis data. Activated oncogenes in spontaneously occurring and chemically induced rodent tumors were examined and compared as one approach to determine the mechanism by which chemical treatment caused an increased incidence of rodent tumors. Different patterns of activated oncogenes were found not only in spontaneous versus chemically induced mouse liver tumors but also in a variety of spontaneous rat tumors versus chemically induced rat lung tumors. In the absence of cytotoxic effects, it could be argued that the chemicals in question activated protooncogenes by a direct genotoxic mechanism. These results provided a basis for the analysis of activated oncogenes in spontaneous and chemically induced rodent tumors to provide information at a molecular level to aid in the extrapolation of rodent carcinogenesis data to human risk assessment.

  3. Photodetection and causality I

    NASA Astrophysics Data System (ADS)

    de Haan, M.

    1985-09-01

    We investigate in this paper the link between the measurement process in quantum mechanics and casuality associated to a finite velocity of field propagation. We use models of interaction of a bound state with a scalar field. We first show that in the existing approaches, time delays resulting from the finite velocity of propagation have been obtained only as a consequence of ad hoc approximations. We show that exact causality can be restored in the case of a single photodetection by a slight change of the observable associated to the measurement process. Moreover, this modification may be justified by the introduction of a simple model for the photodetector. We present qualitative arguments to show that this procedure cannot be extended to the case of multiple photodetections. The process of repeated photodetection clashes therefore with causality. This paradox is closely related to the Zeno paradox described by Misra and Sudarshan 1). Both may be traced back to the positive definite character of the hamiltonian which is the generator of motion in quantum mechanics.

  4. Spectroscopic Observation of Chemical Interaction Between Impact-induced Vapor Clouds and the Ambient Atmosphere

    NASA Technical Reports Server (NTRS)

    Sugita, S.; Heineck, J. T.; Schultz, P. H.

    2000-01-01

    Chemical reactions within impact-induced vapor clouds were observed in laboratory experiments using a spectroscopic method. The results indicate that projectile-derived carbon-rich vapor reacts intensively with atmospheric nitrogen.

  5. Rheological monitoring of phase separation induced by chemical reaction in thermoplastic-modified epoxy

    SciTech Connect

    Vinh-Tung, C.; Lachenal, G.; Chabert, B.

    1996-12-31

    The phase separation induced by chemical reaction in blends of tetraglycidyl-diaminodiphenylmethane epoxy resin with an aromatic diamine hardener and a thermoplastic was monitored. Rheological measurements and morphologies are described.

  6. Experimental test of nonlocal causality

    PubMed Central

    Ringbauer, Martin; Giarmatzi, Christina; Chaves, Rafael; Costa, Fabio; White, Andrew G.; Fedrizzi, Alessandro

    2016-01-01

    Explaining observations in terms of causes and effects is central to empirical science. However, correlations between entangled quantum particles seem to defy such an explanation. This implies that some of the fundamental assumptions of causal explanations have to give way. We consider a relaxation of one of these assumptions, Bell’s local causality, by allowing outcome dependence: a direct causal influence between the outcomes of measurements of remote parties. We use interventional data from a photonic experiment to bound the strength of this causal influence in a two-party Bell scenario, and observational data from a Bell-type inequality test for the considered models. Our results demonstrate the incompatibility of quantum mechanics with a broad class of nonlocal causal models, which includes Bell-local models as a special case. Recovering a classical causal picture of quantum correlations thus requires an even more radical modification of our classical notion of cause and effect. PMID:27532045

  7. Redundant variables and Granger causality

    NASA Astrophysics Data System (ADS)

    Angelini, L.; de Tommaso, M.; Marinazzo, D.; Nitti, L.; Pellicoro, M.; Stramaglia, S.

    2010-03-01

    We discuss the use of multivariate Granger causality in presence of redundant variables: the application of the standard analysis, in this case, leads to under estimation of causalities. Using the un-normalized version of the causality index, we quantitatively develop the notions of redundancy and synergy in the frame of causality and propose two approaches to group redundant variables: (i) for a given target, the remaining variables are grouped so as to maximize the total causality and (ii) the whole set of variables is partitioned to maximize the sum of the causalities between subsets. We show the application to a real neurological experiment, aiming to a deeper understanding of the physiological basis of abnormal neuronal oscillations in the migraine brain. The outcome by our approach reveals the change in the informational pattern due to repetitive transcranial magnetic stimulations.

  8. Experimental test of nonlocal causality.

    PubMed

    Ringbauer, Martin; Giarmatzi, Christina; Chaves, Rafael; Costa, Fabio; White, Andrew G; Fedrizzi, Alessandro

    2016-08-01

    Explaining observations in terms of causes and effects is central to empirical science. However, correlations between entangled quantum particles seem to defy such an explanation. This implies that some of the fundamental assumptions of causal explanations have to give way. We consider a relaxation of one of these assumptions, Bell's local causality, by allowing outcome dependence: a direct causal influence between the outcomes of measurements of remote parties. We use interventional data from a photonic experiment to bound the strength of this causal influence in a two-party Bell scenario, and observational data from a Bell-type inequality test for the considered models. Our results demonstrate the incompatibility of quantum mechanics with a broad class of nonlocal causal models, which includes Bell-local models as a special case. Recovering a classical causal picture of quantum correlations thus requires an even more radical modification of our classical notion of cause and effect. PMID:27532045

  9. Experimental test of nonlocal causality.

    PubMed

    Ringbauer, Martin; Giarmatzi, Christina; Chaves, Rafael; Costa, Fabio; White, Andrew G; Fedrizzi, Alessandro

    2016-08-01

    Explaining observations in terms of causes and effects is central to empirical science. However, correlations between entangled quantum particles seem to defy such an explanation. This implies that some of the fundamental assumptions of causal explanations have to give way. We consider a relaxation of one of these assumptions, Bell's local causality, by allowing outcome dependence: a direct causal influence between the outcomes of measurements of remote parties. We use interventional data from a photonic experiment to bound the strength of this causal influence in a two-party Bell scenario, and observational data from a Bell-type inequality test for the considered models. Our results demonstrate the incompatibility of quantum mechanics with a broad class of nonlocal causal models, which includes Bell-local models as a special case. Recovering a classical causal picture of quantum correlations thus requires an even more radical modification of our classical notion of cause and effect.

  10. Redundant variables and Granger causality.

    PubMed

    Angelini, L; de Tommaso, M; Marinazzo, D; Nitti, L; Pellicoro, M; Stramaglia, S

    2010-03-01

    We discuss the use of multivariate Granger causality in presence of redundant variables: the application of the standard analysis, in this case, leads to under estimation of causalities. Using the un-normalized version of the causality index, we quantitatively develop the notions of redundancy and synergy in the frame of causality and propose two approaches to group redundant variables: (i) for a given target, the remaining variables are grouped so as to maximize the total causality and (ii) the whole set of variables is partitioned to maximize the sum of the causalities between subsets. We show the application to a real neurological experiment, aiming to a deeper understanding of the physiological basis of abnormal neuronal oscillations in the migraine brain. The outcome by our approach reveals the change in the informational pattern due to repetitive transcranial magnetic stimulations.

  11. Causal inference based on counterfactuals

    PubMed Central

    Höfler, M

    2005-01-01

    Background The counterfactual or potential outcome model has become increasingly standard for causal inference in epidemiological and medical studies. Discussion This paper provides an overview on the counterfactual and related approaches. A variety of conceptual as well as practical issues when estimating causal effects are reviewed. These include causal interactions, imperfect experiments, adjustment for confounding, time-varying exposures, competing risks and the probability of causation. It is argued that the counterfactual model of causal effects captures the main aspects of causality in health sciences and relates to many statistical procedures. Summary Counterfactuals are the basis of causal inference in medicine and epidemiology. Nevertheless, the estimation of counterfactual differences pose several difficulties, primarily in observational studies. These problems, however, reflect fundamental barriers only when learning from observations, and this does not invalidate the counterfactual concept. PMID:16159397

  12. Chemically-induced Mouse Lung Tumors: Applications to Human Health Assessments

    EPA Science Inventory

    A state-of-the-science workshop on chemically-induced mouse lung tumors was conducted by U.S. Environmental Protection Agency to better understand the mouse lung tumor data’s role in human health assessments. Three environmental chemicals - naphthalene, styrene, and ethylbe...

  13. Chlorine Dioxide Induced Multiple Chemical Sensitivity: MMPI Validity Problems.

    ERIC Educational Resources Information Center

    Tentoni, Stuart C.

    This paper discusses Minnesota Multiphasic Personality Inventory (MMPI) data obtained from individuals exposed to chlorine dioxide in the workplace who developed Multiple Chemical Sensitivity Syndrome. The paper explores current research on chlorine dioxide exposed persons who were misdiagnosed on the basis of MMPI interpretations. Difficulties…

  14. Causal Poisson bracket via deformation quantization

    NASA Astrophysics Data System (ADS)

    Berra-Montiel, Jasel; Molgado, Alberto; Palacios-García, César D.

    2016-06-01

    Starting with the well-defined product of quantum fields at two spacetime points, we explore an associated Poisson structure for classical field theories within the deformation quantization formalism. We realize that the induced star-product is naturally related to the standard Moyal product through an appropriate causal Green’s functions connecting points in the space of classical solutions to the equations of motion. Our results resemble the Peierls-DeWitt bracket that has been analyzed in the multisymplectic context. Once our star-product is defined, we are able to apply the Wigner-Weyl map in order to introduce a generalized version of Wick’s theorem. Finally, we include some examples to explicitly test our method: the real scalar field, the bosonic string and a physically motivated nonlinear particle model. For the field theoretic models, we have encountered causal generalizations of the creation/annihilation relations, and also a causal generalization of the Virasoro algebra for the bosonic string. For the nonlinear particle case, we use the approximate solution in terms of the Green’s function, in order to construct a well-behaved causal bracket.

  15. Structural Equations and Causal Explanations: Some Challenges for Causal SEM

    ERIC Educational Resources Information Center

    Markus, Keith A.

    2010-01-01

    One common application of structural equation modeling (SEM) involves expressing and empirically investigating causal explanations. Nonetheless, several aspects of causal explanation that have an impact on behavioral science methodology remain poorly understood. It remains unclear whether applications of SEM should attempt to provide complete…

  16. Causality violation and paradoxes

    NASA Astrophysics Data System (ADS)

    Krasnikov, S. V.

    1997-03-01

    Paradoxes that can supposedly occur if causality is violated are discussed. It is shown that the existence of ``trajectories of multiplicity zero'' (i.e., trajectories that describe, say, a ball hitting its younger self so that the latter cannot fall into the time machine) is not paradoxical by itself. This apparent paradox can be resolved (at least sometimes) without any harm to local physics or to the time machine. Also a simple model is adduced for which the absence of true paradoxes caused by self-interaction in an acausal world is proved. The conclusion is made that the paradoxes appear if and (within this model) only if the fact is neglected that no conditions fixed to the past of a time machine guarantee that a system remains isolated after it intersects the Cauchy horizon.

  17. Causal electromagnetic interaction equations

    SciTech Connect

    Zinoviev, Yury M.

    2011-02-15

    For the electromagnetic interaction of two particles the relativistic causal quantum mechanics equations are proposed. These equations are solved for the case when the second particle moves freely. The initial wave functions are supposed to be smooth and rapidly decreasing at the infinity. This condition is important for the convergence of the integrals similar to the integrals of quantum electrodynamics. We also consider the singular initial wave functions in the particular case when the second particle mass is equal to zero. The discrete energy spectrum of the first particle wave function is defined by the initial wave function of the free-moving second particle. Choosing the initial wave functions of the free-moving second particle it is possible to obtain a practically arbitrary discrete energy spectrum.

  18. Stress-induced chemical waves in sediment burial diagenesis.

    PubMed

    Wang, Yifeng; Budd, David A

    2012-01-01

    Lateral metre-scale periodic variations in porosity and composition are found in many dolomite strata. Such variations may embed important information about dolomite formation and transformation. Here we show that these variations could be fossilized chemical waves emerging from stress-mediated mineral-water interaction during sediment burial diagenesis. Under the overlying loading, crystals in higher porosity domains are subjected to a higher effective stress, causing pressure solution. The dissolved species diffuse to and precipitate in neighbouring lower porosity domains, further reducing the porosity. This positive feedback leads to lateral porosity and compositional patterning in dolomite. The pattern geometry depends on fluid flow regimes. In a diffusion-dominated case, the low- and high-porosity domains alternate spatially with no directional preference, while, in the presence of an advective flow, this alternation occurs only along the flow direction, propagating like a chemical wave. Our work provides a new perspective for interpreting diagenetic signatures in sedimentary rocks. PMID:22353716

  19. Stress-induced chemical waves in sediment burial diagenesis.

    PubMed

    Wang, Yifeng; Budd, David A

    2012-01-01

    Lateral metre-scale periodic variations in porosity and composition are found in many dolomite strata. Such variations may embed important information about dolomite formation and transformation. Here we show that these variations could be fossilized chemical waves emerging from stress-mediated mineral-water interaction during sediment burial diagenesis. Under the overlying loading, crystals in higher porosity domains are subjected to a higher effective stress, causing pressure solution. The dissolved species diffuse to and precipitate in neighbouring lower porosity domains, further reducing the porosity. This positive feedback leads to lateral porosity and compositional patterning in dolomite. The pattern geometry depends on fluid flow regimes. In a diffusion-dominated case, the low- and high-porosity domains alternate spatially with no directional preference, while, in the presence of an advective flow, this alternation occurs only along the flow direction, propagating like a chemical wave. Our work provides a new perspective for interpreting diagenetic signatures in sedimentary rocks.

  20. Chemical products induce resistance to Xanthomonas perforans in tomato.

    PubMed

    Itako, Adriana Terumi; Tolentino Júnior, João Batista; Silva Júnior, Tadeu Antônio Fernandes da; Soman, José Marcelo; Maringoni, Antonio Carlos

    2015-01-01

    The bacterial spot of tomato, caused by Xanthomonas spp., is a very important disease, especially in the hot and humid periods of the year. The chemical control of the disease has not been very effective for a number of reasons. This study aimed to evaluate, under greenhouse conditions, the efficacy of leaf-spraying chemicals (acibenzolar-S-methyl (ASM) (0.025 g.L(-1)), fluazinam (0.25 g.L(-1)), pyraclostrobin (0.08 g.L(-1)), pyraclostrobin + methiran (0.02 g.L(-1) + 2.2 g.L(-1)), copper oxychloride (1.50 g.L(-1)), mancozeb + copper oxychloride (0.88 g.L(-1) + 0.60 g.L(-1)), and oxytetracycline (0.40 g.L(-1))) on control of bacterial spot. Tomatoes Santa Clara and Gisele cultivars were pulverized 3 days before inoculation with Xanthomonas perforans. The production of enzymes associated with resistance induction (peroxidase, polyphenol oxidase, phenylalanine ammonia-lyase, β-1,3-glucanase, and protease) was quantified from leaf samples collected 24 hours before and 24 hours after chemical spraying and at 1, 2, 4, 6, and 8 days after bacterial inoculation. All products tested controlled bacterial spot, but only ASM, pyraclostrobin, and pyraclostrobin + metiram increased the production of peroxidase in the leaves of the two tomato cultivars, and increased the production of polyphenol oxidase and β-1,3-glucanase in the Santa Clara cultivar. PMID:26413050

  1. Chemical products induce resistance to Xanthomonas perforans in tomato

    PubMed Central

    Itako, Adriana Terumi; Tolentino, João Batista; da Silva, Tadeu Antônio Fernandes; Soman, José Marcelo; Maringoni, Antonio Carlos

    2015-01-01

    The bacterial spot of tomato, caused by Xanthomonas spp., is a very important disease, especially in the hot and humid periods of the year. The chemical control of the disease has not been very effective for a number of reasons. This study aimed to evaluate, under greenhouse conditions, the efficacy of leaf-spraying chemicals (acibenzolar-S-methyl (ASM) (0.025 g.L−1), fluazinam (0.25 g.L−1), pyraclostrobin (0.08 g.L−1), pyraclostrobin + methiran (0.02 g.L−1 + 2.2 g.L−1), copper oxychloride (1.50 g.L−1), mancozeb + copper oxychloride (0.88 g.L−1 + 0.60 g.L−1), and oxytetracycline (0.40 g.L−1)) on control of bacterial spot. Tomatoes Santa Clara and Gisele cultivars were pulverized 3 days before inoculation with Xanthomonas perforans. The production of enzymes associated with resistance induction (peroxidase, polyphenol oxidase, phenylalanine ammonia-lyase, β-1,3-glucanase, and protease) was quantified from leaf samples collected 24 hours before and 24 hours after chemical spraying and at 1, 2, 4, 6, and 8 days after bacterial inoculation. All products tested controlled bacterial spot, but only ASM, pyraclostrobin, and pyraclostrobin + metiram increased the production of peroxidase in the leaves of the two tomato cultivars, and increased the production of polyphenol oxidase and β-1,3-glucanase in the Santa Clara cultivar. PMID:26413050

  2. Noise-induced multistability in chemical systems: Discrete versus continuum modeling.

    PubMed

    Duncan, Andrew; Liao, Shuohao; Vejchodský, Tomáš; Erban, Radek; Grima, Ramon

    2015-04-01

    The noisy dynamics of chemical systems is commonly studied using either the chemical master equation (CME) or the chemical Fokker-Planck equation (CFPE). The latter is a continuum approximation of the discrete CME approach. It has recently been shown that for a particular system, the CFPE captures noise-induced multistability predicted by the CME. This phenomenon involves the CME's marginal probability distribution changing from unimodal to multimodal as the system size decreases below a critical value. We here show that the CFPE does not always capture noise-induced multistability. In particular we find simple chemical systems for which the CME predicts noise-induced multistability, whereas the CFPE predicts monostability for all system sizes.

  3. Biological relevance and consequences of chemical- or metal-induced DNA cross-linking

    SciTech Connect

    Paustenbach, D.J.; Finley, B.L.

    1996-03-01

    A vast number of chemicals are known to induce mutagenesis and/or carcinogenesis in mammals. Although disruption of cellular nuclear material resulting ultimately in mutagenesis/carcinogenesis can be accomplished by various mechanisms, the search for biomarkers of chemical-induced toxicity continues. This review focuses on the ability of certain metals or chemicals to bind to DNA in a cross-link fashion in whole animal as well as under in vitro conditions. The methodologies currently used to determine DNA cross-linking are described. The biological relevance of the presence of chemical- or metal-induced DNA cross-linking as a measure of carcinogenesis in humans is still under debate, as there is no clear correlation between the disease and the DNA cross-link reaction. 62 refs., 3 tabs.

  4. Causal sets and conservation laws in tests of Lorentz symmetry

    SciTech Connect

    Mattingly, David

    2008-06-15

    Many of the most important astrophysical tests of Lorentz symmetry also assume that energy momentum of the observed particles is exactly conserved. In the causal set approach to quantum gravity a particular kind of Lorentz symmetry holds but energy-momentum conservation may be violated. We show that incorrectly assuming exact conservation can give rise to a spurious signal of Lorentz symmetry violation for a causal set. However, the size of this spurious signal is much smaller than can be currently detected and hence astrophysical Lorentz symmetry tests as currently performed are safe from causal set induced violations of energy-momentum conservation.

  5. Expert Causal Reasoning and Explanation.

    ERIC Educational Resources Information Center

    Kuipers, Benjamin

    The relationship between cognitive psychologists and researchers in artificial intelligence carries substantial benefits for both. An ongoing investigation in causal reasoning in medical problem solving systems illustrates this interaction. This paper traces a dialectic of sorts in which three different types of causal resaoning for medical…

  6. Causal Inference in Retrospective Studies.

    ERIC Educational Resources Information Center

    Holland, Paul W.; Rubin, Donald B.

    1988-01-01

    The problem of drawing causal inferences from retrospective case-controlled studies is considered. A model for causal inference in prospective studies is applied to retrospective studies. Limitations of case-controlled studies are formulated concerning relevant parameters that can be estimated in such studies. A coffee-drinking/myocardial…

  7. Causal Inference and Developmental Psychology

    ERIC Educational Resources Information Center

    Foster, E. Michael

    2010-01-01

    Causal inference is of central importance to developmental psychology. Many key questions in the field revolve around improving the lives of children and their families. These include identifying risk factors that if manipulated in some way would foster child development. Such a task inherently involves causal inference: One wants to know whether…

  8. The Development of Causal Categorization

    ERIC Educational Resources Information Center

    Hayes, Brett K.; Rehder, Bob

    2012-01-01

    Two experiments examined the impact of causal relations between features on categorization in 5- to 6-year-old children and adults. Participants learned artificial categories containing instances with causally related features and noncausal features. They then selected the most likely category member from a series of novel test pairs.…

  9. Pretender punishment induced by chemical signalling in a queenless ant.

    PubMed

    Monnin, Thibaud; Ratnieks, Francis L W; Jones, Graeme R; Beard, Richard

    2002-09-01

    Animal societies are stages for both conflict and cooperation. Reproduction is often monopolized by one or a few individuals who behave aggressively to prevent subordinates from reproducing (for example, naked mole-rats, wasps and ants). Here we report an unusual mechanism by which the dominant individual maintains reproductive control. In the queenless ant Dinoponera quadriceps, only the alpha female reproduces. If the alpha is challenged by another female she chemically marks the pretender who is then punished by low-ranking females. This cooperation between alpha and low-rankers allows the alpha to inflict punishment indirectly, thereby maintaining her reproductive primacy without having to fight. PMID:12214231

  10. Interleukin 19 reduces inflammation in chemically induced experimental colitis.

    PubMed

    Matsuo, Yukiko; Azuma, Yasu-Taka; Kuwamura, Mitsuru; Kuramoto, Nobuyuki; Nishiyama, Kazuhiro; Yoshida, Natsuho; Ikeda, Yoshihito; Fujimoto, Yasuyuki; Nakajima, Hidemitsu; Takeuchi, Tadayoshi

    2015-12-01

    Inflammatory bowel disease results from chronic dysregulation of the mucosal immune system and aberrant activation of both the innate and adaptive immune responses. Interleukin (IL)-19, a member of the IL-10 family, functions as an anti-inflammatory cytokine. Here, we investigated the contribution of IL-19 to intestinal inflammation in a model of T cell-mediated colitis in mice. Inflammatory responses in IL-19-deficient mice were assessed using the 2,4,6-trinitrobenzene sulfonic acid (TNBS) model of acute colitis. IL-19 deficiency aggravated TNBS-induced colitis and compromised intestinal recovery in mice. Additionally, the exacerbation of TNBS-induced colonic inflammation following genetic ablation of IL-19 was accompanied by increased production of interferon-gamma, IL-12 (p40), IL-17, IL-22, and IL-33, and decreased production of IL-4. Moreover, the exacerbation of colitis following IL-19 knockout was also accompanied by increased production of CXCL1, G-CSF and CCL5. Using this model of induced colitis, our results revealed the immunopathological relevance of IL-19 as an anti-inflammatory cytokine in intestinal inflammation in mice.

  11. Chemically induced bidirectional differentiation of embryonal carcinoma cells in vitro.

    PubMed Central

    Speers, W. C.; Birdwell, C. R.; Dixon, F. J.

    1979-01-01

    N,N-dimethylacetamide, hexamethylene bisacetamide, and Polybrene induced rapid and extensive differentiation in vitro in an otherwise slowly differentiating subline of embryonal carcinoma cells. The type of differentiated cell induced was dependent on the spatial organization of the stem cells during drug treatment. In monalayer culture "epithelial" cells were produced exclusively. However, treatment of aggregated suspension cultures yielded predominantly "fibroblast-like" cells. The undifferentiated embryonal carcinoma cells and the two differentiated cell types were morphologically distinct when examined by light microscopy, scanning electron microscopy, and transmission electron microscopy; and they had differences in cell surface antigens. Both differential cell types produced large amounts of fibronectin, whereas the embryonal carcinoma cells produced only minimal amounts. This system provides a convenient way to induce relatively synchronous differentiation of embryonal carcinoma cells into specific differentiated cell types. Images Figure 5 Figure 6 Figure 1 Figure 2 Figure 3 Figure 4 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 Figure 13 Figure 14 PMID:507191

  12. Caspase-2 deficiency accelerates chemically induced liver cancer in mice.

    PubMed

    Shalini, S; Nikolic, A; Wilson, C H; Puccini, J; Sladojevic, N; Finnie, J; Dorstyn, L; Kumar, S

    2016-10-01

    Aberrant cell death/survival has a critical role in the development of hepatocellular carcinoma (HCC). Caspase-2, a cell death protease, limits oxidative stress and chromosomal instability. To study its role in reactive oxygen species (ROS) and DNA damage-induced liver cancer, we assessed diethylnitrosamine (DEN)-mediated tumour development in caspase-2-deficient (Casp2(-/-)) mice. Following DEN injection in young animals, tumour development was monitored for 10 months. We found that DEN-treated Casp2(-/-) mice have dramatically elevated tumour burden and accelerated tumour progression with increased incidence of HCC, accompanied by higher oxidative damage and inflammation. Furthermore, following acute DEN injection, liver injury, DNA damage, inflammatory cytokine release and hepatocyte proliferation were enhanced in mice lacking caspase-2. Our study demonstrates for the first time that caspase-2 limits the progression of tumourigenesis induced by an ROS producing and DNA damaging reagent. Our findings suggest that after initial DEN-induced DNA damage, caspase-2 may remove aberrant cells to limit liver damage and disease progression. We propose that Casp2(-/-) mice, which are more susceptible to genomic instability, are limited in their ability to respond to DNA damage and thus carry more damaged cells resulting in accelerated tumourigenesis.

  13. On causality of extreme events

    PubMed Central

    2016-01-01

    Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets, by analysing how extreme events in one element correspond to the appearance of extreme events in a second one. The metric is able to detect non-linear causalities; to analyse both cross-sectional and longitudinal data sets; and to discriminate between real causalities and correlations caused by confounding factors. We validate the metric through synthetic data, dynamical and chaotic systems, and data representing the human brain activity in a cognitive task. We further show how the proposed metric is able to outperform classical causality metrics, provided non-linear relationships are present and large enough data sets are available. PMID:27330866

  14. [Causality: risk factors and interventions].

    PubMed

    Dekkers, Olaf M; Vandenbroucke, Jan P

    2013-01-01

    A risk factor has a causal effect on a disease when the disease would not have occurred in the absence of the risk factor. Analogous reasoning applies to the effect of a particular therapy. Thinking in terms of contrasts is fundamental to causal reasoning in medicine. The contrast determines the content of the causal claim; the most important assumption here is that the prognosis between groups is comparable. Causal effects of risk factors are not always the same as the causal effect of an intervention: removal of a risk factor (e.g. smoking) for a disease does not necessarily mean that the risk will subsequently normalize. A second problem is that risk factors cannot always easily be translated into interventions. This applies to factors that cannot be changed (e.g. gender) or that can have multiple causes themselves (e.g. obesity).

  15. On causality of extreme events.

    PubMed

    Zanin, Massimiliano

    2016-01-01

    Multiple metrics have been developed to detect causality relations between data describing the elements constituting complex systems, all of them considering their evolution through time. Here we propose a metric able to detect causality within static data sets, by analysing how extreme events in one element correspond to the appearance of extreme events in a second one. The metric is able to detect non-linear causalities; to analyse both cross-sectional and longitudinal data sets; and to discriminate between real causalities and correlations caused by confounding factors. We validate the metric through synthetic data, dynamical and chaotic systems, and data representing the human brain activity in a cognitive task. We further show how the proposed metric is able to outperform classical causality metrics, provided non-linear relationships are present and large enough data sets are available.

  16. Apparent causality affects perceived simultaneity.

    PubMed

    Kohlrausch, Armin; van Eijk, Rob; Juola, James F; Brandt, Inge; van de Par, Steven

    2013-10-01

    The present research addresses the question of how visual predictive information and implied causality affect audio-visual synchrony perception. Previous research has shown a systematic shift in the likelihood of observers to accept audio-leading stimulus pairs as being apparently simultaneous in variants of audio-visual stimulus pairs that differ in (1) the amount of visual predictive information available and (2) the apparent causal relation between the auditory and visual components. An experiment was designed to separate the predictability and causality explanations, and the results indicated that shifts in subjective simultaneity were explained completely by changes in the implied causal relations in the stimuli and that predictability had no added value. Together with earlier findings, these results further indicate that the observed shifts in subjective simultaneity due to causal relations among auditory and visual events do not reflect a mere change in response strategy, but rather result from early multimodal integration processes in event perception.

  17. CausalTrail: Testing hypothesis using causal Bayesian networks

    PubMed Central

    Trampert, Patrick; Lenhof, Hans-Peter

    2015-01-01

    Summary Causal Bayesian Networks are a special class of Bayesian networks in which the hierarchy directly encodes the causal relationships between the variables. This allows to compute the effect of interventions, which are external changes to the system, caused by e.g. gene knockouts or an administered drug. Whereas numerous packages for constructing causal Bayesian networks are available, hardly any program targeted at downstream analysis exists. In this paper we present CausalTrail, a tool for performing reasoning on causal Bayesian networks using the do-calculus. CausalTrail's features include multiple data import methods, a flexible query language for formulating hypotheses, as well as an intuitive graphical user interface. The program is able to account for missing data and thus can be readily applied in multi-omics settings where it is common that not all measurements are performed for all samples. Availability and Implementation CausalTrail is implemented in C++ using the Boost and Qt5 libraries. It can be obtained from https://github.com/dstoeckel/causaltrail PMID:26913195

  18. The Visual Causality Analyst: An Interactive Interface for Causal Reasoning.

    PubMed

    Wang, Jun; Mueller, Klaus

    2016-01-01

    Uncovering the causal relations that exist among variables in multivariate datasets is one of the ultimate goals in data analytics. Causation is related to correlation but correlation does not imply causation. While a number of casual discovery algorithms have been devised that eliminate spurious correlations from a network, there are no guarantees that all of the inferred causations are indeed true. Hence, bringing a domain expert into the casual reasoning loop can be of great benefit in identifying erroneous casual relationships suggested by the discovery algorithm. To address this need we present the Visual Causal Analyst-a novel visual causal reasoning framework that allows users to apply their expertise, verify and edit causal links, and collaborate with the causal discovery algorithm to identify a valid causal network. Its interface consists of both an interactive 2D graph view and a numerical presentation of salient statistical parameters, such as regression coefficients, p-values, and others. Both help users in gaining a good understanding of the landscape of causal structures particularly when the number of variables is large. Our framework is also novel in that it can handle both numerical and categorical variables within one unified model and return plausible results. We demonstrate its use via a set of case studies using multiple practical datasets.

  19. Chemical- and radiation-induced haemorrhagic cystitis: current treatments and challenges

    PubMed Central

    Payne, Heather; Adamson, Andrew; Bahl, Amit; Borwell, Jonathan; Dodds, David; Heath, Catherine; Huddart, Robert; McMenemin, Rhona; Patel, Prashant; Peters, John L; Thompson, Andrew

    2013-01-01

    To review the published data on predisposing risk factors for cancer treatment-induced haemorrhagic cystitis (HC) and the evidence for the different preventive and therapeutic measures that have been used in order to help clinicians optimally define and manage this potentially serious condition. Despite recognition that HC can be a significant complication of cancer treatment, there is currently a lack of UK-led guidelines available on how it should optimally be defined and managed. A systematic literature review was undertaken to evaluate the evidence for preventative measures and treatment options in the management of cancer treatment-induced HC. There is a wide range of reported incidence due to several factors including variability in study design and quality, the type of causal agent, the grading of bleeding, and discrepancies in definition criteria. The most frequently reported causal factors are radiotherapy to the pelvic area, where HC has been reported in up to 20% of patients, and treatment with cyclophosphamide and bacillus Calmette-Guérin, where the incidence has been reported as up to 30%. Mesna (2-mercaptoethane sodium sulphonate), hyperhydration and bladder irrigation have been the most frequently used prophylactic measures to prevent treatment-related cystitis, but are not always effective. Cranberry juice is widely cited as a preventative measure and sodium pentosanpolysulphate as a treatment, although the evidence for both is very limited. The best evidence exists for intravesical hyaluronic acid as an effective preventative and active treatment, and for hyperbaric oxygen as an equally effective treatment option. The lack of robust data and variability in treatment strategies used highlights the need for further research, as well as best practice guidance and consensus on the management of HC. PMID:24000900

  20. Chemically induced strength changes in sandstone. Report of Investigations/1993

    SciTech Connect

    Stroud, W.P.; Dolinar, D.R.

    1993-01-01

    Chemical alteration of the compressive strength of sandstone has been investigated by the U.S. Bureau of Mines (USBM). Successful development of this technology would offer an attractive alternative to the methods now used for stress control in mines. Sandstone cores were stressed to failure under uniaxial compression at two different strain rates. Specimens saturated with either distilled or tap water showed an average 14% reduction in stress at failure compared with those dried in vacuum. Samples saturated with dilute solutions of aluminum chloride, hydrochloric acid, and polyethylene oxide showed no statistically significant difference in failure stress compared with those saturated with water. By contrast, compressive strength of the cores was increased some 7% by saturation with the nonpolar solvent carbon tetrachloride. No correlation was found between zeta potential and compressive strength.

  1. Spin Manipulation in Graphene by Chemically Induced Pseudospin Polarization.

    PubMed

    Van Tuan, Dinh; Roche, Stephan

    2016-03-11

    Spin manipulation is one of the most critical challenges to realize spin-based logic devices and spintronic circuits. Graphene has been heralded as an ideal material to achieve spin manipulation, but so far new paradigms and demonstrators are limited. Here we show that certain impurities such as fluorine adatoms, which locally break sublattice symmetry without the formation of strong magnetic moment, could result in a remarkable variability of spin transport characteristics. The impurity resonance level is found to be associated with a long-range sublattice pseudospin polarization, which by locally decoupling spin and pseudospin dynamics provokes a huge spin lifetime electron-hole asymmetry. In the dilute impurity limit, spin lifetimes could be tuned electrostatically from 100 ps to several nanoseconds, providing a protocol to chemically engineer an unprecedented spin device functionality. PMID:27015500

  2. Altered Acer Rubrum Fecundity Induced By Chemical Climate Change

    NASA Astrophysics Data System (ADS)

    Deforest, J. L.; Peters, A.

    2014-12-01

    Red maple (Acer rubrum L.) is becoming the most dominating tree in North American eastern deciduous forests. Concurrently, human activities have altered the chemical climate of terrestrial ecosystems via acidic deposition, which increases the available of nitrogen (N), while decreasing phosphorus (P) availability. Once a minor forest component prior to European settlement, the abundance of red maple may be a symptom of the modern age. The current paradigm explaining red maple's rise to prominence concerns fire suppression that excludes competitors. However, this still does not explain why red maple is unique compared to other functionally similar trees. The objective of this study was to investigate the interactive influence of acid rain mitigation on the fecundity of red maple. Objectives were achieved by measuring flowering, seed production, germination, and growth from red maple on plots that have been experimentally manipulated to increase soil pH, P, or both in three unglaciated eastern deciduous hardwood forests. At least 50% of the red maple population is seed bearing in our control soils, however the median percent of seed-bearing trees declined to zero when mitigating soils from acidic deposition. This can be explained by the curious fact that red maple is polygamodioecious, or has labile sex-expression, in which an individual tree can change its sex-expression in response to the environment. Furthermore, seed-bearing trees in the mitigated plots grew less, produced less seeds, and germinated at lower rates than their counterparts in control soils. Our results provide evidence that chemical climate change could be the primary contributing factor accelerating the dominance of red maple in eastern North American forests. Our observations can provide a boarder conceptual framework for understanding how nutrient limitations can be applied beyond plant productivity towards explaining distribution changes in vegetation.

  3. CD-REST: a system for extracting chemical-induced disease relation in literature

    PubMed Central

    Xu, Jun; Wu, Yonghui; Zhang, Yaoyun; Wang, Jingqi; Lee, Hee-Jin; Xu, Hua

    2016-01-01

    Mining chemical-induced disease relations embedded in the vast biomedical literature could facilitate a wide range of computational biomedical applications, such as pharmacovigilance. The BioCreative V organized a Chemical Disease Relation (CDR) Track regarding chemical-induced disease relation extraction from biomedical literature in 2015. We participated in all subtasks of this challenge. In this article, we present our participation system Chemical Disease Relation Extraction SysTem (CD-REST), an end-to-end system for extracting chemical-induced disease relations in biomedical literature. CD-REST consists of two main components: (1) a chemical and disease named entity recognition and normalization module, which employs the Conditional Random Fields algorithm for entity recognition and a Vector Space Model-based approach for normalization; and (2) a relation extraction module that classifies both sentence-level and document-level candidate drug–disease pairs by support vector machines. Our system achieved the best performance on the chemical-induced disease relation extraction subtask in the BioCreative V CDR Track, demonstrating the effectiveness of our proposed machine learning-based approaches for automatic extraction of chemical-induced disease relations in biomedical literature. The CD-REST system provides web services using HTTP POST request. The web services can be accessed from http://clinicalnlptool.com/cdr. The online CD-REST demonstration system is available at http://clinicalnlptool.com/cdr/cdr.html. Database URL: http://clinicalnlptool.com/cdr; http://clinicalnlptool.com/cdr/cdr.html PMID:27016700

  4. Causal Rasch models

    PubMed Central

    Stenner, A. Jackson; Fisher, William P.; Stone, Mark H.; Burdick, Donald S.

    2013-01-01

    Rasch's unidimensional models for measurement show how to connect object measures (e.g., reader abilities), measurement mechanisms (e.g., machine-generated cloze reading items), and observational outcomes (e.g., counts correct on reading instruments). Substantive theory shows what interventions or manipulations to the measurement mechanism can be traded off against a change to the object measure to hold the observed outcome constant. A Rasch model integrated with a substantive theory dictates the form and substance of permissible interventions. Rasch analysis, absent construct theory and an associated specification equation, is a black box in which understanding may be more illusory than not. Finally, the quantitative hypothesis can be tested by comparing theory-based trade-off relations with observed trade-off relations. Only quantitative variables (as measured) support such trade-offs. Note that to test the quantitative hypothesis requires more than manipulation of the algebraic equivalencies in the Rasch model or descriptively fitting data to the model. A causal Rasch model involves experimental intervention/manipulation on either reader ability or text complexity or a conjoint intervention on both simultaneously to yield a successful prediction of the resultant observed outcome (count correct). We conjecture that when this type of manipulation is introduced for individual reader text encounters and model predictions are consistent with observations, the quantitative hypothesis is sustained. PMID:23986726

  5. History, causality, and sexology.

    PubMed

    Money, John

    2003-08-01

    In 1896, Krafft-Ebing published Psychopathia Sexualis. Popularly defined as hereditary weakness or taintedness in the family pedigree, degeneracy was called upon as a causal explanation for perversions of the sexual instinct. Although Krafft-Ebing accepted Karl Ulrichs proposal that homosexuality could be innate and probably located in the brain, he paid little attention to neuropathological sexology. Alfred Binet challenged Krafft-Ebing's orthodoxy by explaining fetishism in terms of associative learning, to which Krafft-Ebing's response was that only those with a hereditary taint would be vulnerable. Thus did the venerable nature-nurture antithesis maintain its rhetoric, even to the present day. Krafft-Ebing died too soon to meet the Freudian challenge of endopsychic determinism, and too soon also to encounter the idea of a developmental multivariate outcome of what I have termed the lovemap. Like other brain maps, for example the languagemap, the lovemap requires an intact human brain in which to develop. The personalized content of the lovemap has access to the brain by way of the special senses.

  6. Characterization of Necrosis and Ethylene inducing Proteins (NEP) in the Basidiomycete Moniliophthora perniciosa, the Causal Agent of Witches’ Broom in Theobroma cacao

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The hemibiotrophic basidiomycete Moniliophthora perniciosa causes witches’ broom disease of Theobroma cacao. Analysis of the M. perniciosa draft genome led to the identification of three putative genes encoding Necrosis and Ethylene inducing Proteins (MpNEPs), which are apparently located on the sam...

  7. 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.

    PubMed

    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.

  8. "Head take you": causal attributions of mental illness in Jamaica.

    PubMed

    Arthur, Carlotta M; Whitley, Rob

    2015-02-01

    Causal attributions are a key factor in explanatory models of illness; however, little research on causal attributions of mental illness has been conducted in developing nations in the Caribbean, including Jamaica. Explanatory models of mental illness may be important in understanding illness experience and be a crucial factor in mental health service seeking and utilization. We explored causal attributions of mental illness in Jamaica by conducting 20 focus groups, including 16 community samples, 2 patient samples, and 2 samples of caregivers of patients, with a total of 159 participants. The 5 most commonly endorsed causal attributions of mental illness are discussed: (a) drug-related causes, including ganja (marijuana); (b) biological causes, such as chemical imbalance, familial transmission, and "blood"; (c) psychological causes, including stress and thinking too much; (d) social causes, such as relationship problems and job loss; and (e) spiritual or religious causes, including Obeah.

  9. Hygienic grooming is induced by contact chemicals in Drosophila melanogaster

    PubMed Central

    Yanagawa, Aya; Guigue, Alexandra M. A.; Marion-Poll, Frédéric

    2014-01-01

    In social insects, grooming is considered as a behavioral defense against pathogen and parasite infections since it contributes to remove microbes from their cuticle. However, stimuli which trigger this behavior are not well characterized yet. We examined if activating contact chemoreceptive sensilla could trigger grooming activities in Drosophila melanogaster. We monitored the grooming responses of decapitated flies to compounds known to activate the immune system, e.g., dead Escherichia coli (Ec) and lipopolysaccharides (LPS), and to tastants such as quinine, sucrose, and salt. LPS, quinine, and Ec were quite effective in triggering grooming movements when touching the distal border of the wings and the legs, while sucrose had no effect. Contact chemoreceptors are necessary and sufficient to elicit such responses, as grooming could not be elicited by LPS in poxn mutants deprived of external taste sensilla, and as grooming was elicited by light when a channel rhodopsin receptor was expressed in bitter-sensitive cells expressing Gr33a. Contact chemoreceptors distributed along the distal border of the wings respond to these tastants by an increased spiking activity, in response to quinine, Ec, LPS, sucrose, and KCl. These results demonstrate for the first time that bacterial compounds trigger grooming activities in D. melanogaster, and indicate that contact chemoreceptors located on the wings participate in the detection of such chemicals. PMID:25100963

  10. Hygienic grooming is induced by contact chemicals in Drosophila melanogaster.

    PubMed

    Yanagawa, Aya; Guigue, Alexandra M A; Marion-Poll, Frédéric

    2014-01-01

    In social insects, grooming is considered as a behavioral defense against pathogen and parasite infections since it contributes to remove microbes from their cuticle. However, stimuli which trigger this behavior are not well characterized yet. We examined if activating contact chemoreceptive sensilla could trigger grooming activities in Drosophila melanogaster. We monitored the grooming responses of decapitated flies to compounds known to activate the immune system, e.g., dead Escherichia coli (Ec) and lipopolysaccharides (LPS), and to tastants such as quinine, sucrose, and salt. LPS, quinine, and Ec were quite effective in triggering grooming movements when touching the distal border of the wings and the legs, while sucrose had no effect. Contact chemoreceptors are necessary and sufficient to elicit such responses, as grooming could not be elicited by LPS in poxn mutants deprived of external taste sensilla, and as grooming was elicited by light when a channel rhodopsin receptor was expressed in bitter-sensitive cells expressing Gr33a. Contact chemoreceptors distributed along the distal border of the wings respond to these tastants by an increased spiking activity, in response to quinine, Ec, LPS, sucrose, and KCl. These results demonstrate for the first time that bacterial compounds trigger grooming activities in D. melanogaster, and indicate that contact chemoreceptors located on the wings participate in the detection of such chemicals.

  11. Detecting causality in complex ecosystems.

    PubMed

    Sugihara, George; May, Robert; Ye, Hao; Hsieh, Chih-hao; Deyle, Ethan; Fogarty, Michael; Munch, Stephan

    2012-10-26

    Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. We introduce a method, based on nonlinear state space reconstruction, that can distinguish causality from correlation. It extends to nonseparable weakly connected dynamic systems (cases not covered by the current Granger causality paradigm). The approach is illustrated both by simple models (where, in contrast to the real world, we know the underlying equations/relations and so can check the validity of our method) and by application to real ecological systems, including the controversial sardine-anchovy-temperature problem.

  12. Human causal discovery from observational data.

    PubMed Central

    Hashem, A. I.; Cooper, G. F.

    1996-01-01

    Utilizing Bayesian belief networks as a model of causality, we examined medical students' ability to discover causal relationships from observational data. Nine sets of patient cases were generated from relatively simple causal belief networks by stochastic simulation. Twenty participants examined the data sets and attempted to discover the underlying causal relationships. Performance was poor in general, except at discovering the absence of a causal relationship. This work supports the potential for combining human and computer methods for causal discovery. PMID:8947621

  13. Approaches to immunotoxicologic studies with emphasis on chemical-induced immunomodulation

    SciTech Connect

    Munson, A.E.; McCay, J.A.; Cao, W. )

    1991-06-01

    Immunotoxicology has developed into a subdiscipline of toxicology in a tradition similar to other subdisciplines of toxicology. The use of experimental animals to determine the potential for chemicals to alter the structure and function of the immune system represents a significant part of this subdiscipline. This manuscript describes approaches to assessment of chemical-induced modification of immune status and key issues in interpreting the data for risk assessment.21 references.

  14. Cell Therapy for Chemically Induced Ovarian Failure in Mice

    PubMed Central

    Terraciano, Paula; Durli, Isabel; Baggio, Melchiani; Kuhl, Cristiana Palma; Laurino, Claudia; Passos, Eduardo; Paz, Ana Helena; Cirne-Lima, Elizabeth

    2014-01-01

    Cell therapy has been linked to an unexplained return of ovarian function and fertility in some cancer survivors. Studies modeling this in mice have shown that cells transplantation generates donor-derived oocytes in chemotherapy-treated recipients. This study was conducted to further clarify the impact of cell transplantation from different sources on female reproductive function after chemotherapy using a preclinical mouse model. Methods. Female mice were administered 7.5 mg/kg cisplatin followed by cell transplantation (one week later) using GFP+ female cell donors. For cell tracking, adipose derived stem cell GFP+ (ADSC), female germline stem cell GFP+/MVH+ (FGSC), or ovary cell suspension GFP+ mice were transplanted into cisplatin-treated wild-type recipients. After 7 or 14 days animals were killed and histological analysis, IHQ for GFP cells, and ELISA for estradiol were performed. Results. Histological examinations showed that ADSC, ovary cell suspension, and FGSC transplant increase the number of follicles with apparent normal structure in the cells recipient group euthanized on day 7. Cell tracking showed GFP+ samples 7 days after transplant. Conclusion. These data suggest that intraovarian injection of ADSCs and FGSC into mice with chemotherapy-induced ovarian failure diminished the damage caused by cisplatin. PMID:25548574

  15. Chemically induced Jahn-Teller ordering on manganite surfaces.

    PubMed

    Gai, Zheng; Lin, Wenzhi; Burton, J D; Fuchigami, K; Snijders, P C; Ward, T Z; Tsymbal, Evgeny Y; Shen, J; Jesse, Stephen; Kalinin, Sergei V; Baddorf, Arthur P

    2014-01-01

    Physical and electrochemical phenomena at the surfaces of transition metal oxides and their coupling to local functionality remains one of the enigmas of condensed matter physics. Understanding the emergent physical phenomena at surfaces requires the capability to probe the local composition, map order parameter fields and establish their coupling to electronic properties. Here we demonstrate that measuring the sub-30-pm displacements of atoms from high-symmetry positions in the atomically resolved scanning tunnelling microscopy allows the physical order parameter fields to be visualized in real space on the single-atom level. Here, this local crystallographic analysis is applied to the in-situ-grown manganite surfaces. In particular, using direct bond-angle mapping we report direct observation of structural domains on manganite surfaces, and trace their origin to surface-chemistry-induced stabilization of ordered Jahn-Teller displacements. Density functional calculations provide insight into the intriguing interplay between the various degrees of freedom now resolved on the atomic level. PMID:25058540

  16. Chemical modification of normal tissue damage induced by photodynamic therapy.

    PubMed Central

    Sigdestad, C. P.; Fingar, V. H.; Wieman, T. J.; Lindberg, R. D.

    1996-01-01

    One of the limitations of successful use of photodynamic therapy (PDT) employing porphyrins is the acute and long-term cutaneous photosensitivity. This paper describes results of experiments designed to test the effects of two radiation protective agents (WR-2721, 500 mg kg-1 or WR-3689, 700 mg kg-1) on murine skin damage induced by PDT. C3H mice were shaved and depilated three days prior to injection with the photosensitiser, Photofrin (5 or 10 mg kg-1). Twenty-four hours later, the mice were injected intraperitoneally with a protector 30 min prior to Argon dye laser (630 nm) exposure. The skin response was followed for two weeks post irradiation using an arbitrary response scale. A light dose response as well as a drug dose response was obtained. The results indicate that both protectors reduced the skin response to PDT, however WR-2721 was demonstrated to be the most effective. The effect of the protectors on vascular stasis after PDT was determined using a fluorescein dye exclusion assay. In mice treated with Photofrin (5 mg kg-1), and 630 nm light (180 J cm-2) pretreatment with either WR-2721 or WR-3689 resulted in significant protection of the vascular effects of PDT. These studies document the ability of the phosphorothioate class of radiation protective agents to reduce the effects of light on photosensitized skin. They do so in a drug dose-dependent fashion with maximum protection at the highest drug doses. PMID:8763855

  17. Molecular noise induces concentration oscillations in chemical systems with stable node steady states

    NASA Astrophysics Data System (ADS)

    Toner, D. L. K.; Grima, R.

    2013-02-01

    It is well known that internal or molecular noise induces concentration oscillations in chemical systems whose deterministic models exhibit damped oscillations. In this article we show, using the linear-noise approximation of the chemical master equation, that noise can also induce oscillations in systems whose deterministic descriptions admit no damped oscillations, i.e., systems with a stable node. This non-intuitive phenomenon is remarkable since, unlike noise-induced oscillations in systems with damped deterministic oscillations, it cannot be explained by noise excitation of the deterministic resonant frequency of the system. We here prove the following general properties of stable-node noise-induced oscillations for systems with two species: (i) the upper bound of their frequency is given by the geometric mean of the real eigenvalues of the Jacobian of the system, (ii) the upper bound of the Q-factor of the oscillations is inversely proportional to the distance between the real eigenvalues of the Jacobian, and (iii) these oscillations are not necessarily exhibited by all interacting chemical species in the system. The existence and properties of stable-node oscillations are verified by stochastic simulations of the Brusselator, a cascade Brusselator reaction system, and two other simple chemical systems involving auto-catalysis and trimerization. It is also shown how external noise induces stable node oscillations with different properties than those stimulated by internal noise.

  18. Molecular noise induces concentration oscillations in chemical systems with stable node steady states.

    PubMed

    Toner, D L K; Grima, R

    2013-02-01

    It is well known that internal or molecular noise induces concentration oscillations in chemical systems whose deterministic models exhibit damped oscillations. In this article we show, using the linear-noise approximation of the chemical master equation, that noise can also induce oscillations in systems whose deterministic descriptions admit no damped oscillations, i.e., systems with a stable node. This non-intuitive phenomenon is remarkable since, unlike noise-induced oscillations in systems with damped deterministic oscillations, it cannot be explained by noise excitation of the deterministic resonant frequency of the system. We here prove the following general properties of stable-node noise-induced oscillations for systems with two species: (i) the upper bound of their frequency is given by the geometric mean of the real eigenvalues of the Jacobian of the system, (ii) the upper bound of the Q-factor of the oscillations is inversely proportional to the distance between the real eigenvalues of the Jacobian, and (iii) these oscillations are not necessarily exhibited by all interacting chemical species in the system. The existence and properties of stable-node oscillations are verified by stochastic simulations of the Brusselator, a cascade Brusselator reaction system, and two other simple chemical systems involving auto-catalysis and trimerization. It is also shown how external noise induces stable node oscillations with different properties than those stimulated by internal noise. PMID:23406149

  19. Causal learning with local computations.

    PubMed

    Fernbach, Philip M; Sloman, Steven A

    2009-05-01

    The authors proposed and tested a psychological theory of causal structure learning based on local computations. Local computations simplify complex learning problems via cues available on individual trials to update a single causal structure hypothesis. Structural inferences from local computations make minimal demands on memory, require relatively small amounts of data, and need not respect normative prescriptions as inferences that are principled locally may violate those principles when combined. Over a series of 3 experiments, the authors found (a) systematic inferences from small amounts of data; (b) systematic inference of extraneous causal links; (c) influence of data presentation order on inferences; and (d) error reduction through pretraining. Without pretraining, a model based on local computations fitted data better than a Bayesian structural inference model. The data suggest that local computations serve as a heuristic for learning causal structure.

  20. Purified Si film formation from metallurgical-grade Si by hydrogen plasma induced chemical transport

    SciTech Connect

    Ohmi, Hiromasa; Goto, Akihiro; Kamada, Daiki; Hamaoka, Yoshinori; Kakiuchi, Hiroaki; Yasutake, Kiyoshi

    2009-11-02

    Purified Si film is prepared directly from metallurgical-grade Si (MG-Si) by using hydrogen plasma induced chemical transport at subatmospheric pressure. The purification mechanism is based on the different hydrogenation behaviors of the various impurity elements in MG-Si. The prepared Si films clearly had fewer typical metal impurities (Fe, Al, Ti, Cr, Mn, etc.) than those in the MG-Si. In particular, the Fe concentration was drastically reduced from 6900 mass ppm to less than 0.1 mass ppm by one time chemical transport. Furthermore, metal impurity concentrations were further reduced by repeating chemical transport deposition.

