Pectobacterium carotovorum. subsp. brasiliense is a causal agent of bacterial leaf rot of tobacco in China

USDA-ARS?s Scientific Manuscript database

A new leaf rot disease of tobacco was found in fields of the Shaowu region, Fujian Province of China in 2015. A typical symptom was necrosis along the main or lateral veins of tobacco leaves, eventually causing wilting and death of the leaves, while the necrosis spread no further than the epidermis ...

Agent-Based Modeling in Public Health: Current Applications and Future Directions.

PubMed

Tracy, Melissa; Cerdá, Magdalena; Keyes, Katherine M

2018-04-01

Agent-based modeling is a computational approach in which agents with a specified set of characteristics interact with each other and with their environment according to predefined rules. We review key areas in public health where agent-based modeling has been adopted, including both communicable and noncommunicable disease, health behaviors, and social epidemiology. We also describe the main strengths and limitations of this approach for questions with public health relevance. Finally, we describe both methodologic and substantive future directions that we believe will enhance the value of agent-based modeling for public health. In particular, advances in model validation, comparisons with other causal modeling procedures, and the expansion of the models to consider comorbidity and joint influences more systematically will improve the utility of this approach to inform public health research, practice, and policy.

Domain-specific perceptual causality in children depends on the spatio-temporal configuration, not motion onset

PubMed Central

Schlottmann, Anne; Cole, Katy; Watts, Rhianna; White, Marina

2013-01-01

Humans, even babies, perceive causality when one shape moves briefly and linearly after another. Motion timing is crucial in this and causal impressions disappear with short delays between motions. However, the role of temporal information is more complex: it is both a cue to causality and a factor that constrains processing. It affects ability to distinguish causality from non-causality, and social from mechanical causality. Here we study both issues with 3- to 7-year-olds and adults who saw two computer-animated squares and chose if a picture of mechanical, social or non-causality fit each event best. Prior work fit with the standard view that early in development, the distinction between the social and physical domains depends mainly on whether or not the agents make contact, and that this reflects concern with domain-specific motion onset, in particular, whether the motion is self-initiated or not. The present experiments challenge both parts of this position. In Experiments 1 and 2, we showed that not just spatial, but also animacy and temporal information affect how children distinguish between physical and social causality. In Experiments 3 and 4 we showed that children do not seem to use spatio-temporal information in perceptual causality to make inferences about self- or other-initiated motion onset. Overall, spatial contact may be developmentally primary in domain-specific perceptual causality in that it is processed easily and is dominant over competing cues, but it is not the only cue used early on and it is not used to infer motion onset. Instead, domain-specific causal impressions may be automatic reactions to specific perceptual configurations, with a complex role for temporal information. PMID:23874308

Helicobacter pylori infection as a cause of gastritis, duodenal ulcer, gastric cancer and nonulcer dyspepsia: a systematic overview.

PubMed

Veldhuyzen van Zanten, S J; Sherman, P M

1994-01-15

To evaluate current evidence for a causal relation between Helicobacter pylori infection and gastritis, duodenal ulcer, gastric cancer and nonulcer dyspepsia. A MEDLINE search for articles published in English between January 1983 and December 1992 with the use of MeSH terms Helicobacter pylori, gastritis, duodenal ulcer, gastric cancer, dyspepsia and clinical trial; abstracts were excluded. Six journals and Current Contents were searched manually for pertinent articles published in that time frame. Original studies with at least 25 patients, case reports and reviews that examined the relation between H. pylori and the four gastrointestinal disorders; 350 articles were on gastritis, 122 on duodenal ulcer, 44 on gastric cancer and 96 on nonulcer dyspepsia. The quality of the studies was rated independently on a four-point scale. The strength of the evidence was assessed using a six-point scale for each of the eight established guidelines for determining a causal relation. There was conclusive evidence of a causal relation between H. pylori infection and histologic gastritis. Koch's postulates for the identification of a microorganism as the causative agent of a disease were fulfilled for H. pylori as a causative agent of gastritis. There was strong evidence that H. pylori is the main cause of duodenal ulcers not induced by nonsteroidal anti-inflammatory drugs, but all of Koch's postulates were not fulfilled. There was moderate epidemiologic evidence of an association between chronic H. pylori infection and gastric cancer. There was a lack of convincing evidence of a causal association between H. pylori and nonulcer dyspepsia. The evidence supports a strong causal relation between H. pylori infection and gastritis and duodenal ulcer and a moderate relation between such infection and gastric cancer. Further studies are needed to clarify the role of H. pylori in these disorders. Thus far, there is no evidence of a causal relation between H. pylori and nonulcer dyspepsia.

Helicobacter pylori infection as a cause of gastritis, duodenal ulcer, gastric cancer and nonulcer dyspepsia: a systematic overview.

PubMed Central

Veldhuyzen van Zanten, S J; Sherman, P M

1994-01-01

OBJECTIVE: To evaluate current evidence for a causal relation between Helicobacter pylori infection and gastritis, duodenal ulcer, gastric cancer and nonulcer dyspepsia. DATA SOURCES: A MEDLINE search for articles published in English between January 1983 and December 1992 with the use of MeSH terms Helicobacter pylori, gastritis, duodenal ulcer, gastric cancer, dyspepsia and clinical trial; abstracts were excluded. Six journals and Current Contents were searched manually for pertinent articles published in that time frame. STUDY SELECTION: Original studies with at least 25 patients, case reports and reviews that examined the relation between H. pylori and the four gastrointestinal disorders; 350 articles were on gastritis, 122 on duodenal ulcer, 44 on gastric cancer and 96 on nonulcer dyspepsia. DATA EXTRACTION: The quality of the studies was rated independently on a four-point scale. The strength of the evidence was assessed using a six-point scale for each of the eight established guidelines for determining a causal relation. DATA SYNTHESIS: There was conclusive evidence of a causal relation between H. pylori infection and histologic gastritis. Koch's postulates for the identification of a microorganism as the causative agent of a disease were fulfilled for H. pylori as a causative agent of gastritis. There was strong evidence that H. pylori is the main cause of duodenal ulcers not induced by nonsteroidal anti-inflammatory drugs, but all of Koch's postulates were not fulfilled. There was moderate epidemiologic evidence of an association between chronic H. pylori infection and gastric cancer. There was a lack of convincing evidence of a causal association between H. pylori and nonulcer dyspepsia. CONCLUSIONS: The evidence supports a strong causal relation between H. pylori infection and gastritis and duodenal ulcer and a moderate relation between such infection and gastric cancer. Further studies are needed to clarify the role of H. pylori in these disorders. Thus far, there is no evidence of a causal relation between H. pylori and nonulcer dyspepsia. PMID:8287340

White rot of garlic and onion (Causal agent, Sclerotium cepivorum): A status report from the Pacific Northwest

USDA-ARS?s Scientific Manuscript database

There is evidence from literature, state department of agriculture documents, and recent diagnoses that Sclerotium cepivorum, causal agent of white rot of garlic and onion, is spreading and/or becoming more established in the Pacific Northwest. Previously documented distributions are summarized, an...

A simple culture method inducing sexual reproduction by Fusarium graminearum, the primary causal agent of Fusarium head blight

USDA-ARS?s Scientific Manuscript database

The homothallic ascomycete fungus Fusarium graminearum is the primary causal agent of Fusarium head blight (FHB), a devastating disease of wheat and barley worldwide. The fungus undergoes both asexual and sexual stages in its life cycle. The asexual stage produces conidiospores, whereas the sexual s...

In vitro evidence for sexual reproduction in Venturia effusa, causal agent of pecan scab

USDA-ARS?s Scientific Manuscript database

Venturia effusa is the causal agent of pecan scab, the most prevalent disease of pecan in the southeastern US. Venturia effusa is currently only known to reproduce asexually, yet the genetic diversity among populations of pecan scab suggest it is a sexually reproducing pathogen. Analysis of the mati...

Diversity of endophytic fungal community of cacao (Theobroma cacao L.) and biological control of Crinipellis perniciosa, causal agent of Witches' Broom Disease

PubMed Central

2005-01-01

The basidiomycete fungus Crinipellis perniciosa (Stahel) Singer is the causal agent of Witches' Broom Disease of Cacao (Theobroma cacao L.) which is the main factor limiting cacao production in the Americas. Pod losses of up to 90% are experienced in affected areas as evidenced by the 50% drop in production in Bahia province, Brazil following the arrival of the C. perniciosa in the area in 1989. The disease has proven particularly difficult to control and many farmers in affected areas have given up cacao cultivation. In order to evaluate the potential of endophytes as a biological control agent of this phytopathogen, the endophytic fungal community of resistant and susceptible cacao plants as well as affected branches was studied between 2001 and 2002. The fungal community was identified by morphological traits and rDNA sequencing as belonging to the genera Acremonium, Blastomyces, Botryosphaeria, Cladosporium, Colletotrichum, Cordyceps, Diaporthe, Fusarium, Geotrichum, Gibberella, Gliocladium, Lasiodiplodia, Monilochoetes, Nectria, Pestalotiopsis, Phomopsis, Pleurotus, Pseudofusarium, Rhizopycnis, Syncephalastrum, Trichoderma, Verticillium and Xylaria. These fungi were evaluated both in vitro and in vivo by their ability to inhibit C. perniciosa. Among these, some were identified as potential antagonists, but only one fungus (Gliocladium catenulatum) reduced the incidence of Witches' Broom Disease in cacao seedlings to 70%. PMID:15951847

Diversity of endophytic fungal community of cacao (Theobroma cacao L.) and biological control of Crinipellis perniciosa, causal agent of Witches' Broom Disease.

PubMed

Rubini, Marciano R; Silva-Ribeiro, Rute T; Pomella, Alan W V; Maki, Cristina S; Araújo, Welington L; Dos Santos, Deise R; Azevedo, João L

2005-01-01

The basidiomycete fungus Crinipellis perniciosa (Stahel) Singer is the causal agent of Witches' Broom Disease of Cacao (Theobromacacao L.) which is the main factor limiting cacao production in the Americas. Pod losses of up to 90% are experienced in affected areas as evidenced by the 50% drop in production in Bahia province, Brazil following the arrival of the C. perniciosa in the area in 1989. The disease has proven particularly difficult to control and many farmers in affected areas have given up cacao cultivation. In order to evaluate the potential of endophytes as a biological control agent of this phytopathogen, the endophytic fungal community of resistant and susceptible cacao plants as well as affected branches was studied between 2001 and 2002. The fungal community was identified by morphological traits and rDNA sequencing as belonging to the genera Acremonium, Blastomyces, Botryosphaeria, Cladosporium, Colletotrichum, Cordyceps, Diaporthe, Fusarium, Geotrichum, Gibberella, Gliocladium, Lasiodiplodia, Monilochoetes, Nectria, Pestalotiopsis, Phomopsis, Pleurotus, Pseudofusarium, Rhizopycnis, Syncephalastrum, Trichoderma, Verticillium and Xylaria. These fungi were evaluated both in vitro and in vivo by their ability to inhibit C. perniciosa. Among these, some were identified as potential antagonists, but only one fungus (Gliocladium catenulatum) reduced the incidence of Witches' Broom Disease in cacao seedlings to 70%.

Draft Genome Sequence of an Isolate of Colletotrichum fructicola, a Causal Agent of Mango Anthracnose.

PubMed

Li, Qili; Bu, Junyan; Yu, Zhihe; Tang, Lihua; Huang, Suiping; Guo, Tangxun; Mo, Jianyou; Hsiang, Tom

2018-02-22

Here, we present a draft genome sequence of isolate 15060 of Colletotrichum fructicola , a causal agent of mango anthracnose. The final assembly consists of 1,048 scaffolds totaling 56,493,063 bp (G+C content, 53.38%) and 15,180 predicted genes. Copyright © 2018 Li et al.