  1. Mechanisms of the hepatoprotective effects of tamoxifen against drug-induced and chemical-induced acute liver injuries

    SciTech Connect

    Yoshikawa, Yukitaka; Miyashita, Taishi; Higuchi, Satonori; Tsuneyama, Koichi; Endo, Shinya; Tsukui, Tohru; Toyoda, Yasuyuki; Fukami, Tatsuki; Nakajima, Miki; Yokoi, Tsuyoshi

    2012-10-01

    Although estrogen receptor (ER)α agonists, such as estradiol and ethinylestradiol (EE2), cause cholestasis in mice, they also reduce the degree of liver injury caused by hepatotoxicants as well as ischemia–reperfusion. The functional mechanisms of ERα have yet to be elucidated in drug-induced or chemical-induced liver injury. The present study investigated the effects of an ERα agonist, selective ER modulators (SERMs) and an ER antagonist on drug-induced and chemical-induced liver injuries caused by acetaminophen, bromobenzene, diclofenac, and thioacetamide (TA). We observed hepatoprotective effects of EE2, tamoxifen (TAM) and raloxifene pretreatment in female mice that were exposed to a variety of hepatotoxic compounds. In contrast, the ER antagonist did not show any hepatoprotective effects. DNA microarray analyses suggested that monocyte to macrophage differentiation-associated 2 (Mmd2) protein, which has an unknown function, is commonly increased by TAM and RAL pretreatment, but not by pretreatment with the ER antagonist. In ERα-knockout mice, the hepatoprotective effects of TAM and the increased expression of Mmd2 mRNA were not observed in TA-induced liver injury. To investigate the function of Mmd2, the expression level of Mmd2 mRNA was significantly knocked down to approximately 30% in mice by injection of siRNA for Mmd2 (siMmd2). Mmd2 knockdown resulted in a reduction of the protective effects of TAM on TA-induced liver injury in mice. This is the first report of the involvement of ERα in drug-induced or chemical-induced liver injury. Upregulation of Mmd2 protein in the liver was suggested as the mechanism of the hepatoprotective effects of EE2 and SERMs. -- Highlights: ► Liver injury induced by drugs or chemicals was investigated in mice. ► Liver injury was suppressed by pretreatment with tamoxifen in female mice. ► Mmd2, whose function was unknown, could be a candidate gene for liver protection. ► Tamoxifen up-regulated Mmd2 mRNA expression

  2. Chemical inducible promotor used to obtain transgenic plants with a silent marker

    DOEpatents

    Chua, Nam-Hai; Aoyama, Takashi

    2000-01-01

    A chemically inducible promoter is described which may be used to transform plants with genes which are easily regulatable by adding plants or plant cells to a medium containing an inducer of the promoter or by removing the plants or plant cells from such medium. The promoter described is one which is inducible by a glucocorticoid which is not endogenous to plants. Such promoters may be used with a variety of genes such as ipt or knotted1 to induce shoot formation in the presence of a glucocorticoid. The promoter may also be used with antibiotic or herbicide resistance genes which are then regulatable by the presence or absence of inducer rather than being constitutive. Other examples of genes which may be placed under the control of the inducible promoter are also presented.

  3. Chemical inducible promotor used to obtain transgenic plants with a silent marker

    SciTech Connect

    Chua, N.H.; Aoyama, Takashi

    2000-05-16

    A chemically inducible promoter is described which may be used to transform plants with genes which are easily regulatable by adding plants or plant cells to a medium containing an inducer of the promoter or by removing the plants or plant cells from such medium. The promoter is inducible by a glucocorticoid which is not endogenous to plants. Such promoters may be used with a variety of genes such as ipt or knotted1 to induce shoot formation in the presence of a glucocorticoid. The promoter may also be used with antibiotic or herbicide resistance genes which are then regulatable by the presence or absence of inducer rather than being constitutive. Other examples of genes which may be placed under the control of the inducible promoter are also presented.

  4. Chemical inducible promoter used to obtain transgenic plants with a silent marker

    DOEpatents

    Aoyama, Takashi; Zuo, Jianru; Chua, Nam-Hai

    2004-08-31

    A chemically inducible promoter is described that may be used to transform plants, including tobacco and lettuce, with genes which are easily regulatable by adding the plants or plant cells to a medium containing an inducer of the promoter or by removing the plants or plant cells from such medium. The promoter described is one that is inducible by a glucocorticoid which is not endogenous to plants. Such promoters may be used with a variety of genes such as ipt or knotted1 to induce shoot formation in the presence of a glucocorticoid. The promoter may also be used with antibiotic or herbicide resistance genes which are then regulatable by the presence or absence of inducer rather than being constitutive. Other examples of genes which may be placed under the control of the inducible promoter are also presented.

  5. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule.

    PubMed

    Zheng, Peng; Arantes, Guilherme M; Field, Martin J; Li, Hongbin

    2015-06-25

    Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions.

  6. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule

    NASA Astrophysics Data System (ADS)

    Zheng, Peng; Arantes, Guilherme M.; Field, Martin J.; Li, Hongbin

    2015-06-01

    Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions.

  7. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule

    PubMed Central

    Zheng, Peng; Arantes, Guilherme M.; Field, Martin J.; Li, Hongbin

    2015-01-01

    Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions. PMID:26108369

  8. Radiation induced chemical activity at iron and copper oxide surfaces

    NASA Astrophysics Data System (ADS)

    Reiff, Sarah C.

    The radiolysis of three iron oxides, two copper oxides, and aluminum oxide with varying amounts of water were performed using gamma-rays and 5 MeV 4He ions. The adsorbed water on the surfaces was characterized using temperature programmed desorption and diffuse reflectance infrared spectroscopy, which indicated that all of the oxides had chemisorbed water on the surface. Physisorbed water was observed on the Fe2O 3 and Al2O3 surfaces as well. Molecular hydrogen was produced from adsorbed water only on Fe2O3 and Al 2O3, while the other compounds did not show any hydrogen production due to the low amounts of water on the surfaces. Slurries of varying amounts of water were also examined for hydrogen production, and they showed yields that were greater than the yield for bulk water. However, the yields of hydrogen from the copper compounds were much lower than those of the iron suggesting that the copper oxides are relatively inert to radiation induced damage to nearby water. X-ray diffraction measurements did not show any indication of changes to the bulk crystal structure due to radiolysis for any of the oxides. The surfaces of the oxides were analyzed using Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). For the iron samples, FeO and Fe3O4, Raman spectroscopy revealed areas of Fe2O3 had formed following irradiation with He ions. XPS indicated the formation of a new oxygen species on the iron oxide surfaces. Raman spectroscopy of the copper oxides did not reveal any changes in the surface composition, however, XPS measurements showed a decrease in the amount of OH groups on the surface of Cu2O, while for the CuO samples the amount of OH groups were found to increase following radiolysis. Pristine Al2O3 showed the presence of a surface oxyhydroxide layer which was observed to decrease following radiolysis, consistent with the formation of molecular hydrogen.

  9. One-Directional Fluidic Flow Induced by Chemical Wave Propagation in a Microchannel.

    PubMed

    Arai, Miyu; Takahashi, Kazuhiro; Hattori, Mika; Hasegawa, Takahiko; Sato, Mami; Unoura, Kei; Nabika, Hideki

    2016-05-26

    A one-directional flow induced by chemical wave propagation was investigated to understand the origin of its dynamic flow. A cylindrical injection port was connected with a straight propagation channel; the chemical wave was initiated at the injection port. Chemical waves propagated with a constant velocity irrespective of the channel width, indicating that the dynamics of the chemical waves were governed by a geometry-independent interplay between the chemical reaction and diffusion. In contrast, the velocity of the one-directional flow was dependent on the channel width. Furthermore, enlargement of the injection port volume increased the flow velocity and volume flux. These results imply that the one-directional flow in the microchannel is due to a hydrodynamic effect induced in the injection port. Spectroscopic analysis of a pH indicator revealed the simultaneous behavior between the pH increase near the injection port and the one-directional flow. Hence, we can conclude that the one-directional flow in the microchannel with chemical wave propagation was caused by a proton consumption reaction in the injection port, probably through liquid volume expansion by the reaction products and the reaction heat. It is a characteristic feature of the present system that the hydrodynamic flow started from the chemical wave initiation point and not the propagation wavefront, as observed for previous systems.

  10. Causal Inference in Public Health

    PubMed Central

    Glass, Thomas A.; Goodman, Steven N.; Hernán, Miguel A.; Samet, Jonathan M.

    2014-01-01

    Causal inference has a central role in public health; the determination that an association is causal indicates the possibility for intervention. We review and comment on the long-used guidelines for interpreting evidence as supporting a causal association and contrast them with the potential outcomes framework that encourages thinking in terms of causes that are interventions. We argue that in public health this framework is more suitable, providing an estimate of an action’s consequences rather than the less precise notion of a risk factor’s causal effect. A variety of modern statistical methods adopt this approach. When an intervention cannot be specified, causal relations can still exist, but how to intervene to change the outcome will be unclear. In application, the often-complex structure of causal processes needs to be acknowledged and appropriate data collected to study them. These newer approaches need to be brought to bear on the increasingly complex public health challenges of our globalized world. PMID:23297653

  11. An improved chemically inducible gene switch that functions in the monocotyledonous plant sugar cane.

    PubMed

    Kinkema, Mark; Geijskes, R Jason; Shand, Kylie; Coleman, Heather D; De Lucca, Paulo C; Palupe, Anthony; Harrison, Mark D; Jepson, Ian; Dale, James L; Sainz, Manuel B

    2014-03-01

    Chemically inducible gene switches can provide precise control over gene expression, enabling more specific analyses of gene function and expanding the plant biotechnology toolkit beyond traditional constitutive expression systems. The alc gene expression system is one of the most promising chemically inducible gene switches in plants because of its potential in both fundamental research and commercial biotechnology applications. However, there are no published reports demonstrating that this versatile gene switch is functional in transgenic monocotyledonous plants, which include some of the most important agricultural crops. We found that the original alc gene switch was ineffective in the monocotyledonous plant sugar cane, and describe a modified alc system that is functional in this globally significant crop. A promoter consisting of tandem copies of the ethanol receptor inverted repeat binding site, in combination with a minimal promoter sequence, was sufficient to give enhanced sensitivity and significantly higher levels of ethanol inducible gene expression. A longer CaMV 35S minimal promoter than was used in the original alc gene switch also substantially improved ethanol inducibility. Treating the roots with ethanol effectively induced the modified alc system in sugar cane leaves and stem, while an aerial spray was relatively ineffective. The extension of this chemically inducible gene expression system to sugar cane opens the door to new opportunities for basic research and crop biotechnology.

  12. An improved chemically inducible gene switch that functions in the monocotyledonous plant sugar cane.

    PubMed

    Kinkema, Mark; Geijskes, R Jason; Shand, Kylie; Coleman, Heather D; De Lucca, Paulo C; Palupe, Anthony; Harrison, Mark D; Jepson, Ian; Dale, James L; Sainz, Manuel B

    2014-03-01

    Chemically inducible gene switches can provide precise control over gene expression, enabling more specific analyses of gene function and expanding the plant biotechnology toolkit beyond traditional constitutive expression systems. The alc gene expression system is one of the most promising chemically inducible gene switches in plants because of its potential in both fundamental research and commercial biotechnology applications. However, there are no published reports demonstrating that this versatile gene switch is functional in transgenic monocotyledonous plants, which include some of the most important agricultural crops. We found that the original alc gene switch was ineffective in the monocotyledonous plant sugar cane, and describe a modified alc system that is functional in this globally significant crop. A promoter consisting of tandem copies of the ethanol receptor inverted repeat binding site, in combination with a minimal promoter sequence, was sufficient to give enhanced sensitivity and significantly higher levels of ethanol inducible gene expression. A longer CaMV 35S minimal promoter than was used in the original alc gene switch also substantially improved ethanol inducibility. Treating the roots with ethanol effectively induced the modified alc system in sugar cane leaves and stem, while an aerial spray was relatively ineffective. The extension of this chemically inducible gene expression system to sugar cane opens the door to new opportunities for basic research and crop biotechnology. PMID:24142380

  13. Mammalian models of chemically induced primary malignancies exploitable for imaging-based preclinical theragnostic research

    PubMed Central

    Liu, Yewei; Yin, Ting; Feng, Yuanbo; Cona, Marlein Miranda; Huang, Gang; Liu, Jianjun; Song, Shaoli; Jiang, Yansheng; Xia, Qian; Swinnen, Johannes V.; Bormans, Guy; Himmelreich, Uwe; Oyen, Raymond

    2015-01-01

    Compared with transplanted tumor models or genetically engineered cancer models, chemically induced primary malignancies in experimental animals can mimic the clinical cancer progress from the early stage on. Cancer caused by chemical carcinogens generally develops through three phases namely initiation, promotion and progression. Based on different mechanisms, chemical carcinogens can be divided into genotoxic and non-genotoxic ones, or complete and incomplete ones, usually with an organ-specific property. Chemical carcinogens can be classified upon their origins such as environmental pollutants, cooked meat derived carcinogens, N-nitroso compounds, food additives, antineoplastic agents, naturally occurring substances and synthetic carcinogens, etc. Carcinogen-induced models of primary cancers can be used to evaluate the diagnostic/therapeutic effects of candidate drugs, investigate the biological influential factors, explore preventive measures for carcinogenicity, and better understand molecular mechanisms involved in tumor initiation, promotion and progression. Among commonly adopted cancer models, chemically induced primary malignancies in mammals have several advantages including the easy procedures, fruitful tumor generation and high analogy to clinical human primary cancers. However, in addition to the time-consuming process, the major drawback of chemical carcinogenesis for translational research is the difficulty in noninvasive tumor burden assessment in small animals. Like human cancers, tumors occur unpredictably also among animals in terms of timing, location and the number of lesions. Thanks to the availability of magnetic resonance imaging (MRI) with various advantages such as ionizing-free scanning, superb soft tissue contrast, multi-parametric information, and utility of diverse contrast agents, now a workable solution to this bottleneck problem is to apply MRI for noninvasive detection, diagnosis and therapeutic monitoring on those otherwise

  14. The anti-nociceptive potential of tilmicosin against chemical-induced but not thermal-induced pain in mice.

    PubMed

    El-Mahmoudy, A; Gheith, I

    2016-03-01

    The aim of the present study was to assess the analgesic activity of the macrolide antibiotic tilmicosin at dose levels of 20 and 40 mg/kg of body weight, subcutaneously, against chemical- and thermal-induced acute pains, using acetic acid-induced writhing, formalin-induced pain, hot-plate, and tail-flick models in mice. Tilmicosin showed a dose-dependent significant decrease in the number of writhes in the acetic acid-induced writhing test and significant decrease in hind paw-licking time in the late phase of the formalin test. However, it did not cause any significant changes in the reaction times to heat stimuli in the hot-plate and tail-flick models. In chemically-induced pains, both dose levels of tilmicosin showed significant effects compared to those of the corresponding standard peripheral analgesic, acetylsalicylic acid (200 mg/kg of body weight, subcutaneously) being 26.37±2.88 and 43.64±3.85% vs. 73.35±1.44% in acetic acid test; and 19.23±3.85 and 44.90±1.80% vs. 73.63±2.39% in the late phase of formalin test, respectively. These results may indicate that tilmicosin possesses a significant peripheral but not central analgesic potential that may be beneficial in symptomatic relief of pain when it is used in therapy, in addition to its well-established antibacterial effect.

  15. An Efficient Two-Tier Causal Protocol for Mobile Distributed Systems

    PubMed Central

    Dominguez, Eduardo Lopez; Pomares Hernandez, Saul E.; Gomez, Gustavo Rodriguez; Medina, Maria Auxilio

    2013-01-01

    Causal ordering is a useful tool for mobile distributed systems (MDS) to reduce the non-determinism induced by three main aspects: host mobility, asynchronous execution, and unpredictable communication delays. Several causal protocols for MDS exist. Most of them, in order to reduce the overhead and the computational cost over wireless channels and mobile hosts (MH), ensure causal ordering at and according to the causal view of the Base Stations. Nevertheless, these protocols introduce certain disadvantage, such as unnecessary inhibition at the delivery of messages. In this paper, we present an efficient causal protocol for groupware that satisfies the MDS's constraints, avoiding unnecessary inhibitions and ensuring the causal delivery based on the view of the MHs. One interesting aspect of our protocol is that it dynamically adapts the causal information attached to each message based on the number of messages with immediate dependency relation, and this is not directly proportional to the number of MHs. PMID:23585828

  16. Systematic trends in photonic reagent induced reactions in a homologous chemical family.

    PubMed

    Tibbetts, Katharine Moore; Xing, Xi; Rabitz, Herschel

    2013-08-29

    The growing use of ultrafast laser pulses to induce chemical reactions prompts consideration of these pulses as "photonic reagents" in analogy to chemical reagents. This work explores the prospect that photonic reagents may affect systematic trends in dissociative ionization reactions of a homologous family of halomethanes, much as systematic outcomes are often observed for reactions between homologous families of chemical reagents and chemical substrates. The experiments in this work with photonic reagents of varying pulse energy and linear spectral chirp reveal systematic correlations between observable ion yields and the following set of natural variables describing the substrate molecules: the ionization energy of the parent molecule, the appearance energy of each fragment ion, and the relative strength of carbon-halogen bonds in molecules containing two different halogens. The results suggest that reactions induced by photonic reagents exhibit systematic behavior analogous to that observed in reactions driven by chemical reagents, which provides a basis to consider empirical "rules" for predicting the outcomes of photonic reagent induced reactions.

  17. Sperm assays in man and other mammals as indicators of chemically induced testicular dysfunction

    SciTech Connect

    Wyrobek, A.J.

    1980-07-31

    Human sperm assays can be effective in identifying chemical agents that alter testicular function. Four human sperm assays are available - sperm density, motility, morphology, and the YFF test. Sperm assays have practical advantages over other approaches for assessing chemically induced changes in human testicular function, and they have been used in more than 60 different occupational, environmental, and drug-related chemical exposures. Studies of chemically induced sperm anomalies in other mammals have provided data on several hundred agents and encompass numerous species. The most widely used animal sperm assay is sperm morphology of mice. It is simple, quantitative, and sensitive to carcinogens, mutagens, and teratogens. The availability of both human and animal sperm assays provides a valuable link between human and animal studies which may be of potential benefit in assessing the heritable genetic risk associated with chemically induced sperm defects. Results from sperm assays may be used in conjunction with results from short term mutagenicity assays (those with definitive genetic endpoints) to identify those mutagens that may be active in the mammalian testes.

  18. Chemically-induced mouse lung tumors: applications to human health assessments [Poster 2014

    EPA Science Inventory

    A state-of-the-science workshop on chemically-induced mouse lung tumors was conducted by U.S. Environmental Protection Agency to discuss issues related to the use of mouse lung tumor data in human health assessments. Naphthalene, styrene, and ethylbenzene were chosen for the anal...

  19. MICROWAVE-INDUCED RAPID CHEMICAL FUNCTIONALIZATION OF SINGLE-WALLED CARBON NANOTUBES (R830901)

    EPA Science Inventory


    Abstract

    The microwave-induced chemical functionalization of single-walled carbon nanotubes (SWNTs) is reported. The major advantage of this high-energy procedure is that it reduced the reaction time to the order of minutes and the number of steps in the reac...

  20. Comparison Analysis: Granger Causality and New Causality and Their Applications to Motor Imagery.

    PubMed

    Hu, Sanqing; Wang, Hui; Zhang, Jianhai; Kong, Wanzeng; Cao, Yu; Kozma, Robert

    2016-07-01

    In this paper we first point out a fatal drawback that the widely used Granger causality (GC) needs to estimate the autoregressive model, which is equivalent to taking a series of backward recursive operations which are infeasible in many irreversible chemical reaction models. Thus, new causality (NC) proposed by Hu et al. (2011) is theoretically shown to be more sensitive to reveal true causality than GC. We then apply GC and NC to motor imagery (MI) which is an important mental process in cognitive neuroscience and psychology and has received growing attention for a long time. We study causality flow during MI using scalp electroencephalograms from nine subjects in Brain-computer interface competition IV held in 2008. We are interested in three regions: Cz (central area of the cerebral cortex), C3 (left area of the cerebral cortex), and C4 (right area of the cerebral cortex) which are considered to be optimal locations for recognizing MI states in the literature. Our results show that: 1) there is strong directional connectivity from Cz to C3/C4 during left- and right-hand MIs based on GC and NC; 2) during left-hand MI, there is directional connectivity from C4 to C3 based on GC and NC; 3) during right-hand MI, there is strong directional connectivity from C3 to C4 which is much clearly revealed by NC than by GC, i.e., NC largely improves the classification rate; and 4) NC is demonstrated to be much more sensitive to reveal causal influence between different brain regions than GC.

  1. The Recovery of Locality for Causal Sets and Related Topics

    NASA Astrophysics Data System (ADS)

    Daughton, Alan Ronald

    The theory of causal sets is an attempt at a successful quantum theory of gravity. It is widely expected that any theory of quantum gravity should give rise to a discrete structure to spacetime geometry. This supposition rests upon three features of successfully quantized theories. The first is that quantization usually leads to some form of discrete object, or quantum, which is the source of the term "quantization". The second is the need for renormalization of field theories (which is not alleviated by including gravity, using the usual perturbative approach to quantization, as had once been hoped). An ultraviolet cutoff is introduced, which can be imagined to be either the mathematical manifestation of an underlying theory that contains new structures at some scale (for example the "GUT" fields, strings, etc.) or simply the result of the breakdown of the manifold picture at this same scale. Thirdly, quantized fields exhibit the phenomenon of virtual particles of unlimited energies at short length scales. The coupling of gravity to such quantized fields should induce infinite curvatures of the manifold at short scales, thereby dynamically prohibiting a manifold structure. The theory of causal sets begins with a discrete structure. The classical spacetime manifold is expected to emerge as an approximation (in a large grain limit) to the class of causal sets which dominate a sum over causal sets, each causal set being weighted by the exponentiation of an appropriately defined "action functional". In order for this theory to be successful, several questions need to be addressed. Some of these are directed at the relationship between the causal set theory and the geometry of classical spacetime. Other questions are related to the quantization of the causal set theory and inclusion of quantum fields into the theory's framework. This work addresses the relation between causal sets and classical gravity (specifically the issues of embeddability of a certain class of

  2. Imprint Control of BaTiO3 Thin Films via Chemically Induced Surface Polarization Pinning.

    PubMed

    Lee, Hyungwoo; Kim, Tae Heon; Patzner, Jacob J; Lu, Haidong; Lee, Jung-Woo; Zhou, Hua; Chang, Wansoo; Mahanthappa, Mahesh K; Tsymbal, Evgeny Y; Gruverman, Alexei; Eom, Chang-Beom

    2016-04-13

    Surface-adsorbed polar molecules can significantly alter the ferroelectric properties of oxide thin films. Thus, fundamental understanding and controlling the effect of surface adsorbates are crucial for the implementation of ferroelectric thin film devices, such as ferroelectric tunnel junctions. Herein, we report an imprint control of BaTiO3 (BTO) thin films by chemically induced surface polarization pinning in the top few atomic layers of the water-exposed BTO films. Our studies based on synchrotron X-ray scattering and coherent Bragg rod analysis demonstrate that the chemically induced surface polarization is not switchable but reduces the polarization imprint and improves the bistability of ferroelectric phase in BTO tunnel junctions. We conclude that the chemical treatment of ferroelectric thin films with polar molecules may serve as a simple yet powerful strategy to enhance functional properties of ferroelectric tunnel junctions for their practical applications. PMID:26901570

  3. Causality in physiological signals.

    PubMed

    Müller, Andreas; Kraemer, Jan F; Penzel, Thomas; Bonnemeier, Hendrik; Kurths, Jürgen; Wessel, Niels

    2016-05-01

    Health is one of the most important non-material assets and thus also has an enormous influence on material values, since treating and preventing diseases is expensive. The number one cause of death worldwide today originates in cardiovascular diseases. For these reasons the aim of understanding the functions and the interactions of the cardiovascular system is and has been a major research topic throughout various disciplines for more than a hundred years. The purpose of most of today's research is to get as much information as possible with the lowest possible effort and the least discomfort for the subject or patient, e.g. via non-invasive measurements. A family of tools whose importance has been growing during the last years is known under the headline of coupling measures. The rationale for this kind of analysis is to identify the structure of interactions in a system of multiple components. Important information lies for example in the coupling direction, the coupling strength, and occurring time lags. In this work, we will, after a brief general introduction covering the development of cardiovascular time series analysis, introduce, explain and review some of the most important coupling measures and classify them according to their origin and capabilities in the light of physiological analyses. We will begin with classical correlation measures, go via Granger-causality-based tools, entropy-based techniques (e.g. momentary information transfer), nonlinear prediction measures (e.g. mutual prediction) to symbolic dynamics (e.g. symbolic coupling traces). All these methods have contributed important insights into physiological interactions like cardiorespiratory coupling, neuro-cardio-coupling and many more. Furthermore, we will cover tools to detect and analyze synchronization and coordination (e.g. synchrogram and coordigram). As a last point we will address time dependent couplings as identified using a recent approach employing ensembles of time series. The

  4. Different Kinds of Causality in Event Cognition

    ERIC Educational Resources Information Center

    Radvansky, Gabriel A.; Tamplin, Andrea K.; Armendarez, Joseph; Thompson, Alexis N.

    2014-01-01

    Narrative memory is better for information that is more causally connected and occurs at event boundaries, such as a causal break. However, it is unclear whether there are common or distinct influences of causality. For the event boundaries that arise as a result of causal breaks, the events that follow may subsequently become more causally…

  5. Altered magnesium transport in slices of kidney cortex from chemically-induced diabetic rats

    SciTech Connect

    Hoskins, B.

    1981-10-01

    The uptake of magnesium-28 was measured in slices of kidney cortex from rats with alloxan-diabetes and from rats with streptozotocin-diabetes of increasing durations. In both forms of chemically-induced diabetes, magnesium-28 uptake by kidney cortex slices was significantly increased over uptake measured in kidney cortex slices from control rats. Immediate institution of daily insulin therapy to the diabetic rats prevented the diabetes-induced elevated uptake of magnesium without controlling blood glucose levels. Late institution of daily insulin therapy was ineffective in restoring the magnesium uptake to control values. These alterations in magnesium uptake occurred prior to any evidence of nephropathy (via the classic indices of proteinuria and increased BUN levels). The implications of these findings, together with our earlier demonstrations of altered calcium transport by kidney cortex slices from chemically-induced diabetic rats, are discussed in terms of disordered divalent cation transport being at least part of the basic pathogenesis underlying diabetic nephropathy.

  6. How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates.

    PubMed

    Paul, Fabian; Weikl, Thomas R

    2016-09-01

    Protein binding often involves conformational changes. Important questions are whether a conformational change occurs prior to a binding event ('conformational selection') or after a binding event ('induced fit'), and how conformational transition rates can be obtained from experiments. In this article, we present general results for the chemical relaxation rates of conformational-selection and induced-fit binding processes that hold for all concentrations of proteins and ligands and, thus, go beyond the standard pseudo-first-order approximation of large ligand concentration. These results allow to distinguish conformational-selection from induced-fit processes-also in cases in which such a distinction is not possible under pseudo-first-order conditions-and to extract conformational transition rates of proteins from chemical relaxation data. PMID:27636092

  7. How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates

    PubMed Central

    2016-01-01

    Protein binding often involves conformational changes. Important questions are whether a conformational change occurs prior to a binding event (‘conformational selection’) or after a binding event (‘induced fit’), and how conformational transition rates can be obtained from experiments. In this article, we present general results for the chemical relaxation rates of conformational-selection and induced-fit binding processes that hold for all concentrations of proteins and ligands and, thus, go beyond the standard pseudo-first-order approximation of large ligand concentration. These results allow to distinguish conformational-selection from induced-fit processes—also in cases in which such a distinction is not possible under pseudo-first-order conditions—and to extract conformational transition rates of proteins from chemical relaxation data. PMID:27636092

  8. The crystal structure of necrosis- and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity.

    PubMed

    Zaparoli, Gustavo; Barsottini, Mario Ramos de Oliveira; de Oliveira, Juliana Ferreira; Dyszy, Fabio; Teixeira, Paulo José Pereira Lima; Barau, Joan Grande; Garcia, Odalys; Costa-Filho, Antonio José; Ambrosio, Andre Luis Berteli; Pereira, Gonçalo Amarante Guimarães; Dias, Sandra Martha Gomes

    2011-11-15

    The necrosis- and ethylene-inducing peptide 1 (NEP1)-like proteins (NLPs) are proteins secreted from bacteria, fungi and oomycetes, triggering immune responses and cell death in dicotyledonous plants. Genomic-scale studies of Moniliophthora perniciosa, the fungus that causes the Witches' Broom disease in cacao, which is a serious economic concern for South and Central American crops, have identified five members of this family (termed MpNEP1-5). Here, we show by RNA-seq that MpNEP2 is virtually the only NLP expressed during the fungus infection. The quantitative real-time polymerase chain reaction results revealed that MpNEP2 has an expression pattern that positively correlates with the necrotic symptoms, with MpNEP2 reaching its highest level of expression at the advanced necrotic stage. To improve our understanding of MpNEP2's molecular mechanism of action, we determined the crystallographic structure of MpNEP2 at 1.8 Å resolution, unveiling some key structural features. The implications of a cation coordination found in the crystal structure were explored, and we show that MpNEP2, in contrast to another previously described member of the NLP family, NLP(Pya) from Pythium aphanidermatum, does not depend on an ion to accomplish its necrosis- and electrolyte leakage-promoting activities. Results of site-directed mutagenesis experiments confirmed the importance of a negatively charged cavity and an unforeseen hydrophobic β-hairpin loop for MpNEP2 activity, thus offering a platform for compound design with implications for disease control. Electron paramagnetic resonance and fluorescence assays with MpNEP2 performed in the presence of lipid vesicles of different compositions showed no sign of interaction between the protein and the lipids, implying that MpNEP2 likely requires other anchoring elements from the membrane to promote cytolysis or send death signals.

  9. Chemical excitation of Limulus photoreceptors. I. Phosphatase inhibitors induce discrete-wave production in the dark

    PubMed Central

    1983-01-01

    Molybdate, tungstate, fluoride, vanadate, and GTP-gamma-S [guanosine-5'- 0-(3-thiotriphosphate)] were injected into Limulus ventral photoreceptors by ionophoresis from microelectrodes. All of these drugs induce discrete waves of depolarization similar in waveform to, but smaller in amplitude than, those normally elicited by dim light. As for light-evoked waves, the amplitude of drug-induced waves decreases with light adaptation. For the compounds examined so far (fluoride, vanadate, GTP-gamma-S), the drug-induced waves share a reversal potential with light-induced discrete waves at about +15 mV. The induction of discrete waves by fluoride, vanadate, and molybdate was found to be reversible, whereas the induction of waves by GTP-gamma-S was not. Unlike fluoride and vanadate, which induce waves when added to the bath, molybdate appears to be ineffective when applied extracellularly. Because of the similarity of the drug-induced waves to light-induced discrete waves, we conclude that the drug-induced waves arise from a process similar or perhaps identical to visual excitation of the photoreceptor. However, the smaller size of drug-induced waves suggests that they arise at a stage of phototransduction subsequent to the isomerization of rhodopsin. On the basis of the chemical properties and action of the drugs, we suggest that discrete waves may arise through the activation of a GTP-binding protein. PMID:6315860

  10. The chemical cue tetrabromopyrrole from a biofilm bacterium induces settlement of multiple Caribbean corals.

    PubMed

    Sneed, Jennifer M; Sharp, Koty H; Ritchie, Kimberly B; Paul, Valerie J

    2014-07-01

    Microbial biofilms induce larval settlement for some invertebrates, including corals; however, the chemical cues involved have rarely been identified. Here, we demonstrate the role of microbial biofilms in inducing larval settlement with the Caribbean coral Porites astreoides and report the first instance of a chemical cue isolated from a marine biofilm bacterium that induces complete settlement (attachment and metamorphosis) of Caribbean coral larvae. Larvae settled in response to natural biofilms, and the response was eliminated when biofilms were treated with antibiotics. A similar settlement response was elicited by monospecific biofilms of a single bacterial strain, Pseudoalteromonas sp. PS5, isolated from the surface biofilm of a crustose coralline alga. The activity of Pseudoalteromonas sp. PS5 was attributed to the production of a single compound, tetrabromopyrrole (TBP), which has been shown previously to induce metamorphosis without attachment in Pacific acroporid corals. In addition to inducing settlement of brooded larvae (P. astreoides), TBP also induced larval settlement for two broadcast-spawning species, Orbicella (formerly Montastraea) franksi and Acropora palmata, indicating that this compound may have widespread importance among Caribbean coral species. PMID:24850918

  11. The chemical cue tetrabromopyrrole from a biofilm bacterium induces settlement of multiple Caribbean corals

    PubMed Central

    Sneed, Jennifer M.; Sharp, Koty H.; Ritchie, Kimberly B.; Paul, Valerie J.

    2014-01-01

    Microbial biofilms induce larval settlement for some invertebrates, including corals; however, the chemical cues involved have rarely been identified. Here, we demonstrate the role of microbial biofilms in inducing larval settlement with the Caribbean coral Porites astreoides and report the first instance of a chemical cue isolated from a marine biofilm bacterium that induces complete settlement (attachment and metamorphosis) of Caribbean coral larvae. Larvae settled in response to natural biofilms, and the response was eliminated when biofilms were treated with antibiotics. A similar settlement response was elicited by monospecific biofilms of a single bacterial strain, Pseudoalteromonas sp. PS5, isolated from the surface biofilm of a crustose coralline alga. The activity of Pseudoalteromonas sp. PS5 was attributed to the production of a single compound, tetrabromopyrrole (TBP), which has been shown previously to induce metamorphosis without attachment in Pacific acroporid corals. In addition to inducing settlement of brooded larvae (P. astreoides), TBP also induced larval settlement for two broadcast-spawning species, Orbicella (formerly Montastraea) franksi and Acropora palmata, indicating that this compound may have widespread importance among Caribbean coral species. PMID:24850918

  12. Neuroleptic malignant syndrome: mechanisms, interactions, and causality.

    PubMed

    Gillman, P Ken

    2010-09-15

    This review focuses on new data from recent publications concerning how compounding interactions between different thermoregulatory pathways influence the development of hyperthermia and/or neuroleptic malignant syndrome (NMS), and the fundamental issue of the presumed causal role of antipsychotic drugs. The formal criteria for substantiating cause-effect relationships in medical science, established by Hill, are applied to NMS and, for comparison, also to malignant hyperthermia and serotonin toxicity. The risk of morbidities related to hyperthermia is reviewed from human and experimental data: temperatures in excess of 39.5°C cause physiological and cellular dysfunction and high mortality. The most temperature-sensitive elements of neural cells are mitochondrial and plasma membranes, in which irreversible changes occur around 40°C. Temperatures of up to 39°C are "normal" in mammals, so, the term hyperthermia should be reserved for temperatures of 39.5°C or greater. The implicitly accepted presumption that NMS is a hypermetabolic and hyperthermic syndrome is questionable and does not explain the extensive morbidity in the majority of cases, where the temperature is less than 39°C. The thermoregulatory effects of dopamine and acetylcholine are outlined, especially because they are probably the main pathways by which neuroleptic drugs might affect thermoregulation. It is notable that even potent antagonism of these mechanisms rarely causes temperature elevation and that multiple mechanisms, including the acute phase response, stress-induced hyperthermia, drugs effects, etc., involving compounding interactions, are required to precipitate hyperthermia. The application of the Hill criteria clearly supports causality for drugs inducing both MH and ST but do not support causality for NMS.

  13. Causal reasoning with mental models

    PubMed Central

    Khemlani, Sangeet S.; Barbey, Aron K.; Johnson-Laird, Philip N.

    2014-01-01

    This paper outlines the model-based theory of causal reasoning. It postulates that the core meanings of causal assertions are deterministic and refer to temporally-ordered sets of possibilities: A causes B to occur means that given A, B occurs, whereas A enables B to occur means that given A, it is possible for B to occur. The paper shows how mental models represent such assertions, and how these models underlie deductive, inductive, and abductive reasoning yielding explanations. It reviews evidence both to corroborate the theory and to account for phenomena sometimes taken to be incompatible with it. Finally, it reviews neuroscience evidence indicating that mental models for causal inference are implemented within lateral prefrontal cortex. PMID:25389398

  14. Causal inference from observational data.

    PubMed

    Listl, Stefan; Jürges, Hendrik; Watt, Richard G

    2016-10-01

    Randomized controlled trials have long been considered the 'gold standard' for causal inference in clinical research. In the absence of randomized experiments, identification of reliable intervention points to improve oral health is often perceived as a challenge. But other fields of science, such as social science, have always been challenged by ethical constraints to conducting randomized controlled trials. Methods have been established to make causal inference using observational data, and these methods are becoming increasingly relevant in clinical medicine, health policy and public health research. This study provides an overview of state-of-the-art methods specifically designed for causal inference in observational data, including difference-in-differences (DiD) analyses, instrumental variables (IV), regression discontinuity designs (RDD) and fixed-effects panel data analysis. The described methods may be particularly useful in dental research, not least because of the increasing availability of routinely collected administrative data and electronic health records ('big data'). PMID:27111146

  15. Fluctuations in relativistic causal hydrodynamics

    NASA Astrophysics Data System (ADS)

    Kumar, Avdhesh; Bhatt, Jitesh R.; Mishra, Ananta P.

    2014-05-01

    Formalism to calculate the hydrodynamic fluctuations by applying the Onsager theory to the relativistic Navier-Stokes equation is already known. In this work, we calculate hydrodynamic fluctuations within the framework of the second order hydrodynamics of Müller, Israel and Stewart and its generalization to the third order. We have also calculated the fluctuations for several other causal hydrodynamical equations. We show that the form for the Onsager-coefficients and form of the correlation functions remain the same as those obtained by the relativistic Navier-Stokes equation and do not depend on any specific model of hydrodynamics. Further we numerically investigate evolution of the correlation function using the one dimensional boost-invariant (Bjorken) flow. We compare the correlation functions obtained using the causal hydrodynamics with the correlation function for the relativistic Navier-Stokes equation. We find that the qualitative behavior of the correlation functions remains the same for all the models of the causal hydrodynamics.

  16. The relationship between chemical-induced kidney weight increases and kidney histopathology in rats.

    PubMed

    Craig, Evisabel A; Yan, Zhongyu; Zhao, Q Jay

    2015-07-01

    The kidney is a major site of chemical excretion, which results in its propensity to exhibit chemically-induced toxicological effects at a higher rate than most other organs. Although the kidneys are often weighed in animal toxicity studies, the manner in which these kidney weight measurements are interpreted and the value of this information in predicting renal damage remains controversial. In this study we sought to determine whether a relationship exists between chemically-induced kidney weight changes and renal histopathological alterations. We also examined the relative utility of absolute and relative (kidney-to-body weight ratio) kidney weight in the prediction of renal toxicity. For this, data extracted from oral chemical exposure studies in rats performed by the National Toxicology Program were qualitatively and quantitatively evaluated. Our analysis showed a statistically significant correlation between absolute, but not relative, kidney weight and renal histopathology in chemically-treated rats. This positive correlation between absolute kidney weight and histopathology was observed even with compounds that statistically decreased terminal body weight. Also, changes in absolute kidney weight, which occurred at subchronic exposures, were able to predict the presence or absence of kidney histopathology at both subchronic and chronic exposures. Furthermore, most increases in absolute kidney weight reaching statistical significance (irrespective of the magnitude of change) were found to be relevant for the prediction of histopathological changes. Hence, our findings demonstrate that the evaluation of absolute kidney weight is a useful method for identifying potential renal toxicants.

  17. Investigation of plasma induced electrical and chemical factors and their contribution processes to plasma gene transfection.

    PubMed

    Jinno, Masafumi; Ikeda, Yoshihisa; Motomura, Hideki; Kido, Yugo; Satoh, Susumu

    2016-09-01

    This study has been done to know what kind of factors in plasmas and processes on cells induce plasma gene transfection. We evaluated the contribution weight of three groups of the effects and processes, i.e. electrical, chemical and biochemical ones, inducing gene transfection. First, the laser produced plasma (LPP) was employed to estimate the contribution of the chemical factors. Second, liposomes were fabricated and employed to evaluate the effects of plasma irradiation on membrane under the condition without biochemical reaction. Third, the clathrin-dependent endocytosis, one of the biochemical processes was suppressed. It becomes clear that chemical factors (radicals and reactive oxygen/nitrogen species) do not work by itself alone and electrical factors (electrical current, charge and field) are essential to plasma gene transfection. It turned out the clathrin-dependent endocytosis is the process of the transfection against the 60% in all the transfected cells. The endocytosis and electrical poration are dominant in plasma gene transfection, and neither permeation through ion channels nor chemical poration is dominant processes. The simultaneous achievement of high transfection efficiency and high cell survivability is attributed to the optimization of the contribution weight among three groups of processes by controlling the weight of electrical and chemical factors. PMID:27136710

  18. Bromophenacyl bromide, a phospholipase A2 inhibitor attenuates chemically induced gastroduodenal ulcers in rats

    PubMed Central

    Tariq, Mohammad; Elfaki, Ibrahim; Khan, Haseeb Ahmad; Arshaduddin, Mohammad; Sobki, Samia; Moutaery, Meshal Al

    2006-01-01

    AIM: To study the effect of bromophenacyl bromide (BPB), a phospholipase A2 inhibitor on gastric secretion and to protect chemically induced gastric and duodenal ulcers in rats. METHODS: Acid secretion studies were undertaken in pylorus-ligated rats with BPB treatment (0, 5, 15 and 45 mg/kg). Gastric and duodenal lesions in the rats were induced by ethanol and cysteamine respectively. The levels of gastric wall mucus, nonprotein sulfhydryls (NP-SH) and myeloperoxidase (MPO) were also measured in the glandular stomach of rats following ethanol induced gastric lesions. RESULTS: BPB produced a dose-dependent inhibition of gastric acid secretion and acidity in rats. Pretreatment with BPB significantly attenuated the formation of ethanol induced gastric lesion. BPB also protected intestinal mucosa against cysteamine-induced duodenal ulcers. The antiulcer activity of BPB was associated with significant inhibition of ethanol-induced depletion of gastric wall mucus, NP-SH and MPO. These findings pointed towards the mediation of sulfhydryls in BPB induced gastrointestinal cytoprotection. CONCLUSION: BPB possesses significant antiulcer and cytoprotective activity against experimentally induced gastroduodenal lesions. PMID:17007045

  19. Reasoning about Causal Relationships: Inferences on Causal Networks

    PubMed Central

    Rottman, Benjamin Margolin; Hastie, Reid

    2013-01-01

    Over the last decade, a normative framework for making causal inferences, Bayesian Probabilistic Causal Networks, has come to dominate psychological studies of inference based on causal relationships. The following causal networks—[X→Y→Z, X←Y→Z, X→Y←Z]—supply answers for questions like, “Suppose both X and Y occur, what is the probability Z occurs?” or “Suppose you intervene and make Y occur, what is the probability Z occurs?” In this review, we provide a tutorial for how normatively to calculate these inferences. Then, we systematically detail the results of behavioral studies comparing human qualitative and quantitative judgments to the normative calculations for many network structures and for several types of inferences on those networks. Overall, when the normative calculations imply that an inference should increase, judgments usually go up; when calculations imply a decrease, judgments usually go down. However, two systematic deviations appear. First, people’s inferences violate the Markov assumption. For example, when inferring Z from the structure X→Y→Z, people think that X is relevant even when Y completely mediates the relationship between X and Z. Second, even when people’s inferences are directionally consistent with the normative calculations, they are often not as sensitive to the parameters and the structure of the network as they should be. We conclude with a discussion of productive directions for future research. PMID:23544658

  20. Ultrafast laser induced breakdown spectroscopy for high spatial resolution chemical analysis

    NASA Astrophysics Data System (ADS)

    Zorba, Vassilia; Mao, Xianglei; Russo, Richard E.

    2011-02-01

    Femtosecond laser induced breakdown spectroscopy (LIBS) was used to identify the spatial resolution limitations and assess the minimal detectable mass restrictions in laser-ablation based chemical analysis. The atomic emission of sodium (Na) and potassium (K) dopants in transparent dielectric Mica matrices was studied, to find that both these elements could be detected from 450 nm diameter ablation craters, full-width-at-half-maximum (FWHM). Under optimal conditions, mass as low as 220 ag was measured, demonstrating the feasibility of using laser-ablation based chemical analysis to achieve high spatial resolution elemental analysis in real-time and at atmospheric pressure conditions.

  1. A chemical pollen suppressant inhibits auxin-induced growth in maize coleoptile sections

    SciTech Connect

    Vesper, M.J. ); Cross, J.W. )

    1990-05-01

    Chemical inhibitors of pollen development having a phenylcinnoline carboxylate structure were found to inhibit IAA- and 1-NAA-induced growth in maize coleoptile sections. The inhibitor (100 {mu}M) used in these experiments caused approx. 35% reduction in auxin-induced growth over the auxin concentration range of 0.3 to 100 {mu}M. Growth inhibition was noted as a lengthening of the latent period and a decrease in the rate of an auxin-induced growth response. An acid growth response to pH 5 buffer in abraded sections was not impaired. The velocity of basipetal transport of ({sup 3}H)IAA through the coleoptile sections also was not inhibited by the compound, nor was uptake of ({sup 3}H)IAA. Similarly, the inhibitor does not appear to alter auxin-induced H{sup +} secretion. We suggest that the agent targets some other process necessary for auxin-dependent growth.

  2. Optimization of microwave-induced chemical etching for rapid development of neutron-induced recoil tracks in CR-39 detectors

    NASA Astrophysics Data System (ADS)

    Sahoo, G. S.; Tripathy, S. P.; Bandyopadhyay, T.

    2014-03-01

    A systematic investigation is carried out to optimize the recently established microwave-induced chemical etching (MICE) parameters for rapid development of neutron-induced recoil tracks in CR-39 detectors. Several combinations of all available microwave powers with different etching durations were analysed to determine the most suitable etching condition. The etching duration was found to reduce with increasing microwave power and the tracks were observed at about 18, 15, 12, and 6 min for 300, 450, 600 and 900 W of microwave powers respectively compared to a few hours in chemical etching (CE) method. However, for complete development of tracks the etching duration of 30, 40, 50 and 60 min were found to be suitable for the microwave powers of 900, 600, 450 and 300 W, respectively. Temperature profiles of the etchant for all the available microwave powers at different etching durations were generated to regulate the etching process in a controlled manner. The bulk etch rates at different microwave powers were determined by 2 methods, viz., gravimetric and removed thickness methods. A logarithmic expression was used to fit the variation of bulk etch rate with microwave power. Neutron detection efficiencies were obtained for all the cases and the results on track parameters obtained with MICE technique were compared with those obtained from another detector processed with chemical etching.

  3. Herbal hepatotoxicity: Challenges and pitfalls of causality assessment methods

    PubMed Central

    Teschke, Rolf; Frenzel, Christian; Schulze, Johannes; Eickhoff, Axel

    2013-01-01

    The diagnosis of herbal hepatotoxicity or herb induced liver injury (HILI) represents a particular clinical and regulatory challenge with major pitfalls for the causality evaluation. At the day HILI is suspected in a patient, physicians should start assessing the quality of the used herbal product, optimizing the clinical data for completeness, and applying the Council for International Organizations of Medical Sciences (CIOMS) scale for initial causality assessment. This scale is structured, quantitative, liver specific, and validated for hepatotoxicity cases. Its items provide individual scores, which together yield causality levels of highly probable, probable, possible, unlikely, and excluded. After completion by additional information including raw data, this scale with all items should be reported to regulatory agencies and manufacturers for further evaluation. The CIOMS scale is preferred as tool for assessing causality in hepatotoxicity cases, compared to numerous other causality assessment methods, which are inferior on various grounds. Among these disputed methods are the Maria and Victorino scale, an insufficiently qualified, shortened version of the CIOMS scale, as well as various liver unspecific methods such as the ad hoc causality approach, the Naranjo scale, the World Health Organization (WHO) method, and the Karch and Lasagna method. An expert panel is required for the Drug Induced Liver Injury Network method, the WHO method, and other approaches based on expert opinion, which provide retrospective analyses with a long delay and thereby prevent a timely assessment of the illness in question by the physician. In conclusion, HILI causality assessment is challenging and is best achieved by the liver specific CIOMS scale, avoiding pitfalls commonly observed with other approaches. PMID:23704820

  4. Herbal hepatotoxicity: challenges and pitfalls of causality assessment methods.

    PubMed

    Teschke, Rolf; Frenzel, Christian; Schulze, Johannes; Eickhoff, Axel

    2013-05-21

    The diagnosis of herbal hepatotoxicity or herb induced liver injury (HILI) represents a particular clinical and regulatory challenge with major pitfalls for the causality evaluation. At the day HILI is suspected in a patient, physicians should start assessing the quality of the used herbal product, optimizing the clinical data for completeness, and applying the Council for International Organizations of Medical Sciences (CIOMS) scale for initial causality assessment. This scale is structured, quantitative, liver specific, and validated for hepatotoxicity cases. Its items provide individual scores, which together yield causality levels of highly probable, probable, possible, unlikely, and excluded. After completion by additional information including raw data, this scale with all items should be reported to regulatory agencies and manufacturers for further evaluation. The CIOMS scale is preferred as tool for assessing causality in hepatotoxicity cases, compared to numerous other causality assessment methods, which are inferior on various grounds. Among these disputed methods are the Maria and Victorino scale, an insufficiently qualified, shortened version of the CIOMS scale, as well as various liver unspecific methods such as the ad hoc causality approach, the Naranjo scale, the World Health Organization (WHO) method, and the Karch and Lasagna method. An expert panel is required for the Drug Induced Liver Injury Network method, the WHO method, and other approaches based on expert opinion, which provide retrospective analyses with a long delay and thereby prevent a timely assessment of the illness in question by the physician. In conclusion, HILI causality assessment is challenging and is best achieved by the liver specific CIOMS scale, avoiding pitfalls commonly observed with other approaches.

  5. Transcriptome Sequencing of Chemically Induced Aquilaria sinensis to Identify Genes Related to Agarwood Formation

    PubMed Central

    Ye, Wei; Wu, Hongqing; He, Xin; Wang, Lei; Zhang, Weimin; Li, Haohua; Fan, Yunfei; Tan, Guohui; Liu, Taomei; Gao, Xiaoxia

    2016-01-01

    Background Agarwood is a traditional Chinese medicine used as a clinical sedative, carminative, and antiemetic drug. Agarwood is formed in Aquilaria sinensis when A. sinensis trees are threatened by external physical, chemical injury or endophytic fungal irritation. However, the mechanism of agarwood formation via chemical induction remains unclear. In this study, we characterized the transcriptome of different parts of a chemically induced A. sinensis trunk sample with agarwood. The Illumina sequencing platform was used to identify the genes involved in agarwood formation. Methodology/Principal Findings A five-year-old Aquilaria sinensis treated by formic acid was selected. The white wood part (B1 sample), the transition part between agarwood and white wood (W2 sample), the agarwood part (J3 sample), and the rotten wood part (F5 sample) were collected for transcriptome sequencing. Accordingly, 54,685,634 clean reads, which were assembled into 83,467 unigenes, were obtained with a Q20 value of 97.5%. A total of 50,565 unigenes were annotated using the Nr, Nt, SWISS-PROT, KEGG, COG, and GO databases. In particular, 171,331,352 unigenes were annotated by various pathways, including the sesquiterpenoid (ko00909) and plant–pathogen interaction (ko03040) pathways. These pathways were related to sesquiterpenoid biosynthesis and defensive responses to chemical stimulation. Conclusions/Significance The transcriptome data of the different parts of the chemically induced A. sinensis trunk provide a rich source of materials for discovering and identifying the genes involved in sesquiterpenoid production and in defensive responses to chemical stimulation. This study is the first to use de novo sequencing and transcriptome assembly for different parts of chemically induced A. sinensis. Results demonstrate that the sesquiterpenoid biosynthesis pathway and WRKY transcription factor play important roles in agarwood formation via chemical induction. The comparative analysis of

  6. Role of the Slug Transcription Factor in Chemically-Induced Skin Cancer

    PubMed Central

    von Maltzan, Kristine; Li, Yafan; Rundhaug, Joyce E.; Hudson, Laurie G.; Fischer, Susan M.; Kusewitt, Donna F.

    2016-01-01

    The Slug transcription factor plays an important role in ultraviolet radiation (UVR)-induced skin carcinogenesis, particularly in the epithelial-mesenchymal transition (EMT) occurring during tumor progression. In the present studies, we investigated the role of Slug in two-stage chemical skin carcinogenesis. Slug and the related transcription factor Snail were expressed at high levels in skin tumors induced by 7,12-dimethylbenz[α]anthracene application followed by 12-O-tetradecanoylphorbol-13-acetate (TPA) treatment. TPA-induced transient elevation of Slug and Snail proteins in normal mouse epidermis and studies in Slug transgenic mice indicated that Slug modulates TPA-induced epidermal hyperplasia and cutaneous inflammation. Although Snail family factors have been linked to inflammation via interactions with the cyclooxygenase-2 (COX-2) pathway, a pathway that also plays an important role in skin carcinogenesis, transient TPA induction of Slug and Snail appeared unrelated to COX-2 expression. In cultured human keratinocytes, TPA induced Snail mRNA expression while suppressing Slug expression, and this differential regulation was due specifically to activation of the TPA receptor. These studies show that Slug and Snail exhibit similar patterns of expression during both UVR and chemical skin carcinogenesis, that Slug and Snail can be differentially regulated under some conditions and that in vitro findings may not recapitulate in vivo results. PMID:26848699

  7. Chemical Leucoderma Induced by Ear-ring Stoppers Made of Polyvinyl Chloride

    PubMed Central

    Sharma, Reena; Singal, Archana; Verma, Prashant; Grover, Chander

    2012-01-01

    We report a case of chemical leucoderma (CL) in a 15-year-old girl, who developed patterned depigmentation at the back of both ear lobules after contact with plastic ear-ring stoppers made of polyvinyl chloride (PVC) after continuous use for 6–7 months. Patch test with Indian standard series and cosmetic series was negative after 48 h, but she refused patch testing for extended duration as the possibility of induced depigmentation at the test site was unacceptable to her. To the best of our knowledge, this is the first report of plastic ear-ring stopper induced CL. PMID:23060712

  8. The herbicide atrazine induces hyperactivity and compromises tadpole detection of predator chemical cues.

    PubMed

    Ehrsam, Mackenzie; Knutie, Sarah A; Rohr, Jason R

    2016-09-01

    The ability to detect chemical cues is often critical for freshwater organisms to avoid predation and find food and mates. In particular, reduced activity and avoidance of chemical cues signaling predation risk are generally adaptive behaviors that reduce prey encounter rates with predators. The present study examined the effects of the common herbicide atrazine on the ability of Cuban tree frog (Osteopilus septentrionalis) tadpoles to detect and respond to chemical cues from larval dragonfly (Libellulidae sp.) predators. Tadpoles exposed to an estimated environmental concentration of atrazine (calculated using US Environmental Protection Agency software; measured concentration, 178 μg/L) were significantly hyperactive relative to those exposed to solvent control. In addition, control tadpoles significantly avoided predator chemical cues, but tadpoles exposed to atrazine did not. These results are consistent with previous studies that have demonstrated that ecologically relevant concentrations of atrazine can induce hyperactivity and impair the olfactory abilities of other freshwater vertebrates. The authors call for additional studies examining the role of chemical contaminants in disrupting chemical communication and the quantification of subsequent impacts on the fitness and population dynamics of wildlife. Environ Toxicol Chem 2016;35:2239-2244. © 2016 SETAC.

  9. The herbicide atrazine induces hyperactivity and compromises tadpole detection of predator chemical cues.

    PubMed

    Ehrsam, Mackenzie; Knutie, Sarah A; Rohr, Jason R

    2016-09-01

    The ability to detect chemical cues is often critical for freshwater organisms to avoid predation and find food and mates. In particular, reduced activity and avoidance of chemical cues signaling predation risk are generally adaptive behaviors that reduce prey encounter rates with predators. The present study examined the effects of the common herbicide atrazine on the ability of Cuban tree frog (Osteopilus septentrionalis) tadpoles to detect and respond to chemical cues from larval dragonfly (Libellulidae sp.) predators. Tadpoles exposed to an estimated environmental concentration of atrazine (calculated using US Environmental Protection Agency software; measured concentration, 178 μg/L) were significantly hyperactive relative to those exposed to solvent control. In addition, control tadpoles significantly avoided predator chemical cues, but tadpoles exposed to atrazine did not. These results are consistent with previous studies that have demonstrated that ecologically relevant concentrations of atrazine can induce hyperactivity and impair the olfactory abilities of other freshwater vertebrates. The authors call for additional studies examining the role of chemical contaminants in disrupting chemical communication and the quantification of subsequent impacts on the fitness and population dynamics of wildlife. Environ Toxicol Chem 2016;35:2239-2244. © 2016 SETAC. PMID:26799769

  10. Cortisol influences the antipredator behavior induced by chemical alarm cues in the Frillfin goby.

    PubMed

    Barreto, Rodrigo Egydio; Barbosa-Júnior, Augusto; Urbinati, Elisabeth Criscuolo; Hoffmann, Anette

    2014-04-01

    We evaluated the effect of increased plasma cortisol levels on fish antipredator behavior induced by conspecific chemical alarm cues. The experimental model for the study was the Frillfin goby Bathygobius soporator. We first confirmed that the alarm substance induces typical defensive antipredator responses in Frillfin gobies and described their alarm substance cells (epidermal 'club' cells). Second, we confirmed that intraperitoneal cortisol implants increase plasma cortisol levels in this species. We then demonstrated that exogenous cortisol administration and subsequent exposure to an alarm substance decreased swimming activity to a greater extent than the activity prompted by either stimulus alone. In addition, cortisol did not abolish the sheltering response to the alarm chemical cue even though it decreased activity. As predators use prey movements to guide their first contact with the prey, a factor that decreases swimming activity clearly increases the probability of survival. Consequently, this observation indicates that cortisol helps improve the antipredator response in fish.

  11. Noise induced oscillations and coherence resonance in a generic model of the nonisothermal chemical oscillator

    PubMed Central

    Simakov, David S. A.; Pérez-Mercader, Juan

    2013-01-01

    Oscillating chemical reactions are common in biological systems and they also occur in artificial non-biological systems. Generally, these reactions are subject to random fluctuations in environmental conditions which translate into fluctuations in the values of physical variables, for example, temperature. We formulate a mathematical model for a nonisothermal minimal chemical oscillator containing a single negative feedback loop and study numerically the effects of stochastic fluctuations in temperature in the absence of any deterministic limit cycle or periodic forcing. We show that noise in temperature can induce sustained limit cycle oscillations with a relatively narrow frequency distribution and some characteristic frequency. These properties differ significantly depending on the noise correlation. Here, we have explored white and colored (correlated) noise. A plot of the characteristic frequency of the noise induced oscillations as a function of the correlation exponent shows a maximum, therefore indicating the existence of autonomous stochastic resonance, i.e. coherence resonance. PMID:23929212

  12. Suppressive effects of coffee on the SOS responses induced by UV and chemical mutagens.

    PubMed

    Obana, H; Nakamura, S; Tanaka, R

    1986-10-01

    SOS-inducing activity of UV or chemical mutagens (AF-2, 4NQO and MNNG) was strongly suppressed by instant coffee in Salmonella typhimurium TA1535/pSK1002. As decaffeinated instant coffee showed a similarly strong suppressive effect, it would seem that caffeine, a known inhibitor of SOS responses, is not responsible for the effect observed. The suppression was also shown by freshly brewed coffee extracts. However, the suppression was absent in green coffee-bean extracts. These results suggest that coffee contains some substance(s) which, apart from caffeine, suppresses SOS-inducing activity of UV or chemical mutagens and that the suppressive substance(s) are produced by roasting coffee beans.

  13. Chemical activity induces dynamical force with global structure in a reaction-diffusion-convection system.

    PubMed

    Mahara, Hitoshi; Okada, Koichi; Nomura, Atsushi; Miike, Hidetoshi; Sakurai, Tatsunari

    2009-07-01

    We found a rotating global structure induced by the dynamical force of local chemical activity in a thin solution layer of excitable Belousov-Zhabotinsky reaction coupled with diffusion. The surface flow and deformation associated with chemical spiral waves (wavelength about 1 mm) represents a global unidirectional structure and a global tilt in the entire Petri dish (100 mm in diameter), respectively. For these observations, we scanned the condition of hierarchal pattern selection. From this result, the bromomalonic acid has an important role to induce the rotating global structure. An interaction between a reaction-diffusion process and a surface-tension-driven effect leads to such hierarchal pattern with different scales. PMID:19658764

  14. Learning a Theory of Causality

    ERIC Educational Resources Information Center

    Goodman, Noah D.; Ullman, Tomer D.; Tenenbaum, Joshua B.

    2011-01-01

    The very early appearance of abstract knowledge is often taken as evidence for innateness. We explore the relative learning speeds of abstract and specific knowledge within a Bayesian framework and the role for innate structure. We focus on knowledge about causality, seen as a domain-general intuitive theory, and ask whether this knowledge can be…

  15. Nonlinear connectivity by Granger causality.

    PubMed

    Marinazzo, Daniele; Liao, Wei; Chen, Huafu; Stramaglia, Sebastiano

    2011-09-15

    The communication among neuronal populations, reflected by transient synchronous activity, is the mechanism underlying the information processing in the brain. Although it is widely assumed that the interactions among those populations (i.e. functional connectivity) are highly nonlinear, the amount of nonlinear information transmission and its functional roles are not clear. The state of the art to understand the communication between brain systems are dynamic causal modeling (DCM) and Granger causality. While DCM models nonlinear couplings, Granger causality, which constitutes a major tool to reveal effective connectivity, and is widely used to analyze EEG/MEG data as well as fMRI signals, is usually applied in its linear version. In order to capture nonlinear interactions between even short and noisy time series, a few approaches have been proposed. We review them and focus on a recently proposed flexible approach has been recently proposed, consisting in the kernel version of Granger causality. We show the application of the proposed approach on EEG signals and fMRI data.

  16. Identity, causality, and pronoun ambiguity.

    PubMed

    Sagi, Eyal; Rips, Lance J

    2014-10-01

    This article looks at the way people determine the antecedent of a pronoun in sentence pairs, such as: Albert invited Ron to dinner. He spent hours cleaning the house. The experiment reported here is motivated by the idea that such judgments depend on reasoning about identity (e.g., the identity of the he who cleaned the house). Because the identity of an individual over time depends on the causal-historical path connecting the stages of the individual, the correct antecedent will also depend on causal connections. The experiment varied how likely it is that the event of the first sentence (e.g., the invitation) would cause the event of the second (the house cleaning) for each of the two individuals (the likelihood that if Albert invited Ron to dinner, this would cause Albert to clean the house, versus cause Ron to clean the house). Decisions about the antecedent followed causal likelihood. A mathematical model of causal identity accounted for most of the key aspects of the data from the individual sentence pairs.

  17. Metabolomic Assessment of Induced and Activated Chemical Defence in the Invasive Red Alga Gracilaria vermiculophylla

    PubMed Central

    Nylund, Göran M.; Weinberger, Florian; Rempt, Martin; Pohnert, Georg

    2011-01-01

    In comparison with terrestrial plants the mechanistic knowledge of chemical defences is poor for marine macroalgae. This restricts our understanding in the chemically mediated interactions that take place between algae and other organisms. Technical advances such as metabolomics, however, enable new approaches towards the characterisation of the chemically mediated interactions of organisms with their environment. We address defence responses in the red alga Gracilaria vermiculophylla using mass spectrometry based metabolomics in combination with bioassays. Being invasive in the north Atlantic this alga is likely to possess chemical defences according to the prediction that well-defended exotics are most likely to become successful invaders in systems dominated by generalist grazers, such as marine macroalgal communities. We investigated the effect of intense herbivore feeding and simulated herbivory by mechanical wounding of the algae. Both processes led to similar changes in the metabolic profile. Feeding experiments with the generalist isopod grazer Idotea baltica showed that mechanical wounding caused a significant increase in grazer resistance. Structure elucidation of the metabolites of which some were up-regulated more than 100 times in the wounded tissue, revealed known and novel eicosanoids as major components. Among these were prostaglandins, hydroxylated fatty acids and arachidonic acid derived conjugated lactones. Bioassays with pure metabolites showed that these eicosanoids are part of the innate defence system of macroalgae, similarly to animal systems. In accordance with an induced defence mechanism application of extracts from wounded tissue caused a significant increase in grazer resistance and the up-regulation of other pathways than in the activated defence. Thus, this study suggests that G. vermiculophylla chemically deters herbivory by two lines of defence, a rapid wound-activated process followed by a slower inducible defence. By unravelling

  18. Metabolomic assessment of induced and activated chemical defence in the invasive red alga Gracilaria vermiculophylla.

    PubMed

    Nylund, Göran M; Weinberger, Florian; Rempt, Martin; Pohnert, Georg

    2011-01-01

    In comparison with terrestrial plants the mechanistic knowledge of chemical defences is poor for marine macroalgae. This restricts our understanding in the chemically mediated interactions that take place between algae and other organisms. Technical advances such as metabolomics, however, enable new approaches towards the characterisation of the chemically mediated interactions of organisms with their environment. We address defence responses in the red alga Gracilaria vermiculophylla using mass spectrometry based metabolomics in combination with bioassays. Being invasive in the north Atlantic this alga is likely to possess chemical defences according to the prediction that well-defended exotics are most likely to become successful invaders in systems dominated by generalist grazers, such as marine macroalgal communities. We investigated the effect of intense herbivore feeding and simulated herbivory by mechanical wounding of the algae. Both processes led to similar changes in the metabolic profile. Feeding experiments with the generalist isopod grazer Idotea baltica showed that mechanical wounding caused a significant increase in grazer resistance. Structure elucidation of the metabolites of which some were up-regulated more than 100 times in the wounded tissue, revealed known and novel eicosanoids as major components. Among these were prostaglandins, hydroxylated fatty acids and arachidonic acid derived conjugated lactones. Bioassays with pure metabolites showed that these eicosanoids are part of the innate defence system of macroalgae, similarly to animal systems. In accordance with an induced defence mechanism application of extracts from wounded tissue caused a significant increase in grazer resistance and the up-regulation of other pathways than in the activated defence. Thus, this study suggests that G. vermiculophylla chemically deters herbivory by two lines of defence, a rapid wound-activated process followed by a slower inducible defence. By unravelling

  19. Assessment of immunotoxicity induced by chemicals in human precision-cut lung slices (PCLS).

    PubMed

    Lauenstein, L; Switalla, S; Prenzler, F; Seehase, S; Pfennig, O; Förster, C; Fieguth, H; Braun, A; Sewald, K

    2014-06-01

    Occupational asthma can be induced by a number of chemicals at the workplace. Risk assessment of potential sensitizers is mostly performed in animal experiments. With increasing public demand for alternative methods, human precision-cut lung slices (PCLS) have been developed as an ex vivo model. Human PCLS were exposed to increasing concentrations of 20 industrial chemicals including 4 respiratory allergens, 11 contact allergens, and 5 non-sensitizing irritants. Local respiratory irritation was characterized and expressed as 75% (EC25) and 50% (EC50) cell viability with respect to controls. Dose-response curves of all chemicals except for phenol were generated. Local respiratory inflammation was quantified by measuring the production of cytokines and chemokines. TNF-α and IL-1α were increased significantly in human PCLS after exposure to the respiratory sensitizers trimellitic anhydride (TMA) and ammonium hexachloroplatinate (HClPt) at subtoxic concentrations, while contact sensitizers and non-sensitizing irritants failed to induce the release of these cytokines to the same extent. Interestingly, significant increases in T(H)1/T(H)2 cytokines could be detected only after exposure to HClPt at a subtoxic concentration. In conclusion, allergen-induced cytokines were observed but not considered as biomarkers for the differentiation between respiratory and contact sensitizers. Our preliminary results show an ex vivo model which might be used for prediction of chemical-induced toxicity, but is due to its complex three-dimensional structure not applicable for a simple screening of functional and behavior changes of certain cell populations such as dendritic cells and T-cells in response to allergens.

  20. Music and Spatial Task Performance: A Causal Relationship.

    ERIC Educational Resources Information Center

    Rauscher, Frances H.; And Others

    This research paper reports on testing the hypothesis that music and spatial task performance are causally related. Two complementary studies are presented that replicate and explore previous findings. One study of college students showed that listening to a Mozart sonata induces subsequent short-term spatial reasoning facilitation and tested the…

  1. Modelling biological and chemically induced precipitation of calcium phosphate in enhanced biological phosphorus removal systems.

    PubMed

    Barat, R; Montoya, T; Seco, A; Ferrer, J

    2011-06-01

    The biologically induced precipitation processes can be important in wastewater treatment, in particular treating raw wastewater with high calcium concentration combined with Enhanced Biological Phosphorus Removal. Currently, there is little information and experience in modelling jointly biological and chemical processes. This paper presents a calcium phosphate precipitation model and its inclusion in the Activated Sludge Model No 2d (ASM2d). The proposed precipitation model considers that aqueous phase reactions quickly achieve the chemical equilibrium and that aqueous-solid change is kinetically governed. The model was calibrated using data from four experiments in a Sequencing Batch Reactor (SBR) operated for EBPR and finally validated with two experiments. The precipitation model proposed was able to reproduce the dynamics of amorphous calcium phosphate (ACP) formation and later crystallization to hydroxyapatite (HAP) under different scenarios. The model successfully characterised the EBPR performance of the SBR, including the biological, physical and chemical processes.

  2. Causal Inference for a Population of Causally Connected Units

    PubMed Central

    van der Laan, Mark J.

    2015-01-01

    Suppose that we observe a population of causally connected units. On each unit at each time-point on a grid we observe a set of other units the unit is potentially connected with, and a unit-specific longitudinal data structure consisting of baseline and time-dependent covariates, a time-dependent treatment, and a final outcome of interest. The target quantity of interest is defined as the mean outcome for this group of units if the exposures of the units would be probabilistically assigned according to a known specified mechanism, where the latter is called a stochastic intervention. Causal effects of interest are defined as contrasts of the mean of the unit-specific outcomes under different stochastic interventions one wishes to evaluate. This covers a large range of estimation problems from independent units, independent clusters of units, and a single cluster of units in which each unit has a limited number of connections to other units. The allowed dependence includes treatment allocation in response to data on multiple units and so called causal interference as special cases. We present a few motivating classes of examples, propose a structural causal model, define the desired causal quantities, address the identification of these quantities from the observed data, and define maximum likelihood based estimators based on cross-validation. In particular, we present maximum likelihood based super-learning for this network data. Nonetheless, such smoothed/regularized maximum likelihood estimators are not targeted and will thereby be overly bias w.r.t. the target parameter, and, as a consequence, generally not result in asymptotically normally distributed estimators of the statistical target parameter. To formally develop estimation theory, we focus on the simpler case in which the longitudinal data structure is a point-treatment data structure. We formulate a novel targeted maximum likelihood estimator of this estimand and show that the double robustness of the

  3. Drug-eluting microarrays for cell-based screening of chemical-induced apoptosis

    PubMed Central

    Kwon, Cheong Hoon; Wheeldon, Ian; Kachouie, Nezamoddin N.; Lee, Seung Hwan; Bae, Hojae; Sant, Shilpa; Fukuda, Junji; Kang, Jeong Won; Khademhosseini, Ali

    2011-01-01

    Traditional high throughput screening (HTS) is carried out in centralized facilities that require extensive robotic liquid and plate handling equipment. This model of HTS is restrictive as such facilities are not accessible to many researchers. We have designed a simple microarray platform for cell-based screening that can be carried out at the bench top. The device creates a microarray of 2100 individual cell-based assays in a standard microscope slide format. A microarray of chemical-laden hydrogels addresses a matching array of cell-laden microwells thus creating a microarray of sealed microscale cell cultures each with unique conditions. We demonstrate the utility of the device by screening the extent of apoptosis and necrosis in MCF-7 breast cancer cells in response to exposure to a small library of chemical compounds. From a set of screens we produced a rank order of chemicals that preferentially induce apoptosis over necrosis in MCF-7 cells. Treatment with doxorubicin induced high levels of apoptosis in comparison with staurosporine, ethanol, and hydrogen peroxide, while treatment with 100 μM ethanol induced minimal apoptosis with high levels of necrosis. We anticipate broad application of the device for various research and discovery applications as it is easy to use, scalable and can be fabricated and operated with minimal peripheral equipment. PMID:21476591

  4. Entanglement, holography and causal diamonds

    NASA Astrophysics Data System (ADS)

    de Boer, Jan; Haehl, Felix M.; Heller, Michal P.; Myers, Robert C.

    2016-08-01

    We argue that the degrees of freedom in a d-dimensional CFT can be reorganized in an insightful way by studying observables on the moduli space of causal diamonds (or equivalently, the space of pairs of timelike separated points). This 2 d-dimensional space naturally captures some of the fundamental nonlocality and causal structure inherent in the entanglement of CFT states. For any primary CFT operator, we construct an observable on this space, which is defined by smearing the associated one-point function over causal diamonds. Known examples of such quantities are the entanglement entropy of vacuum excitations and its higher spin generalizations. We show that in holographic CFTs, these observables are given by suitably defined integrals of dual bulk fields over the corresponding Ryu-Takayanagi minimal surfaces. Furthermore, we explain connections to the operator product expansion and the first law of entanglemententropy from this unifying point of view. We demonstrate that for small perturbations of the vacuum, our observables obey linear two-derivative equations of motion on the space of causal diamonds. In two dimensions, the latter is given by a product of two copies of a two-dimensional de Sitter space. For a class of universal states, we show that the entanglement entropy and its spin-three generalization obey nonlinear equations of motion with local interactions on this moduli space, which can be identified with Liouville and Toda equations, respectively. This suggests the possibility of extending the definition of our new observables beyond the linear level more generally and in such a way that they give rise to new dynamically interacting theories on the moduli space of causal diamonds. Various challenges one has to face in order to implement this idea are discussed.

  5. A crowdsourcing workflow for extracting chemical-induced disease relations from free text

    PubMed Central

    Li, Tong Shu; Bravo, Àlex; Furlong, Laura I.; Good, Benjamin M.; Su, Andrew I.

    2016-01-01

    Relations between chemicals and diseases are one of the most queried biomedical interactions. Although expert manual curation is the standard method for extracting these relations from the literature, it is expensive and impractical to apply to large numbers of documents, and therefore alternative methods are required. We describe here a crowdsourcing workflow for extracting chemical-induced disease relations from free text as part of the BioCreative V Chemical Disease Relation challenge. Five non-expert workers on the CrowdFlower platform were shown each potential chemical-induced disease relation highlighted in the original source text and asked to make binary judgments about whether the text supported the relation. Worker responses were aggregated through voting, and relations receiving four or more votes were predicted as true. On the official evaluation dataset of 500 PubMed abstracts, the crowd attained a 0.505 F-score (0.475 precision, 0.540 recall), with a maximum theoretical recall of 0.751 due to errors with named entity recognition. The total crowdsourcing cost was $1290.67 ($2.58 per abstract) and took a total of 7 h. A qualitative error analysis revealed that 46.66% of sampled errors were due to task limitations and gold standard errors, indicating that performance can still be improved. All code and results are publicly available at https://github.com/SuLab/crowd_cid_relex Database URL: https://github.com/SuLab/crowd_cid_relex PMID:27087308

  6. A crowdsourcing workflow for extracting chemical-induced disease relations from free text.

    PubMed

    Li, Tong Shu; Bravo, Àlex; Furlong, Laura I; Good, Benjamin M; Su, Andrew I

    2016-01-01

    Relations between chemicals and diseases are one of the most queried biomedical interactions. Although expert manual curation is the standard method for extracting these relations from the literature, it is expensive and impractical to apply to large numbers of documents, and therefore alternative methods are required. We describe here a crowdsourcing workflow for extracting chemical-induced disease relations from free text as part of the BioCreative V Chemical Disease Relation challenge. Five non-expert workers on the CrowdFlower platform were shown each potential chemical-induced disease relation highlighted in the original source text and asked to make binary judgments about whether the text supported the relation. Worker responses were aggregated through voting, and relations receiving four or more votes were predicted as true. On the official evaluation dataset of 500 PubMed abstracts, the crowd attained a 0.505F-score (0.475 precision, 0.540 recall), with a maximum theoretical recall of 0.751 due to errors with named entity recognition. The total crowdsourcing cost was $1290.67 ($2.58 per abstract) and took a total of 7 h. A qualitative error analysis revealed that 46.66% of sampled errors were due to task limitations and gold standard errors, indicating that performance can still be improved. All code and results are publicly available athttps://github.com/SuLab/crowd_cid_relexDatabase URL:https://github.com/SuLab/crowd_cid_relex. PMID:27087308

  7. A crowdsourcing workflow for extracting chemical-induced disease relations from free text.

    PubMed

    Li, Tong Shu; Bravo, Àlex; Furlong, Laura I; Good, Benjamin M; Su, Andrew I

    2016-01-01

    Relations between chemicals and diseases are one of the most queried biomedical interactions. Although expert manual curation is the standard method for extracting these relations from the literature, it is expensive and impractical to apply to large numbers of documents, and therefore alternative methods are required. We describe here a crowdsourcing workflow for extracting chemical-induced disease relations from free text as part of the BioCreative V Chemical Disease Relation challenge. Five non-expert workers on the CrowdFlower platform were shown each potential chemical-induced disease relation highlighted in the original source text and asked to make binary judgments about whether the text supported the relation. Worker responses were aggregated through voting, and relations receiving four or more votes were predicted as true. On the official evaluation dataset of 500 PubMed abstracts, the crowd attained a 0.505F-score (0.475 precision, 0.540 recall), with a maximum theoretical recall of 0.751 due to errors with named entity recognition. The total crowdsourcing cost was $1290.67 ($2.58 per abstract) and took a total of 7 h. A qualitative error analysis revealed that 46.66% of sampled errors were due to task limitations and gold standard errors, indicating that performance can still be improved. All code and results are publicly available athttps://github.com/SuLab/crowd_cid_relexDatabase URL:https://github.com/SuLab/crowd_cid_relex.

  8. Effect of surface topography in the generation of chemical maps by laser-induced plasma spectroscopy

    NASA Astrophysics Data System (ADS)

    Lopez-Quintas, I.; Piñon, V.; Mateo, M. P.; Nicolas, G.

    2012-09-01

    The development of technologically advanced materials is propelling the improvement of surface analytical techniques. In particular, the composition and hence the properties of most of these new materials are spatial dependent. Between the techniques able to provide chemical spatial information, laser-induced plasma spectroscopy known also as laser-induced breakdown spectroscopy (LIBS) is a very promising analytical technique. During the last decade, LIBS was successfully applied to the analysis of surfaces and the generation of chemical maps of heterogeneous materials. In the LIBS analysis, several experimental factors including surface topography must be taken into account. In this work, the influence of surface roughness in LIBS signal during the point analysis and acquisition of chemical maps was studied. For this purpose, samples of stainless steel with different surface finishes were prepared and analyzed by LIBS. In order to characterize the different surfaces, confocal microscopy images were obtained. Afterwards, both topographic and spectroscopic information were combined to show the relationship between them. Additionally, in order to reveal the effect of surface topography in the acquisition of chemical maps, a three dimensional analysis of a sample exhibiting two different finishes was carried out.

  9. Bioanalytical evidence that chemicals in tattoo ink can induce adaptive stress responses.

    PubMed

    Neale, Peta A; Stalter, Daniel; Tang, Janet Y M; Escher, Beate I

    2015-10-15

    Tattooing is becoming increasingly popular, particularly amongst young people. However, tattoo inks contain a complex mixture of chemical impurities that may pose a long-term risk for human health. As a first step towards the risk assessment of these complex mixtures we propose to assess the toxicological hazard potential of tattoo ink chemicals with cell-based bioassays. Targeted modes of toxic action and cellular endpoints included cytotoxicity, genotoxicity and adaptive stress response pathways. The studied tattoo inks, which were extracted with hexane as a proxy for the bioavailable fraction, caused effects in all bioassays, with the red and yellow tattoo inks having the greatest response, particularly inducing genotoxicity and oxidative stress response endpoints. Chemical analysis revealed the presence of polycyclic aromatic hydrocarbons in the tested black tattoo ink at concentrations twice the recommended level. The detected polycyclic aromatic hydrocarbons only explained 0.06% of the oxidative stress response of the black tattoo ink, thus the majority of the effect was caused by unidentified components. The study indicates that currently available tattoo inks contain components that induce adaptive stress response pathways, but to evaluate the risk to human health further work is required to understand the toxicokinetics of tattoo ink chemicals in the body.

  10. Fluorescence Visualization of the Enteric Nervous Network in a Chemically Induced Aganglionosis Model

    PubMed Central

    Shimojima, Naoki; Morikawa, Yasuhide; Okano, Hideyuki; Kuroda, Tatsuo

    2016-01-01

    Gastrointestinal motility disorders, severe variants in particular, remain a therapeutic challenge in pediatric surgery. Absence of enteric ganglion cells that originate from neural crest cells is a major cause of dysmotility. However, the limitations of currently available animal models of dysmotility continue to impede the development of new therapeutics. Indeed, the short lifespan and/or poor penetrance of existing genetic models of dysmotility prohibit the functional evaluation of promising approaches, such as stem cell replacement strategy. Here, we induced an aganglionosis model using topical benzalkonium chloride in a P0-Cre/GFP transgenic mouse in which the neural crest lineage is labeled by green fluorescence. Pathological abnormalities and functional changes in the gastrointestinal tract were evaluated 2–8 weeks after chemical injury. Laparotomy combined with fluorescence microscopy allowed direct visualization of the enteric neural network in vivo. Immunohistochemical evaluation further confirmed the irreversible disappearance of ganglion cells, glial cells, and interstitial cell of Cajal. Remaining stool weight and bead expulsion time in particular supported the pathophysiological relevance of this chemically-induced model of aganglionosis. Interestingly, we show that chemical ablation of enteric ganglion cells is associated with a long lifespan. By combining genetic labeling of neural crest derivatives and chemical ablation of enteric ganglion cells, we developed a newly customized model of aganglionosis. Our results indicate that this aganglionosis model exhibits decreased gastrointestinal motility and shows sufficient survival for functional evaluation. This model may prove useful for the development of future therapies against motility disorders. PMID:26943905

  11. A mechanistic model for understanding root-induced chemical changes controlling phosphorus availability

    PubMed Central

    Devau, Nicolas; Le Cadre, Edith; Hinsinger, Philippe; Gérard, Frédéric

    2010-01-01

    Background and Aims Plant nutrition models do not properly account for the effects of root-induced chemical changes in the rhizosphere, e.g. pH changes, on the availability of nutrients such as phosphorus (P). As a result, they underestimate the actual P uptake, i.e. P bioavailability to the plant, in low-P soils. The present study aims at simulating root-induced chemical mechanisms controlling P nutrition in a P-limited soil. Methods In this work a mechanistic description for the adsorption of cations and anions by soil constituents (1pK-Triple Plane Model, ion-exchange and Nica–Donnan) was used to simulate changes induced by durum wheat (Triticum durum turgidum) in the P availability of the soil, as measured by water and CaCl2 extraction. Calcium (Ca) availability was also measured and simulated. Key Results The simulations were found to be in close agreement with experimental data. In the rhizosphere, the goodness-of-fit required to account for the measured uptake of Ca by plants, in addition to the measured uptake of P and root-induced alkalization, were satisfactory. Calcium uptake significantly increased P availability, as assessed through water extraction, by decreasing the promoting effect of Ca adsorption on P adsorption. The study thus enabled P and Ca availability to be related to their bioavailability for durum wheat under experimental conditions. It was also shown that P was primarily adsorbed onto Fe oxides and clay minerals (kaolinite and illite) depending on soil pH. The major source of P for durum wheat nutrition was P desorbed from goethite and kaolinite. Conclusions In addition to confirming the validity of our approach to model P availability, the present investigation suggested that in the studied soil, a novel root-induced chemical process was controlling P nutrition under P-deficient conditions, namely the uptake of Ca. PMID:20495198

  12. Half-life measurements of chemical inducers for recombinant gene expression

    PubMed Central

    2014-01-01

    Background Inducible promoters are widely spread genetic tools for triggering, tuning and optimizing the expression of recombinant genes in engineered biological systems. Most of them are controlled by the addition of a specific exogenous chemical inducer that indirectly regulates the promoter transcription rate in a concentration-dependent fashion. In order to have a robust and predictable degree of control on promoter activity, the degradation rate of such chemicals should be considered in many applications like recombinant protein production. Results In this work, we use whole-cell biosensors to assess the half-life of three commonly used chemical inducers for recombinant Escherichia coli: Isopropyl β-D-1-thiogalactopyranoside (IPTG), anhydrotetracycline (ATc) and N-(3-oxohexanoyl)-L-homoserine lactone (HSL). A factorial study was conducted to investigate the conditions that significantly contribute to the decay rate of these inducers. Temperature has been found to be the major factor affecting ATc, while medium and pH have been found to highly affect HSL. Finally, no significant degradation was observed for IPTG among the tested conditions. Conclusions We have quantified the decay rate of IPTG, ATc and HSL in many conditions, some of which were not previously tested in the literature, and the main effects affecting their degradation were identified via a statistics-based framework. Whole-cell biosensors were successfully used to conduct this study, yielding reproducible measurements via simple multiwell-compatible assays. The knowledge of inducer degradation rate in several contexts has to be considered in the rational design of synthetic biological systems for improving the predictability of induction effects, especially for prolonged experiments. PMID:24485151

  13. Cranberry Resistance to Dodder Parasitism: Induced Chemical Defenses and Behavior of a Parasitic Plant.

    PubMed

    Tjiurutue, Muvari Connie; Sandler, Hilary A; Kersch-Becker, Monica F; Theis, Nina; Adler, Lynn A

    2016-02-01

    Parasitic plants are common in many ecosystems, where they can structure community interactions and cause major economic damage. For example, parasitic dodder (Cuscuta spp.) can cause up to 80-100 % yield loss in heavily infested cranberry (Vaccinium macrocarpon) patches. Despite their ecological and economic importance, remarkably little is known about how parasitic plants affect, or are affected by, host chemistry. To examine chemically-mediated interactions between dodder and its cranberry host, we conducted a greenhouse experiment asking whether: (1) dodder performance varies with cranberry cultivar; (2) cultivars differ in levels of phytohormones, volatiles, or phenolics, and whether such variation correlates with dodder parasitism; (3) dodder parasitism induced changes in phytohormones, volatiles, or phenolics, and whether the level of inducible response varied among cultivars. We used five cranberry cultivars to assess host attractiveness to dodder and dodder performance. Dodder performance did not differ across cultivars, but there were marginally significant differences in host attractiveness to dodder, with fewer dodder attaching to Early Black than to any other cultivar. Dodder parasitism induced higher levels of salicylic acid (SA) across cultivars. Cultivars differed in overall levels of flavonols and volatile profiles, but not phenolic acids or proanthocyanidins, and dodder attachment induced changes in several flavonols and volatiles. While cultivars differed slightly in resistance to dodder attachment, we did not find evidence of chemical defenses that mediate these interactions. However, induction of several defenses indicates that parasitism alters traits that could influence subsequent interactions with other species, thus shaping community dynamics. PMID:26905738

  14. Moisture-induced solid state instabilities in α-chymotrypsin and their reduction through chemical glycosylation

    PubMed Central

    2010-01-01

    Background Protein instability remains the main factor limiting the development of protein therapeutics. The fragile nature (structurally and chemically) of proteins makes them susceptible to detrimental events during processing, storage, and delivery. To overcome this, proteins are often formulated in the solid-state which combines superior stability properties with reduced operational costs. Nevertheless, solid protein pharmaceuticals can also suffer from instability problems due to moisture sorption. Chemical protein glycosylation has evolved into an important tool to overcome several instability issues associated with proteins. Herein, we employed chemical glycosylation to stabilize a solid-state protein formulation against moisture-induced deterioration in the lyophilized state. Results First, we investigated the consequences of moisture sorption on the stability and structural conformation of the model enzyme α-chymotrypsin (α-CT) under controlled humidity conditions. Results showed that α-CT aggregates and inactivates as a function of increased relative humidity (RH). Furthermore, α-CT loses its native secondary and tertiary structure rapidly at increasing RH. In addition, H/D exchange studies revealed that α-CT structural dynamics increased at increasing RH. The magnitude of the structural changes in tendency parallels the solid-state instability data (i.e., formation of buffer-insoluble aggregates, inactivation, and loss of native conformation upon reconstitution). To determine if these moisture-induced instability issues could be ameliorated by chemical glycosylation we proceeded to modify our model protein with chemically activated glycans of differing lengths (lactose and dextran (10 kDa)). The various glycoconjugates showed a marked decrease in aggregation and an increase in residual activity after incubation. These stabilization effects were found to be independent of the glycan size. Conclusion Water sorption leads to aggregation, inactivation

  15. Effect of measurement noise on Granger causality.

    PubMed

    Nalatore, Hariharan; Sasikumar, N; Rangarajan, Govindan

    2014-12-01

    Most of the signals recorded in experiments are inevitably contaminated by measurement noise. Hence, it is important to understand the effect of such noise on estimating causal relations between such signals. A primary tool for estimating causality is Granger causality. Granger causality can be computed by modeling the signal using a bivariate autoregressive (AR) process. In this paper, we greatly extend the previous analysis of the effect of noise by considering a bivariate AR process of general order p. From this analysis, we analytically obtain the dependence of Granger causality on various noise-dependent system parameters. In particular, we show that measurement noise can lead to spurious Granger causality and can suppress true Granger causality. These results are verified numerically. Finally, we show how true causality can be recovered numerically using the Kalman expectation maximization algorithm.

  16. Distinguishing time-delayed causal interactions using convergent cross mapping.

    PubMed

    Ye, Hao; Deyle, Ethan R; Gilarranz, Luis J; Sugihara, George

    2015-01-01

    An important problem across many scientific fields is the identification of causal effects from observational data alone. Recent methods (convergent cross mapping, CCM) have made substantial progress on this problem by applying the idea of nonlinear attractor reconstruction to time series data. Here, we expand upon the technique of CCM by explicitly considering time lags. Applying this extended method to representative examples (model simulations, a laboratory predator-prey experiment, temperature and greenhouse gas reconstructions from the Vostok ice core, and long-term ecological time series collected in the Southern California Bight), we demonstrate the ability to identify different time-delayed interactions, distinguish between synchrony induced by strong unidirectional-forcing and true bidirectional causality, and resolve transitive causal chains. PMID:26435402

  17. Distinguishing time-delayed causal interactions using convergent cross mapping

    NASA Astrophysics Data System (ADS)

    Ye, Hao; Deyle, Ethan R.; Gilarranz, Luis J.; Sugihara, George

    2015-10-01

    An important problem across many scientific fields is the identification of causal effects from observational data alone. Recent methods (convergent cross mapping, CCM) have made substantial progress on this problem by applying the idea of nonlinear attractor reconstruction to time series data. Here, we expand upon the technique of CCM by explicitly considering time lags. Applying this extended method to representative examples (model simulations, a laboratory predator-prey experiment, temperature and greenhouse gas reconstructions from the Vostok ice core, and long-term ecological time series collected in the Southern California Bight), we demonstrate the ability to identify different time-delayed interactions, distinguish between synchrony induced by strong unidirectional-forcing and true bidirectional causality, and resolve transitive causal chains.

  18. The latent causal chain of industrial water pollution in China.

    PubMed

    Miao, Xin; Tang, Yanhong; Wong, Christina W Y; Zang, Hongyu

    2015-01-01

    The purpose of this paper is to discover the latent causal chain of industrial water pollution in China and find ways to cure the want on discharge of toxic waste from industries. It draws evidences from the past pollution incidents in China. Through further digging the back interests and relations by analyzing representative cases, extended theory about loophole derivations and causal chain effect is drawn. This theoretical breakthrough reflects deeper causality. Institutional defect instead of human error is confirmed as the deeper reason of frequent outbreaks of water pollution incidents in China. Ways for collaborative environmental governance are proposed. This paper contributes to a better understanding about the deep inducements of industrial water pollution in China, and, is meaningful for ensuring future prevention and mitigation of environmental pollution. It illuminates multiple dimensions for collaborative environmental governance to cure the stubborn problem.

  19. Constraints on Children's Judgments of Magical Causality

    ERIC Educational Resources Information Center

    Woolley, Jacqueline D.; Browne, Cheryl A.; Boerger, Elizabeth A.

    2006-01-01

    In 3 studies we addressed the operation of constraints on children's causal judgments. Our primary focus was whether children's beliefs about magical causality, specifically wishing, are constrained by features that govern the attribution of ordinary causality. In Experiment 1, children witnessed situations in which a confederate's wish appeared…

  20. Expectations and interpretations during causal learning.

    PubMed

    Luhmann, Christian C; Ahn, Woo-Kyoung

    2011-05-01

    In existing models of causal induction, 4 types of covariation information (i.e., presence/absence of an event followed by presence/absence of another event) always exert identical influences on causal strength judgments (e.g., joint presence of events always suggests a generative causal relationship). In contrast, we suggest that, due to expectations developed during causal learning, learners give varied interpretations to covariation information as it is encountered and that these interpretations influence the resulting causal beliefs. In Experiments 1A-1C, participants' interpretations of observations during a causal learning task were dynamic, expectation based, and, furthermore, strongly tied to subsequent causal judgments. Experiment 2 demonstrated that adding trials of joint absence or joint presence of events, whose roles have been traditionally interpreted as increasing causal strengths, could result in decreased overall causal judgments and that adding trials where one event occurs in the absence of another, whose roles have been traditionally interpreted as decreasing causal strengths, could result in increased overall causal judgments. We discuss implications for traditional models of causal learning and how a more top-down approach (e.g., Bayesian) would be more compatible with the current findings.

  1. Expectations and Interpretations during Causal Learning

    ERIC Educational Resources Information Center

    Luhmann, Christian C.; Ahn, Woo-kyoung

    2011-01-01

    In existing models of causal induction, 4 types of covariation information (i.e., presence/absence of an event followed by presence/absence of another event) always exert identical influences on causal strength judgments (e.g., joint presence of events always suggests a generative causal relationship). In contrast, we suggest that, due to…

  2. Expectations and Interpretations During Causal Learning

    PubMed Central

    Luhmann, Christian C.; Ahn, Woo-kyoung

    2012-01-01

    In existing models of causal induction, 4 types of covariation information (i.e., presence/absence of an event followed by presence/absence of another event) always exert identical influences on causal strength judgments (e.g., joint presence of events always suggests a generative causal relationship). In contrast, we suggest that, due to expectations developed during causal learning, learners give varied interpretations to covariation information as it is encountered and that these interpretations influence the resulting causal beliefs. In Experiments 1A–1C, participants’ interpretations of observations during a causal learning task were dynamic, expectation based, and, furthermore, strongly tied to subsequent causal judgments. Experiment 2 demonstrated that adding trials of joint absence or joint presence of events, whose roles have been traditionally interpreted as increasing causal strengths, could result in decreased overall causal judgments and that adding trials where one event occurs in the absence of another, whose roles have been traditionally interpreted as decreasing causal strengths, could result in increased overall causal judgments. We discuss implications for traditional models of causal learning and how a more top-down approach (e.g., Bayesian) would be more compatible with the current findings. PMID:21534705

  3. Designing Effective Supports for Causal Reasoning

    ERIC Educational Resources Information Center

    Jonassen, David H.; Ionas, Ioan Gelu

    2008-01-01

    Causal reasoning represents one of the most basic and important cognitive processes that underpin all higher-order activities, such as conceptual understanding and problem solving. Hume called causality the "cement of the universe" [Hume (1739/2000). Causal reasoning is required for making predictions, drawing implications and inferences, and…

  4. Exploring Individual Differences in Preschoolers' Causal Stance

    ERIC Educational Resources Information Center

    Alvarez, Aubry; Booth, Amy E.

    2016-01-01

    Preschoolers, as a group, are highly attuned to causality, and this attunement is known to facilitate memory, learning, and problem solving. However, recent work reveals substantial individual variability in the strength of children's "causal stance," as demonstrated by their curiosity about and preference for new causal information. In…

  5. Representing Personal Determinants in Causal Structures.

    ERIC Educational Resources Information Center

    Bandura, Albert

    1984-01-01

    Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…

  6. Causal inference in economics and marketing.

    PubMed

    Varian, Hal R

    2016-07-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual-a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference.

  7. Considerations on causality in pharmacovigilance.

    PubMed

    Edwards, I Ralph

    2012-01-01

    Causality has been a topic of debate by philosophers, scientists, lawyers and for centuries. It is essential to define as precisely as possible all steps in the logical chain of events, since each may strengthen or confound an argument. Almost always there are issues of missing and conflicting data that need to be addressed specifically. In pharmacovigilance, as in many other situations, there is not just one possible causation for an effect but several. Each must be evaluated in the given context for probability. There is also likely to be a causal chain of events to the adverse effect under consideration, and each must be considered. In an individual patient diagnosis the components of patient history, clinical findings and various laboratory test findings are combined to point to the probability of the patho-physiological diagnosis, which in turn is related to possible causes with a strength determined by the constellation of findings. The established Bradford-Hill criteria are valuable in considering all the possible causal factors. Pharmacoepidemiology allows for population incidences of causes for particular effects and therefore provides an a priori probability listing for competing possible causes, or at least of one possible cause against the background of all others in a control group. Since adverse effects of medicines are generally rare, it is not possible to exclude drug causation in an individual by reliance on epidemiological evidence alone, only to argue that the incidence is below a level determined by statistical power, of the study or studies combined. Other areas of society are concerned with the process of causal inference, and this is especially true in legal cases in which judgements are made on possible personal injury by drugs.

  8. Modeling of causality with metamaterials

    NASA Astrophysics Data System (ADS)

    Smolyaninov, Igor I.

    2013-02-01

    Hyperbolic metamaterials may be used to model a 2 + 1-dimensional Minkowski space-time in which the role of time is played by one of the spatial coordinates. When a metamaterial is built and illuminated with a coherent extraordinary laser beam, the stationary pattern of light propagation inside the metamaterial may be treated as a collection of particle world lines, which represents a complete ‘history’ of this 2 + 1-dimensional space-time. While this model may be used to build interesting space-time analogs, such as metamaterial ‘black holes’ and a metamaterial ‘big bang’, it lacks causality: since light inside the metamaterial may propagate back and forth along the ‘timelike’ spatial coordinate, events in the ‘future’ may affect events in the ‘past’. Here we demonstrate that a more sophisticated metamaterial model may fix this deficiency via breaking the mirror and temporal (PT) symmetries of the original model and producing one-way propagation along the ‘timelike’ spatial coordinate. The resulting 2 + 1-dimensional Minkowski space-time appears to be causal. This scenario may be considered as a metamaterial model of the Wheeler-Feynman absorber theory of causality.

  9. Velocity Requirements for Causality Violation

    NASA Astrophysics Data System (ADS)

    Modanese, Giovanni

    We re-examine the "Regge-Tolman paradox" with reference to some recent experimental results. It is straightforward to find a formula for the velocity v of the moving system required to produce causality violation. This formula typically yields a velocity very close to the speed of light (for instance, v/c > 0.97 for X-shaped microwaves), which raises some doubts about the real physical observability of the violations. We then compute the velocity requirement introducing a delay between the reception of the primary signal and the emission of the secondary. It turns out that in principle for any delay it is possible to find moving observers able to produce active causal violation. This is mathematically due to the singularity of the Lorentz transformations for β →1. For a realistic delay due to the propagation of a luminal precursor, we find that causality violations in the reported experiments are still more unlikely (v/c > 0.989), and even in the hypothesis that the superluminal propagation velocity goes to infinity, the velocity requirement is bounded by v/c > 0.62. We also prove that if two oscopic bodies exchange energy and momentum through superluminal signals, then the swap of signal source and target is incompatible with the Lorentz transformations; therefore it is not possible to distinguish between source and target, even with reference to a definite reference frame.

  10. Estrogen receptor subtypes selectively mediate female mouse reproductive abnormalities induced by neonatal exposure to estrogenic chemicals.

    PubMed

    Nakamura, Takeshi; Katsu, Yoshinao; Watanabe, Hajime; Iguchi, Taisen

    2008-11-20

    Perinatal exposure to estrogens such as diethylstilbestrol (DES), and to estrogenic chemicals, induces persistent anovulation caused by alteration of hypothalamic-pituitary-gonadal (HPG) axis, polyovular follicles, uterine abnormalities and persistent vaginal changes in mice. Most activities of estrogenic chemicals are mediated through estrogen receptor alpha (ERalpha) and/or ERbeta. However, little was known about the relative contribution of the individual ER subtypes in induction of abnormalities. We tested the effects of neonatal exposure to ER selective ligands and DES on female mice. Transactivation assays using mouse ERalpha and ERbeta showed that 10(-10)M DES activated both ER subtypes and that the ERalpha agonist (propyl pyrazole triol, PPT) and the ERbeta agonist (diarylpropionitrile, DPN) selectively activated their respective ERs at 10(-9)M. Neonatal female mice were injected subcutaneously with DES, PPT or DPN and the animals were examined at 13 and 15 weeks of age, respectively. Persistent estrous smears and anovulation were induced in all mice by 0.025-2.5 microg DES and 2.5-25 microg PPT, but not by DPN, suggesting that the observed anovulation was primarily mediated through ERalpha. Disorganization of uterine musculature and ovary-independent vaginal epithelial cell proliferation accompanied by persistent expression of EGF-related genes and interleukin-1-related genes were also mediated through ERalpha. In contrast, polyovular follicles were induced by neonatal treatment with both ERalpha and ERbeta ligands, suggesting that ovarian abnormalities are mediated through both ER subtypes.

  11. Chemically Induced Reprogramming of Somatic Cells to Pluripotent Stem Cells and Neural Cells

    PubMed Central

    Biswas, Dhruba; Jiang, Peng

    2016-01-01

    The ability to generate transplantable neural cells in a large quantity in the laboratory is a critical step in the field of developing stem cell regenerative medicine for neural repair. During the last few years, groundbreaking studies have shown that cell fate of adult somatic cells can be reprogrammed through lineage specific expression of transcription factors (TFs)-and defined culture conditions. This key concept has been used to identify a number of potent small molecules that could enhance the efficiency of reprogramming with TFs. Recently, a growing number of studies have shown that small molecules targeting specific epigenetic and signaling pathways can replace all of the reprogramming TFs. Here, we provide a detailed review of the studies reporting the generation of chemically induced pluripotent stem cells (ciPSCs), neural stem cells (ciNSCs), and neurons (ciN). We also discuss the main mechanisms of actions and the pathways that the small molecules regulate during chemical reprogramming. PMID:26861316

  12. TRPA1 detects environmental chemicals and induces avoidance behavior and arousal from sleep.

    PubMed

    Yonemitsu, Toru; Kuroki, Chiharu; Takahashi, Nobuaki; Mori, Yasuo; Kanmura, Yuichi; Kashiwadani, Hideki; Ootsuka, Youichirou; Kuwaki, Tomoyuki

    2013-01-01

    Detecting threats and escaping before serious confrontations are important for animals to avoid danger and death. Transient receptor potential ankyrin 1 (TRPA1), a member of the TRP superfamily, is expressed in a subset of sensory neurons and mediates nociception evoked by pungent chemicals. Using behavioral testing, we found that TRPA1 knockout mice failed to avoid entering a chamber filled with vapor of formalin, allyl isothiocyanate, and acrolein. The avoidance behavior was blocked by nasal but not subcutaneous administration of a blocker to TRPA1. We also found that TRPA1 knockout mice did not wake when exposed to formalin during sleep. Additionally, the spinal trigeminal nucleus, the first relay neurons of the trigeminal system, showed massive expression of c-Fos after a brief (3 min) exposure to formalin vapor. TRPA1 seems to be a sentinel for environmental chemicals and induces avoidance behaviors and waking by way of the trigeminal system. PMID:24172941

  13. Laser Induced Breakdown Spectroscopy applications to meteorites: Chemical analysis and composition profiles

    NASA Astrophysics Data System (ADS)

    Dell'Aglio, M.; De Giacomo, A.; Gaudiuso, R.; Pascale, O. De; Senesi, G. S.; Longo, S.

    2010-12-01

    A fast procedure for chemical analysis of different meteorites is presented, based on LIBS (Laser Induced Breakdown Spectroscopy). The technique is applied to several test cases (Dhofar 019, Dhofar 461, Sahara 98222, Toluca, Sikhote Alin and Campo del Cielo) and can be useful for rapid meteorite identification providing geologists with specific chemical information for meteorite classification. Concentration profiles of Fe, Ni and Co are simultaneously detected across the Widmanstätten structure of the iron meteorite Toluca with a view to determining cooling rates. The LIBS analysis of meteorites is also used as a laboratory test for analogous studies on the respective parent bodies (Mars, asteroids) in space exploration missions where one clear advantage of the proposed technique is that no direct contact with the sample is required.

  14. Chemical ordering in magnetic FePd/Pd(001) epitaxial thin films induced by annealing

    SciTech Connect

    Halley, D.; Bayle-Guillemaud, P.; Arenal, R.; Marty, A.; Samson, Y.; Gilles, B.

    2004-11-01

    Chemically disordered FePd epitaxial layers are grown at room temperature by molecular beam epitaxy on a Pd(001) buffer layer and then annealed in order to induce the chemically ordered L1{sub 0} (AuCu I) structure. Contrary to what is observed in the case of ordering during growth above room temperature, the ordered structure appears here with the three possible variants of the L1{sub 0} phase. The ratio of the three different variant volumes is set by the residual epitaxial strain in the layer before annealing. It thus explains that for long annealing times, the long-range order parameter associated with the L1{sub 0} variant with c along the (100) growth direction saturates at a value close to 0.65, and never reaches unity. Magnetic consequences of the ordering are studied.

  15. Time evolution studies of laser induced chemical changes in InAs nanowire using Raman spectroscopy

    SciTech Connect

    Pal, Suparna; Aggarwal, R.; Kumari Gupta, Vandna; Ingale, Alka

    2014-07-07

    We report the study of time evolution of chemical changes on the surface of an InAs nanowire (NW) on laser irradiation in different power density regime, using Raman spectroscopy for a time span of 8–16 min. Mixture of metastable oxides like InAsO{sub 4,} As{sub 2}O{sub 3} are formed upon oxidation, which are reflected as sharp Raman peaks at ∼240–254 and 180–200 cm{sup −1}. Evidence of removal of arsenic layer by layer is also observed at higher power density. Position controlled laser induced chemical modification on a nanometer scale, without changing the core of the NW, can be useful for NW based device fabrication.

  16. Fluctuation Induced Structure in Chemical Reaction with Small Number of Molecules

    NASA Astrophysics Data System (ADS)

    Suzuki, Yasuhiro

    We investigate the behaviors of chemical reactions of the Lotka-Volterra model with small number of molecules; hence the occurrence of random fluctuations modifies the deterministic behavior and the law of mass action is replaced by a stochastic model. We model it by using Abstract Rewriting System on Multisets, ARMS; ARMS is a stochastic method of simulating chemical reactions and it is based on the reaction rate equation. We confirmed that the magnitude of fluctuations on periodicity of oscillations becomes large, as the number of involved molecules is getting smaller; and these fluctuations induce another structure, which have not observed in the reactions with large number of molecules. We show that the underling mechanism through investigating the coarse grained phase space of ARMS.

  17. Self-grooming induced by sexual chemical signals in male root voles (Microtus oeconomus Pallas).

    PubMed

    Yu, Honghao; Yue, Pengpeng; Sun, Ping; Zhao, Xinquan

    2010-03-01

    Sniffing is one-way animals collect chemical signals, and many males self-groom when they encounter the odor of opposite-sex conspecifics. We tested the hypothesis that sexual chemical signals from females can induce self-grooming behavior in male root voles (Microtus oeconomus Pallas). Specifically, we investigated the sniffing pattern of male root voles in response to odors from the head, trunk, and tail areas of lactating and non-lactating females. The self-grooming behavior of males in response to female individual odorant stimuli was documented, and the relationship between self-grooming and sniffing of odors from the head, trunk, and tails areas were analyzed. Sniffing pattern results showed that males are most interested in odors from the head area, and more interested in odors from the tail as compared to the trunk area. Males displayed different sniffing and self-grooming behaviors when they were exposed to odors from lactating females as compared to non-lactating females. Males also spent more time sniffing and engaged in more sniffing behaviors in response to odors from the lactating females' tail area as compared to the same odors from non-lactating females. Similarly, males spent more time self-grooming and engaged in more self-grooming behaviors in the presence of individual odors from lactating females as compared to individual odors from non-lactating females. Partial correlation analyses revealed that the frequency of self-grooming was significantly correlated with the frequency of tail area sniffs. Results from this experiment suggest that sexual attractiveness of lactating females is stronger than that of non-lactating females. Furthermore, the partial correlation analysis demonstrated that self-grooming in males is induced by odors from the tail area of females. Collectively, these results support the hypothesis that sexual chemical signals from females can induce self-grooming behavior in male root voles. Self-grooming may also reflect the

  18. Assessing thalamocortical functional connectivity with Granger causality.

    PubMed

    Chen, Cheng; Maybhate, Anil; Israel, David; Thakor, Nitish V; Jia, Xiaofeng

    2013-09-01

    Assessment of network connectivity across multiple brain regions is critical to understanding the mechanisms underlying various neurological disorders. Conventional methods for assessing dynamic interactions include cross-correlation and coherence analysis. However, these methods do not reveal the direction of information flow, which is important for studying the highly directional neurological system. Granger causality (GC) analysis can characterize the directional influences between two systems. We tested GC analysis for its capability to capture directional interactions within both simulated and in vivo neural networks. The simulated networks consisted of Hindmarsh-Rose neurons; GC analysis was used to estimate the causal influences between two model networks. Our analysis successfully detected asymmetrical interactions between these networks ( , t -test). Next, we characterized the relationship between the "electrical synaptic strength" in the model networks and interactions estimated by GC analysis. We demonstrated the novel application of GC to monitor interactions between thalamic and cortical neurons following ischemia induced brain injury in a rat model of cardiac arrest (CA). We observed that during the post-CA acute period the GC interactions from the thalamus to the cortex were consistently higher than those from the cortex to the thalamus ( 1.983±0.278 times higher, p = 0.021). In addition, the dynamics of GC interactions between the thalamus and the cortex were frequency dependent. Our study demonstrated the feasibility of GC to monitor the dynamics of thalamocortical interactions after a global nervous system injury such as CA-induced ischemia, and offers preferred alternative applications in characterizing other inter-regional interactions in an injured brain.