Potential of Pest and Host Phenological Data in the Attribution of Regional Forest Disturbance Detection Maps According to Causal Agent

NASA Technical Reports Server (NTRS)

Spruce, Joseph; Hargrove, William; Norman Steve; Christie, William

2014-01-01

Near real time forest disturbance detection maps from MODIS NDVI phenology data have been produced since 2010 for the conterminous U.S., as part of the on-line ForWarn national forest threat early warning system. The latter has been used by the forest health community to identify and track many regional forest disturbances caused by multiple biotic and abiotic damage agents. Attribution of causal agents for detected disturbances has been a goal since project initiation in 2006. Combined with detailed cover type maps, geospatial pest phenology data offer a potential means for narrowing the candidate causal agents responsible for a given biotic disturbance. U.S. Aerial Detection Surveys (ADS) employ such phenology data. Historic ADS products provide general locational data on recent insect-induced forest type specific disturbances that may help in determining candidate causal agents for MODIS-based disturbance maps, especially when combined with other historic geospatial disturbance data (e.g., wildfire burn scars and drought maps). Historic ADS disturbance detection polygons can show severe and extensive regional forest disturbances, though they also can show polygons with sparsely scattered or infrequent disturbances. Examples will be discussed that use various historic disturbance data to help determine potential causes of MODIS-detected regional forest disturbance anomalies.

Evaluating Social Causality and Responsibility Models: An Initial Report

DTIC Science & Technology

2005-01-01

ICT Technical Report ICT-TR-03-2005 Evaluating Social Causality and Responsibility ... social intelligent agents. In this report, we present a general computational model of social causality and responsibility , and empirical results of...2005 to 00-00-2005 4. TITLE AND SUBTITLE Evaluating Social Causality and Responsibility Models: An Initial Report 5a. CONTRACT NUMBER 5b. GRANT

Toxicology and Epidemiology: Improving the Science with a Framework for Combining Toxicological and Epidemiological Evidence to Establish Causal Inference

PubMed Central

Adami, Hans-Olov; Berry, Sir Colin L.; Breckenridge, Charles B.; Smith, Lewis L.; Swenberg, James A.; Trichopoulos, Dimitrios; Weiss, Noel S.; Pastoor, Timothy P.

2011-01-01

Historically, toxicology has played a significant role in verifying conclusions drawn on the basis of epidemiological findings. Agents that were suggested to have a role in human diseases have been tested in animals to firmly establish a causative link. Bacterial pathogens are perhaps the oldest examples, and tobacco smoke and lung cancer and asbestos and mesothelioma provide two more recent examples. With the advent of toxicity testing guidelines and protocols, toxicology took on a role that was intended to anticipate or predict potential adverse effects in humans, and epidemiology, in many cases, served a role in verifying or negating these toxicological predictions. The coupled role of epidemiology and toxicology in discerning human health effects by environmental agents is obvious, but there is currently no systematic and transparent way to bring the data and analysis of the two disciplines together in a way that provides a unified view on an adverse causal relationship between an agent and a disease. In working to advance the interaction between the fields of toxicology and epidemiology, we propose here a five-step “Epid-Tox” process that would focus on: (1) collection of all relevant studies, (2) assessment of their quality, (3) evaluation of the weight of evidence, (4) assignment of a scalable conclusion, and (5) placement on a causal relationship grid. The causal relationship grid provides a clear view of how epidemiological and toxicological data intersect, permits straightforward conclusions with regard to a causal relationship between agent and effect, and can show how additional data can influence conclusions of causality. PMID:21561883

Executive Emotional System Disruption as Causal Agent in Frontal Lobishness among Abused Children

ERIC Educational Resources Information Center

Naude, H.; Du Preez, C. S.; Pretorius, E.

2004-01-01

This article aims to explore Executive Emotional System (EES) disruption as causal agent in frontal lobishness among abused children. The "Revised Senior South African Individual Scale" (SSAIS-R) was used to assess a sample population of seventy-five male and female subjects between the ages of 8 years 0 months and 16 years 11 months who were…

Variable Number of Tandem Repeat Markers in the Genome Sequence of Mycosphaerella Fijiensis, the Causal Agent of Black Leaf Streak Disease of Banana (Musa spp.)

USDA-ARS?s Scientific Manuscript database

Mycosphaerella fijiensis, the causal agent of banana leaf streak disease (commonly known as black Sigatoka), is the most devastating pathogen attacking bananas (Musa spp). Recently the whole genome sequence of M. fijiensis became available. This sequence was screened for the presence of Variable Num...

Thermal inactivation of infested plants, nursery equipment, and soil is a management option for the treatment of Phytophthora ramorum, causal agent of sudden oak death

Treesearch

Wolfgang Schweigkofler; Vernon Huffman; Karen Suslow; Kathleen Kosta

2017-01-01

Infected nursery plants play an important role in the spread of Phytophthora ramorum , the causal agent of sudden oak death and ramorum blight. In order to minimize the risk for disease transmission to new areas, nurseries are inspected regularly for P. ramorum , and federal regulations require the eradication of...

Effect of the lactoperoxidase system against three major causal agents of disease in mangoes.

PubMed

Le Nguyen, Doan Duy; Ducamp, Marie-Noelle; Dornier, Manuel; Montet, Didier; Loiseau, Gérard

2005-07-01

The antibacterial activity of the lactoperoxidase system (LPS) on the growth of Xanthomonas campestris, the causal agent of bacterial black spot in mangoes, Botryodiplodia theobromae, the causal agent of stem-end rot disease in mangoes, and Colletotrichum gloeosporioides, the causal agent of anthracnose disease in mangoes, was determined during culture at 30 degrees C and at several pH values (4.5, 5.5, and 6.5). When the results of using the LPS were compared with those from control cultures without the LPS reagents, the growth of the three microorganisms was totally inhibited in all of the conditions tested. Viability tests enumerating cultivable cells of X. campestris showed that the LPS had a bactericidal effect, whatever the pH value. This effect is faster at pH 5.5, corroborating the results reported in the literature (optimal pH for the LPS efficiency). Further, we proved that hydrogen peroxide alone had little inhibition effect on the growth of the microorganisms studied. This compound is essentially used to convert thiocyanate into hypothiocyanate during the lactoperoxidase reaction. The potential of the LPS for the postharvest treatment of the fruits for controlling microbial diseases was thus demonstrated. Nevertheless, further studies are needed on fresh fruits before envisaging any application.

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…

Sources of information on lymphoma associated with anti-tumour necrosis factor agents: comparison of published case reports and cases reported to the French pharmacovigilance system.

PubMed

Théophile, Hélène; Schaeverbeke, Thierry; Miremont-Salamé, Ghada; Abouelfath, Abdelilah; Kahn, Valentine; Haramburu, Françoise; Bégaud, Bernard

2011-07-01

Anti-tumour necrosis factor (TNF) agents, through their intense immunoregulatory effect, have been suspected to increase the risk of malignant lymphoma. However, the classical epidemiological approaches conducted over about the last 10 years have not totally succeeded in addressing the question of a causal or artifactual association. Therefore, the analysis of a substantial set of case reports, although usually considered as poorly generalizable to the general population, could be particularly informative. Two main sources of case reports in postmarketing settings are available; publications in medical journals and reports to pharmacovigilance systems. The aim of the study was to compare the characteristics of case reports from both these sources in order to understand whether they provided the same information for the investigation of the causal link between lymphoma and anti-TNF agents. All case reports of malignant lymphoma in patients treated with an anti-TNF agent published in MEDLINE and all reports to the French pharmacovigilance system up to 1 February 2010 were identified. Cases of malignant lymphoma identified in postmarketing surveillance from both sources were compared regarding the following variables: age, sex, anti-TNF agent involved, indication for use, type of lymphoma, prior or concomitant immunosuppressive drugs and time to onset of lymphoma. A total of 81 published case reports and 61 cases reported to the French pharmacovigilance system were compared. In published reports, patients were younger (p = 0.03) and more frequently receiving a first anti-TNF treatment (p = 0.03), particularly infliximab (p = 0.03). Conversely, in the pharmacovigilance system reports, a succession of different anti-TNFs (p = 0.03) and adalimumab (p < 0.0001) were more frequently reported. Lymphomas in patients treated with anti-TNF agents for Crohn's disease were more prevalent in published cases than in pharmacovigilance reports (p < 0.0001), and in particular involved hepatosplenic T-cell lymphoma. Conversely, rheumatoid arthritis was the main indication for anti-TNF agents in pharmacovigilance reports (p = 0.01). Time to onset was markedly shorter in published cases (median 12 months) than in pharmacovigilance reports (median 30 months; p = 0.0001). Characteristics of published cases and those reported to the French pharmacovigilance system differed markedly for all characteristics tested, except sex and the use of prior or concomitant immunosuppressive drugs. Published case reports favoured convincing arguments for drug causation whereas cases reported to the pharmacovigilance system were more disparate but could describe more accurately the reality of lymphoma occurrence in this particular population. These results argue for the use of the pharmacovigilance reports when case reports are used to investigate the causal link between lymphoma and anti-TNF agents at the population level. Data from cases notified to the French pharmacovigilance system did not indicate an increased risk of lymphoma during the early phase of anti-TNF treatment. To confirm this hypothesis, a study combining pharmacovigilance reports from several countries, or, if feasible, a cohort study both with a large sample size and a long duration of follow-up would be required.

Effects of Manipulation on Attributions of Causation, Free Will, and Moral Responsibility.

PubMed

Murray, Dylan; Lombrozo, Tania

2017-03-01

If someone brings about an outcome without intending to, is she causally and morally responsible for it? What if she acts intentionally, but as the result of manipulation by another agent? Previous research has shown that an agent's mental states can affect attributions of causal and moral responsibility to that agent, but little is known about what effect one agent's mental states can have on attributions to another agent. In Experiment 1, we replicate findings that manipulation lowers attributions of responsibility to manipulated agents. Experiments 2-7 isolate which features of manipulation drive this effect, a crucial issue for both philosophical debates about free will and attributions of responsibility in situations involving social influence more generally. Our results suggest that "bypassing" a manipulated agent's mental states generates the greatest reduction in responsibility, and we explain our results in terms of the effects that one agent's mental states can have on the counterfactual relations between another agent and an outcome. Copyright © 2016 Cognitive Science Society, Inc.

[Drug-induced gynecomastia].

PubMed

Hugues, F C; Gourlot, C; Le Jeunne, C

2000-02-01

Drugs are a very common cause of gynecomastia and should always be entertained as the possible causal agent of such a condition. This drug side-effect is due to an impaired balance in the serum estrogen/serum androgen ratio, whatever the mechanism, or a rise in prolactin level. Sex hormones, antiandrogens, are frequently involved as well as spironolactone, cimetidine, verapamil and cancer chemotherapy (especially alkylating agents). Diazepam, tricyclic antidepressants, neuroleptics, calcium channel blockers, captopril, digitalis glycosides, omeprazole, some antibiotics and growth hormone are all possibly, but less often, the responsible agent. Criteria of the French method for determining drug causality are discussed.

The Reactive-Causal Architecture: Introducing an Emotion Model along with Theories of Needs

NASA Astrophysics Data System (ADS)

Aydin, Ali Orhan; Orgun, Mehmet Ali

In the entertainment application area, one of the major aims is to develop believable agents. To achieve this aim, agents should be highly autonomous, situated, flexible, and display affect. The Reactive-Causal Architecture (ReCau) is proposed to simulate these core attributes. In its current form, ReCau cannot explain the effects of emotions on intelligent behaviour. This study aims is to further improve the emotion model of ReCau to explain the effects of emotions on intelligent behaviour. This improvement allows ReCau to be emotional to support the development of believable agents.

Femoral-facial syndrome with malformations in the central nervous system.

PubMed

Leal, Evelia; Macías-Gómez, Nelly; Rodríguez, Lisa; Mercado, F Miguel; Barros-Núñez, Patricio

2003-01-01

The femoral hypoplasia-unusual facies syndrome (FFS) is a very rare association of femoral and facial abnormalities. Maternal diabetes mellitus has been mainly involved as the causal agent. We report the second case of FFS with anomalies in the central nervous system (CNS) including corticosubcortical atrophy, colpocephaly, partial agenesis of corpus callosum, hypoplasia of the falx cerebri and absent septum pellucidum. The psychomotor development has been normal. We propose that the CNS defects observed in these patients are part of the spectrum of abnormalities in the FFS.

Manipulating Morality: Third-Party Intentions Alter Moral Judgments by Changing Causal Reasoning.

PubMed

Phillips, Jonathan; Shaw, Alex

2015-08-01

The present studies investigate how the intentions of third parties influence judgments of moral responsibility for other agents who commit immoral acts. Using cases in which an agent acts under some situational constraint brought about by a third party, we ask whether the agent is blamed less for the immoral act when the third party intended for that act to occur. Study 1 demonstrates that third-party intentions do influence judgments of blame. Study 2 finds that third-party intentions only influence moral judgments when the agent's actions precisely match the third party's intention. Study 3 shows that this effect arises from changes in participants' causal perception that the third party was controlling the agent. Studies 4 and 5, respectively, show that the effect cannot be explained by changes in the distribution of blame or perceived differences in situational constraint faced by the agent. © 2014 Cognitive Science Society, Inc.