  19. Improving causality induction with category learning.

    PubMed

    Guo, Yi; Wang, Zhihong; Shao, Zhiqing

    2014-01-01

    Causal relations are of fundamental importance for human perception and reasoning. According to the nature of causality, causality has explicit and implicit forms. In the case of explicit form, causal-effect relations exist at either clausal or discourse levels. The implicit causal-effect relations heavily rely on empirical analysis and evidence accumulation. This paper proposes a comprehensive causality extraction system (CL-CIS) integrated with the means of category-learning. CL-CIS considers cause-effect relations in both explicit and implicit forms and especially practices the relation between category and causality in computation. In elaborately designed experiments, CL-CIS is evaluated together with general causality analysis system (GCAS) and general causality analysis system with learning (GCAS-L), and it testified to its own capability and performance in construction of cause-effect relations. This paper confirms the expectation that the precision and coverage of causality induction can be remarkably improved by means of causal and category learning.

  20. Improving Causality Induction with Category Learning

    PubMed Central

    Wang, Zhihong; Shao, Zhiqing

    2014-01-01

    Causal relations are of fundamental importance for human perception and reasoning. According to the nature of causality, causality has explicit and implicit forms. In the case of explicit form, causal-effect relations exist at either clausal or discourse levels. The implicit causal-effect relations heavily rely on empirical analysis and evidence accumulation. This paper proposes a comprehensive causality extraction system (CL-CIS) integrated with the means of category-learning. CL-CIS considers cause-effect relations in both explicit and implicit forms and especially practices the relation between category and causality in computation. In elaborately designed experiments, CL-CIS is evaluated together with general causality analysis system (GCAS) and general causality analysis system with learning (GCAS-L), and it testified to its own capability and performance in construction of cause-effect relations. This paper confirms the expectation that the precision and coverage of causality induction can be remarkably improved by means of causal and category learning. PMID:24883419

  1. Voluntary action and causality in temporal binding.

    PubMed

    Cravo, Andre M; Claessens, Peter M E; Baldo, Marcus V C

    2009-10-01

    Previous studies have documented temporal attraction in perceived times of actions and their effects. While some authors argue that voluntary action is a necessary condition for this phenomenon, others claim that the causal relationship between action and effect is the crucial ingredient. In the present study, we investigate voluntary action and causality as the necessary and sufficient conditions for temporal binding. We used a variation of the launching effect proposed by Michotte, in which participants controlled the launch stimulus in some blocks. Volunteers reported causality ratings and estimated the interval between the two events. Our results show dissociations between causality ratings and temporal estimation. While causality ratings are not affected by voluntary action, temporal bindings were only found in the presence of both voluntary action and high causality. Our results indicate that voluntary action and causality are both necessary for the emergence of temporal binding.

  2. Convection and mass-transport in laser-induced chemical vapor deposition

    NASA Technical Reports Server (NTRS)

    Patnaik, S.; Brown, R. A.

    1988-01-01

    Gas flow and energy and species transport in laser-induced chemical vapor deposition (LICVD) of amorphous silicon films by silane pyrolysis are analyzed by finite element analysis of a two-dimensional model for the process. Spatial nonuniformity of the deposited film is shown to result from diffusion controlled transport of products between the beam and substrate. Deposition profiles are affected by buoyancy-driven convection only at increased gas pressures. Horizontal orientation of the reactor with respect to gravity is optimal because the stagnation-like flow, that results adjacent to the substrate, enhances mixing, and smoothes the film profile.

  3. Observation of two-photon induced three-photon absorption in chemically synthesized silver nanostructures

    NASA Astrophysics Data System (ADS)

    Biswas, S.; Kole, A. K.; Kumbhakar, P.

    2015-06-01

    In this work, we have reported nonlinear optical (NLO) properties of different nanostructures of Ag, namely spherical, nanopentagon, and nanowire, synthesized by single pot chemical technique. NLO properties are measured by open and closed aperture Z-scan techniques at 1064 nm Nd:YAG laser wavelength having pulsed duration of 10 ns. The synthesized Ag nanostructures are exhibiting the rarely reported two-photon induced three-photon absorption along-with self-defocusing nonlinear refraction. A plausible explanation of the observed NLO properties owing to shape variations has been presented. The materials are also exhibiting optical limiting effect making them suitable for applications in advanced photonic devices.

  4. Chemical patterning of Ag(111): Spatially confined oxide formation induced by electron beam irradiation

    SciTech Connect

    Guenther, S.; Reichelt, R.; Wintterlin, J.; Barinov, A.; Mentes, T. O.; Nino, M. A.; Locatelli, A.

    2008-12-08

    Low energy electron irradiation of a Ag(111) surface during NO{sub 2} adsorption at 300 K induces formation of Ag oxide. Using a spatially confined electron beam, small Ag{sub 2}O spots could be grown with a sharp, {approx}100 nm wide, boundary to the nonirradiated metallic surface. Since the structure size will mainly depend on the sharpness of the irradiating electron beam, this process has the potential of a single step nanostructuring process. Temperature treatment offers an easy way to manipulate the boundary between oxide and metallic silver by steering a chemical front.

  5. Effect of etchant concentration on microwave induced chemical etching (MICE) of CR-39 detector

    NASA Astrophysics Data System (ADS)

    Sahoo, G. S.; Tripathy, S. P.; Sharma, S. D.; Bandyopadhyay, T.

    2015-11-01

    The recently introduced microwave induced chemical etching (MICE) has been found to be a fast and effective etching technique for CR-39 detector. In the present work, the MICE technique was used to develop the neutron induced recoil tracks in CR-39 detectors. Special attention was paid in carrying out a systematic investigation to study the effect of etchant concentration and microwave power on the development of tracks and various track parameters. NaOH solution of different concentrations, viz. 3-8 N was tested at 300, 450, 600 and 900 W of microwave power. Temperature profiles for 200 ml solution of each concentration were generated to maintain a fixed operating condition for all concentrations at each microwave power. The bulk etch rate was found to increase with the microwave power as well as with the etchant concentration. Empirical relations were established to relate the variation of bulk etch rate with microwave power and etchant concentration.

  6. Chemically Induced Changes to Membrane Permeability in Living Cells Probed with Nonlinear Light Scattering.

    PubMed

    Wilhelm, Michael J; Sharifian Gh, Mohammad; Dai, Hai-Lung

    2015-07-28

    Second-harmonic light scattering (SHS) permits characterization of membrane-specific molecular transport in living cells. Herein, we demonstrate the use of time-resolved SHS for quantifying chemically induced enhancements in membrane permeability. As proof of concept, we examine the enhanced permeability of the cytoplasmic membrane in living Escherichia coli following addition of extracellular adenosine triphosphate (ATPe). The transport rate of the hydrophobic cation, malachite green, increases nearly an order of magnitude following addition of 0.1 mM ATPe. The absence of an ATPe-enhanced permeability in liposomes strongly suggests the induced effect is protein-mediated. The utility of SHS for elucidating the mechanism of action of antimicrobials is discussed. PMID:26122620

  7. The relevance of spontaneous- and chemically-induced alterations in testicular germ cell apoptosis to toxicology.

    PubMed

    Richburg, J H

    2000-03-15

    Elimination of germ cells via apoptosis occurs spontaneously under normal physiologic conditions and is often heightened after chemical-induced testicular injury. Though many different apoptosis-related elements have been identified in the testis, the molecular and cellular mechanisms that regulate germ cell apoptosis are not thoroughly understood. In this review, the role of germ cell apoptosis in spermatogenesis and possible key regulators of apoptosis is described. The involvement of the Fas-signaling pathway between Sertoli cells and germ cells is highlighted as a crucial paracrine-signaling mechanism that responds to both physiologic- or toxicant-induced declines in the supportive capacity of the testis and reduces the germ cell population accordingly.

  8. Effect of Lepidium meyenii (maca) on testicular function of mice with chemically and physically induced subfertility.

    PubMed

    Valdivia Cuya, M; Yarasca De La Vega, K; Lévano Sánchez, G; Vásquez Cavero, J; Temoche García, H; Torres Torres, L; Cruz Ornetta, V

    2016-10-01

    The aim of this study was to evaluate the effect of Lepidium meyenii (maca) in chemically and physically subfertile mice. After 35 days, the following groups of mice were evaluated: control, sham, chemical subfertility, chemical subfertility-maca-supplemented, physical subfertility, physical subfertility-maca-supplemented and maca-supplemented only. Motility (32.36% ± 5.34%) and sperm count (44.4 ± 5.37 × 10(6) /ml) in the chemically and physically subfertile mice (11.81% ± 4.06%, 17.34 ± 13.07 × 10(6) /ml) decreased compared to the control (75.53% ± 2.97% and 57.4 ± 19.6 10(6) /ml) and sham (53.5% ± 7.86% and 58.4 ± 14.10 10(6) /ml). Maca was able to reverse the deleterious effect of motility (76.36 ± 1.97) as well as sperm count (53.5 ± 9.18 × 10(6) /ml) on chemical subfertility. In contrast, maca did not reverse the effects of induced physical subfertility nor motility (18.78% ± 14.41%) or sperm count (20.17 ± 11.20 × 10(6) /ml). The percentage of sperm DNA fragmentation in the physically subfertile mice increased (11.1% ± 19.29%) compared to the control (0.84% ± 0.85%). However, in the physically subfertile group, maca decreased sperm DNA fragmentation (2.29% ± 2.30%) closer to the sham (1.04% ± 0.62%) and the control (0.84% ± 0.85%). The group supplemented only with maca showed 0.54% ± 0.50% of spermatozoa with DNA fragmentation. Yet, the differences observed were statistically not significant. In conclusion, it appears that maca activates the cytochrome P450 system after chemically induced subfertility. However, it does not reverse the low mitochondrial membrane potential in spermatozoa compromised in the physical subfertility group. PMID:27681650

  9. Common and distinct mechanisms of induced pulmonary fibrosis by particulate and soluble chemical fibrogenic agents

    PubMed Central

    Dong, Jie; Yu, Xiaoqing; Porter, Dale W.; Battelli, Lori A.; Kashon, Michael L.

    2016-01-01

    Pulmonary fibrosis results from the excessive deposition of collagen fibers and scarring in the lungs with or without an identifiable cause. The mechanism(s) underlying lung fibrosis development is poorly understood, and effective treatment is lacking. Here we compared mouse lung fibrosis induced by pulmonary exposure to prototypical particulate (crystalline silica) or soluble chemical (bleomycin or paraquat) fibrogenic agents to identify the underlying mechanisms. Young male C57BL/6J mice were given silica (2 mg), bleomycin (0.07 mg), or paraquat (0.02 mg) by pharyngeal aspiration. All treatments induced significant inflammatory infiltration and collagen deposition, manifesting fibrotic foci in silica-exposed lungs or diffuse fibrosis in bleomycin or paraquat-exposed lungs on day 7 post-exposure, at which time the lesions reached their peaks and represented a junction of transition from an acute response to chronic fibrosis. Lung genomewide gene expression was analyzed, and differential gene expression was confirmed by quantitative RT-PCR, immunohistochemistry, and immunoblotting for representative genes to demonstrate their induced expression and localization in fibrotic lungs. Canonical signaling pathways, gene ontology, and upstream transcription networks modified by each agent were identified. In particular, these inducers elicited marked proliferative responses; at the same time, silica preferentially activated innate immune functions and the defense against foreign bodies, whereas bleomycin and paraquat boosted responses related to cell adhesion, platelet activation, extracellular matrix remodeling, and wound healing. This study identified, for the first time, the shared and unique genes, signaling pathways, and biological functions regulated by particulate and soluble chemical fibrogenic agents during lung fibrosis, providing insights into the mechanisms underlying human lung fibrotic diseases. PMID:26345256

  10. Chemical Inhibition of Histone Deacetylases 1 and 2 Induces Fetal Hemoglobin through Activation of GATA2

    PubMed Central

    Golonzhka, Olga; Chonkar, Apurva; Tamang, David; van Duzer, John H.; Jones, Simon S.; Jarpe, Matthew B.

    2016-01-01

    Therapeutic intervention aimed at reactivation of fetal hemoglobin protein (HbF) is a promising approach for ameliorating sickle cell disease (SCD) and β-thalassemia. Previous studies showed genetic knockdown of histone deacetylase (HDAC) 1 or 2 is sufficient to induce HbF. Here we show that ACY-957, a selective chemical inhibitor of HDAC1 and 2 (HDAC1/2), elicits a dose and time dependent induction of γ-globin mRNA (HBG) and HbF in cultured primary cells derived from healthy individuals and sickle cell patients. Gene expression profiling of erythroid progenitors treated with ACY-957 identified global changes in gene expression that were significantly enriched in genes previously shown to be affected by HDAC1 or 2 knockdown. These genes included GATA2, which was induced greater than 3-fold. Lentiviral overexpression of GATA2 in primary erythroid progenitors increased HBG, and reduced adult β-globin mRNA (HBB). Furthermore, knockdown of GATA2 attenuated HBG induction by ACY-957. Chromatin immunoprecipitation and sequencing (ChIP-Seq) of primary erythroid progenitors demonstrated that HDAC1 and 2 occupancy was highly correlated throughout the GATA2 locus and that HDAC1/2 inhibition led to elevated histone acetylation at well-known GATA2 autoregulatory regions. The GATA2 protein itself also showed increased binding at these regions in response to ACY-957 treatment. These data show that chemical inhibition of HDAC1/2 induces HBG and suggest that this effect is mediated, at least in part, by histone acetylation-induced activation of the GATA2 gene. PMID:27073918

  11. Comparative sensitivity of human and rat neural cultures to chemical-induced inhibition of neurite outgrowth

    SciTech Connect

    Harrill, Joshua A.; Freudenrich, Theresa M.; Robinette, Brian L.; Mundy, William R.

    2011-11-15

    cultures were more sensitive to neurite outgrowth inhibitors, they also had a lower dynamic range for detecting chemical-induced neurite outgrowth inhibition and greater variability from culture-to-culture as compared to rat primary cortical cultures.

  12. Conditional Granger causality and partitioned Granger causality: differences and similarities.

    PubMed

    Malekpour, Sheida; Sethares, William A

    2015-12-01

    Neural information modeling and analysis often requires a measurement of the mutual influence among many signals. A common technique is the conditional Granger causality (cGC) which measures the influence of one time series on another time series in the presence of a third. Geweke has translated this condition into the frequency domain and has explored the mathematical relationships between the time and frequency domain expressions. Chen has observed that in practice, the expressions may return (meaningless) negative numbers, and has proposed an alternative which is based on a partitioned matrix scheme, which we call partitioned Granger causality (pGC). There has been some confusion in the literature about the relationship between cGC and pGC; some authors treat them as essentially identical measures, while others have noted that some properties (such as the relationship between the time and frequency domain expressions) do not hold for the pGC. This paper presents a series of matrix equalities that simplify the calculation of the pGC. In this simplified expression, the essential differences and similarities between the cGC and the pGC become clear; in essence, the pGC is dependent on only a subset of the parameters in the model estimation, and the noise residuals (which are uncorrelated in the cGC) need not be uncorrelated in the pGC. The mathematical results are illustrated with a simulation, and the measures are applied to an EEG dataset.

  13. Scalar Fields via Causal Tapestries

    NASA Astrophysics Data System (ADS)

    Sulis, William

    2012-02-01

    Causal tapestries provide a framework for implementing an explicit Process Theory approach to quantum foundations which models information flow within a physical system. We consider event-transition tapestry pairs. An event tapestry O is a 4-tuple (L, K, M, Ip ) where K is an index set of cardinality κ, M = M x F(M) x D x P(M') a mathematical structure with M a causal space, F(M) a function space, D a descriptor space, P(M') either a Lie algebra or tangent space on a manifold M', Ip an event tapestry. L consists of elements of the form [n]<α>G, n in K, α in M and G an acyclic directed graph whose vertex set is a subset of Lp Likewise, a transition tapestry π is a 4-tuple (L', K', M', I'p ) where M' = M' x F(M') x D' x P'(M). The dynamic generates a consistent succession of O-π pairs by means of a game based on the technique of forcing used in logic to generate models. This dynamic has previously been shown to be compatible with Lorentz invariance. An application of this approach to model scalar fields is presented in which each informon is associated with a function of the form f(πk1 /σ1 ,,πkN /σN )sin ( σ1 t1 --πk1 )/ ( σ1 t1 --πk1 ) .sin ( σN tN --πkN )/ ( σN tN --πkN ) and the WSK interpolation theorem is used to generate the resulting scalar field on the causal manifold.

  14. Lymphohematopoietic Cancers Induced by Chemicals and Other Agents: Overview and Implications for Risk Assessment (External Review Draft)

    EPA Science Inventory

    This draft report provides an overview of the types of mechanisms underlying the lymphohematopoietic cancers induced by chemical agents and radiation in humans, with a primary emphasis on leukemia and leukemia-inducing agents. It focuses on how mechanistic information on human l...

  15. DETECTION OF LOW DOSE RADIATION-AND CHEMICALLY-INDUCED DNA DAMAGE USING TEMPERATURE DIFFERENTIAL FLUORESCENCE ASSAYS

    EPA Science Inventory

    Rapid, sensitive and simple assays for radiation- and chemically-induced DNA damage can be of significant benefit to a number of fields including radiation biology, clinical research, and environmental monitoring. Although temperature-induced DNA strand separation has been use...

  16. Pressure-induced phase and chemical transformations of lithium peroxide (Li2O2).

    PubMed

    Dunuwille, Mihindra; Kim, Minseob; Yoo, Choong-Shik

    2016-08-28

    We present the pressure-induced phase/chemical changes of lithium peroxide (Li2O2) to 63 GPa using diamond anvil cells, confocal micro-Raman spectroscopy, and synchrotron x-ray diffraction. The Raman data show the emergence of the major vibrational peaks associated with O2 above 30 GPa, indicating the subsequent pressure-induced reversible chemical decomposition (disassociation) in dense Li2O2. The x-ray diffraction data of Li2O2, on the other hand, show no dramatic structural change but remain well within a P63/mmc structure to 63 GPa. Nevertheless, the Rietveld refinement indicates a subtle change in the structural order parameter z of the oxygen position O (13, 23, z) at around 35 GPa, which can be considered as a second-order, isostructural phase transition. The nearest oxygen-oxygen distance collapses from 1.56 Å at ambient condition to 1.48 Å at 63 GPa, resulting in a more ionic character of this layered crystal lattice, 3Li(+)+(LiO2)3 (3-). This structural change in turn advocates that Li2O2 decomposes to 2Li and O2, further augmented by the densification in specific molar volumes. PMID:27586935

  17. C-1s NEXAFS spectroscopy reveals chemical fractionation of humic acid by cation-induced coagulation

    SciTech Connect

    Christl,I.; Kretzschmar, R.

    2007-01-01

    The influence of cation-induced coagulation on the chemical composition of dissolved and coagulated fractions of humic acid was investigated in batch coagulation experiments for additions of aluminum at pH 4 and 5, iron at pH 4, and calcium and lead at pH 6. The partitioning of organic carbon and metals was determined by analyzing total organic carbon and total metal contents of the dissolved phase. Both the dissolved and the coagulated humic acid fractions were characterized using synchrotron scanning transmission X-ray microscopy (STXM) and C-1s near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. Intensities of {pi}* transitions of carboxyl carbon and {sigma}* transitions of alkyl, O-alkyl, and carboxyl carbon decreased with increasing metal concentration for the dissolved humic acid fractions. This decrease was accompanied by an increase of the respective intensities in the coagulated fraction as shown for lead. Intensities of aromatic and phenolic carbon were affected to a larger extent only by aluminum and iron additions. The changes observed in the C-1s NEXAFS spectra coincided with an increasing removal of organic carbon from the dissolved phase with increasing total metal concentrations. We conclude that humic acid was chemically fractionated by cation-induced coagulation, which preferentially removed functional groups involved in metal-cation binding from solution.

  18. Proteomic Alterations in B Lymphocytes of Sensitized Mice in a Model of Chemical-Induced Asthma

    PubMed Central

    De Vooght, Vanessa; Schoofs, Liliane; Nemery, Benoit; Clynen, Elke; Hoet, Peter H. M.

    2015-01-01

    Introduction and Aim The role of B-lymphocytes in chemical-induced asthma is largely unknown. Recent work demonstrated that transferring B lymphocytes from toluene diisocyanate (TDI)-sensitized mice into naïve mice, B cell KO mice and SCID mice, triggered an asthma-like response in these mice after a subsequent TDI-challenge. We applied two-dimensional difference gel electrophoresis (2D-DIGE) to describe the “sensitized signature” of B lymphocytes comparing TDI-sensitized mice with control mice. Results Sixteen proteins were identified that were significantly up- or down-regulated in B lymphocytes of sensitized mice. Particularly differences in the expression of cyclophilin A, cofilin 1 and zinc finger containing CCHC domain protein 11 could be correlated to the function of B lymphocytes as initiators of T lymphocyte independent asthma-like responses. Conclusion This study revealed important alterations in the proteome of sensitized B cells in a mouse model of chemical-induced asthma, which will have an important impact on the B cell function. PMID:26398101

  19. Effects of ventromedial and lateral hypothalamic stimulation on chemically-induced liver injury in rats

    SciTech Connect

    Iwai, M.; Shimazu, T.

    1988-01-01

    The effects of hypothalamic stimulation on experimental liver injury induced by carbon tetrachloride (CCL/sub 4/) or dimethylnitrosamine (DMN) were studied in rats, by measuring plasma alanine amino-transferase (ALT) activity as an index of acute liver injury. Electrical stimulation of the ventromedial hypothalamus (VHM) in CCl/sub 4/-treated rats caused a marked increase in plasma ALT activity, accompanied by a significant decrease in ALT activity in the liver, although CCl4 treatment alone had no significant effect on plasma ALT activity. A similar effect of VHM stimulation on plasma ALT activity was observed in rats treated with DMN, another hepatotoxic chemical. No such exaggerated effect of VMH stimulation on plasma ALT activity was observed after stimulation of the lateral hypothalamic area (LH). Surgical sympathetic denervation of the liver greatly suppressed the increase in plasma ALT activity after CCl/sub 4/ injection and VMH stimulation. Measurement of regional blood flow indicated that VMH stimulation did not produce a significant change in blood flow to the liver. These results suggest that the VMH is involved in the progress of chemically-induced liver injury through activation of the sympathetic nerve, possibly by affecting liver metabolism more than the blood flow change to the liver.

  20. Reactivity pattern of bromonucleosides induced by 2-hydroxypropyl radicals: photochemical, radiation chemical, and computational studies.

    PubMed

    Zdrowowicz, Magdalena; Chomicz, Lidia; Miloch, Justyna; Wiczk, Justyna; Rak, Janusz; Kciuk, Gabriel; Bobrowski, Krzysztof

    2015-06-01

    The bromonucleosides (BrdX's) 5-bromo-2'-deoxyuridine (BrdU), 5-bromo-2'-deoxycytidine (BrdC), 8-bromo-2'-deoxyadenosine (BrdA), and 5-bromo-2'-deoxyguanosine (BrdG) may substitute for ordinary nucleosides in DNA. As indicated by electron-stimulated desorption experiments, such a modified biopolymer is greater than 2-3-fold more sensitive to damage induced by excess electrons. The other major product of water radiolysis, the (•)OH radical, may form a number of other radicals in chemical reactions with the complex content of the cell. Thus, the well-proved BrdU-labeled DNA radiosensitivity may be, at least in part, related to secondary organic radicals. Therefore, in the current study, the propensity of BrdX's to damage induced by 2-hydroxypropyl radical (OHisop(•))-a prototype radical species-was investigated. The HPLC and LC-MS analyses revealed the formation of two major products from the brominated pyrimidine nucleosides, a native nucleoside and an adduct of BrdX and OHisop(•) , and only an adduct of BrdX from the bromopurine nucleosides. Quantum chemical calculations ascribed this evident difference between purines and pyrimidines to the electron transfer from OHisop(•) to BrdX that is especially favorable in pyrimidines. PMID:25971814

  1. Improving analytical methods for protein-protein interaction through implementation of chemically inducible dimerization.

    PubMed

    Andersen, Tonni Grube; Nintemann, Sebastian J; Marek, Magdalena; Halkier, Barbara A; Schulz, Alexander; Burow, Meike

    2016-01-01

    When investigating interactions between two proteins with complementary reporter tags in yeast two-hybrid or split GFP assays, it remains troublesome to discriminate true- from false-negative results and challenging to compare the level of interaction across experiments. This leads to decreased sensitivity and renders analysis of weak or transient interactions difficult to perform. In this work, we describe the development of reporters that can be chemically induced to dimerize independently of the investigated interactions and thus alleviate these issues. We incorporated our reporters into the widely used split ubiquitin-, bimolecular fluorescence complementation (BiFC)- and Förster resonance energy transfer (FRET)- based methods and investigated different protein-protein interactions in yeast and plants. We demonstrate the functionality of this concept by the analysis of weakly interacting proteins from specialized metabolism in the model plant Arabidopsis thaliana. Our results illustrate that chemically induced dimerization can function as a built-in control for split-based systems that is easily implemented and allows for direct evaluation of functionality. PMID:27282591

  2. Pressure-induced phase and chemical transformations of lithium peroxide (Li2O2)

    NASA Astrophysics Data System (ADS)

    Dunuwille, Mihindra; Kim, Minseob; Yoo, Choong-Shik

    2016-08-01

    We present the pressure-induced phase/chemical changes of lithium peroxide (Li2O2) to 63 GPa using diamond anvil cells, confocal micro-Raman spectroscopy, and synchrotron x-ray diffraction. The Raman data show the emergence of the major vibrational peaks associated with O2 above 30 GPa, indicating the subsequent pressure-induced reversible chemical decomposition (disassociation) in dense Li2O2. The x-ray diffraction data of Li2O2, on the other hand, show no dramatic structural change but remain well within a P63/mmc structure to 63 GPa. Nevertheless, the Rietveld refinement indicates a subtle change in the structural order parameter z of the oxygen position O (1/3, 2/3, z) at around 35 GPa, which can be considered as a second-order, isostructural phase transition. The nearest oxygen-oxygen distance collapses from 1.56 Å at ambient condition to 1.48 Å at 63 GPa, resulting in a more ionic character of this layered crystal lattice, 3Li++(LiO2)3 3 -. This structural change in turn advocates that Li2O2 decomposes to 2Li and O2, further augmented by the densification in specific molar volumes.

  3. The relationship between chemically-induced meiotic delay and aneuploidy in mouse oocytes and zygotes

    SciTech Connect

    Mailhes, J.B.; Marchetti, F.

    1993-12-31

    Aneuploidy is a relatively common genetic disorder that results in human morbidity and mortality. Approximately 30% of embryonic and fetal deaths and 3.45 per thousand livebirths are associated with an abnormal number of chromosomes. Unfortunately, very little is known about the etiology and mechanism of chromosome missegregation. This situation dictates that considerable research be directed toward understanding the causes of aneuploidy. Although several hypotheses have been advanced for the etiology of aneuploidy, there still exists a paucity of information about the direct cuases and mechanisms of aneuploidy production. Without such specific knowledge, there is little hope of reducing the incidence of aneuploidy in humans. Some progress has been made. We now know that various chemicals can induce aneuploidy by interacting with certain cellular organelles, especially components of the spindle apparatus. These results have been demonstrated in various organisms and cell types both in vivo and in vitro. Since the ultimate objective of aneuploidy research is to obtain information that can be used to reduce the aneuploidy burden in humans, we have concentrated our research efforts on studying chemically-induced aneuploidy in mammalian germ cells and zygotes.

  4. Improving analytical methods for protein-protein interaction through implementation of chemically inducible dimerization

    PubMed Central

    Andersen, Tonni Grube; Nintemann, Sebastian J.; Marek, Magdalena; Halkier, Barbara A.; Schulz, Alexander; Burow, Meike

    2016-01-01

    When investigating interactions between two proteins with complementary reporter tags in yeast two-hybrid or split GFP assays, it remains troublesome to discriminate true- from false-negative results and challenging to compare the level of interaction across experiments. This leads to decreased sensitivity and renders analysis of weak or transient interactions difficult to perform. In this work, we describe the development of reporters that can be chemically induced to dimerize independently of the investigated interactions and thus alleviate these issues. We incorporated our reporters into the widely used split ubiquitin-, bimolecular fluorescence complementation (BiFC)- and Förster resonance energy transfer (FRET)- based methods and investigated different protein-protein interactions in yeast and plants. We demonstrate the functionality of this concept by the analysis of weakly interacting proteins from specialized metabolism in the model plant Arabidopsis thaliana. Our results illustrate that chemically induced dimerization can function as a built-in control for split-based systems that is easily implemented and allows for direct evaluation of functionality. PMID:27282591

  5. How prescriptive norms influence causal inferences.

    PubMed

    Samland, Jana; Waldmann, Michael R

    2016-11-01

    Recent experimental findings suggest that prescriptive norms influence causal inferences. The cognitive mechanism underlying this finding is still under debate. We compare three competing theories: The culpable control model of blame argues that reasoners tend to exaggerate the causal influence of norm-violating agents, which should lead to relatively higher causal strength estimates for these agents. By contrast, the counterfactual reasoning account of causal selection assumes that norms do not alter the representation of the causal model, but rather later causal selection stages. According to this view, reasoners tend to preferentially consider counterfactual states of abnormal rather than normal factors, which leads to the choice of the abnormal factor in a causal selection task. A third view, the accountability hypothesis, claims that the effects of prescriptive norms are generated by the ambiguity of the causal test question. Asking whether an agent is a cause can be understood as a request to assess her causal contribution but also her moral accountability. According to this theory norm effects on causal selection are mediated by accountability judgments that are not only sensitive to the abnormality of behavior but also to mitigating factors, such as intentionality and knowledge of norms. Five experiments are presented that favor the accountability account over the two alternative theories. PMID:27591550

  6. Space and time in perceptual causality.

    PubMed

    Straube, Benjamin; Chatterjee, Anjan

    2010-01-01

    Inferring causality is a fundamental feature of human cognition that allows us to theorize about and predict future states of the world. Michotte suggested that humans automatically perceive causality based on certain perceptual features of events. However, individual differences in judgments of perceptual causality cast doubt on Michotte's view. To gain insights in the neural basis of individual difference in the perception of causality, our participants judged causal relationships in animations of a blue ball colliding with a red ball (a launching event) while fMRI-data were acquired. Spatial continuity and temporal contiguity were varied parametrically in these stimuli. We did not find consistent brain activation differences between trials judged as caused and those judged as non-caused, making it unlikely that humans have universal instantiation of perceptual causality in the brain. However, participants were slower to respond to and showed greater neural activity for violations of causality, suggesting that humans are biased to expect causal relationships when moving objects appear to interact. Our participants demonstrated considerable individual differences in their sensitivity to spatial and temporal characteristics in perceiving causality. These qualitative differences in sensitivity to time or space in perceiving causality were instantiated in individual differences in activation of the left basal ganglia or right parietal lobe, respectively. Thus, the perception that the movement of one object causes the movement of another is triggered by elemental spatial and temporal sensitivities, which themselves are instantiated in specific distinct neural networks. PMID:20463866

  7. Extraction of chemical-induced diseases using prior knowledge and textual information.

    PubMed

    Pons, Ewoud; Becker, Benedikt F H; Akhondi, Saber A; Afzal, Zubair; van Mulligen, Erik M; Kors, Jan A

    2016-01-01

    We describe our approach to the chemical-disease relation (CDR) task in the BioCreative V challenge. The CDR task consists of two subtasks: automatic disease-named entity recognition and normalization (DNER), and extraction of chemical-induced diseases (CIDs) from Medline abstracts. For the DNER subtask, we used our concept recognition tool Peregrine, in combination with several optimization steps. For the CID subtask, our system, which we named RELigator, was trained on a rich feature set, comprising features derived from a graph database containing prior knowledge about chemicals and diseases, and linguistic and statistical features derived from the abstracts in the CDR training corpus. We describe the systems that were developed and present evaluation results for both subtasks on the CDR test set. For DNER, our Peregrine system reached anF-score of 0.757. For CID, the system achieved anF-score of 0.526, which ranked second among 18 participating teams. Several post-challenge modifications of the systems resulted in substantially improvedF-scores (0.828 for DNER and 0.602 for CID). RELigator is available as a web service athttp://biosemantics.org/index.php/software/religator. PMID:27081155

  8. Artificially induced polyploidization in Humulus lupulus L. and its effect on morphological and chemical traits.

    PubMed

    Trojak-Goluch, Anna; Skomra, Urszula

    2013-12-01

    Chemically induced polyploids were obtained by the colchicine treatment of shoot tips of Humulus lupulus L. 'Sybilla'. Flow cytometry revealed that most of the treatments resulted in the production of tetraploids. The highest number of tetraploids was obtained when explants were immersed in 0.05% colchicine for 48 h. A field experiment was conducted to compare diploid and tetraploid plants and assess the effect of genome polyploidization on the morphological and chemical characteristics. Tetraploids showed significant differences in relation to diploids. They had thinner and shorter shoots. The influence of chromosome doubling was also reflected in the length, width and area of leaves. The length of female flowers in the tetraploids was significantly shorter than that observed in diploids. Tetraploids produced a diverse number of lupuline glands that were almost twice as large as those observed in diploids. The most distinct effect of genome polyploidization was a significant increase in the weight of cones and spindles. Contents of major chemical constituents of hop cones was little affected by ploidy level. Total essential oils were significantly lower than those in diploids. However there was a significant increase in the proportion of humulene, caryophyllene and farnesene, oils desired by the brewing industry. PMID:24399911

  9. Chemically induced enucleation of activated bovine oocytes: chromatin and microtubule organization and production of viable cytoplasts.

    PubMed

    Saraiva, Naiara Zoccal; Oliveira, Clara Slade; Leal, Cláudia Lima Verde; de Lima, Marina Ragagnin; Del Collado, Maite; Vantini, Roberta; Monteiro, Fabio Morato; Niciura, Simone Cristina Méo; Garcia, Joaquim Mansano

    2015-12-01

    As the standard enucleation method in mammalian nuclear transfer is invasive and damaging to cytoplast spatial organization, alternative procedures have been developed over recent years. Among these techniques, chemically induced enucleation (IE) is especially interesting because it does not employ ultraviolet light and reduces the amount of cytoplasm eliminated during the procedure. The objective of this study was to optimize the culture conditions with demecolcine of pre-activated bovine oocytes for chemically IE, and to evaluate nuclear and microtubule organization in cytoplasts obtained by this technique and their viability. In the first experiment, a negative effect on oocyte activation was verified when demecolcine was added at the beginning of the process, reducing activation rates by approximately 30%. This effect was not observed when demecolcine was added to the medium after 1.5 h of activation. In the second experiment, although a reduction in the number of microtubules was observed in most oocytes, these structures did not disappear completely during assessment. Approximately 50% of treated oocytes presented microtubule reduction at the end of the evaluation period, while 23% of oocytes were observed to exhibit the complete disappearance of these structures and 28% exhibited visible microtubules. These findings indicated the lack of immediate microtubule repolymerization after culture in demecolcine-free medium, a fact that may negatively influence embryonic development. However, cleavage rates of 63.6-70.0% and blastocyst yield of 15.5-24.2% were obtained in the final experiment, without significant differences between techniques, indicating that chemically induced enucleation produces normal embryos.

  10. A role for c-myc in chemically induced renal-cell death.

    PubMed Central

    Zhan, Y; Cleveland, J L; Stevens, J L

    1997-01-01

    A variety of genes, including c-myc, are activated by chemical toxicants in vivo and in vitro. Although enforced c-myc expression induces apoptosis after withdrawing survival factors, it is not clear if activation of the endogenous c-myc gene is an apoptotic signal after toxicant exposure. The renal tubular epithelium is a target for many toxicants. c-myc expression is activated by tubular damage. In quiescent LLC-PK1 renal epithelial cells, c-myc but not max or mad mRNA is induced by the nephrotoxicant S-(1,2-dichlorovinyl)-L-cysteine (DCVC). The kinetics of DCVC-induced c-myc expression and apoptosis suggested an association between cell death and prolonged activation of c-myc expression after toxicant exposure. Accordingly, prolonged activation of an estrogen receptor-Myc fusion construct, but not a construct in which a c-Myc transactivation domain had been deleted, was sufficient to induce apoptosis in LLC-PK1 cells. Moreover, under conditions in which necrosis was the predominant cell death pathway caused by DCVC in parental cells, overexpressing c-myc biased the cell death pathway toward apoptosis. DCVC also induced ornithine decarboxylase (odc) mRNA and activated the odc promoter. Activation of the odc promoter by DCVC required consensus c-Myc-Max binding sites in odc intron 1. Inhibiting ODC activity with alpha-difluoromethylornithine delayed DCVC-induced cell death. Therefore, odc is a target gene in the DCVC apoptotic pathway involving c-myc activation and contributes to apoptosis. Finally, a structurally related cytotoxic but nongenotoxic analog of DCVC did not induce c-myc and did not activate the odc promoter or induce apoptosis. The data support the hypothesis that activation of apoptotic cell death in quiescent renal epithelial cells involves induction of c-myc. This is the first study to demonstrate that c-myc induction by a specific nephrotoxicant leads to gene activation and cell death. PMID:9343440

  11. Exenatide does not evoke pancreatitis and attenuates chemically induced pancreatitis in normal and diabetic rodents

    PubMed Central

    Smith, Pamela A.; Sablan, Emmanuel J.; Polizzi, Clara J.; Aumann, Donald E.; Villescaz, Christiane; Hargrove, Diane M.; Gedulin, Bronislava R.; Lu, Melissa G. W.; Adams, Lisa; Whisenant, Tina; Roy, Denis; Parkes, David G.

    2010-01-01

    The risk of developing pancreatitis is elevated in type 2 diabetes and obesity. Cases of pancreatitis have been reported in type 2 diabetes patients treated with GLP-1 (GLP-1R) receptor agonists. To examine whether the GLP-1R agonist exenatide potentially induces or modulates pancreatitis, the effect of exenatide was evaluated in normal or diabetic rodents. Normal and diabetic rats received a single exenatide dose (0.072, 0.24, and 0.72 nmol/kg) or vehicle. Diabetic ob/ob or HF-STZ mice were infused with exenatide (1.2 and 7.2 nmol·kg−1·day−1) or vehicle for 4 wk. Post-exenatide treatment, pancreatitis was induced with caerulein (CRN) or sodium taurocholate (ST), and changes in plasma amylase and lipase were measured. In ob/ob mice, plasma cytokines (IL-1β, IL-2, IL-6, MCP-1, IFNγ, and TNFα) and pancreatitis-associated genes were assessed. Pancreata were weighed and examined histologically. Exenatide treatment alone did not modify plasma amylase or lipase in any models tested. Exenatide attenuated CRN-induced release of amylase and lipase in normal rats and ob/ob mice but did not modify the response to ST infusion. Plasma cytokines and pancreatic weight were unaffected by exenatide. Exenatide upregulated Reg3b but not Il6, Ccl2, Nfkb1, or Vamp8 expression. Histological analysis revealed that the highest doses of exenatide decreased CRN- or ST-induced acute inflammation, vacuolation, and acinar single cell necrosis in mice and rats, respectively. Ductal cell proliferation rates were low and similar across all groups of ob/ob mice. In conclusion, exenatide did not modify plasma amylase and lipase concentrations in rodents without pancreatitis and improved chemically induced pancreatitis in normal and diabetic rodents. PMID:20923958

  12. Characteristics of Ca2+- and Mg2+-induced tension development in chemically skinned smooth muscle fibers

    PubMed Central

    1978-01-01

    Chemically skinned fibers from guinea pig taenia caecum were prepared by saponin treatment to study the smooth muscle contractile system in a state as close to the living state as posible. The skinned fibers showed tension development with an increase of Ca2+ in the solution, the threshold tension occurring as 5 X 10(-7) M Ca2+. The maximal tension induced with 10(-4) M Ca2+ was as large and rapid as the potassium-induced contracture in the intact fibers. The slope of the pCa tension curve was less steep than that of skeletal muscle fibers and shifted in the direction of lower pCa with an increase of MgATP. The presence of greater than 1 mM Mg2+ was required for Ca2+-induced contraction in the skinned fibers as well as for the activation of ATPase and superprecipitation in smooth muscle myosin B. Mg2+ above 2 mM caused a slow tension development by itself in the absence of Ca2+. Such a Mg2+-induced tension showed a linear relation to concentrations up to 8 mM in the presence of MgATP. Increase of MgATP concentration revealed a monophasic response without inhibition of Ca2+-induced tension development, unlike the biphasic response in striated muscle. When MgATP was removed from the relaxing solution, the tension developed slowly and slightly, even though the Mg2+ concentrations was fixed at 2 mM. These results suggest a substantial difference in the mode of actin-myosin interaction between smooth and skeletal muscle. PMID:151731

  13. Influence of exothermic chemical reactions on laser-induced shock waves.

    PubMed

    Gottfried, Jennifer L

    2014-10-21

    Differences in the excitation of non-energetic and energetic residues with a 900 mJ, 6 ns laser pulse (1064 nm) have been investigated. Emission from the laser-induced plasma of energetic materials (e.g. triaminotrinitrobenzene [TATB], cyclotrimethylene trinitramine [RDX], and hexanitrohexaazaisowurtzitane [CL-20]) is significantly reduced compared to non-energetic materials (e.g. sugar, melamine, and l-glutamine). Expansion of the resulting laser-induced shock wave into the air above the sample surface was imaged on a microsecond timescale with a high-speed camera recording multiple frames from each laser shot; the excitation of energetic materials produces larger heat-affected zones in the surrounding atmosphere (facilitating deflagration of particles ejected from the sample surface), results in the formation of additional shock fronts, and generates faster external shock front velocities (>750 m s(-1)) compared to non-energetic materials (550-600 m s(-1)). Non-explosive materials that undergo exothermic chemical reactions in air at high temperatures such as ammonium nitrate and magnesium sulfate produce shock velocities which exceed those of the inert materials but are less than those generated by the exothermic reactions of explosive materials (650-700 m s(-1)). The most powerful explosives produced the highest shock velocities. A comparison to several existing shock models demonstrated that no single model describes the shock propagation for both non-energetic and energetic materials. The influence of the exothermic chemical reactions initiated by the pulsed laser on the velocity of the laser-induced shock waves has thus been demonstrated for the first time. PMID:25182866

  14. Selenium and vitamin E inhibit radiogenic and chemically induced transformation in vitro via different mechanisms

    SciTech Connect

    Borek, C.; Ong, A.; Mason, H.; Donahue, L.; Biaglow, J.E.

    1986-03-01

    Results from in vivo and in vitro studies showing that antioxidants may act as anticarcinogens support the role of active oxygen in carcinogenesis and provide impetus for exploring the functions of dietary antioxidants in cancer prevention by using in vitro models. The authors examined the single and combined effects of selenium, a component of glutathione peroxidase, and vitamin E, a known antioxidant, on cell transformation induced in C3H/10T-1/2 cells by x-rays, benzo(a)pyrene, or tryptophan pyrolysate and on the levels of cellular scavenging systems peroxide destruction. Incubation of C3H/10T-1/2 cells with 2.5 ..mu..M Na/sup 2/SeO/sup 3/ (selenium) or with 7 ..mu..M ..cap alpha..-tocopherol succinate (vitamin E) 24 hr prior to exposure to x-rays or the chemical carcinogens resulted in an inhibition of transformation by each of the antioxidants with an additive-inhibitory action when the two nutrients were combined. Cellular pretreatment with selenium resulted in increased levels of cellular glutathione peroxidase, catalase, and nonprotein thiols (glutathione) and in an enhanced destruction of peroxide. The results support our earlier studies showing that free radical-mediated events play a role in radiation and chemically induced transformation. They indicate that selenium and vitamin E act alone and in additive fashion as radioprotecting and chemopreventing agents. The results further suggest that selenium confers protection in part by inducing or activating cellular free-radical scavenging systems and by enhancing peroxide breakdown while vitamin E appears to confer its protection by and alternate complementary mechanism.

  15. Influence of exothermic chemical reactions on laser-induced shock waves.

    PubMed

    Gottfried, Jennifer L

    2014-10-21

    Differences in the excitation of non-energetic and energetic residues with a 900 mJ, 6 ns laser pulse (1064 nm) have been investigated. Emission from the laser-induced plasma of energetic materials (e.g. triaminotrinitrobenzene [TATB], cyclotrimethylene trinitramine [RDX], and hexanitrohexaazaisowurtzitane [CL-20]) is significantly reduced compared to non-energetic materials (e.g. sugar, melamine, and l-glutamine). Expansion of the resulting laser-induced shock wave into the air above the sample surface was imaged on a microsecond timescale with a high-speed camera recording multiple frames from each laser shot; the excitation of energetic materials produces larger heat-affected zones in the surrounding atmosphere (facilitating deflagration of particles ejected from the sample surface), results in the formation of additional shock fronts, and generates faster external shock front velocities (>750 m s(-1)) compared to non-energetic materials (550-600 m s(-1)). Non-explosive materials that undergo exothermic chemical reactions in air at high temperatures such as ammonium nitrate and magnesium sulfate produce shock velocities which exceed those of the inert materials but are less than those generated by the exothermic reactions of explosive materials (650-700 m s(-1)). The most powerful explosives produced the highest shock velocities. A comparison to several existing shock models demonstrated that no single model describes the shock propagation for both non-energetic and energetic materials. The influence of the exothermic chemical reactions initiated by the pulsed laser on the velocity of the laser-induced shock waves has thus been demonstrated for the first time.

  16. Modeling Drug- and Chemical-Induced Hepatotoxicity with Systems Biology Approaches

    PubMed Central

    Bhattacharya, Sudin; Shoda, Lisl K.M.; Zhang, Qiang; Woods, Courtney G.; Howell, Brett A.; Siler, Scott Q.; Woodhead, Jeffrey L.; Yang, Yuching; McMullen, Patrick; Watkins, Paul B.; Andersen, Melvin E.

    2012-01-01

    We provide an overview of computational systems biology approaches as applied to the study of chemical- and drug-induced toxicity. The concept of “toxicity pathways” is described in the context of the 2007 US National Academies of Science report, “Toxicity testing in the 21st Century: A Vision and A Strategy.” Pathway mapping and modeling based on network biology concepts are a key component of the vision laid out in this report for a more biologically based analysis of dose-response behavior and the safety of chemicals and drugs. We focus on toxicity of the liver (hepatotoxicity) – a complex phenotypic response with contributions from a number of different cell types and biological processes. We describe three case studies of complementary multi-scale computational modeling approaches to understand perturbation of toxicity pathways in the human liver as a result of exposure to environmental contaminants and specific drugs. One approach involves development of a spatial, multicellular “virtual tissue” model of the liver lobule that combines molecular circuits in individual hepatocytes with cell–cell interactions and blood-mediated transport of toxicants through hepatic sinusoids, to enable quantitative, mechanistic prediction of hepatic dose-response for activation of the aryl hydrocarbon receptor toxicity pathway. Simultaneously, methods are being developing to extract quantitative maps of intracellular signaling and transcriptional regulatory networks perturbed by environmental contaminants, using a combination of gene expression and genome-wide protein-DNA interaction data. A predictive physiological model (DILIsym™) to understand drug-induced liver injury (DILI), the most common adverse event leading to termination of clinical development programs and regulatory actions on drugs, is also described. The model initially focuses on reactive metabolite-induced DILI in response to administration of acetaminophen, and spans multiple biological

  17. Causal diagrams in systems epidemiology

    PubMed Central

    2012-01-01

    Methods of diagrammatic modelling have been greatly developed in the past two decades. Outside the context of infectious diseases, systematic use of diagrams in epidemiology has been mainly confined to the analysis of a single link: that between a disease outcome and its proximal determinant(s). Transmitted causes ("causes of causes") tend not to be systematically analysed. The infectious disease epidemiology modelling tradition models the human population in its environment, typically with the exposure-health relationship and the determinants of exposure being considered at individual and group/ecological levels, respectively. Some properties of the resulting systems are quite general, and are seen in unrelated contexts such as biochemical pathways. Confining analysis to a single link misses the opportunity to discover such properties. The structure of a causal diagram is derived from knowledge about how the world works, as well as from statistical evidence. A single diagram can be used to characterise a whole research area, not just a single analysis - although this depends on the degree of consistency of the causal relationships between different populations - and can therefore be used to integrate multiple datasets. Additional advantages of system-wide models include: the use of instrumental variables - now emerging as an important technique in epidemiology in the context of mendelian randomisation, but under-used in the exploitation of "natural experiments"; the explicit use of change models, which have advantages with respect to inferring causation; and in the detection and elucidation of feedback. PMID:22429606

  18. The chemical inducibility of mouse cardiac antioxidants and phase 2 enzymes in vivo.

    PubMed

    Cao, Zhuoxiao; Li, Yunbo

    2004-05-14

    The recognition of the critical involvement of oxidative and electrophilic stress in cardiac disorders has led to extensive investigation of the protective effects of exogenous antioxidants on cardiac injury. On the other hand, another strategy for protecting against oxidative/electrophilic cardiac injury may be through induction of the endogenous antioxidants and phase 2 enzymes in myocardium by chemical inducers. However, our understanding of the chemical inducibility of cardiac antioxidants/phase 2 enzymes in vivo is very limited. In addition, careful studies on the basal levels of a scope of endogenous antioxidants/phase 2 enzymes in myocardium as compared with other tissues, such as liver, are lacking. Accordingly, this study was undertaken to determine the basal levels of endogenous antioxidants/phase 2 enzymes, including superoxide dismutase (SOD), catalase, reduced glutathione (GSH), GSH peroxidase (GPx), glutathione reductase (GR), GSH S-transferase (GST), and NAD(P)H:quinone oxidoreductase 1 (NQO1), and investigate the inducibility of the above antioxidants/phase 2 enzymes by the chemoprotectant, 1,2-dithiole-3-thione (D3T), in cardiac as well as hepatic tissues in C57BL/6 mice. Our results demonstrated that in C57BL/6 mice, the levels of catalase, GSH, GPx, GR, and GST were significantly lower in cardiac tissue than in hepatic tissue. The level of total SOD did not differ significantly between mouse heart and liver. Notably, heart contained a much higher NQO1 activity than liver. Immunoblotting and RT-PCR analyses further demonstrated the high expression of NQO1 protein and mRNA in myocardium. Oral administration of D3T at 0.25 and 0.5 mmol/kg body weight for 3 consecutive days resulted in a significant induction of cardiac SOD, catalase, GR, GST, and NQO1. No significant induction of cardiac GSH and GPx was observed with the above D3T treatment. Only GR, GST, and NQO1 in mouse liver were induced by the D3T treatment. Unexpectedly, we observed a

  19. Surface Modification and Chemical Sputtering of Graphite Induced by Low Energy Atomic and Molecular Deuterium Ions

    SciTech Connect

    Zhang, Hengda; Meyer, Fred W; Meyer III, Harry M; Lance, Michael J

    2008-01-01

    The surface morphology, and chemical/structural modifications induced during chemical sputtering of ATJ graphite by low-energy (<200 eV/D) deuterium atomic and molecular ions are explored by Scanning Electron Microscopy (SEM), Raman and Auger Electron Spectroscopy (AES) diagnostics. At the lowest impact energies, the ion range may become less than the probe depth of Raman and AES spectroscopy diagnostics. We show that such diagnostics are still useful probes at these energies. As demonstration, we used these surface diagnostics to confirm the characteristic changes of surface texture, increased amorphization, enhanced surface reactivity to impurity species, and increased sp{sup 3} content that low-energy deuterium ion bombardment to steady-state chemical sputtering conditions produces. To put these studies into proper context, we also present new chemical sputtering yields for methane production of ATJ graphite at room temperature by impact of D{sub 2}{sup +} in the energy range 10-250 eV/D, and by impact of D{sup +} and D{sub 3}{sup +} at 30 eV/D and 125 eV/D, obtained using a Quadrupole Mass Spectroscopy (QMS) approach. Below 100 eV/D, the methane production in ATJ graphite is larger than that in HOPG by a factor of {approx} 2. In the energy range 10-60 eV/D, the methane production yield is almost independent of energy and then decreases with increasing ion energies. The results are in good agreement with recent molecular dynamics simulations.

  20. Characterization of Chemically Induced Liver Injuries Using Gene Co-Expression Modules

    PubMed Central

    Tawa, Gregory J.; AbdulHameed, Mohamed Diwan M.; Yu, Xueping; Kumar, Kamal; Ippolito, Danielle L.; Lewis, John A.; Stallings, Jonathan D.; Wallqvist, Anders

    2014-01-01

    Liver injuries due to ingestion or exposure to chemicals and industrial toxicants pose a serious health risk that may be hard to assess due to a lack of non-invasive diagnostic tests. Mapping chemical injuries to organ-specific damage and clinical outcomes via biomarkers or biomarker panels will provide the foundation for highly specific and robust diagnostic tests. Here, we have used DrugMatrix, a toxicogenomics database containing organ-specific gene expression data matched to dose-dependent chemical exposures and adverse clinical pathology assessments in Sprague Dawley rats, to identify groups of co-expressed genes (modules) specific to injury endpoints in the liver. We identified 78 such gene co-expression modules associated with 25 diverse injury endpoints categorized from clinical pathology, organ weight changes, and histopathology. Using gene expression data associated with an injury condition, we showed that these modules exhibited different patterns of activation characteristic of each injury. We further showed that specific module genes mapped to 1) known biochemical pathways associated with liver injuries and 2) clinically used diagnostic tests for liver fibrosis. As such, the gene modules have characteristics of both generalized and specific toxic response pathways. Using these results, we proposed three gene signature sets characteristic of liver fibrosis, steatosis, and general liver injury based on genes from the co-expression modules. Out of all 92 identified genes, 18 (20%) genes have well-documented relationships with liver disease, whereas the rest are novel and have not previously been associated with liver disease. In conclusion, identifying gene co-expression modules associated with chemically induced liver injuries aids in generating testable hypotheses and has the potential to identify putative biomarkers of adverse health effects. PMID:25226513

  1. Study of permeability changes induced by external stimuli on chemically modified electrodes

    NASA Astrophysics Data System (ADS)

    Perera, Dingiri Mudiyanselage Neluni T.

    This research was focused on understanding how external stimuli affect the permeability of the chemically modified electrodes, and how the materials used in modifying the working electrodes respond to the changes in the surface charge. We adopted a voltammetric type electrochemical sensor to investigate the permeability effects induced by pH and organic solvents. The working electrodes used in this research were chemically modified with thioctic acid self assembled monolayer (TA SAM), track etched polycarbonate membranes (TEPCM) and PS-b-PMMA nanoporous films (polystyrene-block-polymethylmethacrylate). We studied the permeability behavior of each of the material upon application of external stimuli. In chapter 3, the permeability changes induced by change in surface charge of thioctic acid SAM was investigated. The surface charge of the monolayer was tuned by changing pH of the medium, which resulted in decrease of redox current of a negatively charged marker due to deprotonation of the surface --COOH groups of TA SAM. Decrease in redox current reflected a decrease in the reaction rate, and by using closed form equations the effective rate constants at several pKa values were extracted. In chapter 4, permeability changes induced by pH in TEPCM were investigated. We assessed the surface charge of these membranes via cyclic voltammetry generated for neutral and charged redox molecules. Limiting current of charged markers were affected by the surface charge induced by pH, where as the redox current for the neutral marker was not affected. Experimental redox currents were larger than the theoretical current, indicating that redox molecules preferentially distributed in a surface layer on the nanopore. Organic solvent induced permeability changes of PS-b-PMMA nanoporous films were investigated via electrochemical impedance spectroscopy and AFM. Higher response of pore resistance in the presence of organic solvents indicated either swelling of the nanoporous film or

  2. Chemopreventive effect of a mixture of Chinese Herbs (antitumor B) on chemically induced oral carcinogenesis.

    PubMed

    Wang, Yian; Yao, Ruisheng; Gao, Song; Wen, Weidong; Du, Yinqiu; Szabo, Eva; Hu, Ming; Lubet, Ronald A; You, Ming

    2013-01-01

    In this study, we evaluated chemopreventive efficacy of Antitumor B, a Chinese herbal mixture of six plants (Sophora tonkinensis, Polygonum bistorta, Prunella vulgaris, Sonchus arvensis L., Dictamnus dasycarpus, and Dioscorea bulbifera) on the development of 4-nitroquinoline-1-oxide (4NQO) induced oral squamous cell carcinomas in A/J mice. Antitumor B, delivered through diet, inhibited 4NQO-induced oral cancer development by 59.19%. The reduction of cell proliferation appears to be associated with efficacy of Antitumor B against 4NQO-induced oral cancer in A/J mice. The expression of epidermal growth factor receptor (EGFR) and phosphorylated EGFR (Tyr1173) were down-regulated by Antitumor B. Tissue distribution of Antitumor B was determined using obacunone, matrine, and maackiain as marker chemicals. We found significant amounts of obacunone, matrine, and maackiain in the blood after 1-wk treatment. The concentrations of these three compounds did not increase further at 18  wk, suggesting that plasma concentrations had reached a steady-state level at 1  wk. There was no significant body weight loss and there was no other obvious sign of toxicity in Antitumor B-treated mice. These results suggest that Antitumor B is a promising agent for human oral cancer chemoprevention. PMID:22086836

  3. Abnormal Development of Tapetum and Microspores Induced by Chemical Hybridization Agent SQ-1 in Wheat

    PubMed Central

    Wang, Shuping; Zhang, Gaisheng; Song, Qilu; Zhang, Yingxin; Li, Zheng; Guo, Jialin; Niu, Na; Ma, Shoucai; Wang, Junwei

    2015-01-01

    Chemical hybridization agent (CHA)-induced male sterility is an important tool in crop heterosis. To demonstrate that CHA-SQ-1-induced male sterility is associated with abnormal tapetal and microspore development, the cytology of CHA-SQ-1-treated plant anthers at various developmental stages was studied by light microscopy, scanning and transmission electron microscopy, in situ terminal deoxynucleotidyl transferasemediated dUTP nick end-labelling (TUNEL) assay and DAPI staining. The results indicated that the SQ-1-treated plants underwent premature tapetal programmed cell death (PCD), which was initiated at the early-uninucleate stage of microspore development and continued until the tapetal cells were completely degraded; the process of microspore development was then blocked. Microspores with low-viability (fluorescein diacetate staining) were aborted. The study suggests that premature tapetal PCD is the main cause of pollen abortion. Furthermore, it determines the starting period and a key factor in CHA-SQ-1-induced male sterility at the cell level, and provides cytological evidence to further study the mechanism between PCD and male sterility. PMID:25803723

  4. Abnormal development of tapetum and microspores induced by chemical hybridization agent SQ-1 in wheat.

    PubMed

    Wang, Shuping; Zhang, Gaisheng; Song, Qilu; Zhang, Yingxin; Li, Zheng; Guo, Jialin; Niu, Na; Ma, Shoucai; Wang, Junwei

    2015-01-01

    Chemical hybridization agent (CHA)-induced male sterility is an important tool in crop heterosis. To demonstrate that CHA-SQ-1-induced male sterility is associated with abnormal tapetal and microspore development, the cytology of CHA-SQ-1-treated plant anthers at various developmental stages was studied by light microscopy, scanning and transmission electron microscopy, in situ terminal deoxynucleotidyl transferasemediated dUTP nick end-labelling (TUNEL) assay and DAPI staining. The results indicated that the SQ-1-treated plants underwent premature tapetal programmed cell death (PCD), which was initiated at the early-uninucleate stage of microspore development and continued until the tapetal cells were completely degraded; the process of microspore development was then blocked. Microspores with low-viability (fluorescein diacetate staining) were aborted. The study suggests that premature tapetal PCD is the main cause of pollen abortion. Furthermore, it determines the starting period and a key factor in CHA-SQ-1-induced male sterility at the cell level, and provides cytological evidence to further study the mechanism between PCD and male sterility.

  5. Bacterial cell wall-induced arthritis: chemical composition and tissue distribution of four Lactobacillus strains.

    PubMed

    Simelyte, E; Rimpiläinen, M; Lehtonen, L; Zhang, X; Toivanen, P

    2000-06-01

    To study what determines the arthritogenicity of bacterial cell walls, cell wall-induced arthritis in the rat was applied, using four strains of Lactobacillus. Three of the strains used proved to induce chronic arthritis in the rat; all were Lactobacillus casei. The cell wall of Lactobacillus fermentum did not induce chronic arthritis. All arthritogenic bacterial cell walls had the same peptidoglycan structure, whereas that of L. fermentum was different. Likewise, all arthritogenic cell walls were resistant to lysozyme degradation, whereas the L. fermentum cell wall was lysozyme sensitive. Muramic acid was observed in the liver, spleen, and lymph nodes in considerably larger amounts after injection of an arthritogenic L. casei cell wall than following injection of a nonarthritogenic L. fermentum cell wall. The L. casei cell wall also persisted in the tissues longer than the L. fermentum cell wall. The present results, taken together with those published previously, underline the possibility that the chemical structure of peptidoglycan is important in determining the arthritogenicity of the bacterial cell wall. PMID:10816508

  6. Afadin requirement for cytokine expressions in keratinocytes during chemically induced inflammation in mice

    PubMed Central

    Yoshida, Toshiyuki; Iwata, Takanori; Takai, Yoshimi; Birchmeier, Walter; Yamato, Masayuki; Okano, Teruo

    2014-01-01

    Afadin is a filamentous actin-binding protein and a mediator of nectin signaling. Nectins are Ig-like cell adhesion molecules, and the nectin family is composed of four members, nectin-1 to nectin-4. Nectins show homophilic and heterophilic interactions with other nectins or proteins on adjacent cells. Nectin signaling induces formation of cell–cell junctions and is required for the development of epithelial tissues, including skin. This study investigated the role of afadin in epithelial tissue development and established epithelium-specific afadin-deficient (CKO) mice. Although showing no obvious abnormality in the skin development and homeostasis, the mice showed the reduced neutrophil infiltration into the epidermis during chemical-induced inflammation with 12-O-tetradecanoylphorbol 13-acetate (TPA). Immunohistochemical and quantitative real-time PCR analyses showed that the expression levels of cytokines including Cxcl2, Il-1β and Tnf-α were reduced in CKO keratinocytes compared with control keratinocytes during TPA-induced inflammation. Primary-cultured skin keratinocytes from CKO mice also showed reduced expression of these cytokines and weak activation of Rap1 compared with those from control mice after the TPA treatment. These results suggested a remarkable function of afadin, which was able to enhance cytokine expression through Rap1 activation in keratinocytes during inflammation. PMID:25297509

  7. Self-esteem and causal attributions.

    PubMed

    Chandler, T A; Lee, M S; Pengilly, J W

    1997-11-01

    The relationship between self-esteem and causal attributions of success and failure in achievement-related behavior was examined among undergraduate students. An integration of a self-consistency model of causal attribution and self-enhancement theory was attempted. Self-esteem and performance outcome conditions of success and failure served as independent variables. Success and failure conditions were created via feedback regarding the participants' performance on an anagram task. The participants' attributions of six causal elements (ability, effort, immediate effort, task difficulty, luck, and mood) were categorized and combined with three causal dimensions (internal-external locus, stability, and controllability), which served as dependent variables. Participants' expectations regarding performance also served as a dependent variable. The relationship between self-esteem, expectancies of success and failure, performance, and stable causality were reported. In terms of causal dimensions, internal, stable, and controllable dimensions were explained by self-enhancement.

  8. Chemical chaperones reduce ionizing radiation-induced endoplasmic reticulum stress and cell death in IEC-6 cells

    SciTech Connect

    Lee, Eun Sang; Lee, Hae-June; Lee, Yoon-Jin; Jeong, Jae-Hoon; Kang, Seongman; Lim, Young-Bin

    2014-07-25

    Highlights: • UPR activation precedes caspase activation in irradiated IEC-6 cells. • Chemical ER stress inducers radiosensitize IEC-6 cells. • siRNAs that targeted ER stress responses ameliorate IR-induced cell death. • Chemical chaperons prevent cell death in irradiated IEC-6 cells. - Abstract: Radiotherapy, which is one of the most effective approaches to the treatment of various cancers, plays an important role in malignant cell eradication in the pelvic area and abdomen. However, it also generates some degree of intestinal injury. Apoptosis in the intestinal epithelium is the primary pathological factor that initiates radiation-induced intestinal injury, but the mechanism by which ionizing radiation (IR) induces apoptosis in the intestinal epithelium is not clearly understood. Recently, IR has been shown to induce endoplasmic reticulum (ER) stress, thereby activating the unfolded protein response (UPR) signaling pathway in intestinal epithelial cells. However, the consequences of the IR-induced activation of the UPR signaling pathway on radiosensitivity in intestinal epithelial cells remain to be determined. In this study, we investigated the role of ER stress responses in IR-induced intestinal epithelial cell death. We show that chemical ER stress inducers, such as tunicamycin or thapsigargin, enhanced IR-induced caspase 3 activation and DNA fragmentation in intestinal epithelial cells. Knockdown of Xbp1 or Atf6 with small interfering RNA inhibited IR-induced caspase 3 activation. Treatment with chemical chaperones prevented ER stress and subsequent apoptosis in IR-exposed intestinal epithelial cells. Our results suggest a pro-apoptotic role of ER stress in IR-exposed intestinal epithelial cells. Furthermore, inhibiting ER stress may be an effective strategy to prevent IR-induced intestinal injury.

  9. Multiple Causality: Consequences for Medical Practice

    PubMed Central

    Nydegger, Corinne N.

    1983-01-01

    When a scientifically trained health professional is called upon to deal with patients holding differing causal views of illness, the resulting lack of communication is frustrating to both. This discussion traces some implications for medical practice of significant cultural differences in two aspects of causal paradigms of illness: (1) terms accepted and (2) dimension or level of causality typically sought. The second is the more pervasive and intractable problem, having distinctive consequences for the role of curer, symptomatology, diagnosis and treatment. PMID:6858133

  10. Nonparametric causal inference for bivariate time series.

    PubMed

    McCracken, James M; Weigel, Robert S

    2016-02-01

    We introduce new quantities for exploratory causal inference between bivariate time series. The quantities, called penchants and leanings, are computationally straightforward to apply, follow directly from assumptions of probabilistic causality, do not depend on any assumed models for the time series generating process, and do not rely on any embedding procedures; these features may provide a clearer interpretation of the results than those from existing time series causality tools. The penchant and leaning are computed based on a structured method for computing probabilities.

  11. Physical integration: a causal account for consciousness.

    PubMed

    Manzotti, Riccardo; Chella, Antonio

    2014-06-01

    The issue of integration in neural networks is intimately connected with that of consciousness. In this paper, integration as an effective level of physical organization is contrasted with a methodological integrative approach. Understanding how consciousness arises out of neural processes requires a model of integration in just causal physical terms. Based on a set of feasible criteria (physical grounding, causal efficacy, no circularity and scaling), a causal account of physical integration for consciousness centered on joint causation is outlined.

  12. Causal inference in economics and marketing

    PubMed Central

    Varian, Hal R.

    2016-01-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual—a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference. PMID:27382144

  13. Causal inference in economics and marketing.

    PubMed

    Varian, Hal R

    2016-07-01

    This is an elementary introduction to causal inference in economics written for readers familiar with machine learning methods. The critical step in any causal analysis is estimating the counterfactual-a prediction of what would have happened in the absence of the treatment. The powerful techniques used in machine learning may be useful for developing better estimates of the counterfactual, potentially improving causal inference. PMID:27382144

  14. Nonparametric causal inference for bivariate time series

    NASA Astrophysics Data System (ADS)

    McCracken, James M.; Weigel, Robert S.

    2016-02-01

    We introduce new quantities for exploratory causal inference between bivariate time series. The quantities, called penchants and leanings, are computationally straightforward to apply, follow directly from assumptions of probabilistic causality, do not depend on any assumed models for the time series generating process, and do not rely on any embedding procedures; these features may provide a clearer interpretation of the results than those from existing time series causality tools. The penchant and leaning are computed based on a structured method for computing probabilities.

  15. Self-grooming induced by sexual chemical signals in male root voles (Microtus oeconomus Pallas).

    PubMed

    Yu, Honghao; Yue, Pengpeng; Sun, Ping; Zhao, Xinquan

    2010-03-01

    Sniffing is one-way animals collect chemical signals, and many males self-groom when they encounter the odor of opposite-sex conspecifics. We tested the hypothesis that sexual chemical signals from females can induce self-grooming behavior in male root voles (Microtus oeconomus Pallas). Specifically, we investigated the sniffing pattern of male root voles in response to odors from the head, trunk, and tail areas of lactating and non-lactating females. The self-grooming behavior of males in response to female individual odorant stimuli was documented, and the relationship between self-grooming and sniffing of odors from the head, trunk, and tails areas were analyzed. Sniffing pattern results showed that males are most interested in odors from the head area, and more interested in odors from the tail as compared to the trunk area. Males displayed different sniffing and self-grooming behaviors when they were exposed to odors from lactating females as compared to non-lactating females. Males also spent more time sniffing and engaged in more sniffing behaviors in response to odors from the lactating females' tail area as compared to the same odors from non-lactating females. Similarly, males spent more time self-grooming and engaged in more self-grooming behaviors in the presence of individual odors from lactating females as compared to individual odors from non-lactating females. Partial correlation analyses revealed that the frequency of self-grooming was significantly correlated with the frequency of tail area sniffs. Results from this experiment suggest that sexual attractiveness of lactating females is stronger than that of non-lactating females. Furthermore, the partial correlation analysis demonstrated that self-grooming in males is induced by odors from the tail area of females. Collectively, these results support the hypothesis that sexual chemical signals from females can induce self-grooming behavior in male root voles. Self-grooming may also reflect the

  16. Causal supports for early word learning.

    PubMed

    Booth, Amy E

    2009-01-01

    What factors determine whether a young child will learn a new word? Although there are surely numerous contributors, the current investigation highlights the role of causal information. Three-year-old children (N = 36) were taught 6 new words for unfamiliar objects or animals. Items were described in terms of their causal or noncausal properties. When tested only minutes after training, no significant differences between the conditions were evident. However, when tested several days after training, children performed better on words trained in the causal condition. These results demonstrate that the well-documented effect of causal information on learning and categorization extends to word learning in young children. PMID:19630905

  17. Assessing causality in multivariate accident models.

    PubMed

    Elvik, Rune

    2011-01-01

    This paper discusses the application of operational criteria of causality to multivariate statistical models developed to identify sources of systematic variation in accident counts, in particular the effects of variables representing safety treatments. Nine criteria of causality serving as the basis for the discussion have been developed. The criteria resemble criteria that have been widely used in epidemiology. To assess whether the coefficients estimated in a multivariate accident prediction model represent causal relationships or are non-causal statistical associations, all criteria of causality are relevant, but the most important criterion is how well a model controls for potentially confounding factors. Examples are given to show how the criteria of causality can be applied to multivariate accident prediction models in order to assess the relationships included in these models. It will often be the case that some of the relationships included in a model can reasonably be treated as causal, whereas for others such an interpretation is less supported. The criteria of causality are indicative only and cannot provide a basis for stringent logical proof of causality.

  18. Ability of fourteen chemical agents used in dental practice to induce chromosome aberrations in Syrian hamster embryo cells.

    PubMed

    Hikiba, Hirohito; Watanabe, Eiko; Barrett, J Carl; Tsutsui, Takeki

    2005-01-01

    To assess the genotoxicity of 14 chemical agents used in dental practice, the ability of these agents to induce chromosome aberrations was examined using Syrian hamster embryo (SHE) cells. Statistically significant increases in the frequencies of chromosome aberrations were induced in SHE cells treated with 7 of 10 chemical agents used as endodontic medicaments, that is, carbol camphor, m-cresol, eugenol, guaiacol, zinc oxide, hydrogen peroxide, and formaldehyde. The other 3 chemical agents, that is, thymol, glutaraldehyde, and iodoform, did not increase the levels of chromosome aberrations. Of the 4 chemical agents that are used as an antiseptic on the oral mucosa, chromosome aberrations were induced by iodine, but not by the other 3 antiseptics, benzalkonium chloride, benzethonium chloride, and chlorhexidine. Among the 6 chemical agents exhibiting a negative response in the assay, only thymol induced chromosome aberrations in the presence of exogenous metabolic activation. Our results indicate that chemical agents having a positive response in the present study are potentially genotoxic to mammalian cells and need to be studied further in detail. PMID:15665446

  19. Critical role of surface chemical modifications induced by length shortening on multi-walled carbon nanotubes-induced toxicity.

    PubMed

    Bussy, Cyrill; Pinault, Mathieu; Cambedouzou, Julien; Landry, Marion Julie; Jegou, Pascale; Mayne-L'hermite, Martine; Launois, Pascale; Boczkowski, Jorge; Lanone, Sophie

    2012-11-27

    Given the increasing use of carbon nanotubes (CNT) in composite materials and their possible expansion to new areas such as nanomedicine which will both lead to higher human exposure, a better understanding of their potential to cause adverse effects on human health is needed. Like other nanomaterials, the biological reactivity and toxicity of CNT were shown to depend on various physicochemical characteristics, and length has been suggested to play a critical role. We therefore designed a comprehensive study that aimed at comparing the effects on murine macrophages of two samples of multi-walled CNT (MWCNT) specifically synthesized following a similar production process (aerosol-assisted CVD), and used a soft ultrasonic treatment in water to modify the length of one of them. We showed that modification of the length of MWCNT leads, unavoidably, to accompanying structural (i.e. defects) and chemical (i.e. oxidation) modifications that affect both surface and residual catalyst iron nanoparticle content of CNT. The biological response of murine macrophages to the two different MWCNT samples was evaluated in terms of cell viability, pro-inflammatory cytokines secretion and oxidative stress. We showed that structural defects and oxidation both induced by the length reduction process are at least as responsible as the length reduction itself for the enhanced pro-inflammatory and pro-oxidative response observed with short (oxidized) compared to long (pristine) MWCNT. In conclusion, our results stress that surface properties should be considered, alongside the length, as essential parameters in CNT-induced inflammation, especially when dealing with a safe design of CNT, for application in nanomedicine for example.

  20. Chemically induced hepatotoxicity in human stem cell-induced hepatocytes compared with primary hepatocytes and HepG2.

    PubMed

    Kang, Seok-Jin; Lee, Hyuk-Mi; Park, Young-Il; Yi, Hee; Lee, Hunjoo; So, ByungJae; Song, Jae-Young; Kang, Hwan-Goo

    2016-10-01

    Stem cell-induced hepatocytes (SC-iHeps) have been suggested as a valuable model for evaluating drug toxicology. Here, human-induced pluripotent stem cells (QIA7) and embryonic stem cells (WA01) were differentiated into hepatocytes, and the hepatotoxic effects of acetaminophen (AAP) and aflatoxin B1 (AFB1) were compared with primary hepatocytes (p-Heps) and HepG2. In a cytotoxicity assay, the IC50 of SC-iHeps was similar to that in p-Heps and HepG2 in the AAP groups but different from that in p-Heps of the AFB1 groups. In a multi-parameter assay, phenotypic changes in mitochondrial membrane potential, calcium influx and oxidative stress were similar between QIA7-iHeps and p-Heps following AAP and AFB1 treatment but relatively low in WA01-iHeps and HepG2. Most hepatic functional markers (hepatocyte-specific genes, albumin/urea secretion, and the CYP450 enzyme activity) were decreased in a dose-dependent manner following AAP and AFB1 treatment in SC-iHeps and p-Heps but not in HepG2. Regarding CYP450 inhibition, the cell viability of SC-iHeps and p-Heps was increased by ketoconazole, a CYP3A4 inhibitor. Collectively, SC-iHeps and p-Heps showed similar cytotoxicity and hepatocyte functional effects for AAP and AFB1 compared with HepG2. Therefore, SC-iHeps have phenotypic characteristics and sensitivity to cytotoxic chemicals that are more similar to p-Heps than to HepG2 cells.

  1. Lactoferrin protects against chemical-induced rat liver fibrosis by inhibiting stellate cell activation.

    PubMed

    Tung, Yu-Tang; Tang, Ting-Yu; Chen, Hsiao-Ling; Yang, Shang-Hsun; Chong, Kowit-Yu; Cheng, Winston T K; Chen, Chuan-Mu

    2014-01-01

    Liver diseases, which can be caused by alcohol abuse, chemical intoxication, viral hepatitis infection, and autoimmune disorders, are a significant health issue because they can develop into liver fibrosis and cirrhosis. Lactoferrin (LF), a siderophilic protein with 2 iron-binding sites, has been demonstrated to possess a multitude of biological functions, including antiinflammation, anticancer, and antimicrobial effects, as well as immunomodulatory-enhancing functions. In the current study, we induced hepatotoxicity in rats with dimethylnitrosamine (DMN) to establish a situation that would enable us to evaluate the hepatoprotective effects of LF against hepatic injury. Our results showed that DMN-induced hepatic pathological damage significantly decreased the body weight and liver index, increased the mRNA and protein levels of collagen α-1(I) (ColIα-1) and α-smooth muscle actin, and increased the hydroxyproline content. However, treatment with LF significantly increased body weight and liver index, decreased the mRNA and protein levels of ColIα-1 and α-smooth muscle actin, and suppressed the hydroxyproline content when compared with the DMN-treated group. Liver histopathology also showed that low-dose LF (100mg/kg of body weight) or high-dose LF (300 mg/kg of body weight) could significantly reduce the incidences of liver lesions induced by DMN. These results suggest that the LF exhibits potent hepatoprotection against DMN-induced liver damage in rats and that the hepatoprotective effects of LF may be due to the inhibition of collagen production and to stellate cell activation. PMID:24731632

  2. Causal compensated perturbations in cosmology

    NASA Technical Reports Server (NTRS)

    Veeraraghavan, Shoba; Stebbins, Albert

    1990-01-01

    A theoretical framework is developed to calculate linear perturbations in the gravitational and matter fields which arise causally in response to the presence of stiff matter sources in a FRW cosmology. It is shown that, in order to satisfy energy and momentum conservation, the gravitational fields of the source must be compensated by perturbations in the matter and gravitational fields, and the role of such compensation in containing the initial inhomogeneities in their subsequent evolution is discussed. A complete formal solution is derived in terms of Green functions for the perturbations produced by an arbitrary source in a flat universe containing cold dark matter. Approximate Green function solutions are derived for the late-time density perturbations and late-time gravitational waves in a universe containing a radiation fluid. A cosmological energy-momentum pseudotensor is defined to clarify the nature of energy and momentum conservation in the expanding universe.

  3. Individual differences in causal uncertainty.

    PubMed

    Weary, G; Edwards, J A

    1994-08-01

    This article presents a scale that measures chronic individual differences in people's uncertainty about their ability to understand and detect cause-and-effect relationships in the social world: the Causal Uncertainty Scale (CUS). The results of Study 1 indicated that the scale has good internal and adequate test-retest reliability. Additionally, the results of a factor analysis suggested that the scale appears to be tapping a single construct. Study 2 examined the convergent and discriminant validity of the scale, and Studies 3 and 4 examined the predictive and incremental validity of the scale. The importance of the CUS to work on depressives' social information processing and for basic research and theory on human social judgment processes is discussed.

  4. Lysergic acid diethylamide antagonizes shaking induced in rats by five chemically different compounds.

    PubMed

    Cowan, A; Watson, T

    1978-04-14

    Thyrotropin-releasing hormone (TRH), sodium valproate, AF-3-5 (1-[2-hydroxyphenyl]-4-[3-nitrophenyl]-1,2,3,6-tetrahydropyrimidine-2-one), RX336-M (7,8-dihydro-5',6'-dimethylcyclohex-5'-eno-1',2',8',14 codeinone), and Sgd 8473 (alpha-[4-chlorobenzylideneamino)-oxy]-isobutyric acid) each induced repetitive shaking of the body of rats after intraperitoneal injection. This action of the five diverse chemicals appears to be subserved by a common pharmacological component, because pretreatment with d-lysergic acid diethylamide (0.03--1.0 mg kg-1, s.c.) attenuated the shaking behavior in a dose-related manner, and cross tolerance was found between RX336-M and TRH, sodium valproate, and AG-3-5.

  5. Effect of silicon resistivity on its porosification using metal induced chemical etching: morphology and photoluminescence studies

    NASA Astrophysics Data System (ADS)

    Saxena, Shailendra K.; Sahu, Gayatri; Kumar, Vivek; Sahoo, P. K.; Sagdeo, Pankaj R.; Kumar, Rajesh

    2015-03-01

    The structure and light-emitting properties of porous Si nanowires (Si NWs) fabricated by metal induced chemical etching (MIE) process on two different Si substrates of different resistivities have been investigated here. The surface morphological studies have been carried out using scanning electron microscopy. It is observed that porous Si containing well aligned Si NWs is formed from high resistivity (1-20 Ωcm) Si wafer, whereas interconnected pores or cheese-like structures are formed from low resistivity (0.2 Ωcm) Si wafers after MIE. An explanation for the different porosification processes has been proposed based on the initial doping level, where number of dopants seems to be playing an important role in the etching process. Visible photoluminescence (PL) has been observed from all the porous Si samples, that are attributed due to quantum confinement effect.

  6. Molecular Dynamics Study of Thermally Augmented Nanodroplet Motion on Chemical Energy Induced Wettability Gradient Surfaces.

    PubMed

    Chakraborty, Monojit; Chowdhury, Anamika; Bhusan, Richa; DasGupta, Sunando

    2015-10-20

    Droplet motion on a surface with chemical energy induced wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics of molecular movement near the solid-liquid interface including the contact line friction. The simulations mimic experiments in a comprehensive manner wherein microsized droplets are propelled by the surface wettability gradient against forces opposed to motion. The liquid-wall Lennard-Jones interaction parameter and the substrate temperature are varied to explore their effects on the three-phase contact line friction coefficient. The contact line friction is observed to be a strong function of temperature at atomistic scales, confirming their experimentally observed inverse functionality. Additionally, the MD simulation results are successfully compared with those from an analytical model for self-propelled droplet motion on gradient surfaces. PMID:26381847

  7. Light induced chemical vapour deposition of titanium oxide thin films at room temperature

    NASA Astrophysics Data System (ADS)

    Halary, E.; Benvenuti, G.; Wagner, F.; Hoffmann, P.

    2000-02-01

    High resolution patterned deposition of titania is achieved by light induced chemical vapour deposition (LICVD), by imaging a mask onto a glass substrate. A long pulse XeCl Excimer laser (308 nm) provides, by perpendicular irradiation, the energy to convert titanium tetraisopropoxide (TTIP) vapour into titanium dioxide films, in an oxygen atmosphere, on unheated glass substrates. The amorphous titania deposits contain about 6% carbon contamination according to X-ray photoelectron spectroscopy (XPS) measurements. The deposition rate increases with increasing laser fluence until a maximum value is reached, then remains constant over a wide range, and finally decreases with further fluence increase due to titania ablation or thermal effects. The film thickness increases linearly with the number of pulses after a nucleation period. The strong influence of the laser pulse repetition rate on the growth rate and the thickness profile are reported.

  8. High Fidelity Tape Transfer Printing Based On Chemically Induced Adhesive Strength Modulation

    PubMed Central

    Sim, Kyoseung; Chen, Song; Li, Yuhang; Kammoun, Mejdi; Peng, Yun; Xu, Minwei; Gao, Yang; Song, Jizhou; Zhang, Yingchun; Ardebili, Haleh; Yu, Cunjiang

    2015-01-01

    Transfer printing, a two-step process (i.e. picking up and printing) for heterogeneous integration, has been widely exploited for the fabrication of functional electronics system. To ensure a reliable process, strong adhesion for picking up and weak or no adhesion for printing are required. However, it is challenging to meet the requirements of switchable stamp adhesion. Here we introduce a simple, high fidelity process, namely tape transfer printing(TTP), enabled by chemically induced dramatic modulation in tape adhesive strength. We describe the working mechanism of the adhesion modulation that governs this process and demonstrate the method by high fidelity tape transfer printing several types of materials and devices, including Si pellets arrays, photodetector arrays, and electromyography (EMG) sensors, from their preparation substrates to various alien substrates. High fidelity tape transfer printing of components onto curvilinear surfaces is also illustrated. PMID:26553110

  9. Chemical carcinogen-induced decreases in genomic 5-methyldeoxycytidine content of normal human bronchial epithelial cells.

    PubMed Central

    Wilson, V L; Smith, R A; Longoria, J; Liotta, M A; Harper, C M; Harris, C C

    1987-01-01

    The genomic content of DNA 5-methyldeoxycytidine (m5dC) was measured in dividing normal human bronchial epithelial cells treated with a broad range of chemical carcinogens. At noncytotoxic concentrations, all of the carcinogenic agents tested significantly reduced cellular DNA m5dC content whereas the weakly carcinogenic and noncarcinogenic agents, benzo[e]pyrene and phenanthrene (respectively), did not. These reductions varied from 8% to 31% depending on the agent and the donor cells. The reductions in genomic m5dC levels were concentration dependent for the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene. We speculate that carcinogen-induced perturbation of DNA m5dC patterns may lead to heritable changes in gene expression and contribute to the molecular alterations involved in the initiation and the subsequent steps of the carcinogenesis process. PMID:3472209

  10. Silencing of Inducible Immunoproteasome Subunit Expression by Chemically Modified siRNA and shRNA.

    PubMed

    Gvozdeva, Olga V; Prassolov, Vladimir S; Zenkova, Marina A; Vlassov, Valentin V; Chernolovskaya, Elena L

    2016-08-01

    Overexpression of inducible subunits of immunoproteasome is related to pathogenesis of some chronic diseases. Specific inhibition of the immunosubunits may be used for the treatment of these diseases and RNA interference is one of the potent methods used in this area. We designed 2'-O-methyl modified siRNAs with selectively protected nuclease-sensitive sites, which efficiently silence LMP2, LMP7, and MECL-1 genes expression. To provide stable long-lasting inhibition of target genes, short-hairpin RNAs (shRNA) expressed by lentiviral vectors were constructed. Our results demonstrated that chemically modified siRNAs inhibited the expression of target genes with similar efficiency or with efficiency exceeding that of corresponding shRNAs and provide silencing effect for 5 days.

  11. Chemical warfare agent and biological toxin-induced pulmonary toxicity: could stem cells provide potential therapies?

    PubMed

    Angelini, Daniel J; Dorsey, Russell M; Willis, Kristen L; Hong, Charles; Moyer, Robert A; Oyler, Jonathan; Jensen, Neil S; Salem, Harry

    2013-01-01

    Chemical warfare agents (CWAs) as well as biological toxins present a significant inhalation injury risk to both deployed warfighters and civilian targets of terrorist attacks. Inhalation of many CWAs and biological toxins can induce severe pulmonary toxicity leading to the development of acute lung injury (ALI) as well as acute respiratory distress syndrome (ARDS). The therapeutic options currently used to treat these conditions are very limited and mortality rates remain high. Recent evidence suggests that human stem cells may provide significant therapeutic options for ALI and ARDS in the near future. The threat posed by CWAs and biological toxins for both civilian populations and military personnel is growing, thus understanding the mechanisms of toxicity and potential therapies is critical. This review will outline the pulmonary toxic effects of some of the most common CWAs and biological toxins as well as the potential role of stem cells in treating these types of toxic lung injuries.

  12. Decomposition of gaseous organic contaminants by surface discharge induced plasma chemical processing -- SPCP

    SciTech Connect

    Oda, Tetsuji; Yamashita, Ryuichi; Haga, Ichiro; Takahashi, Tadashi; Masuda, Senichi

    1996-01-01

    The decomposition performance of the surface induced plasma chemical processing (SPCP) for chlorofluorocarbon (83 ppm CFC-113 in air), acetone, trichloroethylene, and isopropylalcohol was experimentally examined. In every case, very high decomposition performance, more than 90 or 99% removal rate, is realized when the residence time is about 1 second and the input electric power for a 16 cm{sup 3} reactor is about 10 W. Acetone is the most stable compound and alcohol is most easily decomposed. The decomposed product-analysis by a GasChromato-MassSpectrometer has just started but very poor results are obtained. In fact, some portion of the isopropylalcohol may change to acetone which is worse than alcohol. The necessary energy to decompose one mol gas diluted in the air is calculated form the experiments. The necessary energy level for acetone and trichloroethylene is about one-tenth or one-fiftieth of that for chlorofluorocarbon.

  13. High Fidelity Tape Transfer Printing Based On Chemically Induced Adhesive Strength Modulation

    NASA Astrophysics Data System (ADS)

    Sim, Kyoseung; Chen, Song; Li, Yuhang; Kammoun, Mejdi; Peng, Yun; Xu, Minwei; Gao, Yang; Song, Jizhou; Zhang, Yingchun; Ardebili, Haleh; Yu, Cunjiang

    2015-11-01

    Transfer printing, a two-step process (i.e. picking up and printing) for heterogeneous integration, has been widely exploited for the fabrication of functional electronics system. To ensure a reliable process, strong adhesion for picking up and weak or no adhesion for printing are required. However, it is challenging to meet the requirements of switchable stamp adhesion. Here we introduce a simple, high fidelity process, namely tape transfer printing(TTP), enabled by chemically induced dramatic modulation in tape adhesive strength. We describe the working mechanism of the adhesion modulation that governs this process and demonstrate the method by high fidelity tape transfer printing several types of materials and devices, including Si pellets arrays, photodetector arrays, and electromyography (EMG) sensors, from their preparation substrates to various alien substrates. High fidelity tape transfer printing of components onto curvilinear surfaces is also illustrated.

  14. Chemical taggant detection and analysis by laser-induced breakdown spectroscopy

    SciTech Connect

    Wise, Steven H.; Almirall, Jose R

    2008-11-01

    A commercially available chemical identification taggant that imparts a unique elemental fingerprint to any object and can be analytically distinguished from billions of possible combinations has been developed. The liquid tag is easily applied and, once dry, can be removed and analyzed by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to determine the combination of elements present in the sample. The current study investigates the use of laser-induced breakdown spectroscopy (LIBS) as an alternative, and perhaps more practical, analysis scheme to LA-ICP-MS for this taggant. LIBS provides excellent discrimination potential, sensitivity, and repeatability of analysis for up to 17 rare-earth elements using a Nd:YAG 266 nm or 1064 nm laser and an intensified CCD detector.

  15. Antioxidant Potential of Fagonia arabica against the Chemical Ischemia-Induced in PC12 Cells.

    PubMed

    Satpute, Ravindra; Bhattacharya, Rahul; S Kashyap, Rajpal; J Purohit, Hemant; Y Deopujari, Jayant; M Taori, Girdhar; F Daginawala, Hatim

    2012-01-01

    The imbalance between pro-oxidants and anti-oxidants leads to generation of oxygen/nitrogen free radicals which are implicated in several neurodegenerative diseases. Fagonia arabica is an ethno-pharmacologically important Ayurvedic herb known to have many medicinal properties like anti-inflammatory, analgesic and antipyretic effects. However, its antioxidant potential has not been investigated so far. The present study was designed to investigate the antioxidant potential of F. arabica and its neuroprotective effect on chemical ischemia induced in PC12 cells. Chemical ischemia was induced through exposing the cells to uncoupler of oxidative phosphorylation sodium azide (5.0 mM) and competitive inhibitor of glycolysis 2-deoxy-glucose (2.0 mM) for 2 h followed by 24 h reperfusion with normal culture medium. Total polyphenolic content (TPC) and antioxidant potential of the herb was measured using DPPH and ABTS•+ scavenging and ferric ion reducing antioxidant potential (FRAP) assays; its effect on neuroprotection and energy metabolism was also studied. The ischemic injury was characterized by impaired energy status as indicated by decreased ATP levels in the cells, accompanied by increased lactic acid content. Both the changes favourably responded to F. arabica and offered considerable neuroprotection from ischemia and helped to maintain the cellular viability and mitochondrial integrity of the cells. F. arabica showed considerable amount of TPC and antioxidant activity. This study reveals the antioxidant potential of F. arabica and its protective efficacy against ischemia/reperfusion mediated cell death. F. arabica thus can be considered for further studies for the development of the prophylactic or therapeutic agent for the treatment of ischemic stroke. PMID:24250453

  16. Standoff detection of chemical and biological threats using laser-induced breakdown spectroscopy.

    PubMed

    Gottfried, Jennifer L; De Lucia, Frank C; Munson, Chase A; Miziolek, Andrzej W

    2008-04-01

    Laser-induced breakdown spectroscopy (LIBS) is a promising technique for real-time chemical and biological warfare agent detection in the field. We have demonstrated the detection and discrimination of the biological warfare agent surrogates Bacillus subtilis (BG) (2% false negatives, 0% false positives) and ovalbumin (0% false negatives, 1% false positives) at 20 meters using standoff laser-induced breakdown spectroscopy (ST-LIBS) and linear correlation. Unknown interferent samples (not included in the model), samples on different substrates, and mixtures of BG and Arizona road dust have been classified with reasonable success using partial least squares discriminant analysis (PLS-DA). A few of the samples tested such as the soot (not included in the model) and the 25% BG:75% dust mixture resulted in a significant number of false positives or false negatives, respectively. Our preliminary results indicate that while LIBS is able to discriminate biomaterials with similar elemental compositions at standoff distances based on differences in key intensity ratios, further work is needed to reduce the number of false positives/negatives by refining the PLS-DA model to include a sufficient range of material classes and carefully selecting a detection threshold. In addition, we have demonstrated that LIBS can distinguish five different organophosphate nerve agent simulants at 20 meters, despite their similar stoichiometric formulas. Finally, a combined PLS-DA model for chemical, biological, and explosives detection using a single ST-LIBS sensor has been developed in order to demonstrate the potential of standoff LIBS for universal hazardous materials detection.

  17. Evolution of color vision loss induced by occupational exposure to chemicals.

    PubMed

    Gobba, F; Cavalleri, A

    2000-10-01

    The evolution of occupationally induced color vision loss was studied in workers exposed to various chemicals. Exposure was evaluated by biological monitoring or personal air samplers, and color vision using the Lanthony D-15 desaturated panel (D-15 d). The effect of short-term interruption of exposure was studied in 39 Styrene (St) exposed workers: at a first examination a dose-related color vision loss was disclosed; a re-test performed after one month's interruption of exposure did not show any improvement of the effect. The evolution during longer periods was studied in another group of 30 St workers. Exposure and color vision were evaluated, then a follow-up was done 12 months later: the exposure was unmodified or slightly decreased in 20 subjects, and D-15 d outcomes remained unchanged, while St levels had increased and color vision loss progressed in the other 10. Similar results were obtained in 33 PCE exposed dry-cleaners: no change in color perception was observed in 14 workers whose exposure decreased, while in the other 19 a rise in PCE levels was followed by a significant color vision worsening. In 21 Hg exposed workers whose mean urinary excretion of Hg was threefold the BEI proposed by ACGIH, a dose-related impairment in color perception was observed. 12 months after a marked reduction of exposure, an almost complete recovery of the impairment was observed. Our data show that an increase in exposure can induce a worsening in color vision loss. A short interruption in exposure did not reduce the effect. A more prolonged reduction of dose reversed color vision loss in Hg exposed workers, while in solvent-exposed individuals the progression deserves further evaluation. D-15 d proved a useful test for studies on the evolution of color perception in workers exposed to eye-toxic chemicals.

  18. Antioxidant Activity of Caffeic Acid against Iron-Induced Free Radical Generation—A Chemical Approach

    PubMed Central

    Genaro-Mattos, Thiago C.; Maurício, Ângelo Q.; Rettori, Daniel; Alonso, Antonio; Hermes-Lima, Marcelo

    2015-01-01

    Caffeic acid (CA) is a phenolic compound widely found in coffee beans with known beneficial effects in vivo. Many studies showed that CA has anti-inflammatory, anti-mutagenic, antibacterial and anti-carcinogenic properties, which could be linked to its antioxidant activity. Taking in consideration the reported in vitro antioxidant mechanism of other polyphenols, our working hypothesis was that the CA antioxidant activity could be related to its metal-chelating property. With that in mind, we sought to investigate the chemical antioxidant mechanism of CA against in vitro iron-induced oxidative damage under different assay conditions. CA was able to prevent hydroxyl radical formation promoted by the classical Fenton reaction, as determined by 2-deoxyribose (2-DR) oxidative degradation and DMPO hydroxylation. In addition to its ability to prevent hydroxyl radical formation, CA had a great inhibition of membrane lipid peroxidation. In the lipid peroxidation assays CA acted as both metal-chelator and as hydrogen donor, preventing the deleterious action promoted by lipid-derived peroxyl and alkoxyl radicals. Our results indicate that the observed antioxidant effects were mostly due to the formation of iron-CA complexes, which are able to prevent 2-DR oxidation and DMPO hydroxylation. Noteworthy, the formation of iron-CA complexes and prevention of oxidative damage was directly related to the pH of the medium, showing better antioxidant activity at higher pH values. Moreover, in the presence of lipid membranes the antioxidant potency of CA was much higher, indicating its enhanced effectiveness in a hydrophobic environment. Overall, our results show that CA acts as an antioxidant through an iron chelating mechanism, preventing the formation of free hydroxyl radicals and, therefore, inhibiting Fenton-induced oxidative damage. The chemical properties of CA described here—in association with its reported signaling effects—could be an explanation to its beneficial effects

  19. Antioxidant Activity of Caffeic Acid against Iron-Induced Free Radical Generation--A Chemical Approach.

    PubMed

    Genaro-Mattos, Thiago C; Maurício, Ângelo Q; Rettori, Daniel; Alonso, Antonio; Hermes-Lima, Marcelo

    2015-01-01

    Caffeic acid (CA) is a phenolic compound widely found in coffee beans with known beneficial effects in vivo. Many studies showed that CA has anti-inflammatory, anti-mutagenic, antibacterial and anti-carcinogenic properties, which could be linked to its antioxidant activity. Taking in consideration the reported in vitro antioxidant mechanism of other polyphenols, our working hypothesis was that the CA antioxidant activity could be related to its metal-chelating property. With that in mind, we sought to investigate the chemical antioxidant mechanism of CA against in vitro iron-induced oxidative damage under different assay conditions. CA was able to prevent hydroxyl radical formation promoted by the classical Fenton reaction, as determined by 2-deoxyribose (2-DR) oxidative degradation and DMPO hydroxylation. In addition to its ability to prevent hydroxyl radical formation, CA had a great inhibition of membrane lipid peroxidation. In the lipid peroxidation assays CA acted as both metal-chelator and as hydrogen donor, preventing the deleterious action promoted by lipid-derived peroxyl and alkoxyl radicals. Our results indicate that the observed antioxidant effects were mostly due to the formation of iron-CA complexes, which are able to prevent 2-DR oxidation and DMPO hydroxylation. Noteworthy, the formation of iron-CA complexes and prevention of oxidative damage was directly related to the pH of the medium, showing better antioxidant activity at higher pH values. Moreover, in the presence of lipid membranes the antioxidant potency of CA was much higher, indicating its enhanced effectiveness in a hydrophobic environment. Overall, our results show that CA acts as an antioxidant through an iron chelating mechanism, preventing the formation of free hydroxyl radicals and, therefore, inhibiting Fenton-induced oxidative damage. The chemical properties of CA described here--in association with its reported signaling effects--could be an explanation to its beneficial effects

  20. Antioxidant Activity of Caffeic Acid against Iron-Induced Free Radical Generation--A Chemical Approach.

    PubMed

    Genaro-Mattos, Thiago C; Maurício, Ângelo Q; Rettori, Daniel; Alonso, Antonio; Hermes-Lima, Marcelo

    2015-01-01

    Caffeic acid (CA) is a phenolic compound widely found in coffee beans with known beneficial effects in vivo. Many studies showed that CA has anti-inflammatory, anti-mutagenic, antibacterial and anti-carcinogenic properties, which could be linked to its antioxidant activity. Taking in consideration the reported in vitro antioxidant mechanism of other polyphenols, our working hypothesis was that the CA antioxidant activity could be related to its metal-chelating property. With that in mind, we sought to investigate the chemical antioxidant mechanism of CA against in vitro iron-induced oxidative damage under different assay conditions. CA was able to prevent hydroxyl radical formation promoted by the classical Fenton reaction, as determined by 2-deoxyribose (2-DR) oxidative degradation and DMPO hydroxylation. In addition to its ability to prevent hydroxyl radical formation, CA had a great inhibition of membrane lipid peroxidation. In the lipid peroxidation assays CA acted as both metal-chelator and as hydrogen donor, preventing the deleterious action promoted by lipid-derived peroxyl and alkoxyl radicals. Our results indicate that the observed antioxidant effects were mostly due to the formation of iron-CA complexes, which are able to prevent 2-DR oxidation and DMPO hydroxylation. Noteworthy, the formation of iron-CA complexes and prevention of oxidative damage was directly related to the pH of the medium, showing better antioxidant activity at higher pH values. Moreover, in the presence of lipid membranes the antioxidant potency of CA was much higher, indicating its enhanced effectiveness in a hydrophobic environment. Overall, our results show that CA acts as an antioxidant through an iron chelating mechanism, preventing the formation of free hydroxyl radicals and, therefore, inhibiting Fenton-induced oxidative damage. The chemical properties of CA described here--in association with its reported signaling effects--could be an explanation to its beneficial effects

  1. Antioxidant Potential of Fagonia arabica against the Chemical Ischemia-Induced in PC12 Cells

    PubMed Central

    Satpute, Ravindra; Bhattacharya, Rahul; S Kashyap, Rajpal; J Purohit, Hemant; Y Deopujari, Jayant; M Taori, Girdhar; F. Daginawala, Hatim

    2012-01-01

    The imbalance between pro-oxidants and anti-oxidants leads to generation of oxygen/nitrogen free radicals which are implicated in several neurodegenerative diseases. Fagonia arabica is an ethno-pharmacologically important Ayurvedic herb known to have many medicinal properties like anti-inflammatory, analgesic and antipyretic effects. However, its antioxidant potential has not been investigated so far. The present study was designed to investigate the antioxidant potential of F. arabica and its neuroprotective effect on chemical ischemia induced in PC12 cells. Chemical ischemia was induced through exposing the cells to uncoupler of oxidative phosphorylation sodium azide (5.0 mM) and competitive inhibitor of glycolysis 2-deoxy-glucose (2.0 mM) for 2 h followed by 24 h reperfusion with normal culture medium. Total polyphenolic content (TPC) and antioxidant potential of the herb was measured using DPPH and ABTS•+ scavenging and ferric ion reducing antioxidant potential (FRAP) assays; its effect on neuroprotection and energy metabolism was also studied. The ischemic injury was characterized by impaired energy status as indicated by decreased ATP levels in the cells, accompanied by increased lactic acid content. Both the changes favourably responded to F. arabica and offered considerable neuroprotection from ischemia and helped to maintain the cellular viability and mitochondrial integrity of the cells. F. arabica showed considerable amount of TPC and antioxidant activity. This study reveals the antioxidant potential of F. arabica and its protective efficacy against ischemia/reperfusion mediated cell death. F. arabica thus can be considered for further studies for the development of the prophylactic or therapeutic agent for the treatment of ischemic stroke. PMID:24250453

  2. Secondary Metabolome Variability and Inducible Chemical Defenses in the Mediterranean Sponge Aplysina cavernicola.

    PubMed

    Reverter, M; Perez, T; Ereskovsky, A V; Banaigs, B

    2016-01-01

    Secondary metabolites play a crucial role in marine invertebrate chemical ecology. Thus, it is of great importance to understand factors regulating their production and sources of variability. This work aimed to study the variability of the bromotyrosine derivatives in the Mediterranean sponge Aplysina cavernicola, and also to better understand how biotic (reproductive state) and abiotic factors (seawater temperature) could partly explain this variability. Results showed that the A. cavernicola reproductive cycle has little effect on the variability of the sponges' secondary metabolism, whereas water temperature has a significant influence on the production level of secondary metabolites. Temporal variability analysis of the sponge methanolic extracts showed that bioactivity variability was related to the presence of the minor secondary metabolite dienone, which accounted for 50 % of the bioactivity observed. Further bioassays coupled to HPLC extract fractionation confirmed that dienone was the only compound from Aplysina alkaloids to display a strong bioactivity. Both dienone production and bioactivity showed a notable increase in October 2008, after a late-summer warming episode, indicating that A. cavernicola might be able to induce chemical changes to cope with environmental stressors.

  3. Protection of PC12 cells from chemical ischemia induced oxidative stress by Fagonia arabica.

    PubMed

    Satpute, Ravindra M; Kashyap, Rajpal S; Deopujari, Jayant Y; Purohit, Hemant J; Taori, Girdhar M; Daginawala, Hatim F

    2009-11-01

    Fagonia arabica (Zygophyllaceae) is an important Ayurvedic herb, grows throughout arid regions of India, has been widely used as a folk remedy by the indigenous people for its anti-inflammatory, analgesic and antipyretic effects. In the present study, antioxidant potential of F. arabica and the associated mechanism of antioxidant defence in rat pheochromocytoma (PC12) cells subjected to chemical ischemia was studied. Effect of total extract of F. arabica was studied for its antioxidant potential on the chemical ischemia induced PC12 cells. Alterations in the activities of cellular antioxidant enzymes (SOD, CAT, GSH-Px and GSH-R) were measured. Antioxidant potential of herb (ABTS), extent of lipid peroxidation (MDA and 4-HAE), total antioxidant status (TAS) and total glutathione (reduced, oxidized and their ratio) were evaluated. F. arabica scavenges the free radicals (ABTS(.)+), and showed a concentration dependent antioxidant activity, highest being at 1000 microg/ml. Its treatment with ischemic cells ameliorates the GSH and TAS levels and also helps the cells to restore the activities of the cellular antioxidative enzymes and also reduced the degree of lipid peroxidation. F. arabica scavenges the free radicals and attenuates oxidative stress mediated cell injury during ischemia. PMID:19520135

  4. Host Chemical Footprints Induce Host Sex Discrimination Ability in Egg Parasitoids

    PubMed Central

    Peri, Ezio; Frati, Francesca; Salerno, Gianandrea; Conti, Eric; Colazza, Stefano

    2013-01-01

    Trissolcus egg parasitoids, when perceiving the chemical footprints left on a substrate by pentatomid host bugs, adopt a motivated searching behaviour characterized by longer searching time on patches were signals are present. Once in contact with host chemical footprints, Trissolcus wasps search longer on traces left by associated hosts rather than non-associated species, and, in the former case, they search longer on traces left by females than males. Based on these evidences, we hypothesized that only associated hosts induce the ability to discriminate host sex in wasps. To test this hypothesis we investigated the ability of Trissolcus basalis, T. brochymenae, and Trissolcus sp. to distinguish female from male Nezara viridula, Murgantia histrionica, and Graphosoma semipunctatum footprints. These three pentatomid bugs were selected according to variable association levels. Bioassays were conducted on filter paper sheets, and on Brassica oleracea (broccoli) leaves. The results confirmed our hypothesis showing that wasps spent significantly more time on female rather than male traces left by associated hosts on both substrates. No differences were observed in the presence of traces left by non-associated hosts. The ecological consequences for parasitoid host location behaviour are discussed. PMID:24244417

  5. Extraction of chemical-induced diseases using prior knowledge and textual information

    PubMed Central

    Pons, Ewoud; Becker, Benedikt F.H.; Akhondi, Saber A.; Afzal, Zubair; van Mulligen, Erik M.; Kors, Jan A.