Assessing the Effectiveness of Cumulative Sum Normal- and Poisson-Based Tests for Detecting Rare Diseases

DTIC Science & Technology

2010-12-01

The Francisella tularensis is one of these and is the causal agent of the tularemia disease. Tularemia is used as the motivating problem to evaluate...PAGES 79 14. SUBJECT TERMS Biosurveillance, Rare Disease, Tularemia , Cumulative Sum, CUSUM 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT...is one of these, and is the causal agent of the tularemia disease. Tularemia is used as the motivating problem to evaluate and compare the

The causal structure of utility conditionals.

PubMed

Bonnefon, Jean-François; Sloman, Steven A

2013-01-01

The psychology of reasoning is increasingly considering agents' values and preferences, achieving greater integration with judgment and decision making, social cognition, and moral reasoning. Some of this research investigates utility conditionals, ''if p then q'' statements where the realization of p or q or both is valued by some agents. Various approaches to utility conditionals share the assumption that reasoners make inferences from utility conditionals based on the comparison between the utility of p and the expected utility of q. This article introduces a new parameter in this analysis, the underlying causal structure of the conditional. Four experiments showed that causal structure moderated utility-informed conditional reasoning. These inferences were strongly invited when the underlying structure of the conditional was causal, and significantly less so when the underlying structure of the conditional was diagnostic. This asymmetry was only observed for conditionals in which the utility of q was clear, and disappeared when the utility of q was unclear. Thus, an adequate account of utility-informed inferences conditional reasoning requires three components: utility, probability, and causal structure. Copyright © 2012 Cognitive Science Society, Inc.

ASSOCIATIONS BETWEEN MEASURES OF BEDDED SEDIMENTS AND STREAM LIFE

EPA Science Inventory

Associations between causal agents and biological effects are necessary for the development of water quality criteria and, when combined with information from a site, can provide evidence for causal analysis. These associations can be obtained from controlled laboratory studies ...

Causal Model of Stress and Coping: Women in Management.

ERIC Educational Resources Information Center

Long, Bonita C.; And Others

1992-01-01

Tested model of managerial women's (n=249) stress. Model was developed from Lazarus's theoretical framework of stress/coping and incorporated causal antecedent constructs (demographics, sex role attitudes, agentic traits), mediating constructs (environment, appraisals, engagement coping, disengagement coping), and outcomes (work performance,…

[Burns in childhood. Social implications in the eve of the year 2000].

PubMed

Abad, P; Acosta, D; Martínez Ibáñez, V; Lloret, J; Patiño, B; Gubern, L; Carol, J; Boix Ochoa, J

2000-07-01

The thermic wounds in childhood are the third cause of morbility at hospital in our ambiance. The knowledge about incidence, the causal agents more frequent, and the detailed analysis of different variants about the subject are the unique manner to try to establish precautions against. The aim of this project is to analyse the factors and situations associated with thermic wound, through the retrospective study about the patients admitted. During three years, 362 patients were admitted at hospital, between 0 and 14 years old, following the criterion: barge burn size more than 10%, critical location (hands, face, neck), causal agent (electricity, chemical) or social situation. Different facts were analyzed about provenance, place, causal agent, burned part of the body, degree of lesion and the average stay at hospital. There were 59.6% males, and 40.3% females. Children between 1 and 5 years old, represented the largest group of patients, 205 cases. The 66% were from other hospital were they receive the first aid. The 98.7% were burned at home, and the place more frequent was kitchen, 51%. The causal agent was liquid in 65.4%, specially scald with water about 104 cases. The zones more affected were the face (39.2%), and the superior extremities, about 81% second degree superficial or deep. The size was 10 to 20% in 19% of patients, and more than 40% in 0.2% of children. The average stay was 17.47 days at hospital.

[Intraoperative floppy iris syndrome after treatment with duloxetine: coincidence, association, or causality?].

PubMed

González-Martín-Moro, J; González-López, J J; Zarallo-Gallardo, J; Fernández-Miguel, Y

2015-02-01

The case is presented of a severe Intraoperative Floppy Iris Syndrome (IFIS) in a patient that had been treated with duloxetine. Tamsulosin is the main etiological agent involved in IFIS. However several cases of IFIS, supposedly secondary to drugs of different groups have recently been reported in the literature. The authors use this case report as a means to discuss why most of these cases should be considered anecdotal evidence. Copyright © 2014 Sociedad Española de Oftalmología. Published by Elsevier España, S.L.U. All rights reserved.

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…

Purple spot damage dynamics investigated by an integrated approach on a 1244 A.D. parchment roll from the Secret Vatican Archive.

PubMed

Migliore, Luciana; Thaller, Maria Cristina; Vendittozzi, Giulia; Mejia, Astrid Yazmine; Mercuri, Fulvio; Orlanducci, Silvia; Rubechini, Alessandro

2017-09-07

Ancient parchments are commonly attacked by microbes, producing purple spots and detachment of the superficial layer. Neither standard cultivation nor molecular methods (DGGE) solved the issue: causative agents and colonization model are still unknown. To identify the putative causal agents, we describe the 16 S rRNA gene analysis (454-pyrosequencing) of the microbial communities colonizing a damaged parchment roll dated 1244 A.D. (A.A. Arm. I-XVIII 3328, Vatican Secret Archives). The taxa in damaged or undamaged areas of the same document were different. In the purple spots, marine halotolerant Gammaproteobacteria, mainly Vibrio, were found; these microorganisms are rare or absent in the undamaged areas. Ubiquitous and environmental microorganisms were observed in samples from both damaged and undamaged areas. Pseudonocardiales were the most common, representing the main colonizers of undamaged areas. We hypothesize a successional model of biodeterioration, based on metagenomic data and spectroscopic analysis of pigments, which help to relate the damage to a microbial agent. Furthermore, a new method (Light Transmitted Analysis) was utilized to evaluate the kind and entity of the damage to native collagen. These data give a significant advance to the knowledge in the field and open new perspectives to remediation activity on a huge amount of ancient document.

Molecular characterization and pathogenicity assays of Colletotrichum acutatum, causal agent for lime anthracnose in Texas

USDA-ARS?s Scientific Manuscript database

Several distorted Mexican lime [Citrus aurantiifolia (Christm). Swingle] fruit, leaf, and twig samples with lime anthracnose symptoms were collected from three trees in residential areas of Brownsville, Texas. The causal fungal organism, Colletotrichum acutatum J. H. Simmonds was isolated from leave...

The Agent-based Approach: A New Direction for Computational Models of Development.

ERIC Educational Resources Information Center

Schlesinger, Matthew; Parisi, Domenico

2001-01-01

Introduces the concepts of online and offline sampling and highlights the role of online sampling in agent-based models of learning and development. Compares the strengths of each approach for modeling particular developmental phenomena and research questions. Describes a recent agent-based model of infant causal perception. Discusses limitations…

Preparing Students for Future Learning with Teachable Agents

ERIC Educational Resources Information Center

Chin, Doris B.; Dohmen, Ilsa M.; Cheng, Britte H.; Oppezzo, Marily A.; Chase, Catherine C.; Schwartz, Daniel L.

2010-01-01

Over the past several years, the authors have been developing an instructional technology, called Teachable Agents (TA), which draws on the social metaphor of teaching to help students learn. Students teach a computer character, their "agent," by creating a concept map of nodes connected by qualitative causal links. The authors hypothesize that…

A Non-Mentalistic Cause-Based Heuristic in Human Social Evaluations

ERIC Educational Resources Information Center

Buon, Marine; Jacob, Pierre; Loissel, Elsa; Dupoux, Emmanuel

2013-01-01

In situations where an agent unintentionally causes harm to a victim, the agent's (harmless) intention typically carries "more" weight than his/her (harmful) causal role. Therefore, healthy adults typically judge leniently agents responsible for an accident. Using animated cartoons, we show, however, that in the presence of a difficult concurrent…

Characterization of a Colletotrichum population causing anthracnose disease on Olive in northern Tunisia.

PubMed

Chattaoui, M; Raya, M C; Bouri, M; Moral, J; Perez-Rodriguez, M; Trapero, A; Msallem, M; Rhouma, A

2016-05-01

To phenotypically, physiologically and molecularly characterize the causal agent of olive anthracnose in the northern Tunisia and to study its genetic variability and pathogenicity. A total of 43 isolates were obtained from symptomatic olives collected from four regions in northern Tunisia. A range of morphological and physiological characteristics was recorded; and a phylogenetic study, based on the sequence analysis of both internal transcribed spacers and TUB2 gene regions, was performed. Of the 43 isolates, 41 were identified as Colletotrichum acutatum s.s, and only two were affiliated to Colletotrichum gloeosporioides s.s. Two more representative Spanish isolates, included for comparison, were identified as Colletotrichum godetiae. Using six inter-simple-sequence-repeat markers, homogeneity between isolates from different locations and within the same species was recorded. In pathogenicity and virulence studies, C. gloeosporioides s.s was found to be less virulent, while the Spanish C. godetiae isolate was significantly more virulent than the Tunisian C. acutatum s.s. Olive anthracnose in the North of Tunisia is mainly caused by C. acutatum s.s species. This is the first study of olive anthracnose in Tunisia, which combines both phenotypic and molecular approaches. Colletotrichum acutatum s.s group was recorded for the first time in the country as the causal agent of olive anthracnose. © 2016 The Society for Applied Microbiology.

A novel fungal hyperparasite of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust

USDA-ARS?s Scientific Manuscript database

Puccinia striiformis f. sp. tritici (Pst), the causal fungus of wheat stripe rust, was previously reported to be infected by Lecanicillium lecanii, Microdochium nivale and Typhula idahoensis. Here, we report a novel hyperparasite on Pst. This hyperparasitic fungus was identified as Cladosporium clad...

Exceptionalist naturalism: Human agency and the causal order.

PubMed

Turri, John

2018-02-01

This paper addresses a fundamental question in folk metaphysics: How do we ordinarily view human agency? According to the transcendence account, we view human agency as standing outside of the causal order and imbued with exceptional powers. According to a naturalistic account, we view human agency as subject to the same physical laws as other objects and completely open to scientific investigation. According to exceptionalist naturalism, the truth lies somewhere in between: We view human agency as fitting broadly within the causal order while still being exceptional in important respects. In this paper, I report seven experiments designed to decide between these three competing theories. Across a variety of contexts and types of action, participants agreed that human agents can resist outcomes described as inevitable, guaranteed, and causally determined. Participants viewed non-human animal agents similarly, whereas they viewed computers, robots, and simple inanimate objects differently. At the same time, participants judged that human actions are caused by many things, including psychological, neurological, and social events. Overall, in folk metaphysics, human and non-human animals are viewed as exceptional parts of the natural world.

Money creation and circulation in a credit economy

NASA Astrophysics Data System (ADS)

Xiong, Wanting; Fu, Han; Wang, Yougui

2017-01-01

This paper presents a multi-agent model describing the main mechanisms of money creation and money circulation in a credit economy. Our special attention is paid to the role of debt in the two processes. With the agent-based modeling approach, macro phenomena are well founded in micro-based causalities. A hypothetical economy composed of a banking system and multiple traders is proposed. Instead of being a pure financial intermediary, the banking system is viewed as the center of money creation and an accelerator of money circulation. Agents finance their expenditures not only by their own savings but also through bank loans. Through mathematical calculations and numerical simulation, we identify the determinants of money multiplier and those of velocity of money. In contrast to the traditional money creation model, the money multiplier is determined not only by the behavior of borrowing but also by the behavior of repayment as well. The velocity of money is found to be influenced by both money-related factors such as the expenditure habits of agents with respect to their income and wealth and debt-related factors such as borrowing and repayment behaviors of debtors and the reserve requirements faced by banks.

Experimental antibiotic treatment identifies potential pathogens of white band disease in the endangered Caribbean coral Acropora cervicornis

PubMed Central

Sweet, M. J.; Croquer, A.; Bythell, J. C.