    2016-01-01

    We describe our approach to the chemical–disease relation (CDR) task in the BioCreative V challenge. The CDR task consists of two subtasks: automatic disease-named entity recognition and normalization (DNER), and extraction of chemical-induced diseases (CIDs) from Medline abstracts. For the DNER subtask, we used our concept recognition tool Peregrine, in combination with several optimization steps. For the CID subtask, our system, which we named RELigator, was trained on a rich feature set, comprising features derived from a graph database containing prior knowledge about chemicals and diseases, and linguistic and statistical features derived from the abstracts in the CDR training corpus. We describe the systems that were developed and present evaluation results for both subtasks on the CDR test set. For DNER, our Peregrine system reached an F-score of 0.757. For CID, the system achieved an F-score of 0.526, which ranked second among 18 participating teams. Several post-challenge modifications of the systems resulted in substantially improved F-scores (0.828 for DNER and 0.602 for CID). RELigator is available as a web service at http://biosemantics.org/index.php/software/religator. PMID:27081155

  6. Pollution-Induced Community Tolerance To Diagnose Hazardous Chemicals in Multiple Contaminated Aquatic Systems.

    PubMed

    Rotter, Stefanie; Gunold, Roman; Mothes, Sibylle; Paschke, Albrecht; Brack, Werner; Altenburger, Rolf; Schmitt-Jansen, Mechthild

    2015-08-18

    Aquatic ecosystems are often contaminated with large numbers of chemicals, which cannot be sufficiently addressed by chemical target analyses. Effect-directed analysis (EDA) enables the identification of toxicants in complex contaminated environmental samples. This study suggests pollution-induced community tolerance (PICT) as a confirmation tool for EDA to identify contaminants which actually impact on local communities. The effects of three phytotoxic compounds local periphyton communities, cultivated at a reference (R-site) and a polluted site (P-site), were assessed to confirm the findings of a former EDA study on sediments. The sensitivities of R- and P-communities to prometryn, tributyltin (TBT) and N-phenyl-2-naphthylamine (PNA) were quantified in short-term toxicity tests and exposure concentrations were determined. Prometryn and PNA concentrations were significantly higher at the P-site, whereas TBT concentrations were in the same range at both sites. Periphyton communities differed in biomass, but algal class composition and diatom diversity were similar. Community tolerance of P-communities was significantly enhanced for prometryn, but not for PNA and TBT, confirming site-specific effects on local periphyton for prometryn only. Thus, PICT enables in situ effect confirmation of phytotoxic compounds at the community level and seems to be suitable to support confirmation and enhance ecological realism of EDA. PMID:26196040

  7. Chemical and explosive detection with long-wave infrared laser induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Jin, Feng; Trivedi, Sudhir B.; Yang, Clayton S.; Brown, Ei E.; Kumi-Barimah, Eric; Hommerich, Uwe H.; Samuels, Alan C.

    2016-05-01

    Conventional laser induced breakdown spectroscopy (LIBS) mostly uses silicon-based detectors and measures the atomic emission in the UV-Vis-NIR (UVN) region of the spectrum. It can be used to detect the elements in the sample under test, such as the presence of lead in the solder for electronics during RoHS compliance verification. This wavelength region, however, does not provide sufficient information on the bonding between the elements, because the molecular vibration modes emit at longer wavelength region. Measuring long-wave infrared spectrum (LWIR) in a LIBS setup can instead reveal molecular composition of the sample, which is the information sought in applications including chemical and explosive detection and identification. This paper will present the work and results from the collaboration of several institutions to develop the methods of LWIR LIBS for chemical/explosive/pharmaceutical material detection/identification, such as DMMP and RDX, as fast as using a single excitation laser pulse. In our latest LIBS setup, both UVN and LWIR spectra can be collected at the same time, allowing more accurate detection and identification of materials.

  8. Suppression of SOS-inducing activity of chemical mutagens by metabolites from microbial transformation of (+)-longicyclene.

    PubMed

    Sakata, Kazuki; Miyazawa, Mitsuo

    2010-08-25

    In this study, biotransformation of (+)-longicyclene (1) by Aspergillus niger (NBRC 4414) and the suppressive effect on umuC gene expression by chemical mutagens 2-(2-furyl)-3-(5-nitro-2-furyl)acrylamide (furylfuramide) and aflatoxin B1 (AFB1) of the SOS response in Salmonella typhimurium TA1535/pSK1002 were investigated. Initially, compound 1 was converted to three new terpenoids, (-)-(10R)-10-hydroxy-longicyclic acid (2), (+)-(10S)-10-hydroxy-longicyclic acid (3), and (+)-10-oxo-longicyclic acid (4) by A. niger , and their conversion rates were 27, 23, and 30%, respectively. The metabolites suppressed the SOS-inducing activity of furylfuramide and AFB1 in the umu test. Compounds 1-4 were hardly showing a suppressive effect on umu gene expression of the SOS responses in S. typhimurium TA1535/pSK1002 against furylfuramid. However, metabolites showed a suppressive effect against AFB1. Compound 4 had gene expression by chemical mutagen AFB1, was suppressed 53% at <1.0 mM, and was the most effective compound in this experiment. PMID:20662538

  9. Causal Systems Categories: Differences in Novice and Expert Categorization of Causal Phenomena

    ERIC Educational Resources Information Center

    Rottman, Benjamin M.; Gentner, Dedre; Goldwater, Micah B.

    2012-01-01

    We investigated the understanding of causal systems categories--categories defined by common causal structure rather than by common domain content--among college students. We asked students who were either novices or experts in the physical sciences to sort descriptions of real-world phenomena that varied in their causal structure (e.g., negative…

  10. The Power of Causal Beliefs and Conflicting Evidence on Causal Judgments and Decision Making

    ERIC Educational Resources Information Center

    Garcia-Retamero, Rocio; Muller, Stephanie M.; Catena, Andres; Maldonado, Antonio

    2009-01-01

    In two experiments, we investigated the relative impact of causal beliefs and empirical evidence on both decision making and causal judgments, and whether this relative impact could be altered by previous experience. 2. Selected groups of participants in both experiments received pre-training with either causal or neutral cues, or no pre-training…

  11. Abolished thermal and mechanical antinociception but retained visceral chemical antinociception induced by butorphanol in mu-opioid receptor knockout mice.

    PubMed

    Ide, Soichiro; Minami, Masabumi; Ishihara, Kumatoshi; Uhl, George R; Satoh, Masamichi; Sora, Ichiro; Ikeda, Kazutaka

    2008-06-01

    Butorphanol is hypothesized to induce analgesia via opioid pathways, although the precise mechanisms for its effects remain unknown. In this study, we investigated the role of the mu-opioid receptor (MOP) in thermal, mechanical, and visceral chemical antinociception induced by butorphanol using MOP knockout (KO) mice. Butorphanol-induced thermal antinociception, assessed by the hot-plate and tail-flick tests, was significantly reduced in heterozygous and abolished in homozygous MOP-KO mice compared with wildtype mice. The results obtained from our butorphanol-induced mechanical antinociception experiments, assessed by the Randall-Selitto test, were similar to the results obtained from the thermal antinociception experiments in these mice. Interestingly, however, butorphanol retained its ability to induce significant visceral chemical antinociception, assessed by the writhing test, in homozygous MOP-KO mice. The butorphanol-induced visceral chemical antinociception that was retained in homozygous MOP-KO mice was completely blocked by pretreatment with nor-binaltorphimine, a kappa-opioid receptor (KOP) antagonist. In vitro binding and cyclic adenosine monophosphate assays also showed that butorphanol possessed higher affinity for KOPs and MOPs than for delta-opioid receptors. These results molecular pharmacologically confirmed previous studies implicating MOPs, and partially KOPs, in mediating butorphanol-induced analgesia. PMID:18417173

  12. Chemical and biological insights into uranium-induced apoptosis of rat hepatic cell line.

    PubMed

    Liu, Fang; Du, Ke-Jie; Fang, Zhen; You, Yong; Wen, Ge-Bo; Lin, Ying-Wu

    2015-05-01

    Uranium release into the environment is a threat to human health, and the mechanisms of cytotoxicity caused by uranium are not well-understood. To improve our understanding in this respect, we herein evaluated the effects of uranium exposure on normal rat hepatic BRL cells. As revealed by scanning electron microscopy and transmission electron microscope analysis, uranyl nitrate was found to be transformed into uranyl phosphate particles in the medium and taken up by BRL cells in an endocytotic uptake manner, which presumably initiates apoptosis of the cell, although soluble uranyl ion may also be toxic. The apoptosis of BRL cells upon uranium exposure was also confirmed by both the acridine orange and ethidium bromide double staining assay and the Annexin V/propidium iodide double staining assay. Further studies revealed that uranium induced the loss of mitochondrial membrane potential in a dose-dependent manner. Moreover, the uranium-induced apoptosis was found to be associated with the activation of caspase-3, caspase-8 and caspase-9, indicating both a mitochondria-dependent signaling pathway and a death receptor pathway by a crosstalk. This study provides new chemical and biological insights into the mechanism of uranium toxicity toward hepatic cells, which will help seek approaches for biological remediation of uranium.

  13. Dietary zinc deficiency predisposes mice to the development of preneoplastic lesions in chemically-induced hepatocarcinogenesis.

    PubMed

    Romualdo, Guilherme Ribeiro; Goto, Renata Leme; Henrique Fernandes, Ana Angélica; Cogliati, Bruno; Barbisan, Luis Fernando

    2016-10-01

    Although there is a concomitance of zinc deficiency and high incidence/mortality for hepatocellular carcinoma in certain human populations, there are no experimental studies investigating the modifying effects of zinc on hepatocarcinogenesis. Thus, we evaluated whether dietary zinc deficiency or supplementation alter the development of hepatocellular preneoplastic lesions (PNL). Therefore, neonatal male Balb/C mice were submitted to a diethylnitrosamine/2-acetylaminefluorene-induced hepatocarcinogenesis model. Moreover, mice were fed adequate (35 mg/kg diet), deficient (3 mg/kg) or supplemented (180 mg/kg) zinc diets. Mice were euthanized at 12 (early time-point) or 24 weeks (late time-point) after introducing the diets. At the early time-point, zinc deficiency decreased Nrf2 protein expression and GSH levels while increased p65 and p53 protein expression and the number of PNL/area. At the late time-point, zinc deficiency also decreased GSH levels while increased liver genotoxicity, cell proliferation into PNL and PNL size. In contrast, zinc supplementation increased antioxidant defense at both time-points but not altered PNL development. Our findings are the first to suggest that zinc deficiency predisposes mice to the PNL development in chemically-induced hepatocarcinogenesis. The decrease of Nrf2/GSH pathway and increase of liver genotoxicity, as well as the increase of p65/cell proliferation, are potential mechanisms to this zinc deficiency-mediated effect.

  14. Dietary zinc deficiency predisposes mice to the development of preneoplastic lesions in chemically-induced hepatocarcinogenesis.

    PubMed

    Romualdo, Guilherme Ribeiro; Goto, Renata Leme; Henrique Fernandes, Ana Angélica; Cogliati, Bruno; Barbisan, Luis Fernando

    2016-10-01

    Although there is a concomitance of zinc deficiency and high incidence/mortality for hepatocellular carcinoma in certain human populations, there are no experimental studies investigating the modifying effects of zinc on hepatocarcinogenesis. Thus, we evaluated whether dietary zinc deficiency or supplementation alter the development of hepatocellular preneoplastic lesions (PNL). Therefore, neonatal male Balb/C mice were submitted to a diethylnitrosamine/2-acetylaminefluorene-induced hepatocarcinogenesis model. Moreover, mice were fed adequate (35 mg/kg diet), deficient (3 mg/kg) or supplemented (180 mg/kg) zinc diets. Mice were euthanized at 12 (early time-point) or 24 weeks (late time-point) after introducing the diets. At the early time-point, zinc deficiency decreased Nrf2 protein expression and GSH levels while increased p65 and p53 protein expression and the number of PNL/area. At the late time-point, zinc deficiency also decreased GSH levels while increased liver genotoxicity, cell proliferation into PNL and PNL size. In contrast, zinc supplementation increased antioxidant defense at both time-points but not altered PNL development. Our findings are the first to suggest that zinc deficiency predisposes mice to the PNL development in chemically-induced hepatocarcinogenesis. The decrease of Nrf2/GSH pathway and increase of liver genotoxicity, as well as the increase of p65/cell proliferation, are potential mechanisms to this zinc deficiency-mediated effect. PMID:27544374

  15. IR and UV laser-induced chemical vapor deposition: Chemical mechanism for a-Si:H and Cr (O,C) film formation

    NASA Astrophysics Data System (ADS)

    Hess, Peter

    The characteristic features of laser-induced chemical vapor deposition in the parallel and perpendicular laser beam/surface configurations are discussed. Low temperature chemical processing with directed and spatially localized energy deposition in the system is investigated. Results obtained for the deposition of hydrogenated amorphous silicon (a-Si:H) films in the parallel configuration employing CO 2 and KrFlasers and SiH 4 and Si 2H 6 as precursors are presented. As a second example, the growth of oxygen- and carbon-containing chromium films Cr(O,C) from chromium hexacarbonyl as the precursor using cw and pulse uv lasers is discussed. The chemical pathways leasing to film formation are investigated in detail.

  16. Inference and Action in Early Causal Reasoning.

    ERIC Educational Resources Information Center

    Frye, Douglas; And Others

    1996-01-01

    Two marble-and-ramp experiments investigated whether a simple-to-embedded-rules account can explain changes in children's causal reasoning. Results indicated that the same difference between three- and four-year olds in the prediction experiment appeared in the action experiment, suggesting that the same rules may underlie causal action as well as…

  17. Spin foam models as energetic causal sets

    NASA Astrophysics Data System (ADS)

    Cortês, Marina; Smolin, Lee

    2016-04-01

    Energetic causal sets are causal sets endowed by a flow of energy-momentum between causally related events. These incorporate a novel mechanism for the emergence of space-time from causal relations [M. Cortês and L. Smolin, Phys. Rev. D 90, 084007 (2014); Phys. Rev. D 90, 044035 (2014)]. Here we construct a spin foam model which is also an energetic causal set model. This model is closely related to the model introduced in parallel by Wolfgang Wieland in [Classical Quantum Gravity 32, 015016 (2015)]. What makes a spin foam model also an energetic causal set is Wieland's identification of new degrees of freedom analogous to momenta, conserved at events (or four-simplices), whose norms are not mass, but the volume of tetrahedra. This realizes the torsion constraints, which are missing in previous spin foam models, and are needed to relate the connection dynamics to those of the metric, as in general relativity. This identification makes it possible to apply the new mechanism for the emergence of space-time to a spin foam model. Our formulation also makes use of Markopoulou's causal formulation of spin foams [arXiv:gr-qc/9704013]. These are generated by evolving spin networks with dual Pachner moves. This endows the spin foam history with causal structure given by a partial ordering of the events which are dual to four-simplices.

  18. Updating during Reading Comprehension: Why Causality Matters

    ERIC Educational Resources Information Center

    Kendeou, Panayiota; Smith, Emily R.; O'Brien, Edward J.

    2013-01-01

    The present set of 7 experiments systematically examined the effectiveness of adding causal explanations to simple refutations in reducing or eliminating the impact of outdated information on subsequent comprehension. The addition of a single causal-explanation sentence to a refutation was sufficient to eliminate any measurable disruption in…

  19. Preschoolers' Understanding of Temporal and Causal Relations.

    ERIC Educational Resources Information Center

    Sharp, Kay Colby

    1982-01-01

    Two experiments investigated psychological factors determining preschoolers' success or failure on a sequence-completion task involving temporal and causal ordering of events. Overall findings demonstrate that while preschoolers do understand temporal/causal relationships, their abilities are dependent on process variables demanded by the task…

  20. Causal Inferences in the Campbellian Validity System

    ERIC Educational Resources Information Center

    Lund, Thorleif

    2010-01-01

    The purpose of the present paper is to critically examine causal inferences and internal validity as defined by Campbell and co-workers. Several arguments are given against their counterfactual effect definition, and this effect definition should be considered inadequate for causal research in general. Moreover, their defined independence between…

  1. Campbell's and Rubin's Perspectives on Causal Inference

    ERIC Educational Resources Information Center

    West, Stephen G.; Thoemmes, Felix

    2010-01-01

    Donald Campbell's approach to causal inference (D. T. Campbell, 1957; W. R. Shadish, T. D. Cook, & D. T. Campbell, 2002) is widely used in psychology and education, whereas Donald Rubin's causal model (P. W. Holland, 1986; D. B. Rubin, 1974, 2005) is widely used in economics, statistics, medicine, and public health. Campbell's approach focuses on…

  2. Causal Indicators Can Help to Interpret Factors

    ERIC Educational Resources Information Center

    Bentler, Peter M.

    2016-01-01

    The latent factor in a causal indicator model is no more than the latent factor of the factor part of the model. However, if the causal indicator variables are well-understood and help to improve the prediction of individuals' factor scores, they can help to interpret the meaning of the latent factor. Aguirre-Urreta, Rönkkö, and Marakas (2016)…

  3. Quasi-Experimental Designs for Causal Inference

    ERIC Educational Resources Information Center

    Kim, Yongnam; Steiner, Peter

    2016-01-01

    When randomized experiments are infeasible, quasi-experimental designs can be exploited to evaluate causal treatment effects. The strongest quasi-experimental designs for causal inference are regression discontinuity designs, instrumental variable designs, matching and propensity score designs, and comparative interrupted time series designs. This…

  4. Causal Indicator Models: Identification, Estimation, and Testing

    ERIC Educational Resources Information Center

    Bollen, Kenneth A.; Davis, Walter R.

    2009-01-01

    We discuss the identification, estimation, and testing of structural equation models that have causal indicators. We first provide 2 rules of identification that are particularly helpful in models with causal indicators--the 2C emitted paths rule and the exogenous X rule. We demonstrate how these rules can help us distinguish identified from…

  5. Compact Representations of Extended Causal Models

    ERIC Educational Resources Information Center

    Halpern, Joseph Y.; Hitchcock, Christopher

    2013-01-01

    Judea Pearl (2000) was the first to propose a definition of actual causation using causal models. A number of authors have suggested that an adequate account of actual causation must appeal not only to causal structure but also to considerations of "normality." In Halpern and Hitchcock (2011), we offer a definition of actual causation…

  6. A Causal Model of Faculty Research Productivity.

    ERIC Educational Resources Information Center

    Bean, John P.

    A causal model of faculty research productivity was developed through a survey of the literature. Models of organizational behavior, organizational effectiveness, and motivation were synthesized into a causal model of productivity. Two general types of variables were assumed to affect individual research productivity: institutional variables and…

  7. Causal Moderation Analysis Using Propensity Score Methods

    ERIC Educational Resources Information Center

    Dong, Nianbo

    2012-01-01

    This paper is based on previous studies in applying propensity score methods to study multiple treatment variables to examine the causal moderator effect. The propensity score methods will be demonstrated in a case study to examine the causal moderator effect, where the moderators are categorical and continuous variables. Moderation analysis is an…

  8. A copula approach to assessing Granger causality.

    PubMed

    Hu, Meng; Liang, Hualou

    2014-10-15

    In neuroscience, as in many other fields of science and engineering, it is crucial to assess the causal interactions among multivariate time series. Granger causality has been increasingly used to identify causal influence between time series based on multivariate autoregressive models. Such an approach is based on linear regression framework with implicit Gaussian assumption of model noise residuals having constant variance. As a consequence, this measure cannot detect the cause-effect relationship in high-order moments and nonlinear causality. Here, we propose an effective model-free, copula-based Granger causality measure that can be used to reveal nonlinear and high-order moment causality. We first formulate Granger causality as the log-likelihood ratio in terms of conditional distribution, and then derive an efficient estimation procedure using conditional copula. We use resampling techniques to build a baseline null-hypothesis distribution from which statistical significance can be derived. We perform a series of simulations to investigate the performance of our copula-based Granger causality, and compare its performance against other state-of-the-art techniques. Our method is finally applied to neural field potential time series recorded from visual cortex of a monkey while performing a visual illusion task.

  9. Controlling for causally relevant third variables.

    PubMed

    Goodie, Adam S; Williams, Cristina C; Crooks, C L

    2003-10-01

    In 3 experiments, the authors tested the conditions under which 3rd variables are controlled for in making causal judgments. The authors hypothesized that 3rd variables are controlled for when the 3rd variables are themselves perceived as causal. In Experiment 1, the participants predicted test performance after seeing information about wearing a lucky garment, taking a test-preparation course, and staying up late. The course (perceived as more causally relevant) was controlled for more than was the garment (perceived as less causally relevant) in assessing the effectiveness of staying up late. In Experiments 2 and 3, to obviate the many alternative accounts that arise from the realistic cover story of Experiment 1, participants predicted flowers' blooming after the presentation or nonpresentation of liquids. When one liquid was trained as causal, it was controlled for more in judging another liquid than when it was trained as neutral. Overall, stimuli perceived as causal were controlled for more when judging other stimuli. The authors concluded that the effect of perceived causal relevance on causal conditionalizing is real and normatively reasonable. PMID:14672103

  10. On the spectral formulation of Granger causality.

    PubMed

    Chicharro, D

    2011-12-01

    Spectral measures of causality are used to explore the role of different rhythms in the causal connectivity between brain regions. We study several spectral measures related to Granger causality, comprising the bivariate and conditional Geweke measures, the directed transfer function, and the partial directed coherence. We derive the formulation of dependence and causality in the spectral domain from the more general formulation in the information-theory framework. We argue that the transfer entropy, the most general measure derived from the concept of Granger causality, lacks a spectral representation in terms of only the processes associated with the recorded signals. For all the spectral measures we show how they are related to mutual information rates when explicitly considering the parametric autoregressive representation of the processes. In this way we express the conditional Geweke spectral measure in terms of a multiple coherence involving innovation variables inherent to the autoregressive representation. We also link partial directed coherence with Sims' criterion of causality. Given our results, we discuss the causal interpretation of the spectral measures related to Granger causality and stress the necessity to explicitly consider their specific formulation based on modeling the signals as linear Gaussian stationary autoregressive processes.

  11. Causal Mediation Analysis: Warning! Assumptions Ahead

    ERIC Educational Resources Information Center

    Keele, Luke

    2015-01-01

    In policy evaluations, interest may focus on why a particular treatment works. One tool for understanding why treatments work is causal mediation analysis. In this essay, I focus on the assumptions needed to estimate mediation effects. I show that there is no "gold standard" method for the identification of causal mediation effects. In…

  12. Essays on Causal Inference for Public Policy

    ERIC Educational Resources Information Center

    Zajonc, Tristan

    2012-01-01

    Effective policymaking requires understanding the causal effects of competing proposals. Relevant causal quantities include proposals' expected effect on different groups of recipients, the impact of policies over time, the potential trade-offs between competing objectives, and, ultimately, the optimal policy. This dissertation studies causal…

  13. Near-field photochemical and radiation-induced chemical fabrication of nanopatterns of a self-assembled silane monolayer.

    PubMed

    Fischer, Ulrich Christian; Hentschel, Carsten; Fontein, Florian; Stegemann, Linda; Hoeppener, Christiane; Fuchs, Harald; Hoeppener, Stefanie

    2014-01-01

    A general concept for parallel near-field photochemical and radiation-induced chemical processes for the fabrication of nanopatterns of a self-assembled monolayer (SAM) of (3-aminopropyl)triethoxysilane (APTES) is explored with three different processes: 1) a near-field photochemical process by photochemical bleaching of a monomolecular layer of dye molecules chemically bound to an APTES SAM, 2) a chemical process induced by oxygen plasma etching as well as 3) a combined near-field UV-photochemical and ozone-induced chemical process, which is applied directly to an APTES SAM. All approaches employ a sandwich configuration of the surface-supported SAM, and a lithographic mask in form of gold nanostructures fabricated through colloidal sphere lithography (CL), which is either exposed to visible light, oxygen plasma or an UV-ozone atmosphere. The gold mask has the function to inhibit the photochemical reactions by highly localized near-field interactions between metal mask and SAM and to inhibit the radiation-induced chemical reactions by casting a highly localized shadow. The removal of the gold mask reveals the SAM nanopattern.

  14. Canonical Granger causality between regions of interest.

    PubMed

    Ashrafulla, Syed; Haldar, Justin P; Joshi, Anand A; Leahy, Richard M

    2013-12-01

    Estimating and modeling functional connectivity in the brain is a challenging problem with potential applications in the understanding of brain organization and various neurological and neuropsychological conditions. An important objective in connectivity analysis is to determine the connections between regions of interest in the brain. However, traditional functional connectivity analyses have frequently focused on modeling interactions between time series recordings at individual sensors, voxels, or vertices despite the fact that a single region of interest will often include multiple such recordings. In this paper, we present a novel measure of interaction between regions of interest rather than individual signals. The proposed measure, termed canonical Granger causality, combines ideas from canonical correlation and Granger causality analysis to yield a measure that reflects directed causality between two regions of interest. In particular, canonical Granger causality uses optimized linear combinations of signals from each region of interest to enable accurate causality measurements from substantially less data compared to alternative multivariate methods that have previously been proposed for this scenario. The optimized linear combinations are obtained using a variation of a technique developed for optimization on the Stiefel manifold. We demonstrate the advantages of canonical Granger causality in comparison to alternative causality measures for a range of different simulated datasets. We also apply the proposed measure to local field potential data recorded in a macaque brain during a visuomotor task. Results demonstrate that canonical Granger causality can be used to identify causal relationships between striate and prestriate cortexes in cases where standard Granger causality is unable to identify statistically significant interactions.

  15. Analysis of α-particle-induced chromosomal aberrations by chemically-induced PCC. Elaboration of dose-effect curves.

    PubMed

    Puig, Roser; Pujol, Mònica; Barrios, Leonardo; Caballín, María Rosa; Barquinero, Joan-Francesc

    2016-09-01

    In a similar way to high-dose exposures to low-LET radiations, cells show difficulties reaching mitosis after high-LET radiation exposure. For this reason, techniques have been proposed that are able to analyze chromosome aberrations in interphase by prematurely condensing the chromosomes (PCC-techniques). Few dose-effect curves for high-LET radiation types have been reported, and none for α-particles. The aim of this study was to evaluate, by chemically-induced PCC, the chromosome aberrations induced by several doses of α-particles. Monolayers of peripheral lymphocytes were exposed to an α-source of Americium-241 with a mean energy entering the cells of 2.7 MeV. Lymphocytes were exposed to 10 doses, from 0-2.5 Gy, and then cultured for 48 h. Colcemid and Calyculin-A were added at 24 and 1 h before harvesting, respectively. During microscope analysis, chromosome rings and extra chromosome pieces were scored in G2/M-PCC and M cells, while dicentric chromosomes were only scored in M cells. As the dose increased, fewer cells were able to reach mitosis and the proportion of G2/M-PCC cells increased. Chromosome rings were hardly observed in M cells when compared to G2/M-PCC cells. Extra fragments were more frequent than rings in both G2/M-PCC and M cells, but with lower frequencies than in G2/M-PCC cells. The distribution of dicentrics and extra fragments showed a clear overdispersion; this was not so evident for rings. The dose-effect curves obtained fitted very well to a linear model. Damaged cells after α-particle irradiation show more difficulties in reaching mitosis than cells exposed to γ-rays. After α-particle irradiation the frequency of all the chromosome aberrations considered increased linearly with the dose, and α-particles clearly produced more dicentrics and extra chromosome pieces with respect to γ-rays. After α-particle exposure, the existence of extra chromosome fragments in PCC cells seems to be a good candidate for use as a biomarker

  16. Analysis of α-particle-induced chromosomal aberrations by chemically-induced PCC. Elaboration of dose-effect curves.

    PubMed

    Puig, Roser; Pujol, Mònica; Barrios, Leonardo; Caballín, María Rosa; Barquinero, Joan-Francesc

    2016-09-01

    In a similar way to high-dose exposures to low-LET radiations, cells show difficulties reaching mitosis after high-LET radiation exposure. For this reason, techniques have been proposed that are able to analyze chromosome aberrations in interphase by prematurely condensing the chromosomes (PCC-techniques). Few dose-effect curves for high-LET radiation types have been reported, and none for α-particles. The aim of this study was to evaluate, by chemically-induced PCC, the chromosome aberrations induced by several doses of α-particles. Monolayers of peripheral lymphocytes were exposed to an α-source of Americium-241 with a mean energy entering the cells of 2.7 MeV. Lymphocytes were exposed to 10 doses, from 0-2.5 Gy, and then cultured for 48 h. Colcemid and Calyculin-A were added at 24 and 1 h before harvesting, respectively. During microscope analysis, chromosome rings and extra chromosome pieces were scored in G2/M-PCC and M cells, while dicentric chromosomes were only scored in M cells. As the dose increased, fewer cells were able to reach mitosis and the proportion of G2/M-PCC cells increased. Chromosome rings were hardly observed in M cells when compared to G2/M-PCC cells. Extra fragments were more frequent than rings in both G2/M-PCC and M cells, but with lower frequencies than in G2/M-PCC cells. The distribution of dicentrics and extra fragments showed a clear overdispersion; this was not so evident for rings. The dose-effect curves obtained fitted very well to a linear model. Damaged cells after α-particle irradiation show more difficulties in reaching mitosis than cells exposed to γ-rays. After α-particle irradiation the frequency of all the chromosome aberrations considered increased linearly with the dose, and α-particles clearly produced more dicentrics and extra chromosome pieces with respect to γ-rays. After α-particle exposure, the existence of extra chromosome fragments in PCC cells seems to be a good candidate for use as a biomarker

  17. Field and laboratory studies of chemical contamination and environmentally related diseases in fish and molluscs of New England

    SciTech Connect

    Gardner, G.R.

    1993-01-01

    The concentration of PCBs, PAHs, insecticides and metals in some aquatic ecosystems have reached high levels placing identified populations at risk to chemical, physical, and biological agents in estuarine and open coastal areas of the United States. In the last three decades scientific studies bolstered evidence for a causal relationship between spontaneous and chemically induced pathological effects on marine organisms and exposure to industrial and agricultural pollutants discharged into aquatic ecosystems. In subsequent years research, both in the laboratory and at polluted estuarine or marine sites, has elucidated causal relationships between processes of pathogenesis of lesions (including carcinogenesis) and exposure to specific toxic agents. Today, research investigating mechanisms of chemical- and pollutant-induced lesions is demonstrating that chemicals can exert toxic, mutagenic, carcinogenic, and immunogenic effects on marine organisms.

  18. Long-chain polyunsaturated fatty acids and chemically induced diabetes mellitus. Effect of omega-3 fatty acids.

    PubMed

    Suresh, Y; Das, U N

    2003-03-01

    In a previous study, we showed that prior oral feeding of oils rich in omega-3 eicosapentaenoic acid and docosahexaenoic acid and omega-6 gamma-linolenic acid and arachidonic acid prevent the development of alloxan-induced diabetes mellitus in experimental animals. We also observed that 99% pure omega-6 fatty acids gamma-linolenic acid and arachidonic acid protect against chemically induced diabetes mellitus. Here we report the results of our studies with omega-3 fatty acids. Alloxan-induced in vitro cytotoxicity and apoptosis in an insulin-secreting rat insulinoma cell line, RIN, was prevented by prior exposure of these cells to alpha-linolenic acid, eicosapentaenoic acid, and docosahexaenoic acid. Prior oral supplementation with alpha-linolenic acid, eicosapentaenoic acid, and docosahexaenoic acid prevented alloxan-induced diabetes mellitus. alpha-Linolenic acid, eicosapentaenoic acid, and docosahexaenoic acid not only attenuated chemical-induced diabetes mellitus but also restored the anti-oxidant status to normal range in various tissues. These results suggested that omega-3 fatty acids can abrogate chemically induced diabetes in experimental animals and attenuate the oxidant stress that occurs in diabetes mellitus.

  19. Causal systems categories: differences in novice and expert categorization of causal phenomena.

    PubMed

    Rottman, Benjamin M; Gentner, Dedre; Goldwater, Micah B

    2012-07-01

    We investigated the understanding of causal systems categories--categories defined by common causal structure rather than by common domain content--among college students. We asked students who were either novices or experts in the physical sciences to sort descriptions of real-world phenomena that varied in their causal structure (e.g., negative feedback vs. causal chain) and in their content domain (e.g., economics vs. biology). Our hypothesis was that there would be a shift from domain-based sorting to causal sorting with increasing expertise in the relevant domains. This prediction was borne out: the novice groups sorted primarily by domain and the expert group sorted by causal category. These results suggest that science training facilitates insight about causal structures.

  20. Spread of entanglement and causality

    NASA Astrophysics Data System (ADS)

    Casini, Horacio; Liu, Hong; Mezei, Márk

    2016-07-01

    We investigate causality constraints on the time evolution of entanglement entropy after a global quench in relativistic theories. We first provide a general proof that the so-called tsunami velocity is bounded by the speed of light. We then generalize the free particle streaming model of [1] to general dimensions and to an arbitrary entanglement pattern of the initial state. In more than two spacetime dimensions the spread of entanglement in these models is highly sensitive to the initial entanglement pattern, but we are able to prove an upper bound on the normalized rate of growth of entanglement entropy, and hence the tsunami velocity. The bound is smaller than what one gets for quenches in holographic theories, which highlights the importance of interactions in the spread of entanglement in many-body systems. We propose an interacting model which we believe provides an upper bound on the spread of entanglement for interacting relativistic theories. In two spacetime dimensions with multiple intervals, this model and its variations are able to reproduce intricate results exhibited by holographic theories for a significant part of the parameter space. For higher dimensions, the model bounds the tsunami velocity at the speed of light. Finally, we construct a geometric model for entanglement propagation based on a tensor network construction for global quenches.

  1. Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics.

    PubMed

    Wu, Jian-Li; Wu, Chanjian; Lei, Cailin; Baraoidan, Marietta; Bordeos, Alicia; Madamba, Ma Reina Suzette; Ramos-Pamplona, Marilou; Mauleon, Ramil; Portugal, Arlett; Ulat, Victor Jun; Bruskiewich, Richard; Wang, Guoliang; Leach, Jan; Khush, Gurdev; Leung, Hei

    2005-09-01

    IR64, the most widely grown indica rice in South and Southeast Asia, possesses many positive agronomic characteristics (e.g., wide adaptability, high yield potential, tolerance to multiple diseases and pests, and good eating quality,) that make it an ideal genotype for identifying mutational changes in traits of agronomic importance. We have produced a large collection of chemical and irradiation-induced IR64 mutants with different genetic lesions that are amenable to both forward and reverse genetics. About 60,000 IR64 mutants have been generated by mutagenesis using chemicals (diepoxybutane and ethylmethanesulfonate) and irradiation (fast neutron and gamma ray). More than 38,000 independent lines have been advanced to M4 generation enabling evaluation of quantitative traits by replicated trials. Morphological variations at vegetative and reproductive stages, including plant architecture, growth habit, pigmentation and various physiological characters, are commonly observed in the four mutagenized populations. Conditional mutants such as gain or loss of resistance to blast, bacterial blight, and tungro disease have been identified at frequencies ranging from 0.01% to 0.1%. Results from pilot experiments indicate that the mutant collections are suitable for reverse genetics through PCR-detection of deletions and TILLING. Furthermore, deletions can be detected using oligomer chips suggesting a general technique to pinpoint deletions when genome-wide oligomer chips are broadly available. M4 mutant seeds are available for users for screening of altered response to multiple stresses. So far, more than 15,000 mutant lines have been distributed. To facilitate broad usage of the mutants, a mutant database has been constructed in the International Rice Information System (IRIS; http: //www.iris.irri.org) to document the phenotypes and gene function discovered by users.

  2. Epigenetic alterations induced by genotoxic occupational and environmental human chemical carcinogens: A systematic literature review.

    PubMed

    Chappell, Grace; Pogribny, Igor P; Guyton, Kathryn Z; Rusyn, Ivan

    2016-01-01

    Accumulating evidence suggests that epigenetic alterations play an important role in chemically-induced carcinogenesis. Although the epigenome and genome may be equally important in carcinogenicity, the genotoxicity of chemical agents and exposure-related transcriptomic responses have been more thoroughly studied and characterized. To better understand the evidence for epigenetic alterations of human carcinogens, and the potential association with genotoxic endpoints, we conducted a systematic review of published studies of genotoxic carcinogens that reported epigenetic endpoints. Specifically, we searched for publications reporting epigenetic effects for the 28 agents and occupations included in Monograph Volume 100F of the International Agency for the Research on Cancer (IARC) that were classified as "carcinogenic to humans" (Group 1) with strong evidence of genotoxic mechanisms of carcinogenesis. We identified a total of 158 studies that evaluated epigenetic alterations for 12 of these 28 carcinogenic agents and occupations (1,3-butadiene, 4-aminobiphenyl, aflatoxins, benzene, benzidine, benzo[a]pyrene, coke production, formaldehyde, occupational exposure as a painter, sulfur mustard, and vinyl chloride). Aberrant DNA methylation was most commonly studied, followed by altered expression of non-coding RNAs and histone changes (totaling 85, 59 and 25 studies, respectively). For 3 carcinogens (aflatoxins, benzene and benzo[a]pyrene), 10 or more studies reported epigenetic effects. However, epigenetic studies were sparse for the remaining 9 carcinogens; for 4 agents, only 1 or 2 published reports were identified. While further research is needed to better identify carcinogenesis-associated epigenetic perturbations for many potential carcinogens, published reports on specific epigenetic endpoints can be systematically identified and increasingly incorporated in cancer hazard assessments. PMID:27234561

  3. Attitudes toward Others Depend upon Self and Other Causal Uncertainty

    PubMed Central

    Tobin, Stephanie J.; Osika, Matylda M.; McLanders, Mia

    2014-01-01

    People who are high in causal uncertainty doubt their own ability to understand the causes of social events. In three studies, we examined the effects of target and perceiver causal uncertainty on attitudes toward the target. Target causal uncertainty was manipulated via responses on a causal uncertainty scale in Studies 1 and 2, and with a scenario in Study 3. In Studies 1 and 2, we found that participants liked the low causal uncertainty target more than the high causal uncertainty target. This preference was stronger for low relative to high causal uncertainty participants because high causal uncertainty participants held more uncertain ideals. In Study 3, we examined the value individuals place upon causal understanding (causal importance) as an additional moderator. We found that regardless of their own causal uncertainty level, participants who were high in causal importance liked the low causal uncertainty target more than the high causal uncertainty target. However, when participants were low in causal importance, low causal uncertainty perceivers showed no preference and high causal uncertainty perceivers preferred the high causal uncertainty target. These findings reveal that goal importance and ideals can influence how perceivers respond to causal uncertainty in others. PMID:24504048

  4. Attitudes toward others depend upon self and other causal uncertainty.

    PubMed

    Tobin, Stephanie J; Osika, Matylda M; McLanders, Mia

    2014-01-01

    People who are high in causal uncertainty doubt their own ability to understand the causes of social events. In three studies, we examined the effects of target and perceiver causal uncertainty on attitudes toward the target. Target causal uncertainty was manipulated via responses on a causal uncertainty scale in Studies 1 and 2, and with a scenario in Study 3. In Studies 1 and 2, we found that participants liked the low causal uncertainty target more than the high causal uncertainty target. This preference was stronger for low relative to high causal uncertainty participants because high causal uncertainty participants held more uncertain ideals. In Study 3, we examined the value individuals place upon causal understanding (causal importance) as an additional moderator. We found that regardless of their own causal uncertainty level, participants who were high in causal importance liked the low causal uncertainty target more than the high causal uncertainty target. However, when participants were low in causal importance, low causal uncertainty perceivers showed no preference and high causal uncertainty perceivers preferred the high causal uncertainty target. These findings reveal that goal importance and ideals can influence how perceivers respond to causal uncertainty in others.

  5. Causal localizations in relativistic quantum mechanics

    SciTech Connect

    Castrigiano, Domenico P. L. Leiseifer, Andreas D.

    2015-07-15

    Causal localizations describe the position of quantum systems moving not faster than light. They are constructed for the systems with finite spinor dimension. At the center of interest are the massive relativistic systems. For every positive mass, there is the sequence of Dirac tensor-localizations, which provides a complete set of inequivalent irreducible causal localizations. They obey the principle of special relativity and are fully Poincaré covariant. The boosters are determined by the causal position operator and the other Poincaré generators. The localization with minimal spinor dimension is the Dirac localization. Thus, the Dirac equation is derived here as a mere consequence of the principle of causality. Moreover, the higher tensor-localizations, not known so far, follow from Dirac’s localization by a simple construction. The probability of localization for positive energy states results to be described by causal positive operator valued (PO-) localizations, which are the traces of the causal localizations on the subspaces of positive energy. These causal Poincaré covariant PO-localizations for every irreducible massive relativistic system were, all the more, not known before. They are shown to be separated. Hence, the positive energy systems can be localized within every open region by a suitable preparation as accurately as desired. Finally, the attempt is made to provide an interpretation of the PO-localization operators within the frame of conventional quantum mechanics attributing an important role to the negative energy states.

  6. Quantum correlations with no causal order

    PubMed Central

    Oreshkov, Ognyan; Costa, Fabio; Brukner, Časlav

    2012-01-01

    The idea that events obey a definite causal order is deeply rooted in our understanding of the world and at the basis of the very notion of time. But where does causal order come from, and is it a necessary property of nature? Here, we address these questions from the standpoint of quantum mechanics in a new framework for multipartite correlations that does not assume a pre-defined global causal structure but only the validity of quantum mechanics locally. All known situations that respect causal order, including space-like and time-like separated experiments, are captured by this framework in a unified way. Surprisingly, we find correlations that cannot be understood in terms of definite causal order. These correlations violate a 'causal inequality' that is satisfied by all space-like and time-like correlations. We further show that in a classical limit causal order always arises, which suggests that space-time may emerge from a more fundamental structure in a quantum-to-classical transition. PMID:23033068

  7. Stimulation of serotonin-1A receptors in mammals to alleviate motion sickness and emesis induced by chemical agents

    NASA Technical Reports Server (NTRS)

    Lucot, James B. (Inventor); Crampton, George H. (Inventor)

    1990-01-01

    A method for the alleviation of both motion sickness and chemically-induced emesis is provided which includes the administration of a nontoxic, therapeutically effective amount of a composition which stimulates serotonin-1A receptors in a mammal in need of such treatment. The preferred compounds for use are buspirone and 8-hydroxy-2(di-n-propylamino)-tetralin (8-OH-DPAT).

  8. Evaluation of the chemical model of vestibular lesions induced by arsanilate in rats

    SciTech Connect

    Vignaux, G.; Chabbert, C.; Gaboyard-Niay, S.; Travo, C.; Machado, M.L.; Denise, P.; Comoz, F.; Hitier, M.; Landemore, G.; Philoxène, B.; Besnard, S.

    2012-01-01

    Several animal models of vestibular deficits that mimic the human pathology phenotype have previously been developed to correlate the degree of vestibular injury to cognate vestibular deficits in a time-dependent manner. Sodium arsanilate is one of the most commonly used substances for chemical vestibular lesioning, but it is not well described in the literature. In the present study, we used histological and functional approaches to conduct a detailed exploration of the model of vestibular lesions induced by transtympanic injection of sodium arsanilate in rats. The arsanilate-induced damage was restricted to the vestibular sensory organs without affecting the external ear, the oropharynx, or Scarpa's ganglion. This finding strongly supports the absence of diffusion of arsanilate into the external ear or Eustachian tubes, or through the eighth cranial nerve sheath leading to the brainstem. One of the striking observations of the present study is the complete restructuring of the sensory epithelia into a non sensory epithelial monolayer observed at 3 months after arsanilate application. This atrophy resembles the monolayer epithelia observed postmortem in the vestibular epithelia of patients with a history of lesioned vestibular deficits such as labyrinthectomy, antibiotic treatment, vestibular neuritis, or Ménière's disease. In cases of Ménière's disease, aminoglycosides, and platinum-based chemotherapy, vestibular hair cells are destroyed, regardless of the physiopathological process, as reproduced with the arsanilate model of vestibular lesion. These observations, together with those presented in this study of arsanilate vestibular toxicity, suggest that this atrophy process relies on a common mechanism of degeneration of the sensory epithelia.

  9. Chemoprevention of chemical-induced skin cancer by Panax ginseng root extract

    PubMed Central

    Sharma, Jyoti; Goyal, Pradeep K.

    2015-01-01

    Background Cancer has emerged as a major health problem globally as a consequence to the increased longevity of the population, changing the environment and life style. Chemoprevention is a new and promising strategy for reducing cancer burden. Recently, some natural products have been identified for their chemopreventive activity to reduce the cancer incidence. Ginseng is known for its potential to treat various ailments in human beings. The present study was designed to explore the anticancer and antioxidative potential of Panax ginseng against chemical-induced skin carcinogenesis in mammals. Methods Skin tumors were induced in Swiss albino mice by a single topical application of 7,12-dimethylbenz(a)anthracene (100 μg/100 μL acetone) and, 2 wks later, promoted by repeated applications of croton oil (thrice in a wk in 1% acetone) till the end of the experiment (i.e., 16 wk). Hydroalcoholic ginseng root extract at a dose of 25 mg/kg body weight/d was orally administered at the peri-initiation, postinitiation, and peri–post-initiation stages. Results Ginseng root extract treatment caused a significant reduction in tumor incidence, cumulative number of tumors, tumor yield, and tumor burden, as compared to the 7,12-dimethylbenz(a)anthracene–croton oil-treated control group. Further, biochemical assays revealed a significant enhancement in the levels of reduced glutathione, superoxide dismutase, catalase, vitamin C, and total proteins but a significant reduction in lipid peroxidation levels in both the liver and skin with ginseng root extract treatment, as compared to carcinogen-treated control group. Conclusion These results suggest that P. ginseng has the potential to become a pivotal chemopreventive agent that can reduce cancer in mammals. PMID:26199559

  10. What is the Role of the Transition State in Soret and Chemical Diffusion Induced Isotopic Fractionation?

    NASA Astrophysics Data System (ADS)

    Dominguez, G.

    2013-12-01

    For over six decades, Urey's (1) statistical mechanical model of isotopic fractionation based on partition functions with quantized energy levels have enjoyed enormous success in quantitatively explaining equilibrium isotopic fractionation in a wide variety of geochemical systems For example, the interpretation of oxygen isotopic variations in carbonate systems (e.g. foraminiferas), in terms of partition functions with quantized energy levels, forms the basis for paleothermometry (2). Recent observations of isotopic fractionation from chemical and thermal (Soret) diffusion (3-7) appear to challenge our theoretical understanding of mass-transport and isotopic fractionation (8, 9). For example, a recently proposed quantum mechanical model of Soret diffusion, which correctly predicts the isotopic fractionation in thermal gradients for isotopes of Mg, Ca, Fe, Si, and possibly oxygen, was critiqued as being unphysical. First, it was argued that the zero point energies needed to explain the magnitude of isotopic fractionation in basalt melts were unrealistically high based on infrared spectra of these melts. Second, it was argued that the chemical diffusion isotopic fractionation (beta) factors expected from these zero-point energies were also unphysical (10). A recently proposed collision-momentum transfer model partially explains observed fractionation factors, although it fails miserably (by a factor of 3) to account for the isotopic fractionation of Mg isotopes (11). In this presentation, I will review recent observations and models of isotopic fractionation in geochemical melts with thermal gradients and expand upon previous work (8, 12) to show how transition state theory can simultaneously explain mass-transport induced isotopic fractionation, including kinetic, equilibrium, and Soret isotopic fractionation. I show this by providing a few example calculations of the kinetic fractionation factors (a.k.a. beta factors) expected in chemical diffusion as well as

  11. Perception of causality in schizophrenia spectrum disorder.

    PubMed

    Tschacher, Wolfgang; Kupper, Zeno

    2006-10-01

    Patients with schizophrenia spectrum disorders often maintain deviating views on cause-effect relationships, especially when positive and disorganization symptoms are manifest. Altered perceived causality is prominent in delusional ideation, in ideas of reference, and in the mentalizing ability (theory of mind [ToM]) of patients. Perceiving causal relationships may be understood either as higher order cognitive reasoning or as low-level information processing. In the present study, perception of causality was investigated as a low-level, preattentional capability similar to gestalt-like perceptual organization. Thirty-one patients (24 men and 7 women with mean age 27.7 years) and the same number of healthy control subjects matched to patients with respect to age and sex were tested. A visual paradigm was used in which 2 identical discs move, from opposite sides of a monitor, steadily toward and then past one another. Their coincidence generates an ambiguous, bistable percept (discs either "stream through" or "bounce off" one another). The bouncing perception, ie, perceived causality, is enhanced when auditory stimuli are presented at the time of coincidence. Psychopathology was measured using the Positive and Negative Syndrome Scale. It was found that positive symptoms were strongly associated with increased perceived causality and disorganization with attenuated perceived causality. Patients in general were not significantly different from controls, but symptom subgroups showed specifically altered perceived causality. Perceived causality as a basic preattentional process may contribute to higher order cognitive alterations and ToM deficiencies. It is suggested that cognitive remediation therapy should address both increased and reduced perception of causality. PMID:16896057

  12. On the origin of Hill's causal criteria.

    PubMed

    Morabia, A

    1991-09-01

    The rules to assess causation formulated by the eighteenth century Scottish philosopher David Hume are compared to Sir Austin Bradford Hill's causal criteria. The strength of the analogy between Hume's rules and Hill's causal criteria suggests that, irrespective of whether Hume's work was known to Hill or Hill's predecessors, Hume's thinking expresses a point of view still widely shared by contemporary epidemiologists. The lack of systematic experimental proof to causal inferences in epidemiology may explain the analogy of Hume's and Hill's, as opposed to Popper's, logic.

  13. Causality and methodology. Notes on thanatochronological estimations.

    PubMed

    Boniolo, Giovanni; Libero, Mirella; Aprile, Anna

    2005-01-01

    The authors propose some methodological considerations on thanatochronological estimations. They first consider the problem of the definition of death, and then they deal with the issue of the estimations of death time, that is, with the Post-Mortem Interval (PMI). As regards the first question, they note that it does not concern only the definition of death, but also the choice of a particular kind of definition of 'definition'. With reference to the second question, the authors suggest a causal model showing that the presence of many causal chains must be taken into consideration. Finally they discuss what 'most convenient and reliable causal chain' means for a thanatochronologist.

  14. [Leukoderma caused by chemicals: mechanisms underlying 4-alkyl/aryl-substituted phenols- and rhododendrol-induced melanocyte loss].

    PubMed

    Nishimaki-Mogami, Tomoko

    2015-01-01

    Chemical leukoderma is a skin depigmentation disorder known to occur in manufactural workplace through contact with chemicals, such as monobenzyl ether of hydroquinone (MBEH) and 4-tert- butylphenol (4-TBP). In the skin depigmented -legions induced by these chemicals, the number of melanocyte was severely decreased. Anti-melanoma agent 4-cysteaminylphenol (4-SCAP) and its derivatives are also known to cause leukoderma. Evidence has accumulated supporting that typical class of chemicals causing leukoderma is "4-alkyl/aryl-substituted phenols/catechols", which are structurally similar to melanin precursor tyrosine. Tyrosinase-mediated oxidation of these chemicals yields toxic ortho-quinones which bind to cellular proteins and produce reactive oxygen species. Accordingly, this tyrosinase-dependent metabolic activation is thought to cause melanocyte-specific damage and subsequent immune reactions toward melanocytes. Recently, rhododendrol, an inhibitor of tyrosinase developed for so-called lightening/whitening cosmetics, was shown to cause leukoderma in the users. In this review, I document the causes of known chemical leukoderma and rhododendrol- induced leukoderma, focusing on their common mechanisms underlying melanocyte loss. PMID:26821466

  15. Accounting for respiration is necessary to reliably infer Granger causality from cardiovascular variability series.

    PubMed

    Porta, Alberto; Bassani, Tito; Bari, Vlasta; Pinna, Gian D; Maestri, Roberto; Guzzetti, Stefano

    2012-03-01

    This study was designed to demonstrate the need of accounting for respiration (R) when causality between heart period (HP) and systolic arterial pressure (SAP) is under scrutiny. Simulations generated according to a bivariate autoregressive closed-loop model were utilized to assess how causality changes as a function of the model parameters. An exogenous (X) signal was added to the bivariate autoregressive closed-loop model to evaluate the bias on causality induced when the X source was disregarded. Causality was assessed in the time domain according to a predictability improvement approach (i.e., Granger causality). HP and SAP variability series were recorded with R in 19 healthy subjects during spontaneous and controlled breathing at 10, 15, and 20 breaths/min. Simulations proved the importance of accounting for X signals. During spontaneous breathing, assessing causality without taking into consideration R leads to a significantly larger percentage of closed-loop interactions and a smaller fraction of unidirectional causality from HP to SAP. This finding was confirmed during paced breathing and it was independent of the breathing rate. These results suggest that the role of baroreflex cannot be correctly assessed without accounting for R.

  16. AKT1E¹⁷K Is Oncogenic in Mouse Lung and Cooperates with Chemical Carcinogens in Inducing Lung Cancer.

    PubMed

    Malanga, Donatella; Belmonte, Stefania; Colelli, Fabiana; Scarfò, Marzia; De Marco, Carmela; Oliveira, Duarte Mendes; Mirante, Teresa; Camastra, Caterina; Gagliardi, Monica; Rizzuto, Antonia; Mignogna, Chiara; Paciello, Orlando; Papparella, Serenella; Fagman, Henrik; Viglietto, Giuseppe

    2016-01-01

    The hotspot AKT1E17K mutation in the pleckstrin homology domain of AKT1 occurs in approximately 0.6-2% of human lung cancers. Recently, we have demonstrated that AKT1E17K transforms immortalized human bronchial cells. Here by use of a transgenic Cre-inducible murine strain in the wild type Rosa26 (R26) locus (R26-AKT1E17K mice) we demonstrate that AKT1E17K is a bona-fide oncogene and plays a role in the development of lung cancer in vivo. In fact, we report that mutant AKT1E17K induces bronchial and/or bronchiolar hyperplastic lesions in murine lung epithelium, which progress to frank carcinoma at very low frequency, and accelerates tumor formation induced by chemical carcinogens. In conclusion, AKT1E17K induces hyperplasia of mouse lung epithelium in vivo and cooperates with urethane to induce the fully malignant phenotype.

  17. Chemically induced graft copolymerization of 2-hydroxyethyl methacrylate onto polyurethane surface for improving blood compatibility

    NASA Astrophysics Data System (ADS)

    He, Chunli; Wang, Miao; Cai, Xianmei; Huang, Xiaobo; Li, Li; Zhu, Haomiao; Shen, Jian; Yuan, Jiang

    2011-11-01

    To improve hydrophilicity and blood compatibility properties of polyurethane (PU) film, we chemically induced graft copolymerization of 2-hydroxyethyl methacrylate (HEMA) onto the surface of polyurethane film using benzoyl peroxide as an initiator. The effects of grafting temperature, grafting time, monomer and initiator concentrations on the grafting yields were studied. The maximum grafting yield value was obtained 0.0275 g/cm2 for HEMA. Characterization of the films was carried out by attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), water contact angle measurements. ATR-FTIR data showed that HEMA was successfully grafted onto the PU films surface. Water contact angle measurement demonstrated the grafted films possessed a relatively hydrophilic surface. The blood compatibility of the grafted films was preliminarily evaluated by a platelet-rich plasma adhesion test and hemolysis test. The results of platelet adhesion experiment showed that polyurethane grafted polymerization with monomer of 2-hydroxyethyl methacrylate had good blood compatibility featured by the low platelet adhesion. Hemolysis rate of the PU-g-PHEMA films was dramatically decreased than the ungrafted PU films. This kind of new biomaterials grafted with HEMA monomers might have a potential usage for biomedical applications.