2014-01-01

Coral diseases have been increasingly reported over the past few decades and are a major contributor to coral decline worldwide. The Caribbean, in particular, has been noted as a hotspot for coral disease, and the aptly named white syndromes have caused the decline of the dominant reef building corals throughout their range. White band disease (WBD) has been implicated in the dramatic loss of Acropora cervicornis and Acropora palmata since the 1970s, resulting in both species being listed as critically endangered on the International Union for Conservation of Nature Red list. The causal agent of WBD remains unknown, although recent studies based on challenge experiments with filtrate from infected hosts concluded that the disease is probably caused by bacteria. Here, we report an experiment using four different antibiotic treatments, targeting different members of the disease-associated microbial community. Two antibiotics, ampicillin and paromomycin, arrested the disease completely, and by comparing with community shifts brought about by treatments that did not arrest the disease, we have identified the likely candidate causal agent or agents of WBD. Our interpretation of the experimental treatments is that one or a combination of up to three specific bacterial types, detected consistently in diseased corals but not detectable in healthy corals, are likely causal agents of WBD. In addition, a histophagous ciliate (Philaster lucinda) identical to that found consistently in association with white syndrome in Indo-Pacific acroporas was also consistently detected in all WBD samples and absent in healthy coral. Treatment with metronidazole reduced it to below detection limits, but did not arrest the disease. However, the microscopic disease signs changed, suggesting a secondary role in disease causation for this ciliate. In future studies to identify a causal agent of WBD via tests of Henle–Koch's postulates, it will be vital to experimentally control for populations of the other potential pathogens identified in this study. PMID:24943374

Experimental antibiotic treatment identifies potential pathogens of white band disease in the endangered Caribbean coral Acropora cervicornis.

PubMed

Sweet, M J; Croquer, A; Bythell, J C

2014-08-07

Coral diseases have been increasingly reported over the past few decades and are a major contributor to coral decline worldwide. The Caribbean, in particular, has been noted as a hotspot for coral disease, and the aptly named white syndromes have caused the decline of the dominant reef building corals throughout their range. White band disease (WBD) has been implicated in the dramatic loss of Acropora cervicornis and Acropora palmata since the 1970s, resulting in both species being listed as critically endangered on the International Union for Conservation of Nature Red list. The causal agent of WBD remains unknown, although recent studies based on challenge experiments with filtrate from infected hosts concluded that the disease is probably caused by bacteria. Here, we report an experiment using four different antibiotic treatments, targeting different members of the disease-associated microbial community. Two antibiotics, ampicillin and paromomycin, arrested the disease completely, and by comparing with community shifts brought about by treatments that did not arrest the disease, we have identified the likely candidate causal agent or agents of WBD. Our interpretation of the experimental treatments is that one or a combination of up to three specific bacterial types, detected consistently in diseased corals but not detectable in healthy corals, are likely causal agents of WBD. In addition, a histophagous ciliate (Philaster lucinda) identical to that found consistently in association with white syndrome in Indo-Pacific acroporas was also consistently detected in all WBD samples and absent in healthy coral. Treatment with metronidazole reduced it to below detection limits, but did not arrest the disease. However, the microscopic disease signs changed, suggesting a secondary role in disease causation for this ciliate. In future studies to identify a causal agent of WBD via tests of Henle-Koch's postulates, it will be vital to experimentally control for populations of the other potential pathogens identified in this study.

SALMON RECOVERY: CATEGORIZING AGENTS, DRIVERS, AND DELUSIONS

EPA Science Inventory

Throughout the southern region of western North America, many wild salmon stocks have declined and some have disappeared. The decline was induced by an extensively studied combination of causal agents. The public appears to support reversing the downward trajectory for wild sal...

SAN-RL: combining spreading activation networks and reinforcement learning to learn configurable behaviors

NASA Technical Reports Server (NTRS)

White, J.; Gaines, D. M.; Wilkes, M.; Kusumalnukool, K.; Thongchai, S.; Kawamura, K.

2001-01-01

This approach provides the agent with a causal structure, the spreading activation network, relating goals to the actions that can achieve those goals. This enables the agent to select actions relative to the goal priorities.

Modeling and Evaluating Emotions Impact on Cognition

DTIC Science & Technology

2013-07-01

Causality and Responsibility Judgment in Multi-Agent Interactions: Extended abstract. 23rd International Joint Conference on Artificial Inteligence ...responsibility judgment in multi-agent interactions." Journal of Artificial Intelligence Research v44(1), 223- 273. • Morteza Dehghani, Jonathan Gratch... Artificial Intelligence (AAAI’11). Grant related invited talks: • Keynote speaker, Workshop on Empathic and Emotional Agents at the International

Domain Generality and Specificity in Children's Causal Inference about Ambiguous Data

ERIC Educational Resources Information Center

Sobel, David M.; Munro, Sarah E.

2009-01-01

In 5 experiments the authors examined children's understanding of causal mechanisms and their reasoning about base rates across domains of knowledge. Experiment 1 showed that 3-year-olds interpret objects activating a machine differently from a novel agent liking each object; children are more likely to treat the latter as indicating the objects…

The Role of Causal and Intentional Judgments in Moral Reasoning in Individuals with High Functioning Autism

ERIC Educational Resources Information Center

Buon, Marine; Dupoux, Emmanuel; Jacob, Pierre; Chaste, Pauline; Leboyer, Marion; Zalla, Tiziana

2013-01-01

In the present study, we investigated the ability to assign moral responsibility and punishment in adults with high functioning autism or Asperger Syndrome (HFA/AS), using non-verbal cartoons depicting an aggression, an accidental harm or a mere coincidence. Participants were asked to evaluate the agent's causal and intentional roles, his…

A Causal Model of Career Development and Quality of Life of College Students with Disabilities

ERIC Educational Resources Information Center

Chun, Jina

2017-01-01

Researchers have assumed that social cognitive factors play significant roles in the career development of transition youth and young adults with disabilities and those without disabilities. However, research on the influence of the career decision-making process as a primary causal agent in one's psychosocial outcomes such as perceived level of…

Combining Human and Machine Intelligence to Derive Agents' Behavioral Rules for Groundwater Irrigation

NASA Astrophysics Data System (ADS)

Hu, Y.; Quinn, C.; Cai, X.

2015-12-01

One major challenge of agent-based modeling is to derive agents' behavioral rules due to behavioral uncertainty and data scarcity. This study proposes a new approach to combine a data-driven modeling based on the directed information (i.e., machine intelligence) with expert domain knowledge (i.e., human intelligence) to derive the behavioral rules of agents considering behavioral uncertainty. A directed information graph algorithm is applied to identifying the causal relationships between agents' decisions (i.e., groundwater irrigation depth) and time-series of environmental, socio-economical and institutional factors. A case study is conducted for the High Plains aquifer hydrological observatory (HO) area, U.S. Preliminary results show that four factors, corn price (CP), underlying groundwater level (GWL), monthly mean temperature (T) and precipitation (P) have causal influences on agents' decisions on groundwater irrigation depth (GWID) to various extents. Based on the similarity of the directed information graph for each agent, five clusters of graphs are further identified to represent all the agents' behaviors in the study area as shown in Figure 1. Using these five representative graphs, agents' monthly optimal groundwater pumping rates are derived through the probabilistic inference. Such data-driven relationships and probabilistic quantifications are then coupled with a physically-based groundwater model to investigate the interactions between agents' pumping behaviors and the underlying groundwater system in the context of coupled human and natural systems.

Human agency in social cognitive theory.

PubMed

Bandura, A

1989-09-01

The present article examines the nature and function of human agency within the conceptual model of triadic reciprocal causation. In analyzing the operation of human agency in this interactional causal structure, social cognitive theory accords a central role to cognitive, vicarious, self-reflective, and self-regulatory processes. The issues addressed concern the psychological mechanisms through which personal agency is exercised, the hierarchical structure of self-regulatory systems, eschewal of the dichotomous construal of self as agent and self as object, and the properties of a nondualistic but nonreductional conception of human agency. The relation of agent causality to the fundamental issues of freedom and determinism is also analyzed.

Chilli anthracnose disease caused by Colletotrichum species.

PubMed

Than, Po Po; Prihastuti, Haryudian; Phoulivong, Sitthisack; Taylor, Paul W J; Hyde, Kevin D

2008-10-01

Anthracnose disease is one of the major economic constraints to chilli production worldwide, especially in tropical and subtropical regions. Accurate taxonomic information is necessary for effective disease control management. In the Colletotrichum patho-system, different Colletotrichum species can be associated with anthracnose of the same host. Little information is known concerning the interactions of the species associated with the chilli anthracnose although several Colletotrichum species have been reported as causal agents of chilli anthracnose disease worldwide. The ambiguous taxonomic status of Colletotrichum species has resulted in inaccurate identification which may cause practical problems in plant breeding and disease management. Although the management and control of anthracnose disease are still being extensively researched, commercial cultivars of Capsicum annuum that are resistant to the pathogens that cause chilli anthracnose have not yet been developed. This paper reviews the causal agents of chilli anthracnose, the disease cycle, conventional methods in identification of the pathogen and molecular approaches that have been used for the identification of Colletotrichum species. Pathogenetic variation and population structure of the causal agents of chilli anthracnose along with the current taxonomic status of Colletotrichum species are discussed. Future developments leading to the disease management strategies are suggested.

Chilli anthracnose disease caused by Colletotrichum species§

PubMed Central

Than, Po Po; Prihastuti, Haryudian; Phoulivong, Sitthisack; Taylor, Paul W.J.; Hyde, Kevin D.

2008-01-01

Anthracnose disease is one of the major economic constraints to chilli production worldwide, especially in tropical and subtropical regions. Accurate taxonomic information is necessary for effective disease control management. In the Colletotrichum patho-system, different Colletotrichum species can be associated with anthracnose of the same host. Little information is known concerning the interactions of the species associated with the chilli anthracnose although several Colletotrichum species have been reported as causal agents of chilli anthracnose disease worldwide. The ambiguous taxonomic status of Colletotrichum species has resulted in inaccurate identification which may cause practical problems in plant breeding and disease management. Although the management and control of anthracnose disease are still being extensively researched, commercial cultivars of Capsicum annuum that are resistant to the pathogens that cause chilli anthracnose have not yet been developed. This paper reviews the causal agents of chilli anthracnose, the disease cycle, conventional methods in identification of the pathogen and molecular approaches that have been used for the identification of Colletotrichum species. Pathogenetic variation and population structure of the causal agents of chilli anthracnose along with the current taxonomic status of Colletotrichum species are discussed. Future developments leading to the disease management strategies are suggested. PMID:18837103

Obesity and infection: reciprocal causality.

PubMed

Hainer, V; Zamrazilová, H; Kunešová, M; Bendlová, B; Aldhoon-Hainerová, I

2015-01-01

Associations between different infectious agents and obesity have been reported in humans for over thirty years. In many cases, as in nosocomial infections, this relationship reflects the greater susceptibility of obese individuals to infection due to impaired immunity. In such cases, the infection is not related to obesity as a causal factor but represents a complication of obesity. In contrast, several infections have been suggested as potential causal factors in human obesity. However, evidence of a causal linkage to human obesity has only been provided for adenovirus 36 (Adv36). This virus activates lipogenic and proinflammatory pathways in adipose tissue, improves insulin sensitivity, lipid profile and hepatic steatosis. The E4orf1 gene of Adv36 exerts insulin senzitizing effects, but is devoid of its pro-inflammatory modalities. The development of a vaccine to prevent Adv36-induced obesity or the use of E4orf1 as a ligand for novel antidiabetic drugs could open new horizons in the prophylaxis and treatment of obesity and diabetes. More experimental and clinical studies are needed to elucidate the mutual relations between infection and obesity, identify additional infectious agents causing human obesity, as well as define the conditions that predispose obese individuals to specific infections.

A causal analysis framework for land-use change and the potential role of bioenergy policy

DOE PAGES

Efroymson, Rebecca A.; Kline, Keith L.; Angelsen, Arild; ...