  18. Ion-Beam-Induced Chemical Mixing at a Nanocrystalline CeO2 Si Interface

    SciTech Connect

    Edmondson, Dr. Philip; Young, Neil P.; Parish, Chad M; Moll, Sandra; Namavar, Fereydoon; Weber, William J; Zhang, Yanwen

    2013-01-01

    Thin films of nanocrystalline ceria deposited onto a silicon substrate have been irradiated with 3 MeV Au+ ions to a total dose of 34 displacements per atom to examine the film/substrate interfacial response upon displacement damage. Under irradiation, a band of contrast is observed to form that grows under further irradiation. Scanning and high-resolution transmission electron microscopy imaging and analysis suggest that this band of contrast is a cerium silicate phase with an approximate Ce:Si:O composition ratio of 1:1:3 in an amorphous nature. The slightly nonstoichiometric composition arises due to the loss of mobile oxygen within the cerium silicate phase under the current irradiation condition. This nonequilibrium phase is formed as a direct result of ion-beam-induced chemical mixing caused by ballistic collisions between the incoming ion and the lattice atoms. This may hold promise in ion beam engineering of cerium silicates for microelectronic applications e.g., the fabrication of blue LEDs.

  19. Chemical Profiles and Protective Effect of Hedyotis diffusa Willd in Lipopolysaccharide-Induced Renal Inflammation Mice

    PubMed Central

    Ye, Jian-Hong; Liu, Meng-Hua; Zhang, Xu-Lin; He, Jing-Yu

    2015-01-01

    Protective effect of Hedyotis diffusa (H. diffusa) Willd against lipopolysaccharide (LPS)-induced renal inflammation was evaluated by the productions of cytokines and chemokine, and the bioactive constituents of H. diffusa were detected by the ultra-fast liquid chromatography -diode array detector-quadrupole-time of flight mass spectrometry (UFLC-DAD-Q-TOF-MS/MS) method. As the results showed, water extract of H. diffusa (equal to 5.0 g/kg body weight) obviously protected renal tissues, significantly suppressed the productions of tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, IL-6, and monocyte chemoattractant protein (MCP)-1, as well as significantly promoted the production of IL-10 in serum and renal tissues. According the chemical profiles of H. diffusa, flavonoids, iridoid glycosides and anthraquinones were greatly detected in serum from H. diffusa extract treatment mice. Two main chemotypes, including eight flavonoids and four iridoid glycosides were found in renal tissues from H. diffusa extract treatment mice. The results demonstrated that water extract of H. diffusa had protective effect on renal inflammation, which possibly resulted from the bioactive constituents consisting of flavonoids, iridoids and anthraquinones. PMID:26580602

  20. Chemical reactions between CF2HCl and NH3 induced by IR double-beam excitation

    NASA Astrophysics Data System (ADS)

    Sigüenza, C. L.; Simeonov, S. A.; Díaz, L.; González-Díaz, P. F.

    1993-06-01

    Infrared multiphoton dissociation experiments with two wavelengths in different mixtures of chlorodifluoromethane and ammonia have been carried out. It is shown that the presence of ammonia in the sample induces a decrease in the chlorodifluoromethane dissociation yield. It has been observed that the distinct chemical reaction channels are differently activated as the time delay between the two laser pulses is varied. The ratio of the obtained products in the infrared multiphoton dissociation changes with the composition of the initial mixture and are not compatible with the mechanism suggested by Sugita and Arai for this reaction in single IR wavelength excitation if it is assumed to be the only contributing mechanism other than that for direct CF2HCl dissociation and subsequent C2F4 formation from the resulting CF2 radicals. It appears that, although for simultaneous two-wavelength irradiation the presence of an accumulated solid NH4Cl deposit does not significantly influence the reaction, this is no longer the case when time delays are introduced between the two beams.

  1. Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text.

    PubMed

    Bravo, Àlex; Li, Tong Shu; Su, Andrew I; Good, Benjamin M; Furlong, Laura I

    2016-01-01

    Drug toxicity is a major concern for both regulatory agencies and the pharmaceutical industry. In this context, text-mining methods for the identification of drug side effects from free text are key for the development of up-to-date knowledge sources on drug adverse reactions. We present a new system for identification of drug side effects from the literature that combines three approaches: machine learning, rule- and knowledge-based approaches. This system has been developed to address the Task 3.B of Biocreative V challenge (BC5) dealing with Chemical-induced Disease (CID) relations. The first two approaches focus on identifying relations at the sentence-level, while the knowledge-based approach is applied both at sentence and abstract levels. The machine learning method is based on the BeFree system using two corpora as training data: the annotated data provided by the CID task organizers and a new CID corpus developed by crowdsourcing. Different combinations of results from the three strategies were selected for each run of the challenge. In the final evaluation setting, the system achieved the highest Recall of the challenge (63%). By performing an error analysis, we identified the main causes of misclassifications and areas for improving of our system, and highlighted the need of consistent gold standard data sets for advancing the state of the art in text mining of drug side effects.Database URL: https://zenodo.org/record/29887?ln¼en#.VsL3yDLWR_V.

  2. A mint purified extract protects human keratinocytes from short-term, chemically induced oxidative stress.

    PubMed

    Berselli, Patrizia Valeria Rita; Zava, Stefania; Montorfano, Gigliola; Corsetto, Paola Antonia; Krzyzanowska, Justyna; Oleszek, Wieslaw; Berra, Bruno; Rizzo, Angela Maria

    2010-11-10

    Oxidative stress is strictly correlated to the pathogenesis of many diseases, and a diet rich in fruits and vegetables, or adequately integrated, is currently considered to be a protective and preventive factor. This study aimed to analyze the efficacy of a 1 h preincubation with the highest nontoxic dose of a characterized Mentha longifolia extract (80 μg/mL) in protecting human keratinocytes (NCTC2544) from chemically induced oxidative stress (500 μM H2O2 for 2, 16, and 24 h). As reference synthetic pure compounds rosmarinic acid (360.31 μg/mL), a major mint phenolic constituent, and resveratrol (31.95 mg/mL), a well-known antioxidant, were used. Cellular viability was significantly protected by mint, which limited protein and DNA damage, decreased lipid peroxidation, and preserved glutathione and superoxide dismutase activity in the shorter phases of oxidative stress induction, in extents comparable to or better than those of pure compounds. These data suggest that mint use as only a flavoring has to be revised, taking into consideration its enrichment in foodstuff and cosmetics.

  3. A microsuspension adaptation of the Bacillus subtilis ''rec'' assay. [Detection of chemically induced DNA damage

    SciTech Connect

    McCarroll, N.E.; Keech, B.H.; Piper, C.E.

    1981-01-01

    We have demonstrated the utility of an Escherichia coli microsuspension assay to detect and characterize chemical mediation of DNA damage by a wide variety of mutagens and carcinogens. The assay have been improved by the development of a microsuspension modification to the Bacillus subtilis ''rec'' assay. The addition of these gram-positive organisms has allowed detection of DNA damage induced by benzo(a)pyrene (B(a)P), 3-aminopyrene (3-AP), 7, 12-dimethylbenz(a)anthrancene (DMBA), 3-methylcholanthrene (3-MC), and 4-nitrobiphenyl (4-NBP). Data presented in this paper from tests of 61 additional compounds, including a representative number of direct and promutagenic agents, indicate that the B subtilis H17 and M45 strains provide an effective microbial system for identification of DNA damage susceptible to postreplicational repair. The results of this study further suggests that the inclusion of these strains in the microsuspension assay for DNA damage will markedly enhance the detection of agents which cannot readily penetrate the intact cell wall of E coli.

  4. Changes in chemical interactions and protein conformation during heat-induced wheat gluten gel formation.

    PubMed

    Wang, Kai-Qiang; Luo, Shui-Zhong; Zhong, Xi-Yang; Cai, Jing; Jiang, Shao-Tong; Zheng, Zhi

    2017-01-01

    In order to elucidate the heat-induced wheat gluten gel formation mechanism, changes in chemical interactions and protein conformation were investigated during gelation. The contribution of ionic and hydrogen bonds were found to decrease from 0.746 and 4.133g/L to 0.397 and 2.733g/L, respectively, as the temperature increased from 25 to 90°C. Moreover, the free SH content remarkably decreased from 37.91 to 19.79μmol/g during gelation. Ultraviolet absorption spectra and intrinsic fluorescence spectra suggested that wheat gluten unfolded during the heating process. In addition, wheat gluten gels treated at 80 and 90°C exhibited a "steric hindrance" effect, which can be attributed to the formation of aggregates. Fourier transform infrared spectra suggested that the random coil content increased at low temperatures (40 and 50°C), whereas the content of intermolecular β-sheets due to protein aggregation increased from 38.10% to 44.28% when the gelation temperature was 90°C. PMID:27507490

  5. Characterisation of TiO 2 deposited by photo-induced chemical vapour deposition

    NASA Astrophysics Data System (ADS)

    Kaliwoh, Never; Zhang, Jun-Ying; Boyd, Ian W.

    2002-01-01

    We report the deposition of thin TiO 2 films on crystalline Si and quartz by photo-induced chemical vapour deposition (CVD) using UV excimer lamps employing a dielectric barrier discharge in krypton chloride (KrCl ∗) to provide intense narrow band radiation at λ=222 nm. The precursor used was titanium isopropoxide (TTIP). Films from around 20-510 nm in thickness with refractive indices from 2.20 to 2.54 were grown at temperatures between 50 and 350 °C. The higher refractive index values compare favourably with the value of 2.58 recorded for the bulk material. The measured deposition rate was around 50 nm/min at 350 °C. Fourier transform infrared spectroscopy (FTIR) revealed the presence of TiO 2 through the observation of a Ti-O absorption peak and the absence of OH in films deposited at 250-350 °C indicated relatively good quality films. The phase of films deposited at 200-350 °C was anatase as determined by X-ray diffraction.

  6. Chemical reactions in liquid induced by atmospheric-pressure dc glow discharge in contact with liquid

    NASA Astrophysics Data System (ADS)

    Tochikubo, Fumiyoshi; Shimokawa, Yudai; Shirai, Naoki; Uchida, Satoshi

    2014-12-01

    We experimentally investigated some of the initial reactions in a liquid induced by electron or positive-ion irradiation from an atmospheric-pressure dc glow discharge in contact with the liquid. Aqueous solutions of NaCl, AgNO3, and HAuCl4 are used as the electrolyte. We measured the pH and conductivity in the liquid at approximately 1 cm below the solution surfaces. OH radical generation in the liquid was observed by a chemical probe method. Experimental results showed that electron irradiation of the liquid surface generates OH- in water and that positive-ion irradiation of the liquid surface generates H+ in water even without the dissolution of gas-phase nitrogen oxide. A possible reaction process is qualitatively discussed. In particular, the contribution of charge transfer collision between impinging low-energy positive ions and water molecules to the ionic species in the liquid is used to explain the overall tendency of the experimental results.

  7. Corona-induced chemical scrubber for the control of NO{sub x} emissions

    SciTech Connect

    Yang, C.L.; Beltran, M.; Kravets, Z.; Yamamoto, Toshiaki

    1998-12-31

    Two dielectric materials (barium titanate and glass pellets) were evaluated for their ability to decompose/oxidize nitric oxide (NO) by nonthermal plasma discharge. Both barium titanate and glass pellets were tested in a packed bed dielectric barrier plasma reactor. The plasma reactor using barium, titanate completely destroys 130 ppm of NO in an air stream at an electric field strength of 9 kV/cm. A majority of the incoming NO is decomposed to N{sub 2} and O{sub 2}. However, 30% of the NO is oxidized to NO{sub 2}. The plasma reactor using glass pellets in a similar system is just as effective, but at a 3 k V/cm higher electric field strength. The 40 ppm NO{sub 2} in the effluent of the plasma reactor is then removed quantitatively by a caustic sodium sulfite aqueous scrubbing system. The outlet concentrations of both NO and NO{sub 2} from the plasma-scrubber combination system (corona-induced chemical scrubber) are beyond the detection limit of the chemiluminescent NO{sub x} analyzer.

  8. Combination of Sleeping Beauty transposition and chemically induced dimerization selection for robust production of engineered cells

    PubMed Central

    Kacherovsky, Nataly; Harkey, Michael A.; Blau, C. Anthony; Giachelli, Cecilia M.; Pun, Suzie H.

    2012-01-01

    The main methods for producing genetically engineered cells use viral vectors for which safety issues and manufacturing costs remain a concern. In addition, selection of desired cells typically relies on the use of cytotoxic drugs with long culture times. Here, we introduce an efficient non-viral approach combining the Sleeping Beauty (SB) Transposon System with selective proliferation of engineered cells by chemically induced dimerization (CID) of growth factor receptors. Minicircles carrying a SB transposon cassette containing a reporter transgene and a gene for the F36VFGFR1 fusion protein were delivered to the hematopoietic cell line Ba/F3. Stably-transduced Ba/F3 cell populations with >98% purity were obtained within 1 week using this positive selection strategy. Copy number analysis by quantitative PCR (qPCR) revealed that CID-selected cells contain on average higher copy numbers of transgenes than flow cytometry-selected cells, demonstrating selective advantage for cells with multiple transposon insertions. A diverse population of cells is present both before and after culture in CID media, although site-specific qPCR of transposon junctions show that population diversity is significantly reduced after selection due to preferential expansion of clones with multiple integration events. This non-viral, positive selection approach is an attractive alternative for producing engineered cells. PMID:22402491

  9. Measurement Of Atmospheric Peroxy Radicals By Chemical Conversion And Laser-induced Fluorescence Technique

    NASA Astrophysics Data System (ADS)

    Ren, X.; Naik, C.; Mao, J.; Harder, H.; Martinez, M.; Lesher, R.; Brune, W. H.

    2005-12-01

    A new method for measuring atmospheric peroxy radicals is described based on chemical conversion and laser-induced fluorescence (LIF) technique. Peroxy radicals are quantitatively converted into hydroperoxyl radicals (HO2) by the reactions with NO in a low-pressure reactor. The produced HO2 is then detected with an LIF instrument. The characterization and response of this instrument has been evaluated through the laboratory experiments as well as numeric simulations. Relative responses of different organic groups of peroxy radicals to HO2 were measured and the conversion coefficients agree generally well with the model calculations. The dependence of conversion coefficients on different experiment conditions was investigated. For HO2, the LIF signal is calibrated with an HO2 source produced by the photolysis of H2O via a low-pressure mercury lamp. Field measurements of peroxy radicals using this method were conducted at a rural site and preliminary results are presented. The estimated accuracy of the derived HOxROx concentrations is about 40% with a 2σ confidence level. Typical detection limit is about 0.2 pptv for 1-minute averaging times.

  10. Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text.

    PubMed

    Bravo, Àlex; Li, Tong Shu; Su, Andrew I; Good, Benjamin M; Furlong, Laura I

    2016-01-01

    Drug toxicity is a major concern for both regulatory agencies and the pharmaceutical industry. In this context, text-mining methods for the identification of drug side effects from free text are key for the development of up-to-date knowledge sources on drug adverse reactions. We present a new system for identification of drug side effects from the literature that combines three approaches: machine learning, rule- and knowledge-based approaches. This system has been developed to address the Task 3.B of Biocreative V challenge (BC5) dealing with Chemical-induced Disease (CID) relations. The first two approaches focus on identifying relations at the sentence-level, while the knowledge-based approach is applied both at sentence and abstract levels. The machine learning method is based on the BeFree system using two corpora as training data: the annotated data provided by the CID task organizers and a new CID corpus developed by crowdsourcing. Different combinations of results from the three strategies were selected for each run of the challenge. In the final evaluation setting, the system achieved the highest Recall of the challenge (63%). By performing an error analysis, we identified the main causes of misclassifications and areas for improving of our system, and highlighted the need of consistent gold standard data sets for advancing the state of the art in text mining of drug side effects.Database URL: https://zenodo.org/record/29887?ln¼en#.VsL3yDLWR_V. PMID:27307137

  11. Thrombolytic effect of nattokinase on a chemically induced thrombosis model in rat.

    PubMed

    Fujita, M; Hong, K; Ito, Y; Fujii, R; Kariya, K; Nishimuro, S

    1995-10-01

    Nattokinase is a new fibrinolytic enzyme which cleaves directly cross-linked fibrin in vitro. In this study, we investigated the thrombolytic effect of nattokinase on a thrombus in the common carotid artery of rat in which the endothelial cells of the vessel wall were injured by acetic acid. When a section of occluded vessel was stained for CD61 antigen by immunofluorescence utilizing a monoclonal antibody, the antigen was localized around the surface of the occluded blood vessels. This result suggests that the occlusive thrombosis was caused by platelet aggregation. In addition, thrombolysis with urokinase (UK; 50000 IU/kg, i.v.) or tissue plasminogen activator (tPA; 13300 IU/kg, i.v.) in our model was observed to restore the blood flow over a 60 min monitoring period. The results indicate that our chemically induced model is useful for screening and evaluating a thrombolytic agent. We evaluated the thrombolytic activity of nattokinase using this model and compared it with fibrino(geno)lytic enzyme, plasmin or elastase. On a molar basis, the recovery of the arterial blood flow with nattokinase, plasmin and elastase were 62.0 +/- 5.3%, 15.8 +/- 0.7% and 0%, respectively. The results indicate that the thrombolytic activity of nattokinase is stronger than that of plasmin or elastase in vivo.

  12. Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text

    PubMed Central

    Bravo, Àlex; Li, Tong Shu; Su, Andrew I.; Good, Benjamin M.; Furlong, Laura I.

    2016-01-01

    Drug toxicity is a major concern for both regulatory agencies and the pharmaceutical industry. In this context, text-mining methods for the identification of drug side effects from free text are key for the development of up-to-date knowledge sources on drug adverse reactions. We present a new system for identification of drug side effects from the literature that combines three approaches: machine learning, rule- and knowledge-based approaches. This system has been developed to address the Task 3.B of Biocreative V challenge (BC5) dealing with Chemical-induced Disease (CID) relations. The first two approaches focus on identifying relations at the sentence-level, while the knowledge-based approach is applied both at sentence and abstract levels. The machine learning method is based on the BeFree system using two corpora as training data: the annotated data provided by the CID task organizers and a new CID corpus developed by crowdsourcing. Different combinations of results from the three strategies were selected for each run of the challenge. In the final evaluation setting, the system achieved the highest Recall of the challenge (63%). By performing an error analysis, we identified the main causes of misclassifications and areas for improving of our system, and highlighted the need of consistent gold standard data sets for advancing the state of the art in text mining of drug side effects. Database URL: https://zenodo.org/record/29887?ln¼en#.VsL3yDLWR_V PMID:27307137

  13. Swift heavy ion induced structural and chemical changes in BOPP film

    NASA Astrophysics Data System (ADS)

    Chawla, S.; Ghosh, A. K.; Ahmad, S.; Avasthi, D. K.

    2006-03-01

    Swift heavy ions (SHIs), such as, 80 MeV Si7+ and 120 MeV Ag9+ ions were used to irradiate 15 μm bi-axially oriented polypropylene (BOPP) films. The fluence (Φ) dependence of the structural and chemical changes in BOPP was investigated. The irradiated BOPP films were analyzed ex situ by means of FTIR, UV and DSC. Due to SHI irradiation, the isotactic helical structure of polypropylene (PP) gets reduced. PP undergoes distortion of its crystal lattice in magnitude proportional to the fluence. The scission of C-H bonds and production of unsaturated groups like dienes and trienes occurred after irradiation with Si ions for Φ ⩾ 1012 ions/cm2 and Ag ions for Φ ⩾ 1011 ions/cm2. It was found that Ag ions are better than Si ions for creation of free radical active sites on BOPP. The observed findings are very useful particularly in the selection of optimum experimental conditions for SHI induced graft copolymerization.

  14. 5'-structural analysis of genes encoding polymorphic antigens of chemically induced tumors

    SciTech Connect

    Srivastava, R.K.; Chen, Y.T.; Old, L.J.

    1987-06-01

    The authors have proposed that the distinct tumor rejection antigens of chemically induced sarcomas in inbred mice belong to a family of M/sub r/ 96,000 glycoproteins (gp96). An identical 14-amino acid sequence was found at the amino terminus of gp96 from two antigenically distinct BALB/c sarcomas. Oligonucleotide probes, end-labeled with (/sup 12/P)-ATP, derived from this sequence permitted isolation of 5' cDNA and genomic fragments coding for gp96. Three short exons interrupted by relatively long introns were identified at the 5' terminus of the gp96 gene. The first exon encodes a signal peptide, which is consistent with gp96 being a cell surface antigen. Southern blot analysis indicated that the gp96 family is encoded by a single gene, and 3-kilobase transcripts were detected in all normal and tumor cells tested. Nucleotide and deduced amino acid sequences from 311 base pairs at the 5' terminus showed no homology with any know protein. The availability of molecular probes for the gp96 system permits analysis of the structural polymorphism of these antigens.

  15. Laser-Induced Acoustic Desorption/Atmospheric Pressure Chemical Ionization Mass Spectrometry

    PubMed Central

    Gao, Jinshan; Borton, David J.; Owen, Benjamin C.; Jin, Zhicheng; Hurt, Matt; Amundson, Lucas M.; Madden, Jeremy T.; Qian, Kuangnan; Kenttämaa, Hilkka I.

    2010-01-01

    Laser-induced acoustic desorption (LIAD) was successfully coupled to a conventional atmospheric pressure chemical ionization (APCI) source in a linear quadrupole ion trap mass spectrometer (LQIT). Model compounds representing a wide variety of different types, including basic nitrogen and oxygen compounds, aromatic and aliphatic compounds, as well as unsaturated and saturated hydrocarbons, were tested separately and as a mixture. These model compounds were successfully evaporated into the gas phase by using LIAD and then ionized by using APCI with different reagents. Four APCI reagent systems were tested: the traditionally used mixture of methanol and water, neat benzene, neat carbon disulfide, and nitrogen gas (no liquid reagent). The mixture of methanol and water produced primarily protonated molecules, as expected. However, only the most basic compounds yielded ions under these conditions. In sharp contrast, using APCI with either neat benzene or neat carbon disulfide as the reagent resulted in the ionization of all the analytes studied to predominantly yield stable molecular ions. Benzene yielded a larger fraction of protonated molecules than carbon disulfide, which is a disadvantage. A similar amount of fragmentation was observed for these reagents. When the experiment was performed without a liquid reagent(nitrogen gas was the reagent), more fragmentation was observed. Analysis of a known mixture as well as a petroleum cut was also carried out. In summary, the new experiment presented here allows the evaporation of thermally labile compounds, both polar and nonpolar, without dissociation or aggregation, and their ionization to form stable molecular ions. PMID:21472571

  16. Graphenol defects induced blue emission enhancement in chemically reduced graphene quantum dots.

    PubMed

    Zhang, Wenkai; Liu, Yingqiu; Meng, Xianrui; Ding, Tao; Xu, Yuanqing; Xu, Hao; Ren, Yanrong; Liu, Baoying; Huang, Jiajia; Yang, Jinghe; Fang, Xiaomin

    2015-09-14

    In this work, few layer graphene quantum dots (GQDs) with a size of 3-5 nm are purposely treated with highly concentrated aqueous NaBH4 solutions to obtain the reduced graphene quantum dots (rGQDs). Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy demonstrate that the number of carbonyl groups decreases but -OH related defects increase during chemical reduction. Green and weak emissions of original GQDs originate from carrier recombination in the disorder-induced localized state (mainly including carbonyl and carboxyl and epoxy groups). As the reduction degree increases, the photoluminescence (PL) quantum efficiency of GQDs increases dramatically from 2.6% to 10.1%. In the meantime, the PL peak position blue shifts rapidly, and full width at half maximum (FWHM) becomes narrower. Thus we can infer that graphenol topological defects (hydroxyl functionalized graphene) are gradually formed during reduction. Besides, graphenol defect related PL features a longer fluorescence lifetime, excitation wavelength dependence but less pH sensitivity. PMID:26247890

  17. A new route to nanoscale tomographic chemical analysis: Focused ion beam-induced auger electron spectrosocpy

    NASA Astrophysics Data System (ADS)

    Parvaneh, Hamed

    This research project is aimed to study the application of ion-induced Auger electron spectroscopy (IAES) in combination with the characteristics of focused ion beam (FIB) microscopy for performing chemical spectroscopy and further evaluate its potential for 3-dimensional chemical tomography applications. The mechanism for generation of Auger electrons by bombarding ions is very different from its electron induced counterpart. In the conventional electron-induced Auger electron spectroscopy (EAES), an electron beam with energy typically in the range 1-10kV is used to excite inner-shell (core) electrons of the solid. An electron from a higher electron energy state then de-excites to fill the hole and the extra energy is then transferred to either another electron, i.e. the Auger electron, or generation of an X-ray (photon). In both cases the emitting particles have charac-teristic energies and could be used to identify the excited target atoms. In IAES, however, large excitation cross sections can occur by promotion of in-ner shell electrons through crossing of molecular orbitals. Originally such phenomenological excitation processes were first proposed [3] for bi-particle gas phase collision systems to explain the generation of inner shell vacancies in violent collisions. In addition to excitation of incident or target atoms, due to a much heavier mass of ions compared to electrons, there would also be a substantial momentum transfer from the incident to the target atoms. This may cause the excited target atom to recoil from the lattice site or alternatively sputter off the surface with the possibility of de-excitation while the atom is either in motion in the matrix or traveling in vacuum. As a result, one could expect differences between the spectra induced by incident electrons and ions and interpretation of the IAE spectra requires separate consideration of both excitation and decay processes. In the first stage of the project, a state-of-the-art mass

  18. Ex vivo analysis of irradiated fingernails: chemical yields and properties of radiation-induced and mechanically-induced radicals.

    PubMed

    Black, Paul J; Swarts, Steven G

    2010-02-01

    A qualitative and quantitative analysis of the radicals underlying the radiation-induced signal (RIS) in fingernails was conducted in an attempt to identify properties of these radicals that could be used for biodosimetry purposes. A qualitative analysis of RIS showed the presence of at least three components, two of which were observed at low doses (<50 Gy) and the third required higher doses (>500 Gy). The low dose signal, obtained by reconstruction, consists of a 10 gauss singlet at g = 2.0053 and an 18 gauss doublet centered at g = 2.0044. Based on the initial slope of the dose-response curve, the chemical (radical) yields of the radicals giving rise to the singlet and doublet were 327 (+/-113) and 122 (+/-9) nmol J-1 (standard error, SE), respectively. At doses below 50 Gy, the singlet signal is the dominant component. Above this dose range, the signal intensity of the singlet rapidly dose-saturates. At doses <50 Gy, there is a small contribution of the doublet signal that increases in its proportion of the RIS as dose increases. A third component was revealed at high dose with a spectral extent of approximately 100 gauss and displayed peaks due to g anisotropy at g = 2.056, 2.026, and 1.996. The total radical yield calculated from the initial slope of the dose-response curve averaged 458 +/- (116) nmol J-1 (SE) in irradiated nail clippings obtained from six volunteers. Such high yields indicate that nails are a strong candidate for biodosimetry at low doses. In a comparison of relative stabilities of the radicals underlying the singlet and doublet signals, the stability of the doublet signal is more sensitive to the moisture content of the nail than the singlet. This differential in radical stabilities could provide a method for removing the doublet signal under controlled exposures to high humidities (>70% relative humidity). The decay of the singlet signal in RIS varies with exposure of a nail clipping to differing ambient humidities. However, long

  19. Ex vivo analysis of irradiated fingernails: chemical yields and properties of radiation-induced and mechanically-induced radicals.

    PubMed

    Black, Paul J; Swarts, Steven G

    2010-02-01

    A qualitative and quantitative analysis of the radicals underlying the radiation-induced signal (RIS) in fingernails was conducted in an attempt to identify properties of these radicals that could be used for biodosimetry purposes. A qualitative analysis of RIS showed the presence of at least three components, two of which were observed at low doses (<50 Gy) and the third required higher doses (>500 Gy). The low dose signal, obtained by reconstruction, consists of a 10 gauss singlet at g = 2.0053 and an 18 gauss doublet centered at g = 2.0044. Based on the initial slope of the dose-response curve, the chemical (radical) yields of the radicals giving rise to the singlet and doublet were 327 (+/-113) and 122 (+/-9) nmol J-1 (standard error, SE), respectively. At doses below 50 Gy, the singlet signal is the dominant component. Above this dose range, the signal intensity of the singlet rapidly dose-saturates. At doses <50 Gy, there is a small contribution of the doublet signal that increases in its proportion of the RIS as dose increases. A third component was revealed at high dose with a spectral extent of approximately 100 gauss and displayed peaks due to g anisotropy at g = 2.056, 2.026, and 1.996. The total radical yield calculated from the initial slope of the dose-response curve averaged 458 +/- (116) nmol J-1 (SE) in irradiated nail clippings obtained from six volunteers. Such high yields indicate that nails are a strong candidate for biodosimetry at low doses. In a comparison of relative stabilities of the radicals underlying the singlet and doublet signals, the stability of the doublet signal is more sensitive to the moisture content of the nail than the singlet. This differential in radical stabilities could provide a method for removing the doublet signal under controlled exposures to high humidities (>70% relative humidity). The decay of the singlet signal in RIS varies with exposure of a nail clipping to differing ambient humidities. However, long

  20. The gravity dual of boundary causality

    NASA Astrophysics Data System (ADS)

    Engelhardt, Netta; Fischetti, Sebastian

    2016-09-01

    In gauge/gravity duality, points which are not causally related on the boundary cannot be causally related through the bulk; this is the statement of boundary causality. By the Gao-Wald theorem, the averaged null energy condition in the bulk is sufficient to ensure this property. Here we proceed in the converse direction: we derive a necessary as well as sufficient condition for the preservation of boundary causality under perturbative (quantum or stringy) corrections to the bulk. The condition that we find is a (background-dependent) constraint on the amount by which light cones can ‘open’ over all null bulk geodesics. We show that this constraint is weaker than the averaged null energy condition.

  1. Risk and causality in newspaper reporting.

    PubMed

    Boholm, Max

    2009-11-01

    The study addresses the textual representation of risk and causality in news media reporting. The analytical framework combines two theoretical perspectives: media frame analysis and the philosophy of causality. Empirical data derive from selected newspaper articles on risks in the Göta älv river valley in southwest Sweden from 1994 to 2007. News media content was coded and analyzed with respect to causal explanations of risk issues. At the level of individual articles, this study finds that the media provide simple causal explanations of risks such as water pollution, landslides, and flooding. Furthermore, these explanations are constructed, or framed, in various ways, the same risk being attributed to different causes in different articles. However, the study demonstrates that a fairly complex picture of risks in the media emerges when extensive material is analyzed systematically.

  2. Rate-Agnostic (Causal) Structure Learning

    PubMed Central

    Plis, Sergey; Danks, David; Freeman, Cynthia; Calhoun, Vince

    2016-01-01

    Causal structure learning from time series data is a major scientific challenge. Extant algorithms assume that measurements occur sufficiently quickly; more precisely, they assume approximately equal system and measurement timescales. In many domains, however, measurements occur at a significantly slower rate than the underlying system changes, but the size of the timescale mismatch is often unknown. This paper develops three causal structure learning algorithms, each of which discovers all dynamic causal graphs that explain the observed measurement data, perhaps given undersampling. That is, these algorithms all learn causal structure in a “rate-agnostic” manner: they do not assume any particular relation between the measurement and system timescales. We apply these algorithms to data from simulations to gain insight into the challenge of undersampling. PMID:27182188

  3. Synergy, redundancy and unnormalized Granger causality.

    PubMed

    Stramaglia, S; Angelini, L; Cortes, J M; Marinazzo, D

    2015-08-01

    We analyze by means of Granger causality the effect of synergy and redundancy in the inference (from time series data) of the information flow between subsystems of a complex network. Whilst fully conditioned Granger causality is not affected by synergy, the pairwise analysis fails to put in evidence synergetic effects. We show that maximization of the total Granger causality to a given target, over all the possible partitions of the set of driving variables, puts in evidence redundant multiplets of variables influencing the target, provided that an unnormalized definition of Granger causality is adopted. Along the same lines we also introduce a pairwise index of synergy (w.r.t. to information flow to a third variable) which is zero when two independent sources additively influence a common target; thus, this definition differs from previous definitions of synergy.

  4. Granger-causality maps of diffusion processes.

    PubMed

    Wahl, Benjamin; Feudel, Ulrike; Hlinka, Jaroslav; Wächter, Matthias; Peinke, Joachim; Freund, Jan A

    2016-02-01

    Granger causality is a statistical concept devised to reconstruct and quantify predictive information flow between stochastic processes. Although the general concept can be formulated model-free it is often considered in the framework of linear stochastic processes. Here we show how local linear model descriptions can be employed to extend Granger causality into the realm of nonlinear systems. This novel treatment results in maps that resolve Granger causality in regions of state space. Through examples we provide a proof of concept and illustrate the utility of these maps. Moreover, by integration we convert the local Granger causality into a global measure that yields a consistent picture for a global Ornstein-Uhlenbeck process. Finally, we recover invariance transformations known from the theory of autoregressive processes. PMID:26986337

  5. Quantum probability assignment limited by relativistic causality

    PubMed Central

    Han, Yeong Deok; Choi, Taeseung

    2016-01-01

    Quantum theory has nonlocal correlations, which bothered Einstein, but found to satisfy relativistic causality. Correlation for a shared quantum state manifests itself, in the standard quantum framework, by joint probability distributions that can be obtained by applying state reduction and probability assignment that is called Born rule. Quantum correlations, which show nonlocality when the shared state has an entanglement, can be changed if we apply different probability assignment rule. As a result, the amount of nonlocality in quantum correlation will be changed. The issue is whether the change of the rule of quantum probability assignment breaks relativistic causality. We have shown that Born rule on quantum measurement is derived by requiring relativistic causality condition. This shows how the relativistic causality limits the upper bound of quantum nonlocality through quantum probability assignment. PMID:26971717

  6. The gravity dual of boundary causality

    NASA Astrophysics Data System (ADS)

    Engelhardt, Netta; Fischetti, Sebastian

    2016-09-01

    In gauge/gravity duality, points which are not causally related on the boundary cannot be causally related through the bulk; this is the statement of boundary causality. By the Gao–Wald theorem, the averaged null energy condition in the bulk is sufficient to ensure this property. Here we proceed in the converse direction: we derive a necessary as well as sufficient condition for the preservation of boundary causality under perturbative (quantum or stringy) corrections to the bulk. The condition that we find is a (background-dependent) constraint on the amount by which light cones can ‘open’ over all null bulk geodesics. We show that this constraint is weaker than the averaged null energy condition.

  7. Granger-causality maps of diffusion processes.

    PubMed

    Wahl, Benjamin; Feudel, Ulrike; Hlinka, Jaroslav; Wächter, Matthias; Peinke, Joachim; Freund, Jan A

    2016-02-01

    Granger causality is a statistical concept devised to reconstruct and quantify predictive information flow between stochastic processes. Although the general concept can be formulated model-free it is often considered in the framework of linear stochastic processes. Here we show how local linear model descriptions can be employed to extend Granger causality into the realm of nonlinear systems. This novel treatment results in maps that resolve Granger causality in regions of state space. Through examples we provide a proof of concept and illustrate the utility of these maps. Moreover, by integration we convert the local Granger causality into a global measure that yields a consistent picture for a global Ornstein-Uhlenbeck process. Finally, we recover invariance transformations known from the theory of autoregressive processes.

  8. Novel quantitative methods for characterization of chemical induced functional alteration in developing neuronal cultures

    EPA Science Inventory

    ABSTRACT BODY: Thousands of chemicals lack adequate testing for adverse effects on nervous system development, stimulating research into alternative methods to screen chemicals for potential developmental neurotoxicity. Microelectrode arrays (MEA) collect action potential spiking...

  9. Singular clues to causality and their use in human causal judgment.

    PubMed

    White, Peter A

    2014-01-01

    It is argued that causal understanding originates in experiences of acting on objects. Such experiences have consistent features that can be used as clues to causal identification and judgment. These are singular clues, meaning that they can be detected in single instances. A catalog of 14 singular clues is proposed. The clues function as heuristics for generating causal judgments under uncertainty and are a pervasive source of bias in causal judgment. More sophisticated clues such as mechanism clues and repeated interventions are derived from the 14. Research on the use of empirical information and conditional probabilities to identify causes has used scenarios in which several of the clues are present, and the use of empirical association information for causal judgment depends on the presence of singular clues. It is the singular clues and their origin that are basic to causal understanding, not multiple instance clues such as empirical association, contingency, and conditional probabilities. PMID:23957568

  10. Ploidy differences between hormone- and chemical carcinogen-induced rat mammary neoplasms: comparison to invasive human ductal breast cancer.

    PubMed

    Li, Jonathan J; Papa, Dan; Davis, Marilyn F; Weroha, S John; Aldaz, C Marcelo; El-Bayoumy, Karam; Ballenger, Jodi; Tawfik, Ossama; Li, Sara Antonia

    2002-01-01

    To ascertain differences between solely hormone- and chemical carcinogen-induced murine mammary gland tumors (MGTs), a direct comparison of their ploidy status was assessed. Nuclear image cytometry (NIC) was used to evaluate ploidy in ductal carcinoma in situ (DCIS) and MGTs induced solely by 17beta-estradiol (E(2)) in female A-strain Copenhagen Irish hooded gene rats (ACI) and E(2) plus testosterone propionate in male Noble rats. These results were compared to ploidy data from primary MGTs induced by two synthetic carcinogens, 7,12-dimethylbenz[a]antracene and nitrosomethylurea in female Brown Lewis Norway rats and an environmental carcinogen, 6-nitrochrysene, in female Sprague-Dawley rats. Both DCIS and primary MGTs induced solely by hormones were highly aneuploid (> 84%), whereas MGTs induced by either synthetic or environmental carcinogens were primarily diploid (> 85%). Examination of 76 metaphase plates obtained from eight individual E(2)-induced ACI female rat MGTs revealed the following consistent chromosome alterations: gains in chromosomes 7, 11, 12, 13, 19, and 20 and loss of chromosome 12. On Southern blot analysis, six of nine ACI female rat primary E(2)-induced MGTs (66%) exhibited amplified copy numbers (range: 3.4-6.9 copies) of the c-myc gene. Fluorescence in situ hybridization (FISH) analysis of these MGTs revealed specific fluorescent hybridization signals for c-myc (7q33) on all three homologs of a trisomy in chromosome 7. NIC analysis of 140 successive nonfamilial sporadic invasive human ductal breast cancers (BCs) showed an aneuploid frequency of 61%, while 31 DCISs revealed a 71% aneuploid frequency. These results clearly demonstrate that the female ACI rat E(2)-induced MGTs more closely resemble invasive human DCIS and ductal BC in two pertinent aspects: they are highly aneuploid compared with chemical carcinogen-induced MGTs and exhibit a high frequency of c-myc amplification. PMID:11807958

  11. Kant on causal laws and powers.

    PubMed

    Henschen, Tobias

    2014-12-01

    The aim of the paper is threefold. Its first aim is to defend Eric Watkins's claim that for Kant, a cause is not an event but a causal power: a power that is borne by a substance, and that, when active, brings about its effect, i.e. a change of the states of another substance, by generating a continuous flow of intermediate states of that substance. The second aim of the paper is to argue against Watkins that the Kantian concept of causal power is not the pre-critical concept of real ground but the category of causality, and that Kant holds with Hume that causal laws cannot be inferred non-inductively (that he accordingly has no intention to show in the Second analogy or elsewhere that events fall under causal laws). The third aim of the paper is to compare the Kantian position on causality with central tenets of contemporary powers ontology: it argues that unlike the variants endorsed by contemporary powers theorists, the Kantian variants of these tenets are resistant to objections that neo-Humeans raise to these tenets. PMID:25571742

  12. Causal Inference for Vaccine Effects on Infectiousness

    PubMed Central

    Halloran, M. Elizabeth; Hudgens, Michael G.

    2012-01-01

    If a vaccine does not protect individuals completely against infection, it could still reduce infectiousness of infected vaccinated individuals to others. Typically, vaccine efficacy for infectiousness is estimated based on contrasts between the transmission risk to susceptible individuals from infected vaccinated individuals compared with that from infected unvaccinated individuals. Such estimates are problematic, however, because they are subject to selection bias and do not have a causal interpretation. Here, we develop causal estimands for vaccine efficacy for infectiousness for four different scenarios of populations of transmission units of size two. These causal estimands incorporate both principal stratification, based on the joint potential infection outcomes under vaccine and control, and interference between individuals within transmission units. In the most general scenario, both individuals can be exposed to infection outside the transmission unit and both can be assigned either vaccine or control. The three other scenarios are special cases of the general scenario where only one individual is exposed outside the transmission unit or can be assigned vaccine. The causal estimands for vaccine efficacy for infectiousness are well defined only within certain principal strata and, in general, are identifiable only with strong unverifiable assumptions. Nonetheless, the observed data do provide some information, and we derive large sample bounds on the causal vaccine efficacy for infectiousness estimands. An example of the type of data observed in a study to estimate vaccine efficacy for infectiousness is analyzed in the causal inference framework we developed. PMID:22499732

  13. Causality violation, gravitational shockwaves and UV completion

    NASA Astrophysics Data System (ADS)

    Hollowood, Timothy J.; Shore, Graham M.

    2016-03-01

    The effective actions describing the low-energy dynamics of QFTs involving gravity generically exhibit causality violations. These may take the form of superluminal propagation or Shapiro time advances and allow the construction of "time machines", i.e. spacetimes admitting closed non-spacelike curves. Here, we discuss critically whether such causality violations may be used as a criterion to identify unphysical effective actions or whether, and how, causality problems may be resolved by embedding the action in a fundamental, UV complete QFT. We study in detail the case of photon scattering in an Aichelburg-Sexl gravitational shockwave background and calculate the phase shifts in QED for all energies, demonstrating their smooth interpolation from the causality-violating effective action values at low-energy to their manifestly causal high-energy limits. At low energies, these phase shifts may be interpreted as backwards-in-time coordinate jumps as the photon encounters the shock wavefront, and we illustrate how the resulting causality problems emerge and are resolved in a two-shockwave time machine scenario. The implications of our results for ultra-high (Planck) energy scattering, in which graviton exchange is modelled by the shockwave background, are highlighted.

  14. Chemical speciation of chlorine in atmospheric aerosol samples by high-resolution proton induced X-ray emission spectroscopy

    NASA Astrophysics Data System (ADS)

    Kertész, Zsófia; Furu, Enikő; Kavčič, Matjaž

    2013-01-01

    Chlorine is a main elemental component of atmospheric particulate matter (APM). The knowledge of the chemical form of chlorine is of primary importance for source apportionment and for estimation of health effects of APM. In this work the applicability of high-resolution wavelength dispersive proton induced X-ray emission (PIXE) spectroscopy for chemical speciation of chlorine in fine fraction atmospheric aerosols is studied. A Johansson-type crystal spectrometer with energy resolution below the natural linewidth of Cl K lines was used to record the high-resolution Kα and Kβ proton induced spectra of several reference Cl compounds and two atmospheric aerosol samples, which were collected for conventional PIXE analysis. The Kα spectra which refers to the oxidation state, showed very minor differences due to the high electronegativity of Cl. However, the Kβ spectra exhibited pronounced chemical effects which were significant enough to perform chemical speciation. The major chlorine component in two fine fraction aerosol samples collected during a 2010 winter campaign in Budapest was clearly identified as NaCl by comparing the high-resolution Cl Kβ spectra from the aerosol samples with the corresponding reference spectra. This work demonstrates the feasibility of high-resolution PIXE method for chemical speciation of Cl in aerosols.

  15. The role of causal criteria in causal inferences: Bradford Hill's "aspects of association"

    PubMed Central

    Ward, Andrew C

    2009-01-01

    As noted by Wesley Salmon and many others, causal concepts are ubiquitous in every branch of theoretical science, in the practical disciplines and in everyday life. In the theoretical and practical sciences especially, people often base claims about causal relations on applications of statistical methods to data. However, the source and type of data place important constraints on the choice of statistical methods as well as on the warrant attributed to the causal claims based on the use of such methods. For example, much of the data used by people interested in making causal claims come from non-experimental, observational studies in which random allocations to treatment and control groups are not present. Thus, one of the most important problems in the social and health sciences concerns making justified causal inferences using non-experimental, observational data. In this paper, I examine one method of justifying such inferences that is especially widespread in epidemiology and the health sciences generally – the use of causal criteria. I argue that while the use of causal criteria is not appropriate for either deductive or inductive inferences, they do have an important role to play in inferences to the best explanation. As such, causal criteria, exemplified by what Bradford Hill referred to as "aspects of [statistical] associations", have an indispensible part to play in the goal of making justified causal claims. PMID:19534788

  16. H-2 restriction of the T cell response to chemically induced tumors: evidence from F/sub 1/. -->. parent chimeras

    SciTech Connect

    Lannin, D.R.; Yu, S.; McKhann, C.F.

    1982-01-01

    It has been well established that T cells that react to tumor antigen on virus-induced tumors must share H-2D or H-2K specificities with the tumor. It has been impossible to perform similar studies with chemically induced tumors because each chemically induced tumor expresses a unique tumor antigen that cannot be studied in association with other H-2 types. This study provies evidence that H-2 recognition is also necessary for recognition of chemically induced tumors. We have found that F/sub 1/ ..-->.. parent chimeras preferentially recognize chemically induced tumors of parental H-2 type. C3H/HeJ and C57BL/6 mice were lethally irradiated and restored with (C3H x C57BL/6) F/sub 1/ hybrid bone marrow. The F/sub 1/ ..-->.. C3H chimera but not the F/sub 1/ ..-->.. C57BL/6 chimera was able to respond to a C3H fibrosarcoma in mixed lymphocyte-tumor cell culture and also to neutralize the tumor in an in vivo tumor neutralization assay. On the other hand, the F/sub 1/ ..-->.. C57BL/6 chimera but not the F/sub 1/ ..-->.. C3H chimera was able to kill the C57BL/6 lymphoma EL4 in an in vitro cytotoxicity assay. Both chimeras were tolerant to C3H and C57BL/6 alloantigens but could respond normally to Con A and to BALB/c spleen cells in mixed lymphocyte cultures and cytotoxicity assay.

  17. Stress-induced chemical detection using flexible metal-organic frameworks.

    SciTech Connect

    Allendorf, Mark D.; Hesketh, Peter J.; Gall, Kenneth A.; Choudhury, A.; Pikarsky, J.; Andruszkiewicz, Leanne; Houk, Ronald J. T.; Talin, Albert Alec

    2009-09-01

    In this work we demonstrate the concept of stress-induced chemical detection using metal-organic frameworks (MOFs) by integrating a thin film of the MOF HKUST-1 with a microcantilever surface. The results show that the energy of molecular adsorption, which causes slight distortions in the MOF crystal structure, can be efficiently converted to mechanical energy to create a highly responsive, reversible, and selective sensor. This sensor responds to water, methanol, and ethanol vapors, but yields no response to either N{sub 2} or O{sub 2}. The magnitude of the signal, which is measured by a built-in piezoresistor, is correlated with the concentration and can be fitted to a Langmuir isotherm. Furthermore, we show that the hydration state of the MOF layer can be used to impart selectivity to CO{sub 2}. We also report the first use of surface-enhanced Raman spectroscopy to characterize the structure of a MOF film. We conclude that the synthetic versatility of these nanoporous materials holds great promise for creating recognition chemistries to enable selective detection of a wide range of analytes. A force field model is described that successfully predicts changes in MOF properties and the uptake of gases. This model is used to predict adsorption isotherms for a number of representative compounds, including explosives, nerve agents, volatile organic compounds, and polyaromatic hydrocarbons. The results show that, as a result of relatively large heats of adsorption (> 20 kcal mol{sup -1}) in most cases, we expect an onset of adsorption by MOF as low as 10{sup -6} kPa, suggesting the potential to detect compounds such as RDX at levels as low as 10 ppb at atmospheric pressure.

  18. Effects of Ginkgo biloba on chemically-induced mammary tumors in rats receiving tamoxifen

    PubMed Central

    2013-01-01

    Background Ginkgo biloba extract (GbE) is used extensively by breast cancer patients undergoing treatment with Tamoxifen (TAM). Thus, the present study investigated the effects of GbE in female Sprague–Dawley (SD) rats bearing chemically-induced mammary tumors and receiving TAM. Methods Animals bearing mammary tumors (≥1 cm in diameter) were divided into four groups: TAM [10 mg/kg, intragastrically (i.g.)], TAM plus GbE [50 and 100 mg/kg, intraperitoneally (i.p.)] or an untreated control group. After 4 weeks, the therapeutic efficacy of the different treatments was evaluated by measuring the tumor volume (cm3) and the proportions of each tumor that were alive, necrotic or degenerative (mm2). In addition, labeling indexes (LI%) were calculated for cell proliferation (PCNA LI%) and apoptosis (cleaved caspase-3 LI%), expression of estrogen receptor-alpha (ER-α) and p63 biomarkers. Results Overall, the tumor volume and the PCNA LI% within live tumor areas were reduced by 83% and 99%, respectively, in all TAM-treated groups when compared to the untreated control group. GbE treatment (100 mg/kg) reduced the proportions of live (24.8%) and necrotic areas (2.9%) (p = 0.046 and p = 0.038, respectively) and significantly increased the proportion of degenerative areas (72.9%) (p = 0.004) in mammary tumors when compared to the group treated only with TAM. The expression of ER-α, p63 and cleaved caspase-3 in live tumor tissues was not modified by GbE treatment. Conclusions Co-treatment with 100 mg/kg GbE presented a slightly beneficial effect on the therapeutic efficacy of TAM in female SD rats bearing mammary tumors. PMID:23634930

  19. Thermal, Chemical and pH Induced Unfolding of Turmeric Root Lectin: Modes of Denaturation

    PubMed Central

    Biswas, Himadri; Chattopadhyaya, Rajagopal

    2014-01-01

    Curcuma longa rhizome lectin, of non-seed origin having antifungal, antibacterial and α-glucosidase inhibitory activities, forms a homodimer with high thermal stability as well as acid tolerance. Size exclusion chromatography and dynamic light scattering show it to be a dimer at pH 7, but it converts to a monomer near pH 2. Circular dichroism spectra and fluorescence emission maxima are virtually indistinguishable from pH 7 to 2, indicating secondary and tertiary structures remain the same in dimer and monomer within experimental error. The tryptophan environment as probed by acrylamide quenching data yielded very similar data at pH 2 and pH 7, implying very similar folding for monomer and dimer. Differential scanning calorimetry shows a transition at 350.3 K for dimer and at 327.0 K for monomer. Thermal unfolding and chemical unfolding induced by guanidinium chloride for dimer are both reversible and can be described by two-state models. The temperatures and the denaturant concentrations at which one-half of the protein molecules are unfolded, are protein concentration-dependent for dimer but protein concentration-independent for monomer. The free energy of unfolding at 298 K was found to be 5.23 Kcal mol−1 and 14.90 Kcal mol−1 for the monomer and dimer respectively. The value of change in excess heat capacity upon protein denaturation (ΔCp) is 3.42 Kcal mol−1 K−1 for dimer. The small ΔCp for unfolding of CLA reflects a buried hydrophobic core in the folded dimeric protein. These unfolding experiments, temperature dependent circular dichroism and dynamic light scattering for the dimer at pH 7 indicate its higher stability than for the monomer at pH 2. This difference in stability of dimeric and monomeric forms highlights the contribution of inter-subunit interactions in the former. PMID:25140525

  20. Illness causal beliefs in Turkish immigrants

    PubMed Central

    Minas, Harry; Klimidis, Steven; Tuncer, Can

    2007-01-01

    Background People hold a wide variety of beliefs concerning the causes of illness. Such beliefs vary across cultures and, among immigrants, may be influenced by many factors, including level of acculturation, gender, level of education, and experience of illness and treatment. This study examines illness causal beliefs in Turkish-immigrants in Australia. Methods Causal beliefs about somatic and mental illness were examined in a sample of 444 members of the Turkish population of Melbourne. The socio-demographic characteristics of the sample were broadly similar to those of the Melbourne Turkish community. Five issues were examined: the structure of causal beliefs; the relative frequency of natural, supernatural and metaphysical beliefs; ascription of somatic, mental, or both somatic and mental conditions to the various causes; the correlations of belief types with socio-demographic, modernizing and acculturation variables; and the relationship between causal beliefs and current illness. Results Principal components analysis revealed two broad factors, accounting for 58 percent of the variation in scores on illness belief scales, distinctly interpretable as natural and supernatural beliefs. Second, beliefs in natural causes were more frequent than beliefs in supernatural causes. Third, some causal beliefs were commonly linked to both somatic and mental conditions while others were regarded as more specific to either somatic or mental disorders. Last, there was a range of correlations between endorsement of belief types and factors defining heterogeneity within the community, including with demographic factors, indicators of modernizing and acculturative processes, and the current presence of illness. Conclusion Results supported the classification of causal beliefs proposed by Murdock, Wilson & Frederick, with a division into natural and supernatural causes. While belief in natural causes is more common, belief in supernatural causes persists despite modernizing and

  1. Molecular Mechanism Underlying Pathogenesis of Lewisite-Induced Cutaneous Blistering and Inflammation: Chemical Chaperones as Potential Novel Antidotes.

    PubMed

    Li, Changzhao; Srivastava, Ritesh K; Weng, Zhiping; Croutch, Claire R; Agarwal, Anupam; Elmets, Craig A; Afaq, Farrukh; Athar, Mohammad

    2016-10-01

    Lewisite is a potent arsenic-based chemical warfare agent known to induce painful cutaneous inflammation and blistering. Only a few modestly effective antidotes have so far been described in the literature. However, the discovery of effective antidotes for lewisite was hampered by the paucity of the exact molecular mechanism underlying its cutaneous pathogenesis. We investigated the molecular mechanism underlying lewisite-induced cutaneous blistering and inflammation and describe its novel antidotes. On the basis of our initial screening, we used a highly sensitive murine model that recapitulates the known human pathogenesis of arsenicals-induced cutaneous inflammation and blistering. Topically administered lewisite induced potent acute inflammation and microvesication in the skin of Ptch1(+/-)/SKH-1 mice. Even at a very low dose, lewisite up-regulates unfolded protein response signaling, inflammatory response, and apoptosis. These cutaneous lesions were associated with production of reactive oxygen species and extensive apoptosis of the epidermal keratinocytes. We confirmed that activation of reactive oxygen species-dependent unfolded protein response signaling is the underlying molecular mechanism of skin damage. Similar alterations were noticed in lewisite-treated cultured human skin keratinocytes. We discovered that chemical chaperone 4-phenyl butyric acid and antioxidant N-acetylcysteine, which significantly attenuate lewisite-mediated skin injury, can serve as potent antidotes. These data reveal a novel molecular mechanism underlying the cutaneous pathogenesis of lewisite-induced lesions. We also identified novel potential therapeutic targets for lewisite-mediated cutaneous injury. PMID:27528504

  2. Linear structures, causal sets and topology

    NASA Astrophysics Data System (ADS)

    Hudetz, Laurenz

    2015-11-01

    Causal set theory and the theory of linear structures (which has recently been developed by Tim Maudlin as an alternative to standard topology) share some of their main motivations. In view of that, I raise and answer the question how these two theories are related to each other and to standard topology. I show that causal set theory can be embedded into Maudlin's more general framework and I characterise what Maudlin's topological concepts boil down to when applied to discrete linear structures that correspond to causal sets. Moreover, I show that all topological aspects of causal sets that can be described in Maudlin's theory can also be described in the framework of standard topology. Finally, I discuss why these results are relevant for evaluating Maudlin's theory. The value of this theory depends crucially on whether it is true that (a) its conceptual framework is as expressive as that of standard topology when it comes to describing well-known continuous as well as discrete models of spacetime and (b) it is even more expressive or fruitful when it comes to analysing topological aspects of discrete structures that are intended as models of spacetime. On one hand, my theorems support (a). The theory is rich enough to incorporate causal set theory and its definitions of topological notions yield a plausible outcome in the case of causal sets. On the other hand, the results undermine (b). Standard topology, too, has the conceptual resources to capture those topological aspects of causal sets that are analysable within Maudlin's framework. This fact poses a challenge for the proponents of Maudlin's theory to prove it fruitful.

  3. You are what you eat: diet-induced chemical crypsis in a coral-feeding reef fish

    PubMed Central

    Brooker, Rohan M.; Munday, Philip L.; Chivers, Douglas P.; Jones, Geoffrey P.

    2015-01-01

    The vast majority of research into the mechanisms of camouflage has focused on forms that confound visual perception. However, many organisms primarily interact with their surroundings using chemosensory systems and may have evolved mechanisms to ‘blend in’ with chemical components of their habitat. One potential mechanism is ‘chemical crypsis' via the sequestration of dietary elements, causing a consumer's odour to chemically match that of its prey. Here, we test the potential for chemical crypsis in the coral-feeding filefish, Oxymonacanthus longirostris, by examining olfactory discrimination in obligate coral-dwelling crabs and a predatory cod. The crabs, which inhabit the corals consumed by O. longirostris, were used as a bioassay to determine the effect of coral diet on fish odour. Crabs preferred the odour of filefish fed their preferred coral over the odour of filefish fed a non-preferred coral, suggesting coral-specific dietary elements that influence odour are sequestered. Crabs also exhibited a similar preference for the odour of filefish fed their preferred coral and odour directly from that coral, suggesting a close chemical match. In behavioural trials, predatory cod were less attracted to filefish odour when presented alongside the coral it had been fed on, suggesting diet can reduce detectability. This is, we believe, the first evidence of diet-induced chemical crypsis in a vertebrate. PMID:25621328

  4. Heat-induced Irreversible Denaturation of the Camelid Single Domain VHH Antibody Is Governed by Chemical Modifications

    PubMed Central

    Akazawa-Ogawa, Yoko; Takashima, Mizuki; Lee, Young-Ho; Ikegami, Takahisa; Goto, Yuji; Uegaki, Koichi; Hagihara, Yoshihisa

    2014-01-01

    The variable domain of camelid heavy chain antibody (VHH) is highly heat-resistant and is therefore ideal for many applications. Although understanding the process of heat-induced irreversible denaturation is essential to improve the efficacy of VHH, its inactivation mechanism remains unclear. Here, we showed that chemical modifications predominantly governed the irreversible denaturation of VHH at high temperatures. After heat treatment, the activity of VHH was dependent only on the incubation time at 90 °C and was insensitive to the number of heating (90 °C)-cooling (20 °C) cycles, indicating a negligible role for folding/unfolding intermediates on permanent denaturation. The residual activity was independent of concentration; therefore, VHH lost its activity in a unimolecular manner, not by aggregation. A VHH mutant lacking Asn, which is susceptible to chemical modifications, had significantly higher heat resistance than did the wild-type protein, indicating the importance of chemical modifications to VHH denaturation. PMID:24739391

  5. Systems toxicology of chemically induced liver and kidney injuries: histopathology-associated gene co-expression modules.

    PubMed

    Te, Jerez A; AbdulHameed, Mohamed Diwan M; Wallqvist, Anders

    2016-09-01

    Organ injuries caused by environmental chemical exposures or use of pharmaceutical drugs pose a serious health risk that may be difficult to assess because of a lack of non-invasive diagnostic tests. Mapping chemical injuries to organ-specific histopathology outcomes via biomarkers will provide a foundation for designing precise and robust diagnostic tests. We identified co-expressed genes (modules) specific to injury endpoints using the Open Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System (TG-GATEs) - a toxicogenomics database containing organ-specific gene expression data matched to dose- and time-dependent chemical exposures and adverse histopathology assessments in Sprague-Dawley rats. We proposed a protocol for selecting gene modules associated with chemical-induced injuries that classify 11 liver and eight kidney histopathology endpoints based on dose-dependent activation of the identified modules. We showed that the activation of the modules for a particular chemical exposure condition, i.e., chemical-time-dose combination, correlated with the severity of histopathological damage in a dose-dependent manner. Furthermore, the modules could distinguish different types of injuries caused by chemical exposures as well as determine whether the injury module activation was specific to the tissue of origin (liver and kidney). The generated modules provide a link between toxic chemical exposures, different molecular initiating events among underlying molecular pathways and resultant organ damage. Published 2016. This article is a U.S. Government work and is in the public domain in the USA. Journal of Applied Toxicology published by John Wiley & Sons, Ltd.

  6. Singular Clues to Causality and Their Use in Human Causal Judgment

    ERIC Educational Resources Information Center

    White, Peter A.

    2014-01-01

    It is argued that causal understanding originates in experiences of acting on objects. Such experiences have consistent features that can be used as clues to causal identification and judgment. These are singular clues, meaning that they can be detected in single instances. A catalog of 14 singular clues is proposed. The clues function as…

  7. The Cradle of Causal Reasoning: Newborns' Preference for Physical Causality

    ERIC Educational Resources Information Center

    Mascalzoni, Elena; Regolin, Lucia; Vallortigara, Giorgio; Simion, Francesca

    2013-01-01

    Perception of mechanical (i.e. physical) causality, in terms of a cause-effect relationship between two motion events, appears to be a powerful mechanism in our daily experience. In spite of a growing interest in the earliest causal representations, the role of experience in the origin of this sensitivity is still a matter of dispute. Here, we…

  8. Dimensions of Causal Understanding: The Role of Complex Causal Models in Students' Understanding of Science

    ERIC Educational Resources Information Center

    Perkins, David N.; Grotzer, Tina A.

    2005-01-01

    This article argues that an important source of the difficulties posed by particular concepts and theories is the narrow range of "types of causal models" with which most learners are familiar. Most learners are familiar with relatively simple styles of causal models, but many concepts and theories in science depend on styles substantially more…

  9. The Mental Representation of Causal Conditional Reasoning: Mental Models or Causal Models

    ERIC Educational Resources Information Center

    Ali, Nilufa; Chater, Nick; Oaksford, Mike

    2011-01-01

    In this paper, two experiments are reported investigating the nature of the cognitive representations underlying causal conditional reasoning performance. The predictions of causal and logical interpretations of the conditional diverge sharply when inferences involving "pairs" of conditionals--such as "if P[subscript 1] then Q" and "if P[subscript…

  10. SOK1 translocates from the Golgi to the nucleus upon chemical anoxia and induces apoptotic cell death.

    PubMed

    Nogueira, Emilio; Fidalgo, Miguel; Molnar, Arpad; Kyriakis, John; Force, Thomas; Zalvide, Juan; Pombo, Celia M

    2008-06-01

    SOK1 is a Ste20 protein kinase of the germinal center kinase (GCK) family that has been shown to be activated by oxidant stress and chemical anoxia, a cell culture model of ischemia. More recently, it has been shown to be localized to the Golgi apparatus, where it functions in a signaling pathway required for cell migration and polarization. Herein, we demonstrate that SOK1 regulates cell death after chemical anoxia, as its down-regulation by RNA interference enhances cell survival. Furthermore, expression of SOK1 elicits apoptotic cell death by activating the intrinsic pathway. We also find that a cleaved form of SOK1 translocates from the Golgi to the nucleus after chemical anoxia and that this translocation is dependent on both caspase activity and on amino acids 275-292, located immediately C-terminal to the SOK1 kinase domain. Furthermore, SOK1 entry into the nucleus is important for the cell death response since SOK1 mutants unable to enter the nucleus do not induce cell death. In summary, SOK1 is necessary to induce cell death and can induce death when overexpressed. Furthermore, SOK1 appears to play distinctly different roles in stressed versus non-stressed cells, regulating cell death in the former.

  11. A Cell-Based High-Throughput Screen for Novel Chemical Inducers of Fetal Hemoglobin for Treatment of Hemoglobinopathies

    PubMed Central

    Peterson, Kenneth R.; Costa, Flávia C.; Fedosyuk, Halyna; Neades, Renee Y.; Chazelle, Allen M.; Zelenchuk, Lesya; Fonteles, Andrea H.; Dalal, Parmita; Roy, Anuradha; Chaguturu, Rathnam; Li, Biaoru; Pace, Betty S.

    2014-01-01

    Decades of research have established that the most effective treatment for sickle cell disease (SCD) is increased fetal hemoglobin (HbF). Identification of a drug specific for inducing γ-globin expression in pediatric and adult patients, with minimal off-target effects, continues to be an elusive goal. One hurdle has been an assay amenable to a high-throughput screen (HTS) of chemicals that displays a robust γ-globin off-on switch to identify potential lead compounds. Assay systems developed in our labs to understand the mechanisms underlying the γ- to β-globin gene expression switch during development has allowed us to generate a cell-based assay that was adapted for a HTS of 121,035 compounds. Using chemical inducer of dimerization (CID)-dependent bone marrow cells (BMCs) derived from human γ-globin promoter-firefly luciferase β-globin promoter-Renilla luciferase β-globin yeast artificial chromosome (γ-luc β-luc β-YAC) transgenic mice, we were able to identify 232 lead chemical compounds that induced γ-globin 2-fold or higher, with minimal or no β-globin induction, minimal cytotoxicity and that did not directly influence the luciferase enzyme. Secondary assays in CID-dependent wild-type β-YAC BMCs and human primary erythroid progenitor cells confirmed the induction profiles of seven of the 232 hits that were cherry-picked for further analysis. PMID:25225870

  12. TRPV4 inhibition counteracts edema and inflammation and improves pulmonary function and oxygen saturation in chemically induced acute lung injury

    PubMed Central

    Balakrishna, Shrilatha; Song, Weifeng; Achanta, Satyanarayana; Doran, Stephen F.; Liu, Boyi; Kaelberer, Melanie M.; Yu, Zhihong; Sui, Aiwei; Cheung, Mui; Leishman, Emma; Eidam, Hilary S.; Ye, Guosen; Willette, Robert N.; Thorneloe, Kevin S.; Bradshaw, Heather B.; Matalon, Sadis

    2014-01-01

    The treatment of acute lung injury caused by exposure to reactive chemicals remains challenging because of the lack of mechanism-based therapeutic approaches. Recent studies have shown that transient receptor potential vanilloid 4 (TRPV4), an ion channel expressed in pulmonary tissues, is a crucial mediator of pressure-induced damage associated with ventilator-induced lung injury, heart failure, and infarction. Here, we examined the effects of two novel TRPV4 inhibitors in mice exposed to hydrochloric acid, mimicking acid exposure and acid aspiration injury, and to chlorine gas, a severe chemical threat with frequent exposures in domestic and occupational environments and in transportation accidents. Postexposure treatment with a TRPV4 inhibitor suppressed acid-induced pulmonary inflammation by diminishing neutrophils, macrophages, and associated chemokines and cytokines, while improving tissue pathology. These effects were recapitulated in TRPV4-deficient mice. TRPV4 inhibitors had similar anti-inflammatory effects in chlorine-exposed mice and inhibited vascular leakage, airway hyperreactivity, and increase in elastance, while improving blood oxygen saturation. In both models of lung injury we detected increased concentrations of N-acylamides, a class of endogenous TRP channel agonists. Taken together, we demonstrate that TRPV4 inhibitors are potent and efficacious countermeasures against severe chemical exposures, acting against exaggerated inflammatory responses, and protecting tissue barriers and cardiovascular function. PMID:24838754

  13. TRPV4 inhibition counteracts edema and inflammation and improves pulmonary function and oxygen saturation in chemically induced acute lung injury.

    PubMed

    Balakrishna, Shrilatha; Song, Weifeng; Achanta, Satyanarayana; Doran, Stephen F; Liu, Boyi; Kaelberer, Melanie M; Yu, Zhihong; Sui, Aiwei; Cheung, Mui; Leishman, Emma; Eidam, Hilary S; Ye, Guosen; Willette, Robert N; Thorneloe, Kevin S; Bradshaw, Heather B; Matalon, Sadis; Jordt, Sven-Eric

    2014-07-15

    The treatment of acute lung injury caused by exposure to reactive chemicals remains challenging because of the lack of mechanism-based therapeutic approaches. Recent studies have shown that transient receptor potential vanilloid 4 (TRPV4), an ion channel expressed in pulmonary tissues, is a crucial mediator of pressure-induced damage associated with ventilator-induced lung injury, heart failure, and infarction. Here, we examined the effects of two novel TRPV4 inhibitors in mice exposed to hydrochloric acid, mimicking acid exposure and acid aspiration injury, and to chlorine gas, a severe chemical threat with frequent exposures in domestic and occupational environments and in transportation accidents. Postexposure treatment with a TRPV4 inhibitor suppressed acid-induced pulmonary inflammation by diminishing neutrophils, macrophages, and associated chemokines and cytokines, while improving tissue pathology. These effects were recapitulated in TRPV4-deficient mice. TRPV4 inhibitors had similar anti-inflammatory effects in chlorine-exposed mice and inhibited vascular leakage, airway hyperreactivity, and increase in elastance, while improving blood oxygen saturation. In both models of lung injury we detected increased concentrations of N-acylamides, a class of endogenous TRP channel agonists. Taken together, we demonstrate that TRPV4 inhibitors are potent and efficacious countermeasures against severe chemical exposures, acting against exaggerated inflammatory responses, and protecting tissue barriers and cardiovascular function. PMID:24838754

  14. Causal impressions: predicting when, not just whether.

    PubMed

    Young, Michael E; Rogers, Ester T; Beckmann, Joshua S

    2005-03-01

    In 1739, David Hume established the so-called cues to causality--environmental cues that are important to the inference of causality. Although this descriptive account has been corroborated experimentally, it has not been established why these cues are useful, except that they may reflect statistical regularities in the environment. One of the cues to causality, covariation, helps predict whether an effect will occur, but not its time of occurrence. In the present study, evidence is provided that spatial and temporal contiguity improve an observer's ability to predict when an effect will occur, thus complementing the utility of covariation as a predictor of whether an effect will occur. While observing Michotte's (1946/1963) launching effect, participants showed greater accuracy and precision in their predictions of the onset of movement by the launched object when there was spatial and temporal contiguity. Furthermore, when auditory cues that bridged a delayed launch were included, causal ratings and predictability were similarly affected. These results suggest that the everyday inference of causality relies on our ability to predict whether and when an effect will occur.

  15. Involvement of phospholipase D-related signal transduction in chemical-induced programmed cell death in tomato cell cultures.

    PubMed

    Iakimova, Elena T; Michaeli, Rina; Woltering, Ernst J

    2013-10-01

    Phospholipase D (PLD) and its product phosphatidic acid (PA) are incorporated in a complex metabolic network in which the individual PLD isoforms are suggested to regulate specific developmental and stress responses, including plant programmed cell death (PCD). Despite the accumulating knowledge, the mechanisms through which PLD/PA operate during PCD are still poorly understood. In this work, the role of PLDα1 in PCD and the associated caspase-like proteolysis, ethylene and hydrogen peroxide (H(2)O(2)) synthesis in tomato suspension cells was studied. Wild-type (WT) and PLDα1-silenced cell lines were exposed to the cell death-inducing chemicals camptothecin (CPT), fumonisin B1 (FB1) and CdSO(4). A range of caspase inhibitors effectively suppressed CPT-induced PCD in WT cells, but failed to alleviate cell death in PLDα1-deficient cells. Compared to WT, in CPT-treated PLDα1 mutant cells, reduced cell death and decreased production of H(2)O(2) were observed. Application of ethylene significantly enhanced CPT-induced cell death both in WT and PLDα1 mutants. Treatments with the PA derivative lyso-phosphatidic acid and mastoparan (agonist of PLD/PLC signalling downstream of G proteins) caused severe cell death. Inhibitors, specific to PLD and PLC, remarkably decreased the chemical-induced cell death. Taken together with our previous findings, the results suggest that PLDα1 contributes to caspase-like-dependent cell death possibly communicated through PA, reactive oxygen species and ethylene. The dead cells expressed morphological features of PCD such as protoplast shrinkage and nucleus compaction. The presented findings reveal novel elements of PLD/PA-mediated cell death response and suggest that PLDα1 is an important factor in chemical-induced PCD signal transduction.

  16. A FLUORESCENCE BASED ASSAY FOR DNA DAMAGE INDUCED BY TOXIC INDUSTRIAL CHEMICALS

    EPA Science Inventory

    One of the reported effects for exposure to many of the toxic industrial chemicals is DNA damage. The present study describes a simple, rapid and innovative assay to detect DNA damage resulting from exposure of surrogate DNA to toxic industrial chemicals (acrolein, allylamine, ch...

  17. Causal conjunction fallacies: the roles of causal strength and mental resources.

    PubMed

    Crisp, Aimée Kay; Feeney, Aidan

    2009-12-01

    In two experiments we tested the prediction derived from Tversky and Kahneman's (1983) work on the causal conjunction fallacy that the strength of the causal connection between constituent events directly affects the magnitude of the causal conjunction fallacy. We also explored whether any effects of perceived causal strength were due to graded output from heuristic Type 1 reasoning processes or the result of analytic Type 2 reasoning processes. As predicted, Experiment 1 demonstrated that fallacy rates were higher for strongly than for weakly related conjunctions. Weakly related conjunctions in turn attracted higher rates of fallacious responding than did unrelated conjunctions. Experiment 2 showed that a concurrent memory load increased rates of fallacious responding for strongly related but not for weakly related conjunctions. We interpret these results as showing that manipulations of the strength of the perceived causal relationship between the conjuncts result in graded output from heuristic reasoning process and that additional mental resources are required to suppress strong heuristic output.

  18. Ingested plastic transfers hazardous chemicals to fish and induces hepatic stress

    PubMed Central

    Rochman, Chelsea M.; Hoh, Eunha; Kurobe, Tomofumi; Teh, Swee J.

    2013-01-01

    Plastic debris litters aquatic habitats globally, the majority of which is microscopic (< 1 mm), and is ingested by a large range of species. Risks associated with such small fragments come from the material itself and from chemical pollutants that sorb to it from surrounding water. Hazards associated with the complex mixture of plastic and accumulated pollutants are largely unknown. Here, we show that fish, exposed to a mixture of polyethylene with chemical pollutants sorbed from the marine environment, bioaccumulate these chemical pollutants and suffer liver toxicity and pathology. Fish fed virgin polyethylene fragments also show signs of stress, although less severe than fish fed marine polyethylene fragments. We provide baseline information regarding the bioaccumulation of chemicals and associated health effects from plastic ingestion in fish and demonstrate that future assessments should consider the complex mixture of the plastic material and their associated chemical pollutants. PMID:24263561

  19. Slit2 promotes tumor growth and invasion in chemically induced skin carcinogenesis.

    PubMed

    Qi, Cuiling; Lan, Haimei; Ye, Jie; Li, Weidong; Wei, Ping; Yang, Yang; Guo, Simei; Lan, Tian; Li, Jiangchao; Zhang, Qianqian; He, Xiaodong; Wang, Lijing

    2014-07-01

    Slit, a neuronal guidance cue, binds to Roundabout (Robo) receptors to modulate neuronal, leukocytic, and endothelial migration. Slit has been reported to have an important effect on tumor growth and metastasis. In the current study, we evaluated the role of Slit2 in skin tumor growth and invasion in mice using a two-step chemical carcinogenesis protocol. We found that Slit2 expression correlated with the loss of basement membrane in the samples of human skin squamous cell carcinoma at different stages of disease progression. Slit2-Tg mice developed significantly more skin tumors than wild-type mice. Furthermore, the skin tumors that occurred in Slit2-Tg mice were significantly larger than those in the wild-type mice 10 weeks after 7,12-dimethylbenz[a]anthracene initiation until the end of the experiment. We also found that pathological development of the wild-type mice was delayed compared with that of Slit2-Tg mice. To further investigate the mechanism of increasing tumors in Slit2-Tg mice, we analyzed the expression of 5-bromo-2'-deoxyuridine (BrdU) in mouse skin lesions and found that the number of BrdU-positive cells and microvessel density in skin lesions were significantly higher in Slit2-Tg mice than in wild-type mice. Histological staining of PAS and type IV collagen and the colocalization of Slit2 and type IV collagen demonstrated varying degrees of loss of the basement membrane in the skin lesions from Slit2-Tg mice that were at the stage of carcinoma in situ. However, the basement membrane was well defined in the wild-type mice. In addition, MMP2, but not MMP9, was upregulated in the skin tissue of Slit2-Tg mice. Interruption of Slit2-Robo1 signaling by the antibody R5 significantly repressed the invasive capability of the squamous cell carcinoma cell line A431. Taken together, our findings reveal that Slit2 promotes DMBA/TPA-induced skin tumorigenesis by increasing cell proliferation, microvessel density, and invasive behavior of cutaneous squamous

  20. Photon-induced electro-chemical processes in airless icy bodies analogues

    NASA Astrophysics Data System (ADS)

    Marchione, Demian; Gudipati, Murthy

    2016-10-01

    Previous laboratory studies have shown that radiation-induced ionization of impurities in water-rich ices drives the formation of ionized species resulting in charge generation and accumulation in ices [1-3]. It is expected that some of these impurity ions are decomposed into smaller volatile species and ejected into the vacuum. These processes are relevant to the chemical composition of the near-surface tenuous (thin) atmosphere of icy bodies such as the Jovian satellites like Europa.Our work aims at investigating photocurrents from organic impurity embedded water ices of several microns thick and understanding how these measurements correlate with the desorption of volatiles during UV and electron irradiation. These experiments are performed in an ultrahigh vacuum chamber around Europa's surface temperature (100 – 150 K) conditions using a low-pressure hydrogen flow-discharge lamp emitting primarily at Lyα (121.6 nm), a 2 keV electron source, and a substrate-less electrode. Photoionization of organic impurities in the water matrix results in charge pair (electron and ion) separation within the ice, and hence in detectable currents that are measured as a function of the applied bias and the temperature (5 K – 200 K). Photodesorption products are also identified by a quadrupole mass spectrometer (QMS) and correlated with conductivity measurements. We will discuss these results in the context of expected Europa's surface photoconductivity and near-surface volatile production.References:[1] M. S. Gudipati, and L. J. Allamandola, Astrophysical Journal Letters, 2003, 596(2), L195-L198.[2] M. S. Gudipati, Journal of Physical Chemistry A, 2004, 108(20), 4412-4419.[3] S. H. Cuylle, L. J. Allamandola, and H. Linnartz, Astronomy and Astrophysics, 2014, 562, A22.This work has been carried out at Jet Propulsion Laboratory, California Institute of Technology under a contract with the National Aeronautics and Space Administration, and funded by NASA under Planetary

  1. Permeability Enhancement in Fine-Grained Sediments by Chemically Induced Clay Fabric Shrinkage

    SciTech Connect

    Wijesinghe, A M; Kansa, E J; Viani, B E; Blake, R G; Roberts, J J; Huber, R D

    2004-02-26

    The National Research Council [1] identified the entrapment of contaminants in fine-grained clay-bearing soils as a major impediment to the timely and cost-effective remediation of groundwater to regulatory standards. Contaminants trapped in low-permeability, low-diffusivity, high-sorptivity clays are not accessible to advective flushing by treatment fluids from permeable zones, and slowly diffuse out to recontaminate previously cleaned permeable strata. We propose to overcome this barrier to effective remediation by exploiting the ability of certain nontoxic EPA-approved chemicals (e.g., ethanol) to shrink and alter the fabric of clays, and thereby create macro-porosity and crack networks in fine-grained sediments. This would significantly reduce the distance and time scales of diffusive mass transport to advectively flushed boundaries, to yield orders of magnitude reduction in the time required to complete remediation. Given that effective solutions to this central problem of subsurface remediation do not yet exist, the cost and time benefits of successful deployment of this novel concept, both as a stand-alone technology and as an enabling pre-treatment for other remedial technologies that rely on advective delivery, is likely to be very large. This project, funded as a 1-year feasibility study by LLNL's LDRD Program, is a multi-directorate, multi-disciplinary effort that leverages expertise from the Energy & Environment Directorate, the Environmental Restoration Division, and the Manufacturing & Materials Evaluation Division of Mechanical Engineering. In this feasibility study, a ''proof-of-principle'' experiment was performed to answer the central question: ''Can clay shrinkage induced by ethanol in clay-bearing sediments overcome realistic confining stresses, crack clay, and increase its effective permeability by orders of magnitude within a time that is much smaller than the time required for diffusive mass transport of ethanol in the unaltered sediment

  2. Differentiation of human kidney stones induced by melamine and uric acid using surface desorption atmospheric pressure chemical ionization mass spectrometry.

    PubMed

    Jia, Bin; Ouyang, Yongzhong; Sodhi, Rana N S; Hu, Bin; Zhang, Tingting; Li, Jianqiang; Chen, Huanwen

    2011-03-01

    Clinically obtained human kidney stones of different pathogenesis were dissolved in acetic acid/methanol solutions and then rapidly analyzed by surface desorption atmospheric pressure chemical ionization mass spectrometry (SDAPCI-MS) without any desalination treatment. The mass spectral fingerprints of six groups of kidney stone samples were rapidly recorded in the mass range of m/z 50-400. A set of ten melamine-induced kidney stone samples and nine uric acid derived kidney stone samples were successfully differentiated from other groups by principal component analysis of SDAPCI-MS fingerprints upon positive-ion detection mode. In contrast, the mass spectra recorded using negative-ion detection mode did not give enough information to differentiate those stone samples. The results showed that in addition to the melamine, the chemical compounds enwrapped in the melamine-induced kidney stone samples differed from other kidney stone samples, providing useful hints for studying on the formation mechanisms of melamine-induced kidney stones. This study also provides useful information on establishing a MS-based platform for rapid analysis of the melamine-induced human kidney stones at molecular levels.

  3. Investigation of Shock-Induced Chemical Reactions in Mo-Si Powder Mixtures Using Instrumented Experiments with PVDF Stress Gauges

    SciTech Connect

    Vandersall, K S; Thadhani, N N

    2001-05-29

    Shock-induced chemical reactions in {approx}58% dense Mo+2Si powder mixtures were investigated using time-resolved instrumented experiments, employing PVDF-piezoelectric stress gauges placed at the front and rear surfaces of the powders to measure the input and propagated stresses, and wave speed through the powder mixture. Experiments performed on the powders at input stresses less than 4 GPa, showed characteristics of powder densification and dispersed propagated wave stress profiles with rise time > {approx}40 nanoseconds. At input stress between 4-6 GPa, the powder mixtures showed a sharp rise time (<{approx}10 ns) of propagated wave profile and an expanded state of products revealing evidence of shock-induced chemical reaction. At input stresses greater than 6 GPa, the powder mixtures showed a slower propagated-stress-wave rise time and transition to a low-compressibility (melt) state indicating lack of shock-induced reaction. The results illustrate that premature melting of Si, at input stresses less than the crush-strength of the powder mixtures, restricts mixing between reactants and inhibits ''shock-induced'' reaction initiation.

  4. Causal Phenotype Discovery via Deep Networks

    PubMed Central

    Kale, David C.; Che, Zhengping; Bahadori, Mohammad Taha; Li, Wenzhe; Liu, Yan; Wetzel, Randall

    2015-01-01

    The rapid growth of digital health databases has attracted many researchers interested in using modern computational methods to discover and model patterns of health and illness in a research program known as computational phenotyping. Much of the work in this area has focused on traditional statistical learning paradigms, such as classification, prediction, clustering, pattern mining. In this paper, we propose a related but different paradigm called causal phenotype discovery, which aims to discover latent representations of illness that are causally predictive. We illustrate this idea with a two-stage framework that combines the latent representation learning power of deep neural networks with state-of-the-art tools from causal inference. We apply this framework to two large ICU time series data sets and show that it can learn features that are predictively useful, that capture complex physiologic patterns associated with critical illnesses, and that are potentially more clinically meaningful than manually designed features. PMID:26958203

  5. Normalizing the causality between time series

    NASA Astrophysics Data System (ADS)

    Liang, X. San

    2015-08-01

    Recently, a rigorous yet concise formula was derived to evaluate information flow, and hence the causality in a quantitative sense, between time series. To assess the importance of a resulting causality, it needs to be normalized. The normalization is achieved through distinguishing a Lyapunov exponent-like, one-dimensional phase-space stretching rate and a noise-to-signal ratio from the rate of information flow in the balance of the marginal entropy evolution of the flow recipient. It is verified with autoregressive models and applied to a real financial analysis problem. An unusually strong one-way causality is identified from IBM (International Business Machines Corporation) to GE (General Electric Company) in their early era, revealing to us an old story, which has almost faded into oblivion, about "Seven Dwarfs" competing with a giant for the mainframe computer market.

  6. The causal meaning of Hamilton's rule.

    PubMed

    Okasha, Samir; Martens, Johannes

    2016-03-01

    Hamilton's original derivation of his rule for the spread of an altruistic gene (rb>c) assumed additivity of costs and benefits. Recently, it has been argued that an exact version of the rule holds under non-additive pay-offs, so long as the cost and benefit terms are suitably defined, as partial regression coefficients. However, critics have questioned both the biological significance and the causal meaning of the resulting rule. This paper examines the causal meaning of the generalized Hamilton's rule in a simple model, by computing the effect of a hypothetical experiment to assess the cost of a social action and comparing it to the partial regression definition. The two do not agree. A possible way of salvaging the causal meaning of Hamilton's rule is explored, by appeal to R. A. Fisher's 'average effect of a gene substitution'.

  7. Causal binding of actions to their effects.

    PubMed

    Buehner, Marc J; Humphreys, Gruffydd R

    2009-10-01

    According to widely held views in cognitive science harking back to David Hume, causality cannot be perceived directly, but instead is inferred from patterns of sensory experience, and the quality of these inferences is determined by perceivable quantities such as contingency and contiguity. We report results that suggest a reversal of Hume's conjecture: People's sense of time is warped by the experience of causality. In a stimulus-anticipation task, participants' response behavior reflected a shortened experience of time in the case of target stimuli participants themselves had generated, relative to equidistant, equally predictable stimuli they had not caused. These findings suggest that causality in the mind leads to temporal binding of cause and effect, and extend and generalize beyond earlier claims of intentional binding between action and outcome.

  8. The causal meaning of Hamilton's rule.

    PubMed

    Okasha, Samir; Martens, Johannes

    2016-03-01

    Hamilton's original derivation of his rule for the spread of an altruistic gene (rb>c) assumed additivity of costs and benefits. Recently, it has been argued that an exact version of the rule holds under non-additive pay-offs, so long as the cost and benefit terms are suitably defined, as partial regression coefficients. However, critics have questioned both the biological significance and the causal meaning of the resulting rule. This paper examines the causal meaning of the generalized Hamilton's rule in a simple model, by computing the effect of a hypothetical experiment to assess the cost of a social action and comparing it to the partial regression definition. The two do not agree. A possible way of salvaging the causal meaning of Hamilton's rule is explored, by appeal to R. A. Fisher's 'average effect of a gene substitution'. PMID:27069669

  9. On causality in polymer scalar field theory

    NASA Astrophysics Data System (ADS)

    García-Chung, Angel A.; Morales-Técotl, Hugo A.

    2011-10-01

    The properties of spacetime corresponding to a proposed quantum gravity theory might modify the high energy behavior of quantum fields. Motivated by loop quantum gravity, recently, Hossain et al [1] have considered a polymer field algebra that replaces the standard canonical one in order to calculate the propagator of a real scalar field in flat spacetime. This propagator features Lorentz violations. Motivated by the relation between Lorentz invariance and causality in standard Quantum Field Theory, in this work we investigate the causality behavior of the polymer scalar field.

  10. Identification of transcriptional networks involved in peroxisome proliferator chemical-induced hepatocyte proliferation

    EPA Science Inventory

    Peroxisome proliferator chemical (PPC) exposure leads to increases in rodent liver tumors through a non-genotoxic mode of action (MOA). The PPC MOA includes increased oxidative stress, hepatocyte proliferation and decreased apoptosis. We investigated the putative genetic regulato...

  11. MIXTURES OF THYROID DISRUPTING CHEMICALS: TESTING ADDITIVITY OF HEPATIC INDUCERS AND THYROID PEROXIDASE INHIBITORS.

    EPA Science Inventory

    Humans are exposed to chemical mixtures via diet, occupation, and the environment. Previous data demonstrated that low doses of polycyclic halogenated aromatic hydrocarbons (PHAHs) acting through similar mechanisms result in an additive reduction of thyroxine (T4). If xenobioti...

  12. Use of high content image analysis to detect chemical-induced changes in synaptogenesis in vitro

    EPA Science Inventory

    Synaptogenesis is a critical process in nervous system development whereby neurons establish specialized contact sites which facilitate neurotransmission. There is evidence that early life exposure to chemicals can result in persistent deficits in nervous system function, cogniti...

  13. ToxCast: Developing Predictive Signatures of Chemically Induced Toxicity (S)

    EPA Science Inventory

    ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry, bioactivity profiling and toxicogenomic data to predict potential for toxicity and prioritize limited testing resour...

  14. Protective effects of black rice bran against chemically-induced inflammation of mouse skin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated the inhibitory effects of black rice (cv. LK1-3-6-12-1-1) bran against 12-O-tetradecanolylphorbol-13-acetate (TPA)-induced skin edema and 2,4-dinitroflurobenzene (DNFB)-induced allergic contact dermatitis (ACD) in inflammatory mouse models. We also determined the effects of the bran...

  15. Causality assessment for suspected DILI during clinical phases of drug development.

    PubMed

    Regev, Arie; Seeff, Leonard B; Merz, Michael; Ormarsdottir, Sif; Aithal, Guruprasad P; Gallivan, Jim; Watkins, Paul B

    2014-11-01

    Causality assessment is a critical step in establishing the diagnosis of drug induced liver injury (DILI) during drug development. DILI may resemble almost any type of liver disease, and often presents a serious challenge to clinical investigators and drug makers. The diagnosis of DILI is largely based upon a combination of a compatible clinical course, exclusion of all other reasonable causes, resemblance of clinical and pathological features to known features of liver injury due to the drug (i.e., "drug's signature"), and incidence of liver injury among patients treated with the drug compared to placebo or comparator. Causality assessment for suspected DILI is currently performed using either evaluation by physicians with expertise in liver disorders (i.e., expert opinion) or standardized scoring instruments such as the Roussel Uclaf Causality Assessment Method (RUCAM). Both approaches are widely used in the post marketing setting. Causality assessment based on expert opinion is considered superior to standardized instruments such as RUCAM, in the setting of drug development, and is currently the preferred approach during clinical trials. There is a need for a systematic revision of RUCAM that will render it more suitable for the setting of clinical trials and drug development. Careful monitoring and meticulous data collection during clinical trials are essential in all cases with established liver injury to allow for a proper causality assessment. A workshop was convened to discuss best practices for the assessment of drug-induced liver injury (DILI) in clinical trials. This publication is based on the conclusions of this workshop.

  16. The Load and Time Dependence of Chemical Bonding-Induced Frictional Ageing of Silica at the Nanoscale

    NASA Astrophysics Data System (ADS)

    Tian, K.; Gosvami, N. N.; Goldsby, D. L.; Carpick, R. W.

    2015-12-01

    Rate and state friction (RSF) laws are empirical relationships that describe the frictional behavior of rocks and other materials in experiments, and reproduce a variety of observed natural behavior when employed in earthquake models. A pervasive observation from rock friction experiments is the linear increase of static friction with the log of contact time, or 'ageing'. Ageing is usually attributed to an increase in real area of contact associated with asperity creep. However, recent atomic force microscopy (AFM) experiments demonstrate that ageing of nanoscale silica-silica contacts is due to progressive formation of interfacial chemical bonds in the absence of plastic deformation, in a manner consistent with the multi-contact ageing behavior of rocks [Li et al., 2011]. To further investigate chemical bonding-induced ageing, we explored the influence of normal load (and thus contact normal stress) and contact time on ageing. Experiments that mimic slide-hold-slide rock friction experiments were conducted in the AFM for contact loads and hold times ranging from 23 to 393 nN and 0.1 to 100 s, respectively, all in humid air (~50% RH) at room temperature. Experiments were conducted by sequentially sliding the AFM tip on the sample at a velocity V of 0.5 μm/s, setting V to zero and holding the tip stationary for a given time, and finally resuming sliding at 0.5 μm/s to yield a peak value of friction followed by a drop to the sliding friction value. Chemical bonding-induced ageing, as measured by the peak friction minus the sliding friction, increases approximately linearly with the product of normal load and the log of the hold time. Theoretical studies of the roles of reaction energy barriers in nanoscale ageing indicate that frictional ageing depends on the total number of reaction sites and the hold time [Liu & Szlufarska, 2012]. We combine chemical kinetics analyses with contact mechanics models to explain our results, and develop a new approach for curve

  17. Halogen-induced organic aerosol (XOA): a study on ultra-fine particle formation and time-resolved chemical characterization.

    PubMed

    Ofner, Johannes; Kamilli, Katharina A; Held, Andreas; Lendl, Bernhard; Zetzsch, Cornelius

    2013-01-01

    The concurrent presence of high values of organic SOA precursors and reactive halogen species (RHS) at very low ozone concentrations allows the formation of halogen-induced organic aerosol, so-called XOA, in maritime areas where high concentrations of RHS are present, especially at sunrise. The present study combines aerosol smog-chamber and aerosol flow-reactor experiments for the characterization of XOA. XOA formation yields from alpha-pinene at low and high concentrations of chlorine as reactive halogen species (RHS) were determined using a 700 L aerosol smog-chamber with a solar simulator. The chemical transformation of the organic precursor during the aerosol formation process and chemical aging was studied using an aerosol flow-reactor coupled to an FTIR spectrometer. The FTIR dataset was analysed using 2D correlation spectroscopy. Chlorine induced homogeneous XOA formation takes place at even 2.5 ppb of molecular chlorine, which was photolysed by the solar simulator. The chemical pathway of XOA formation is characterized by the addition of chlorine and abstraction of hydrogen atoms, causing simultaneous carbon-chlorine bond formation. During further steps of the formation process, carboxylic acids are formed, which cause a SOA-like appearance of XOA. During the ozone-free formation of secondary organic aerosol with RHS a special kind of particulate matter (XOA) is formed, which is afterwards transformed to SOA by atmospheric aging or degradation pathways.

  18. Gene expression patterns during the early stages of chemically induced larval metamorphosis and settlement of the coral Acropora millepora.

    PubMed

    Siboni, Nachshon; Abrego, David; Motti, Cherie A; Tebben, Jan; Harder, Tilmann

    2014-01-01

    The morphogenetic transition of motile coral larvae into sessile primary polyps is triggered and genetically programmed upon exposure to environmental biomaterials, such as crustose coralline algae (CCA) and bacterial biofilms. Although the specific chemical cues that trigger coral larval morphogenesis are poorly understood there is much more information available on the genes that play a role in this early life phase. Putative chemical cues from natural biomaterials yielded defined chemical samples that triggered different morphogenetic outcomes: an extract derived from a CCA-associated Pseudoalteromonas bacterium that induced metamorphosis, characterized by non-attached metamorphosed juveniles; and two fractions of the CCA Hydrolithon onkodes (Heydrich) that induced settlement, characterized by attached metamorphosed juveniles. In an effort to distinguish the genes involved in these two morphogenetic transitions, competent larvae of the coral Acropora millepora were exposed to these predictable cues and the expression profiles of 47 coral genes of interest (GOI) were investigated after only 1 hour of exposure using multiplex RT-qPCR. Thirty-two GOI were differentially expressed, indicating a putative role during the early regulation of morphogenesis. The most striking differences were observed for immunity-related genes, hypothesized to be involved in cell recognition and adhesion, and for fluorescent protein genes. Principal component analysis of gene expression profiles resulted in separation between the different morphogenetic cues and exposure times, and not only identified those genes involved in the early response but also those which influenced downstream biological changes leading to larval metamorphosis or settlement.

  19. Rat epidermal keratinocyte organotypic culture (ROC) as a model for chemically induced skin irritation testing

    SciTech Connect

    Pappinen, Sari . E-mail: sari.pappinen@uku.fi; Pasonen-Seppaenen, Sanna; Suhonen, Marjukka; Tammi, Raija; Urtti, Arto

    2005-11-01

    The potential of rat epidermal keratinocyte (REK) organotypic culture (ROC) with proper stratum corneum barrier as a model for screening skin irritants was evaluated. The test chemicals were selected from ECETOC database (1995) and the observed in vitro irritation potential was compared to ECETOC in vivo primary irritation index (PII), to EU risk phrases, and to the harmonized OECD criteria. Chemicals were applied onto the stratum corneum surface of ROC for 30 min and samples were taken from the underlying medium at 4 and 8 h after exposure. Cell membrane integrity (determined by LDH assay) and pro-inflammatory effect (determined by IL-1{alpha} release) were verified at both time points and correlated to PII values. The best correlation (R {sup 2} = 0.831) was seen with LDH leakage test. Based on obtained data, chemicals were classified according to criteria defined by EU and OECD. From 12 chemicals, only two were incorrectly classified according to OECD criteria when using LDH leakage and IL-1{alpha} release as irritation markers. At the end of experiment, chemical-treated ROC cultures were fixed and histological changes were assessed. Typical signs for irritation were lightly stained cytoplasm, condensed nuclei, cellular vacuolization, eosinophilic cytoplasms, and blebbing. These irritation effects of chemicals were graded visually into four classes (A-D). The extent of morphological perturbations of the cultures mostly correlated with PII. The present results indicate the validity of the ROC model in predicting skin irritation potential of chemicals and show that the use of set of irritation markers with different mechanistic responses gives more information on irritation than if only one marker was used.

  20. AKT1E17K Is Oncogenic in Mouse Lung and Cooperates with Chemical Carcinogens in Inducing Lung Cancer

    PubMed Central

    Malanga, Donatella; Belmonte, Stefania; Colelli, Fabiana; Scarfò, Marzia; De Marco, Carmela; Oliveira, Duarte Mendes; Mirante, Teresa; Camastra, Caterina; Gagliardi, Monica; Rizzuto, Antonia; Mignogna, Chiara; Paciello, Orlando; Papparella, Serenella; Fagman, Henrik; Viglietto, Giuseppe

    2016-01-01

    The hotspot AKT1E17K mutation in the pleckstrin homology domain of AKT1 occurs in approximately 0.6–2% of human lung cancers. Recently, we have demonstrated that AKT1E17K transforms immortalized human bronchial cells. Here by use of a transgenic Cre-inducible murine strain in the wild type Rosa26 (R26) locus (R26-AKT1E17K mice) we demonstrate that AKT1E17K is a bona-fide oncogene and plays a role in the development of lung cancer in vivo. In fact, we report that mutant AKT1E17K induces bronchial and/or bronchiolar hyperplastic lesions in murine lung epithelium, which progress to frank carcinoma at very low frequency, and accelerates tumor formation induced by chemical carcinogens. In conclusion, AKT1E17K induces hyperplasia of mouse lung epithelium in vivo and cooperates with urethane to induce the fully malignant phenotype. PMID:26859676

  1. Pride and Prejudice and Causal Indicators

    ERIC Educational Resources Information Center

    Lee, Nick; Chamberlain, Laura

    2016-01-01

    Aguirre-Urreta, Rönkkö, and Marakas' (2016) paper in "Measurement: Interdisciplinary Research and Perspectives" (hereafter referred to as ARM2016) is an important and timely piece of scholarship, in that it provides strong analytic support to the growing theoretical literature that questions the underlying ideas behind causal and…

  2. Comments: Causal Interpretations of Mediation Effects

    ERIC Educational Resources Information Center

    Jo, Booil; Stuart, Elizabeth A.

    2012-01-01

    The authors thank Dr. Lindsay Page for providing a nice illustration of the use of the principal stratification framework to define causal effects, and a Bayesian model for effect estimation. They hope that her well-written article will help expose education researchers to these concepts and methods, and move the field of mediation analysis in…

  3. Escaping Myopia: Teaching Students about Historical Causality

    ERIC Educational Resources Information Center

    Waring, Scott M.

    2010-01-01

    There are so many aspects to teaching history that are vital to creating well-rounded historical thinkers, but one of the most fundamental and most overlooked elements is the idea of causality. Far too many students do not understand the idea of causation, that there are multiple reasons for why historical events occurred and transpired in the way…

  4. Causality and Teleology in High School Biology.

    ERIC Educational Resources Information Center

    Tamir, Pinchas

    1985-01-01

    Ability to distinguish between causal (cause-effect) and teleological (means-ends) explanations was measured in 1905 twelfth-grade biology students and found to be dependent on student knowledge. Although the inability to make these distinctions contributes to misconceptions in biology, appropriate instruction can easily remedy the problem. Sample…

  5. Inductive Reasoning about Causally Transmitted Properties

    ERIC Educational Resources Information Center

    Shafto, Patrick; Kemp, Charles; Bonawitz, Elizabeth Baraff; Coley, John D.; Tenenbaum, Joshua B.

    2008-01-01

    Different intuitive theories constrain and guide inferences in different contexts. Formalizing simple intuitive theories as probabilistic processes operating over structured representations, we present a new computational model of category-based induction about causally transmitted properties. A first experiment demonstrates undergraduates'…

  6. Marriage and Anomie: A Causal Argument

    ERIC Educational Resources Information Center

    Lee, Gary R.

    1974-01-01

    A sample of 394 married couples is employed to test the possibility of an association between marital satisfaction and personal (attitudinal) anomie. The hypothesis is supported. Conclusions are offered relevant to anomie theory, and to utilization of marital and family phenomena as independent variables in causal explanations of nonfamily events.…

  7. Causal Measurement Models: Can Criticism Stimulate Clarification?

    ERIC Educational Resources Information Center

    Markus, Keith A.

    2016-01-01

    In their 2016 work, Aguirre-Urreta et al. provided a contribution to the literature on causal measurement models that enhances clarity and stimulates further thinking. Aguirre-Urreta et al. presented a form of statistical identity involving mapping onto the portion of the parameter space involving the nomological net, relationships between the…

  8. THE CHILD'S CONCEPTION OF PHYSICAL CAUSALITY.

    ERIC Educational Resources Information Center

    PIAGET, JEAN

    THE CHILD'S CONCEPTION OF PHYSICAL CAUSALITY WAS INVESTIGATED. THREE METHODS OF INVESTIGATION WERE USED. THE FIRST METHOD WAS PURELY VERBAL, AND CONSISTED OF A SERIES OF QUESTIONS DIRECTED TO CHILDREN, REGARDING SOME NATURAL PHENOMENON. THE SECOND METHOD INVOLVED A HALF-VERBAL, HALF-PRACTICAL APPROACH, WHEREIN A SPECIFIC REFERENCE TO NATURAL…

  9. A Quantum Probability Model of Causal Reasoning

    PubMed Central

    Trueblood, Jennifer S.; Busemeyer, Jerome R.

    2012-01-01

    People can often outperform statistical methods and machine learning algorithms in situations that involve making inferences about the relationship between causes and effects. While people are remarkably good at causal reasoning in many situations, there are several instances where they deviate from expected responses. This paper examines three situations where judgments related to causal inference problems produce unexpected results and describes a quantum inference model based on the axiomatic principles of quantum probability theory that can explain these effects. Two of the three phenomena arise from the comparison of predictive judgments (i.e., the conditional probability of an effect given a cause) with diagnostic judgments (i.e., the conditional probability of a cause given an effect). The third phenomenon is a new finding examining order effects in predictive causal judgments. The quantum inference model uses the notion of incompatibility among different causes to account for all three phenomena. Psychologically, the model assumes that individuals adopt different points of view when thinking about different causes. The model provides good fits to the data and offers a coherent account for all three causal reasoning effects thus proving to be a viable new candidate for modeling human judgment. PMID:22593747

  10. Constructing Causal Diagrams to Learn Deliberation

    ERIC Educational Resources Information Center

    Easterday, Matthew W.; Aleven, Vincent; Scheines, Richard; Carver, Sharon M.

    2009-01-01

    Policy problems like "What should we do about global warming?" are ill-defined in large part because we do not agree on a system to represent them the way we agree Algebra problems should be represented by equations. As a first step toward building a policy deliberation tutor, we investigated: (a) whether causal diagrams help students learn to…

  11. Strong curvature singularities and causal simplicity

    SciTech Connect

    Krolak, A. )

    1992-02-01

    Techniques of differential topology in Lorentzian manifolds developed by Geroch, Hawking, and Penrose are used to rule out a class of locally naked strong curvature singularities in strongly causal space-times. This result yields some support to the validity of Penrose's strong cosmic censorship hypothesis.

  12. Linear Response Laws and Causality in Electrodynamics

    ERIC Educational Resources Information Center

    Yuffa, Alex J.; Scales, John A.

    2012-01-01

    Linear response laws and causality (the effect cannot precede the cause) are of fundamental importance in physics. In the context of classical electrodynamics, students often have a difficult time grasping these concepts because the physics is obscured by the intermingling of the time and frequency domains. In this paper, we analyse the linear…

  13. Time and Order Effects on Causal Learning

    ERIC Educational Resources Information Center

    Alvarado, Angelica; Jara, Elvia; Vila, Javier; Rosas, Juan M.

    2006-01-01

    Five experiments were conducted to explore trial order and retention interval effects upon causal predictive judgments. Experiment 1 found that participants show a strong effect of trial order when a stimulus was sequentially paired with two different outcomes compared to a condition where both outcomes were presented intermixed. Experiment 2…

  14. Income inequality and health: a causal review.

    PubMed

    Pickett, Kate E; Wilkinson, Richard G

    2015-03-01

    There is a very large literature examining income inequality in relation to health. Early reviews came to different interpretations of the evidence, though a large majority of studies reported that health tended to be worse in more unequal societies. More recent studies, not included in those reviews, provide substantial new evidence. Our purpose in this paper is to assess whether or not wider income differences play a causal role leading to worse health. We conducted a literature review within an epidemiological causal framework and inferred the likelihood of a causal relationship between income inequality and health (including violence) by considering the evidence as a whole. The body of evidence strongly suggests that income inequality affects population health and wellbeing. The major causal criteria of temporality, biological plausibility, consistency and lack of alternative explanations are well supported. Of the small minority of studies which find no association, most can be explained by income inequality being measured at an inappropriate scale, the inclusion of mediating variables as controls, the use of subjective rather than objective measures of health, or follow up periods which are too short. The evidence that large income differences have damaging health and social consequences is strong and in most countries inequality is increasing. Narrowing the gap will improve the health and wellbeing of populations.

  15. [FROM STATISTICAL ASSOCIATIONS TO SCIENTIFIC CAUSALITY].

    PubMed

    Golan, Daniel; Linn, Shay

    2015-06-01

    The pathogenesis of most chronic diseases is complex and probably involves the interaction of multiple genetic and environmental risk factors. One way to learn about disease triggers is from statistically significant associations in epidemiological studies. However, associations do not necessarily prove causation. Associations can commonly result from bias, confounding and reverse causation. Several paradigms for causality inference have been developed. Henle-Koch postulates are mainly applied for infectious diseases. Austin Bradford Hill's criteria may serve as a practical tool to weigh the evidence regarding the probability that a single new risk factor for a given disease is indeed causal. These criteria are irrelevant for estimating the causal relationship between exposure to a risk factor and disease whenever biological causality has been previously established. Thus, it is highly probable that past exposure of an individual to definite carcinogens is related to his cancer, even without proving an association between this exposure and cancer in his group. For multifactorial diseases, Rothman's model of interacting sets of component causes can be applied.

  16. The metagenomic approach and causality in virology.

    PubMed

    Castrignano, Silvana Beres; Nagasse-Sugahara, Teresa Keico

    2015-01-01

    Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease.

  17. Introducing Mechanics by Tapping Core Causal Knowledge

    ERIC Educational Resources Information Center

    Klaassen, Kees; Westra, Axel; Emmett, Katrina; Eijkelhof, Harrie; Lijnse, Piet

    2008-01-01

    This article concerns an outline of an introductory mechanics course. It is based on the argument that various uses of the concept of force (e.g. from Kepler, Newton and everyday life) share an explanatory strategy based on core causal knowledge. The strategy consists of (a) the idea that a force causes a deviation from how an object would move of…

  18. Causality and the Levels of Selection.

    PubMed

    Krupp, D B

    2016-04-01

    When is it sensible to say that group selection has shaped organismal design? This question has prompted many replies but few credible solutions. New work that exposes the causal relationships between phenotypes and fitness may finally settle the matter - and a few other things besides.

  19. The metagenomic approach and causality in virology

    PubMed Central

    Castrignano, Silvana Beres; Nagasse-Sugahara, Teresa Keico

    2015-01-01

    Nowadays, the metagenomic approach has been a very important tool in the discovery of new viruses in environmental and biological samples. Here we discuss how these discoveries may help to elucidate the etiology of diseases and the criteria necessary to establish a causal association between a virus and a disease. PMID:25902566

  20. Causal and Teleological Explanations in Biology

    ERIC Educational Resources Information Center

    Yip, Cheng-Wai

    2009-01-01

    A causal explanation in biology focuses on the mechanism by which a biological process is brought about, whereas a teleological explanation considers the end result, in the context of the survival of the organism, as a reason for certain biological processes or structures. There is a tendency among students to offer a teleological explanation…