2016-10-05

Here we propose a causal analysis framework to increase the reliability of land-use change (LUC) models and the accuracy of net greenhouse gas (GHG) emissions calculations for biofuels. The health-sciences-inspired framework is used here to determine probable causes of LUC, with an emphasis on bioenergy and deforestation. Calculations of net GHG emissions for LUC are critical in determining whether a fuel qualifies as a biofuel or advanced biofuel category under national (U.S., U.K.), state (California), and European Union regulations. Biofuel policymakers and scientists continue to discuss whether presumed indirect land-use change (ILUC) estimates, which often involve deforestation, should be includedmore » in GHG accounting for biofuel pathways. Current estimates of ILUC for bioenergy rely largely on economic simulation models that focus on causal pathways involving global commodity trade and use coarse land cover data with simple land classification systems. ILUC estimates are highly uncertain, partly because changes are not clearly defined and key causal links are not sufficiently included in the models. The proposed causal analysis framework begins with a definition of the change that has occurred and proceeds to a strength-of-evidence approach based on types of epidemiological evidence including plausibility of the relationship, completeness of the causal pathway, spatial co-occurrence, time order, analogous agents, simulation model results, and quantitative agent response relationships.Lastly, we discuss how LUC may be allocated among probable causes for policy purposes and how the application of the framework has the potential to increase the validity of LUC models and resolve ILUC and biofuel controversies.« less

A causal analysis framework for land-use change and the potential role of bioenergy policy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Efroymson, Rebecca A.; Kline, Keith L.; Angelsen, Arild

Here we propose a causal analysis framework to increase the reliability of land-use change (LUC) models and the accuracy of net greenhouse gas (GHG) emissions calculations for biofuels. The health-sciences-inspired framework is used here to determine probable causes of LUC, with an emphasis on bioenergy and deforestation. Calculations of net GHG emissions for LUC are critical in determining whether a fuel qualifies as a biofuel or advanced biofuel category under national (U.S., U.K.), state (California), and European Union regulations. Biofuel policymakers and scientists continue to discuss whether presumed indirect land-use change (ILUC) estimates, which often involve deforestation, should be includedmore » in GHG accounting for biofuel pathways. Current estimates of ILUC for bioenergy rely largely on economic simulation models that focus on causal pathways involving global commodity trade and use coarse land cover data with simple land classification systems. ILUC estimates are highly uncertain, partly because changes are not clearly defined and key causal links are not sufficiently included in the models. The proposed causal analysis framework begins with a definition of the change that has occurred and proceeds to a strength-of-evidence approach based on types of epidemiological evidence including plausibility of the relationship, completeness of the causal pathway, spatial co-occurrence, time order, analogous agents, simulation model results, and quantitative agent response relationships.Lastly, we discuss how LUC may be allocated among probable causes for policy purposes and how the application of the framework has the potential to increase the validity of LUC models and resolve ILUC and biofuel controversies.« less

On the Self-Organizing Origins of Agency.

PubMed

Kelso, J A Scott

2016-07-01

The question of agency and directedness in living systems has puzzled philosophers and scientists for centuries. What principles and mechanisms underlie the emergence of agency? Analysis and dynamical modeling of experiments on human infants suggest that the birth of agency is due to a eureka-like, pattern-forming phase transition in which the infant suddenly realizes it can make things happen in the world. The main mechanism involves positive feedback: when the baby's initially spontaneous movements cause the world to change, their perceived consequences have a sudden and sustained amplifying effect on the baby's further actions. The baby discovers itself as a causal agent. Some implications of this theory are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

A new approach for embedding causal sets into Minkowski space

NASA Astrophysics Data System (ADS)

Liu, He; Reid, David D.

2018-06-01

This paper reports on recent work toward an approach for embedding causal sets into two-dimensional Minkowski space. The main new feature of the present scheme is its use of the spacelike distance measure to construct an ordering of causal set elements within anti-chains of a causal set as an aid to the embedding procedure.

Draft genome sequence of Xylaria sp., the causal agent of taproot decline of soybean in the southern United States.

PubMed

Sharma, Sandeep; Zaccaron, Alex Z; Ridenour, John B; Allen, Tom W; Conner, Kassie; Doyle, Vinson P; Price, Trey; Sikora, Edward; Singh, Raghuwinder; Spurlock, Terry; Tomaso-Peterson, Maria; Wilkerson, Tessie; Bluhm, Burton H

2018-04-01

The draft genome of Xylaria sp. isolate MSU_SB201401, causal agent of taproot decline of soybean in the southern U.S., is presented here. The genome assembly was 56.7 Mb in size with an L50 of 246. A total of 10,880 putative protein-encoding genes were predicted, including 647 genes encoding carbohydrate-active enzymes and 1053 genes encoding secreted proteins. This is the first draft genome of a plant-pathogenic Xylaria sp. associated with soybean. The draft genome of Xylaria sp. isolate MSU_SB201401 will provide an important resource for future experiments to determine the molecular basis of pathogenesis.

Evidence implicating Thamnostylum lucknowense as an etiological agent of Rhino-orbital Mucormycosis

USDA-ARS?s Scientific Manuscript database

In this report, we present a case of rhino-orbital mucormycosis in a 57-year-old female with poorly controlled diabetes mellitus. The causal agent was cultured from a specimen of the nasal crust and identified phenotypically and independently using nuclear ribosomal DNA sequence data as Thamnostylum...

Heterothallic sexual reproduction in three canker-inducing tree pathogens within the Fusarium torreyae clade

USDA-ARS?s Scientific Manuscript database

Fusarium zanthoxyli and F. continuum are sister taxa that were recently discovered to be the etiological agents of an economically important canker disease of prickly ash trees (Zanthoxylum bungeanum) in northern China. These two pathogens together with F. torreyae, the causal agent of canker diseas...

The Host-Agent-Environment Concept of Accidents.

ERIC Educational Resources Information Center

Phillips, Don

Background information is presented to indicate that accidents are an environmental health problem. While accidents are seldom thought to be a disease process, in many ways there are remarkable similarities--not only in terms of causal relationships, but also in preventive aspects. These parallels are described in terms of host-agent-environment…

One wouldn't expect an expert bowler to hit only two pins: Hierarchical predictive processing of agent-caused events.

PubMed

Heil, Lieke; Kwisthout, Johan; van Pelt, Stan; van Rooij, Iris; Bekkering, Harold

2018-01-01

Evidence is accumulating that our brains process incoming information using top-down predictions. If lower level representations are correctly predicted by higher level representations, this enhances processing. However, if they are incorrectly predicted, additional processing is required at higher levels to "explain away" prediction errors. Here, we explored the potential nature of the models generating such predictions. More specifically, we investigated whether a predictive processing model with a hierarchical structure and causal relations between its levels is able to account for the processing of agent-caused events. In Experiment 1, participants watched animated movies of "experienced" and "novice" bowlers. The results are in line with the idea that prediction errors at a lower level of the hierarchy (i.e., the outcome of how many pins fell down) slow down reporting of information at a higher level (i.e., which agent was throwing the ball). Experiments 2 and 3 suggest that this effect is specific to situations in which the predictor is causally related to the outcome. Overall, the study supports the idea that a hierarchical predictive processing model can account for the processing of observed action outcomes and that the predictions involved are specific to cases where action outcomes can be predicted based on causal knowledge.

CAUSAL ANALYSIS OF BIOLOGICAL IMPAIRMENT IN LONG CREEK, A SANDY-BOTTOMED STREAM IN COASTAL SOUTHERN MAINE (Final Report)

EPA Science Inventory

This assessment presents results from a complex causal assessment of a biologically impaired, urbanized coastal watershed located primarily in South Portland, Maine, USA—the Long Creek watershed. This case study serves as an example implementation of U.S. Environmental Protectio...

A Comparison of Agent-Based Models and the Parametric G-Formula for Causal Inference.

PubMed

Murray, Eleanor J; Robins, James M; Seage, George R; Freedberg, Kenneth A; Hernán, Miguel A

2017-07-15

Decision-making requires choosing from treatments on the basis of correctly estimated outcome distributions under each treatment. In the absence of randomized trials, 2 possible approaches are the parametric g-formula and agent-based models (ABMs). The g-formula has been used exclusively to estimate effects in the population from which data were collected, whereas ABMs are commonly used to estimate effects in multiple populations, necessitating stronger assumptions. Here, we describe potential biases that arise when ABM assumptions do not hold. To do so, we estimated 12-month mortality risk in simulated populations differing in prevalence of an unknown common cause of mortality and a time-varying confounder. The ABM and g-formula correctly estimated mortality and causal effects when all inputs were from the target population. However, whenever any inputs came from another population, the ABM gave biased estimates of mortality-and often of causal effects even when the true effect was null. In the absence of unmeasured confounding and model misspecification, both methods produce valid causal inferences for a given population when all inputs are from that population. However, ABMs may result in bias when extrapolated to populations that differ on the distribution of unmeasured outcome determinants, even when the causal network linking variables is identical. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Summarizing Simulation Results using Causally-relevant States

PubMed Central

Parikh, Nidhi; Marathe, Madhav; Swarup, Samarth

2016-01-01

As increasingly large-scale multiagent simulations are being implemented, new methods are becoming necessary to make sense of the results of these simulations. Even concisely summarizing the results of a given simulation run is a challenge. Here we pose this as the problem of simulation summarization: how to extract the causally-relevant descriptions of the trajectories of the agents in the simulation. We present a simple algorithm to compress agent trajectories through state space by identifying the state transitions which are relevant to determining the distribution of outcomes at the end of the simulation. We present a toy-example to illustrate the working of the algorithm, and then apply it to a complex simulation of a major disaster in an urban area. PMID:28042620

Characterization of Mycobacterium salmoniphilum as causal agent of mycobacteriosis in Atlantic salmon, Salmo salar L., from a freshwater recirculation system.

PubMed

Aro, L; Correa, K; Martínez, A; Ildefonso, R; Yáñez, J M

2014-04-01

Thirty Atlantic salmon, Salmo salar L., with low corporal condition relative to other fish present in the culture system, were sampled from a freshwater recirculation pisciculture located in Chile. The most characteristic signs and lesions were cachexia and presence of multiple greyish-white granulomas within internal organs. The external and internal lesions, along with the microscopic, histologic and biochemical findings, were consistent with mycobacteriosis. The identification of Mycobacterium salmoniphilum as the causal agent of the lesions was possible through the use of molecular analyses. This study represents the first report of Mycobacterium salmoniphilum in a freshwater recirculation system and the first case of fish mycobacteriosis described in Chile. © 2013 John Wiley & Sons Ltd.

Bioaerosol exposure assessment in the workplace: the past, present and recent advances.

PubMed

Eduard, Wijnand; Heederik, Dick; Duchaine, Caroline; Green, Brett James

2012-02-01

Louis Pasteur described the first measurements of airborne microorganisms in 1861. A century later, the inhalation of spores from thermophilic microorganisms was shown to induce attacks of farmers' lung in patients with this disease, while endotoxins originating from Gram-negative bacteria were identified as causal agents for byssinosis in cotton workers. Further epidemiological and toxicological studies have demonstrated inflammatory, respiratory, and pathogenic effects following exposure to bioaerosols. Exposure assessment is often confounded by the diversity of bioaerosol agents in the environment. Microorganisms represent a highly diverse group that may vary in toxicity. Fungi and bacteria are mainly quantified as broad groups using a variety of viable and nonviable assessment methods. Endotoxins and β(1 → 3)-glucans are mainly measured by their activity in the Limulus amebocyte lysate assay, enzymes by immuno-chemical methods and mycotoxins by liquid chromatography-mass spectrometry. Few health-based occupational exposure limits (OELs) are available for risk assessment. For endotoxins, a health-based OEL of 90 endotoxin units m(-3) has been proposed in the Netherlands. A criteria document for fungal spores recently proposed a lowest observed effect level of 100,000 spores m(-3) for non-pathogenic and non-mycotoxin producing species based on inflammatory respiratory effects. Recent developments in bioaerosol assessment were presented at the Organic Dust Tromsø Symposium including molecular biological methods for infectious agents and organisms that are difficult to cultivate; studies of submicronic and hyphal fragments from fungi; the effect of biodiversity of microorganisms in asthma studies; and new/improved measurement methods for fungal antigens, enzymes and allergens. Although exposure assessment of bioaerosol agents is complex and limited by the availability of methods and criteria, the field is rapidly evolving.

Changes in the Fusarium Head Blight Complex of Malting Barley in a Three-Year Field Experiment in Italy

PubMed Central

Beccari, Giovanni; Prodi, Antonio; Tini, Francesco; Bonciarelli, Umberto; Onofri, Andrea; Oueslati, Souheib; Limayma, Marwa; Covarelli, Lorenzo

2017-01-01

In this study, conducted for three years on eleven malting barley varieties cultivated in central Italy, the incidence of different mycotoxigenic fungal genera, the identification of the Fusarium species associated with the Fusarium Head Blight (FHB) complex, and kernels contamination with deoxynivalenol (DON) and T-2 mycotoxins were determined. The influence of climatic conditions on Fusarium infections and FHB complex composition was also investigated. Fusarium species were always present in the three years and the high average and maximum temperatures during anthesis mainly favored their occurrence. The FHB complex was subject to changes during the three years and the main causal agents were F. poae, F. avenaceum, F. tricinctum and F. graminearum, which, even if constantly present, never represented the principal FHB agent. The relative incidence of Fusarium species changed because of climatic conditions occurring during the seasons. The FHB complex was composed of many different Fusarium species and some of them were associated with a specific variety and/or with specific weather parameters, indicating that the interaction between a certain plant genotype and climatic conditions may influence the presence of Fusarium spp. causing infections. With regard to mycotoxin contamination, T-2 toxin, in some cases, was found in kernels at levels that exceeded EU recommended values. PMID:28353653

Accounting for occurrences: an explanation for some novel tendencies in causal judgment from contingency information.

PubMed

White, Peter A

2009-06-01

Contingency information is information about empirical associations between possible causes and outcomes. In the present research, it is shown that, under some circumstances, there is a tendency for negative contingencies to lead to positive causal judgments and for positive contingencies to lead to negative causal judgments. If there is a high proportion of instances in which a candidate cause (CC) being judged is present, these tendencies are predicted by weighted averaging models of causal judgment. If the proportion of such instances is low, the predictions of weighted averaging models break down. It is argued that one of the main aims of causal judgment is to account for occurrences of the outcome. Thus, a CC is not given a high causal judgment if there are few or no occurrences of it, regardless of the objective contingency. This argument predicts that, if there is a low proportion of instances in which a CC is present, causal judgments are determined mainly by the number of Cell A instances (i.e., CC present, outcome occurs), and that this explains why weighted averaging models fail to predict judgmental tendencies under these circumstances. Experimental results support this argument.

On Non-Universality of Solar-Terrestrial Connections

NASA Astrophysics Data System (ADS)

Pustilnik, Lev; Yom Din, Gregory

The discussion on the principal possibility of a causal chain from solar activity and space weather to the earth weather and agriculture price dynamics continues over 200 years from the first publication of Herschel (1801) up to the current time. We analyze main arguments of the two sides and show that the root of the critics of this possibility lies in the wide accepted conception of the universality of the solar-terrestrial connection (that can appear, for example, in daily and seasonal variations) what suggest that the effect can be observed in any historical period and in any region. We show that this expectation is not correct because of the solar-terrestrial connections generated by different sides of solar activity with different agents of solar magnetic dynamo process that have different and non-stable phase patterns. We remind that the realization of the causal chain “solar activity/space weather” - “earth weather” - “crops” -“market reaction” may have a place only in specific historical periods and in specific zones where and when the three necessary conditions hold true. This limitation leads to one of four possible scenarios of the market reaction. We show that the critical arguments used for rejecting a principal possibility of the causal connection “solar activity” - Earth agriculture markets” are based on neglecting the three necessary conditions for realization of this connection, and on analyzing periods and regions when and where the necessary conditions are not hold.

Volatile organic compounds produced by a soil-isolate, Bacillus subtilis FA26 induce adverse ultra-structural changes to the cells of Clavibacter michiganensis ssp. sepedonicus, the causal agent of bacterial ring rot of potato.

PubMed

Rajer, Faheem Uddin; Wu, Huijun; Xie, Yongli; Xie, Shanshan; Raza, Waseem; Tahir, Hafiz Abdul Samad; Gao, Xuewen

2017-04-01

Rhizobacterial volatile organic compounds (VOCs) play an important role in the suppression of soil-borne phytopathogens. In this study, the VOCs produced by a soil-isolate, Bacillus subtilis FA26, were evaluated in vitro for their antibacterial activity against Clavibacter michiganensis ssp. sepedonicus (Cms), the causal agent of bacterial ring rot of potato. The VOCs emitted by FA26 inhibited the growth of Cms significantly compared with the control. Scanning and transmission electron microscopy analyses revealed distorted colony morphology and a wide range of abnormalities in Cms cells exposed to the VOCs of FA26. Varying the inoculation strategy and inoculum size showed that the production and activity of the antibacterial VOCs of FA26 were dependent on the culture conditions. Headspace solid-phase microextraction/gas chromatography-mass spectrometry analyses revealed that FA26 produced 11 VOCs. Four VOCs (benzaldehyde, nonanal, benzothiazole and acetophenone) were associated with the antibacterial activity against Cms. The results suggested that the VOCs produced by FA26 could control the causal agent of bacterial ring rot of potato. This information will increase our understanding of the microbial interactions mediated by VOCs in nature and aid the development of safer strategies for controlling plant disease.

Candidate Species Selection and Controlled Environment Injuries

NASA Technical Reports Server (NTRS)

Tibbitts, T. W.

1982-01-01

Research was undertaken to attempt to identify the causal agents for intumescences that develop on many different species of plants in controlled environments. Concentration and filtration procedures were not successful in identifying any particular compounds. The injury was found to develop, even though the atmosphere for the plants is filtered through activated charcoal, potassium permanganate, or is subjected to catalytic combustion at 450 C. Thus, the causal agent is apparently either an oxidized compound or specific element, or the result of some unrecognized variation in physical conditions around the plants. The research has demonstrated that the injury is controlled to a significant extent by temperature. Growing temperatures of 20 degrees and 25 degrees C resulted in serious injury on plants, but temperatures of 30 C resulted in very little injury.

Tafenoquine: a promising new antimalarial agent.

PubMed

Crockett, Maryanne; Kain, Kevin C

2007-05-01

Malaria remains an important cause of global morbidity and mortality. As antimalarial drug resistance escalates, new safe and effective medications are necessary to prevent and treat malarial infection. Tafenoquine is an 8-aminoquinoline antimalarial that is presently under development. It has a long half-life of approximately 14 days and is generally safe and well tolerated, although it cannot be used in pregnant women and individuals who are deficient in the enzyme glucose-6-phosphate dehydrogenase. In well-designed studies, tafenoquine was highly effective in both the radical cure of relapsing malaria and causal prophylaxis of Plasmodium vivax and P. falciparum infections with protective efficacies of > or = 90%. Given its causal activity and safety profile, tafenoquine represents a potentially exciting alternative to standard agents for the prevention and radical cure of malaria.

Converging and Competing Cues in the Acquisition of Syntactic Structures: The Conjoined Agent Intransitive

ERIC Educational Resources Information Center

Noble, Claire; Iqbal, Faria; Lieven, Elena; Theakston, Anna

2016-01-01

In two studies we use a pointing task to explore developmentally the nature of the knowledge that underlies three- and four-year-old children's ability to assign meaning to the intransitive structure. The results suggest that early in development children are sensitive to a first-noun-as-causal-agent cue and animacy cues when interpreting…

Causal reports: Context-dependent contributions of intuitive physics and visual impressions of launching.

PubMed

Vicovaro, Michele

2018-05-01

Everyday causal reports appear to be based on a blend of perceptual and cognitive processes. Causality can sometimes be perceived automatically through low-level visual processing of stimuli, but it can also be inferred on the basis of an intuitive understanding of the physical mechanism that underlies an observable event. We investigated how visual impressions of launching and the intuitive physics of collisions contribute to the formation of explicit causal responses. In Experiment 1, participants observed collisions between realistic objects differing in apparent material and hence implied mass, whereas in Experiment 2, participants observed collisions between abstract, non-material objects. The results of Experiment 1 showed that ratings of causality were mainly driven by the intuitive physics of collisions, whereas the results of Experiment 2 provide some support to the hypothesis that ratings of causality were mainly driven by visual impressions of launching. These results suggest that stimulus factors and experimental design factors - such as the realism of the stimuli and the variation in the implied mass of the colliding objects - may determine the relative contributions of perceptual and post-perceptual cognitive processes to explicit causal responses. A revised version of the impetus transmission heuristic provides a satisfactory explanation for these results, whereas the hypothesis that causal responses and intuitive physics are based on the internalization of physical laws does not. Copyright © 2018 Elsevier B.V. All rights reserved.

Is There a Causal Relation between Mathematical Creativity and Mathematical Problem-Solving Performance?

ERIC Educational Resources Information Center

Tyagi, Tarun Kumar

2016-01-01

The relationship between mathematical creativity (MC) and mathematical problem-solving performance (MP) has often been studied but the causal relation between these two constructs has yet to be clearly reported. The main purpose of this study was to define the causal relationship between MC and MP. Data from a representative sample of 480…

The epidemiology of sudden oak death in Oregon forests

Treesearch

Ebba K. Peterson

2011-01-01

The phytopathogen Phytophthora ramorum (Werres, DeCock & Man in't Veld), causal agent of Sudden Oak Death (SOD) of oaks (Quercus spp.) and tanoaks (Notholithocarpus densiflorus syn. Lithocarpus densiflorus...

Characterization of bacterial knot disease caused by Pseudomonas savastanoi pv. savastanoi on pomegranate (Punica granatum L.) trees: a new host of the pathogen.

PubMed

Bozkurt, I A; Soylu, S; Mirik, M; Ulubas Serce, C; Baysal, Ö

2014-11-01

This study aimed to isolate and identify the causal organism causing hyperplastic outgrowths (knots) on stems and branches of pomegranate trees in the Eastern Mediterranean region of Turkey. Bacterial colonies were isolated from young knots on plates containing selective nutrient media. Biochemical tests, fatty acid analysis and PCR were performed to identify possible causal disease agent. Representative isolates were identified as Pseudomonas.pv.savastanoi (Psv) using biochemical tests, fatty acid profiling and PCR. Following inoculation of pomegranate plants (cv. hicaz) with bacterial suspensions, 25 of 54 bacterial isolates caused typical knots at the site of inoculation. PCR analysis, using specific primer for Psv, generated a single amplicon from all isolates. The similarity of the sequence of Turkish pomegranate isolate was 99% similar to the corresponding gene sequences of Psv in the databases. Based on symptoms, biochemical, molecular, pathogenicity tests and sequence analyses, the disease agent of knots observed on the pomegranate trees is Psv. To the best of our knowledge, this research has revealed pomegranate as a natural host of Psv, which extends the list of host plant species affected by the pathogen in the world and Turkey. Pomegranate trees were affected by the disease with outgrowths (galls or knot) disease. Currently, there is no published study on disease agent(s) causing the galls or knots on pomegranate trees in worldwide. Bacterial colonies were isolated from young knots. The causal agent of the knot Pseudomonas savastanoi pv.savastanoi (Psv) was identified based on symptoms, biochemical, molecular methods, pathogenicity tests and sequence analysis. To the best of our knowledge, this is the first report of Psv on pomegranate as a natural host, which extends the growing list of plant species affected by this bacterium in the world and Turkey. © 2014 The Society for Applied Microbiology.

Jasmonic Acid, Abscisic Acid, and Salicylic Acid Are Involved in the Phytoalexin Responses of Rice to Fusarium fujikuroi, a High Gibberellin Producer Pathogen.

PubMed

Siciliano, Ilenia; Amaral Carneiro, Greice; Spadaro, Davide; Garibaldi, Angelo; Gullino, Maria Lodovica

2015-09-23

Fusarium fujikuroi, the causal agent of bakanae disease, is the main seedborne pathogen on rice. To understand the basis of rice resistance, a quantitative method to simultaneously detect phytohormones and phytoalexins was developed by using HPLC-MS/MS. With this method dynamic profiles and possible interactions of defense-related phytohormones and phytoalexins were investigated on two rice cultivars, inoculated or not with F. fujikuroi. In the resistant cultivar Selenio, the presence of pathogen induced high production of phytoalexins, mainly sakuranetin, and symptoms of bakanae were not observed. On the contrary, in the susceptible genotype Dorella, the pathogen induced the production of gibberellin and abscisic acid and inhibited jasmonic acid production, phytoalexins were very low, and bakanae symptoms were observed. The results suggested that a wide range of secondary metabolites are involved in plant defense against pathogens and phytoalexin synthesis could be an important factor for rice resistance against bakanae disease.

Erwinia mallotivora sp., a New Pathogen of Papaya (Carica papaya) in Peninsular Malaysia

PubMed Central

Amin, Noriha Mat; Bunawan, Hamidun; Redzuan, Rohaiza Ahmad; Jaganath, Indu Bala S.

2011-01-01

Erwinia mallotivora was isolated from papaya infected with dieback disease showing the typical symptoms of greasy, water-soaked lesions and spots on leaves. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belonged to the genus Erwinia and was united in a monophyletic group with E. mallotivora DSM 4565 (AJ233414). Earlier studies had indicated that the causal agent for this disease was E. papayae. However, our current studies, through Koch’s postulate, have confirmed that papaya dieback disease is caused by E. mallotivora. To our knowledge, this is the first new discovery of E. mallotivora as a causal agent of papaya dieback disease in Peninsular Malaysia. Previous reports have suggested that E. mallotivora causes leaf spot in Mallotus japonicus. However, this research confirms it also to be pathogenic to Carica papaya. PMID:21339975

Huanglongbing: An overview of a complex pathosystem ravaging the world's citrus.

PubMed

da Graça, John V; Douhan, Greg W; Halbert, Susan E; Keremane, Manjunath L; Lee, Richard F; Vidalakis, Georgios; Zhao, Hongwei

2016-04-01

Citrus huanglongbing (HLB) has become a major disease and limiting factor of production in citrus areas that have become infected. The destruction to the affected citrus industries has resulted in a tremendous increase to support research that in return has resulted in significant information on both applied and basic knowledge concerning this important disease to the global citrus industry. Recent research indicates the relationship between citrus and the causal agent of HLB is shaped by multiple elements, in which host defense responses may also play an important role. This review is intended to provide an overview of the importance of HLB to a wider audience of plant biologists. Recent advances on host-pathogen interactions, population genetics and vectoring of the causal agent are discussed. © 2015 Institute of Botany, Chinese Academy of Sciences.

Erwinia mallotivora sp., a new pathogen of papaya (Carica papaya) in Peninsular Malaysia.

PubMed

Amin, Noriha Mat; Bunawan, Hamidun; Redzuan, Rohaiza Ahmad; Jaganath, Indu Bala S

2010-12-24

Erwinia mallotivora was isolated from papaya infected with dieback disease showing the typical symptoms of greasy, water-soaked lesions and spots on leaves. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belonged to the genus Erwinia and was united in a monophyletic group with E. mallotivora DSM 4565 (AJ233414). Earlier studies had indicated that the causal agent for this disease was E. papayae. However, our current studies, through Koch's postulate, have confirmed that papaya dieback disease is caused by E. mallotivora. To our knowledge, this is the first new discovery of E. mallotivora as a causal agent of papaya dieback disease in Peninsular Malaysia. Previous reports have suggested that E. mallotivora causes leaf spot in Mallotus japonicus. However, this research confirms it also to be pathogenic to Carica papaya.

Clinical guidelines for the management of acute viral infections in patients with systemic lupus erythematosus.

PubMed

Ramos-Casals, M; Cuadrado, M J; Alba, P; Sanna, G; Brito-Zerón, P; Bertolaccini, L; Babini, A; Moreno, A; D'Cruz, D; Khamashta, M A

2009-12-01

In recent decades, many research groups have focused on the role of viral infections in the etiopathogenesis of systemic lupus erythematosus (SLE), the so-called "viral hypothesis". The main candidates are herpes viruses such as Epstein-Barr virus (EBV) and cytomegalovirus (CMV), which have a high seroprevalence in the general population. However, a viral causal agent of SLE has not yet been discovered, although many interesting clinical findings on the complex interactions between viruses and SLE have been made. This review analyzes 88 cases of acute viral infections in adult patients with SLE and identifies situations in which viral infections influenced the diagnosis, prognosis or treatment of SLE. We also propose clinical guidelines for the management of these infections in patients with SLE.

Zoonotic risks from small ruminants.

PubMed

Ganter, M

2015-12-14

Zoonoses are infections that spread naturally between species (sometimes by a vector) from animals to other animal species or to humans or from humans to animals. Most of the zoonoses diagnosed in sheep and goats are transmitted by close contact of man with these animals and are, more often, occupational diseases that principally affect breeders, veterinarians and/or slaughterhouse workers. Some other diseases have an airborne transmission and affect the population in the vicinity of sheep/goat farms. Due to the fact that small ruminants are almost the only remaining animals which are migrating in industrialised countries, there is a severe risk for transmitting the diseases. Some other zoonotic diseases are foodborne diseases, which are mainly transmitted from animals to humans and to other animal species by contaminated food and water. Within the last decade central Europe was threatened by some new infections, e.g., bluetongue disease and schmallenberg disease, which although not of zoonotic interest, are caused by pathogens transmitted by vectors. Causal agents of both diseases have found highly effective indigenous vectors. In the future, climate change may possibly modify conditions for the vectors and influence their distribution and competence. By this, other vector-borne zoonotic infections may propagate into former disease free countries. Changes in human behaviour in consummation and processing of food, in animal housing and management may also influence future risks for zoonosis. Monitoring, prevention and control measures are proposed to limit further epidemics and to enable the containment of outbreaks. Measures depend mainly on the damage evoked or anticipated by the disease, the local situation, and the epidemiology of the zoonoses, the presence of the infective agent in wild and other animals, as well as the resistance of the causal microorganisms in the environment and the possibility to breed sheep and goats which are resistant to specific infections. In this review, the clinical signs in animals and humans of the main sheep and goat zoonoses, as well as the transmission route and the control measures are reported. Brucellosis, chlamydophilosis, Q fever, Orf, Rift valley fever and Bovine Spongiform Encephalopathy are described in greater detail, in order to determine factors that contribute to the choice of the control strategies. Copyright © 2015 Elsevier B.V. All rights reserved.

Situation models and memory: the effects of temporal and causal information on recall sequence.

PubMed

Brownstein, Aaron L; Read, Stephen J

2007-10-01

Participants watched an episode of the television show Cheers on video and then reported free recall. Recall sequence followed the sequence of events in the story; if one concept was observed immediately after another, it was recalled immediately after it. We also made a causal network of the show's story and found that recall sequence followed causal links; effects were recalled immediately after their causes. Recall sequence was more likely to follow causal links than temporal sequence, and most likely to follow causal links that were temporally sequential. Results were similar at 10-minute and 1-week delayed recall. This is the most direct and detailed evidence reported on sequential effects in recall. The causal network also predicted probability of recall; concepts with more links and concepts on the main causal chain were most likely to be recalled. This extends the causal network model to more complex materials than previous research.

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

A critical review of the epidemiology of Agent Orange/TCDD and prostate cancer.

PubMed

Chang, Ellen T; Boffetta, Paolo; Adami, Hans-Olov; Cole, Philip; Mandel, Jack S

2014-10-01

To inform risk assessment and regulatory decision-making, the relationship between 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and prostate cancer requires clarification. This article systematically and critically reviews the epidemiologic evidence on the association between exposure to TCDD or Agent Orange, a TCDD-contaminated herbicide used during the Vietnam War, and prostate cancer risk. Articles evaluated include 11 studies of three cohorts, four case-control or cross-sectional studies, and three case-only studies of military veterans with information on estimated Agent Orange or TCDD exposure; 13 studies of seven cohorts, one case-control study, and eight proportionate morbidity or mortality studies of Vietnam veterans without information on Agent Orange exposure; 11 cohort studies of workers with occupational exposure to TCDD; and two studies of one community cohort with environmental exposure to TCDD. The most informative studies, including those of Vietnam veterans involved in Agent Orange spraying or other handling, herbicide manufacturing or spraying workers with occupational TCDD exposure, and community members exposed to TCDD through an industrial accident, consistently reported no significant increase in prostate cancer incidence or mortality. Only some potentially confounded studies of Vietnam veterans compared with the general population, studies with unreliable estimates of Agent Orange exposure, and analyses of selected subgroups of Vietnam veterans reported positive associations. Overall, epidemiologic research offers no consistent or convincing evidence of a causal relationship between exposure to Agent Orange or TCDD and prostate cancer. More accurate exposure assessment is needed in large epidemiologic studies to rule out a causal association more conclusively.

Preeminence of Staphylococcus aureus in infective endocarditis: a 1-year population-based survey.

PubMed

Selton-Suty, Christine; Célard, Marie; Le Moing, Vincent; Doco-Lecompte, Thanh; Chirouze, Catherine; Iung, Bernard; Strady, Christophe; Revest, Matthieu; Vandenesch, François; Bouvet, Anne; Delahaye, François; Alla, François; Duval, Xavier; Hoen, Bruno

2012-05-01

Observational studies showed that the profile of infective endocarditis (IE) significantly changed over the past decades. However, most studies involved referral centers. We conducted a population-based study to control for this referral bias. The objective was to update the description of characteristics of IE in France and to compare the profile of community-acquired versus healthcare-associated IE. A prospective population-based observational study conducted in all medical facilities from 7 French regions (32% of French individuals aged ≥18 years) identified 497 adults with Duke-Li-definite IE who were first admitted to the hospital in 2008. Main measures included age-standardized and sex-standardized incidence of IE and multivariate Cox regression analysis for risk factors of in-hospital death. The age-standardized and sex-standardized annual incidence of IE was 33.8 (95% confidence interval [CI], 30.8-36.9) cases per million inhabitants. The incidence was highest in men aged 75-79 years. A majority of patients had no previously known heart disease. Staphylococci were the most common causal agents, accounting for 36.2% of cases (Staphylococcus aureus, 26.6%; coagulase-negative staphylococci, 9.7%). Healthcare-associated IE represented 26.7% of all cases and exhibited a clinical pattern significantly different from that of community-acquired IE. S. aureus as the causal agent of IE was the most important factor associated with in-hospital death in community-acquired IE (hazard ratio [HR], 2.82 [95% CI, 1.72-4.61]) and the single factor in healthcare-associated IE (HR, 2.54 [95% CI, 1.33-4.85]). S. aureus became both the leading cause and the most important prognostic factor of IE, and healthcare-associated IE appeared as a major subgroup of the disease.

Control of Root Rot and Wilt Diseases of Roselle under Field Conditions

PubMed Central

Hassan, Naglaa; Elsharkawy, Mohsen Mohamed; Shimizu, Masafumi

2014-01-01

Roselle (Hibiscus sabdariffa L.) is one of the most important medicinal crops in many parts of the world. In this study, the effects of microelements, antioxidants, and bioagents on Fusarium oxysporum, F. solani, and Macrophomina phaseolina, the causal pathogens of root rot and wilt diseases in roselle, were examined under field conditions. Preliminary studies were carried out in vitro in order to select the most effective members to be used in field control trials. Our results showed that microelements (copper and manganese), antioxidants (salicylic acid, ascorbic acid, and EDTA), a fungicide (Dithane M45) and biological control agents (Trichoderma harzianum and Bacillus subtilis) were significantly reduced the linear growth of the causal pathogens. Additionally, application of the previous microelements, antioxidants, a fungicide and biological control agents significantly reduced disease incidence of root rot and wilt diseases under field conditions. Copper, salicylic acid, and T. harzianum showed the best results in this respect. In conclusion, microelements, antioxidants, and biocontrol agents could be used as alternative strategies to fungicides for controlling root rot and wilt diseases in roselle. PMID:25606010

How to diagnose black walnut damage.

Treesearch

Barbara C. Weber; Robert L. Anderson; William H. Hoffard

1980-01-01

Presents a key to common insect, disease, animal, and other damages to black walnut. Also includes illustrations of many of the damage types and descriptions of the causal agents. Preventive or control recommendations are made where appropriate.

Structure and Connectivity Analysis of Financial Complex System Based on G-Causality Network

NASA Astrophysics Data System (ADS)

Xu, Chuan-Ming; Yan, Yan; Zhu, Xiao-Wu; Li, Xiao-Teng; Chen, Xiao-Song

2013-11-01

The recent financial crisis highlights the inherent weaknesses of the financial market. To explore the mechanism that maintains the financial market as a system, we study the interactions of U.S. financial market from the network perspective. Applied with conditional Granger causality network analysis, network density, in-degree and out-degree rankings are important indicators to analyze the conditional causal relationships among financial agents, and further to assess the stability of U.S. financial systems. It is found that the topological structure of G-causality network in U.S. financial market changed in different stages over the last decade, especially during the recent global financial crisis. Network density of the G-causality model is much higher during the period of 2007-2009 crisis stage, and it reaches the peak value in 2008, the most turbulent time in the crisis. Ranked by in-degrees and out-degrees, insurance companies are listed in the top of 68 financial institutions during the crisis. They act as the hubs which are more easily influenced by other financial institutions and simultaneously influence others during the global financial disturbance.

Is There a Relationship Between Use of Anti-Vascular Endothelial Growth Factor Agents and Atrophic Changes in Age-Related Macular Degeneration Patients?

PubMed

Kaynak, Süleyman; Kaya, Mahmut; Kaya, Derya

2018-04-01

Choroidal neovascularization due to age-related macular degeneration (AMD) is currently treated successfully with anti-vascular endothelial growth factor (VEGF) intravitreal agents. Emerging evidence suggests that anti-VEGF treatment may potentially increase development of geographic atrophy. However, there is not yet direct proof of a causal relationship between geographic atrophy and use of anti-VEGF agents in neovaskuler AMD. The aim of this review is to discuss the evidence concerning the association between anti-VEGF therapy and progression of geographic atrophy.

Emergent Societal Effects of Crimino-Social Forces in an Animat Agent Model

NASA Astrophysics Data System (ADS)

Scogings, Chris J.; Hawick, Ken A.

Societal behaviour can be studied at a causal level by perturbing a stable multi-agent model with new microscopic behaviours and observing the statistical response over an ensemble of simulated model systems. We report on the effects of introducing criminal and law-enforcing behaviours into a large scale animat agent model and describe the complex spatial agent patterns and population changes that result. Our well-established predator-prey substrate model provides a background framework against which these new microscopic behaviours can be trialled and investigated. We describe some quantitative results and some surprising conclusions concerning the overall societal health when individually anti-social behaviour is introduced.

Gnomonia canker, shoot blight, and leaf spot of yellow birch.

Treesearch

Kenneth J. Jr. Kessler

1978-01-01

Describes a canker, shoot blight, and leaf spot disease of yellow birch seedlings in the northern Great Lakes region and tells how and when trees become infected by the fungal causal agent, Gnomonia setacea.

‘Candidatus Liberibacter asiaticus’, causal agent of citrus Huanglongbing, is reduced by treatment with Brassinosteroids

DOE PAGES

Canales, Eduardo; Coll, Yamilet; Hernández, Ingrid; ...

2016-01-05

Huanglongbing (HLB) constitutes the most destructive disease of citrus worldwide, yet no established efficient management measures exist for it. Brassinosteroids, a family of plant steroidal compounds, are essential for plant growth, development and stress tolerance. As a possible control strategy for HLB, epibrassinolide was applied to as a foliar spray to citrus plants infected with the causal agent of HLB, ‘Candidatus Liberibacter asiaticus’. The bacterial titers were reduced after treatment with epibrassinolide under both greenhouse and field conditions but were stronger in the greenhouse. Known defense genes were induced in leaves by epibrassinolide. With the SuperSAGE technology combined with nextmore » generation sequencing, induction of genes known to be associated with defense response to bacteria and hormone transduction pathways were identified. Lastly, the results demonstrate that epibrassinolide may provide a useful tool for the management of HLB.« less

New insights in the pathogenesis of atopic disease.

PubMed

Ionescu, John G

2009-01-01

A causal link between the increasing environmental pollution and the fast spreading of allergic diseases is currently discussed. The exogenic and endogenic noxious agents contributing to the total environmental load are primarily acting through immunotoxic, sensitizing and neurotoxic mechanisms in animal experiments and in humans. Beside classic allergic-triggering factors (allergen potency, intermittent exposure to different allergen concentrations, presence of microbial bodies and sensitizing phenols), the adjuvant role of environmental pollutants gains increasing importance in allergy induction. Our therapy experience with more than 18.000 atopic eczema patients shows that beside allergic reactions pseudoallergic mechanisms through toxic environmental agents (formaldehyde, industrial and traffic smog, wood preservatives, microbial toxins, additive-rich food, nicotine, alcohol, pesticides, solvents, amalgam-heavy metals) are increasingly incriminated as causal factors for the complex symptomatology. The avoidance and elimination of such triggering factors before and during pregnancy and in early childhood may result in a significant decrease of the incidence of atopic diseases.

Bladder carcinoma in a transplant recipient: evidence to implicate the BK human polyomavirus as a causal transforming agent.

PubMed

Geetha, Duvuru; Tong, Betty C; Racusen, Lorraine; Markowitz, Jay S; Westra, William H

2002-06-27

The BK polyomavirus (BKV) infects most of the human population, but clinically relevant infections are mostly limited to individuals who are immunosuppressed. In transplant recipients, BKV has been associated with ureteral stenosis, interstitial nephritis, and hemorrhagic cystitis. The role of BKV in the development of human tumors is intriguing but uncertain. BKV has been identified in various tumor types including urothelial carcinoma, but the ubiquitous presence of BKV as a latent infection has confounded efforts to validate any causal role in cancer development. We report the case of a simultaneous pancreas and kidney transplant recipient who developed BKV interstitial nephritis and carcinoma of the bladder with widespread metastases. High level expression of BKV large T antigen in the primary and metastatic carcinoma, but not in the nonneoplastic urothelium, implicates BKV as an etiologic agent in the development of this tumor.

‘Candidatus Liberibacter asiaticus’, causal agent of citrus Huanglongbing, is reduced by treatment with Brassinosteroids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Canales, Eduardo; Coll, Yamilet; Hernández, Ingrid

Huanglongbing (HLB) constitutes the most destructive disease of citrus worldwide, yet no established efficient management measures exist for it. Brassinosteroids, a family of plant steroidal compounds, are essential for plant growth, development and stress tolerance. As a possible control strategy for HLB, epibrassinolide was applied to as a foliar spray to citrus plants infected with the causal agent of HLB, ‘Candidatus Liberibacter asiaticus’. The bacterial titers were reduced after treatment with epibrassinolide under both greenhouse and field conditions but were stronger in the greenhouse. Known defense genes were induced in leaves by epibrassinolide. With the SuperSAGE technology combined with nextmore » generation sequencing, induction of genes known to be associated with defense response to bacteria and hormone transduction pathways were identified. Lastly, the results demonstrate that epibrassinolide may provide a useful tool for the management of HLB.« less

New Insights in the Pathogenesis of Atopic Disease

PubMed Central

Ionescu, GJ

2009-01-01

A causal link between the increasing environmental pollution and the fast spreading of allergic diseases is currently discussed. The exogenic and endogenic noxious agents contributing to the total environmental load are primarily acting through immunotoxic, sensitizing and neurotoxic mechanisms in animal experiments and in humans. Beside classic allergic–triggering factors (allergen potency, intermittent exposure to different allergen concentrations, presence of microbial bodies and sensitizing phenols), the adjuvant role of environmental pollutants gains increasing importance in allergy induction. Our therapy experience with more than 18.000 atopic eczema patients shows that beside allergic reactions pseudoallergic mechanisms through toxic environmental agents (formaldehyde, industrial and traffic smog, wood preservatives, microbial toxins, additive–rich food, nicotine, alcohol, pesticides, solvents, amalgam–heavy metals) are increasingly incriminated as causal factors for the complex symptomatology. The avoidance and elimination of such triggering factors before and during pregnancy and in early childhood may result in a significant decrease of the incidence of atopic diseases.

New Insights in the Pathogenesis of Atopic Disease

PubMed Central

John G., Ionescu

2009-01-01

A causal link between the increasing environmental pollution and the fast spreading of allergic diseases is currently discussed. The exogenic and endogenic noxious agents contributing to the total environmental load are primarily acting through immunotoxic, sensitizing and neurotoxic mechanisms in animal experiments and in humans. Beside classic allergic-triggering factors (allergen potency, intermittent exposure to different allergen concentrations, presence of microbial bodies and sensitizing phenols), the adjuvant role of environmental pollutants gains increasing importance in allergy induction. Our therapy experience with more than 18.000 atopic eczema patients shows that beside allergic reactions pseudoallergic mechanisms through toxic environmental agents (formaldehyde, industrial and traffic smog, wood preservatives, microbial toxins, additive-rich food, nicotine, alcohol, pesticides, solvents, amalgam-heavy metals) are increasingly incriminated as causal factors for the complex symptomatology. The avoidance and elimination of such triggering factors before and during pregnancy and in early childhood may result in a significant decrease of the incidence of atopic diseases. PMID:20108533

Effect of bodily fluids from honey bee (Apis mellifera) larvae on growth and genome-wide transcriptional response of the causal agent of American Foulbrood disease (Paenibacillus larvae).

PubMed

De Smet, Lina; De Koker, Dieter; Hawley, Alyse K; Foster, Leonard J; De Vos, Paul; de Graaf, Dirk C

2014-01-01

Paenibacillus larvae, the causal agent of American Foulbrood disease (AFB), affects honey bee health worldwide. The present study investigates the effect of bodily fluids from honey bee larvae on growth velocity and transcription for this Gram-positive, endospore-forming bacterium. It was observed that larval fluids accelerate the growth and lead to higher bacterial densities during stationary phase. The genome-wide transcriptional response of in vitro cultures of P. larvae to larval fluids was studied by microarray technology. Early responses of P. larvae to larval fluids are characterized by a general down-regulation of oligopeptide and sugar transporter genes, as well as by amino acid and carbohydrate metabolic genes, among others. Late responses are dominated by general down-regulation of sporulation genes and up-regulation of phage-related genes. A theoretical mechanism of carbon catabolite repression is discussed.

A Novel Fungal Hyperparasite of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

PubMed Central

Zhan, Gangming; Tian, Yuan; Wang, Fuping; Chen, Xianming; Guo, Jun; Jiao, Min; Huang, Lili; Kang, Zhensheng

2014-01-01

Puccinia striiformis f. sp. tritici (Pst), the causal fungus of wheat stripe rust, was previously reported to be infected by Lecanicillium lecanii, Microdochium nivale and Typhula idahoensis. Here, we report a novel hyperparasite on Pst. This hyperparasitic fungus was identified as Cladosporium cladosporioides (Fresen.) GA de Vries based on morphological characteristics observed by light and scanning electron microscopy together with molecular data. The hyperparasite reduced the production and viability of urediniospores and, therefore, could potentially be used for biological control of wheat stripe rust. PMID:25369036

A novel fungal hyperparasite of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.

PubMed

Zhan, Gangming; Tian, Yuan; Wang, Fuping; Chen, Xianming; Guo, Jun; Jiao, Min; Huang, Lili; Kang, Zhensheng

2014-01-01

Puccinia striiformis f. sp. tritici (Pst), the causal fungus of wheat stripe rust, was previously reported to be infected by Lecanicillium lecanii, Microdochium nivale and Typhula idahoensis. Here, we report a novel hyperparasite on Pst. This hyperparasitic fungus was identified as Cladosporium cladosporioides (Fresen.) GA de Vries based on morphological characteristics observed by light and scanning electron microscopy together with molecular data. The hyperparasite reduced the production and viability of urediniospores and, therefore, could potentially be used for biological control of wheat stripe rust.

Human toxocariasis: diagnosis, worldwide seroprevalences and clinical expression of the systemic and ocular forms.

PubMed

Rubinsky-Elefant, G; Hirata, C E; Yamamoto, J H; Ferreira, M U

2010-01-01

Although human toxocariasis ranks among the most common zoonotic infections worldwide, it remains relatively unknown to the public. The causal agents are the nematode parasites Toxocara canis and T. cati, whose definitive hosts are dogs and cats, respectively. When embryonated eggs are accidentally ingested by humans, larvae hatch in the small intestine, penetrate the intestinal wall and migrate, via the bloodstream, to the liver, lungs, muscles, eye and central nervous system. Although most human infections are asymptomatic, two well-defined clinical syndromes are classically recognised: visceral larva migrans (a systemic disease caused by larval migration through major organs) and ocular larva migrans (a disease limited to the eyes and optic nerves). Two less-severe syndromes have recently been described, one mainly in children (covert toxocariasis) and the other mainly in adults (common toxocariasis). Here, the current laboratory diagnosis, epidemiology and main clinical features of both the systemic and ocular forms of human toxocariasis are reviewed. New developments in serological diagnosis are described, the available seroprevalence data are analysed, and the results of relevant clinical studies that have been published over the last decade are explored, to provide an updated overview of this neglected but highly prevalent human infection.

Investigation of occupational asthma: Do clinicians fail to identify relevant occupational exposures?

PubMed Central

de Olim, Carlo; Bégin, Denis; Boulet, Louis-Philippe; Cartier, André; Gérin, Michel; Lemière, Catherine

2015-01-01

BACKGROUND: Specific inhalation challenges (SIC) enable the identification of the agent responsible of occupational asthma (OA). A clinician may fail to identify a specific agent in the workplace, which may potentially lead to a misdiagnosis. The expert assessment method performed by an occupational hygienist has been used to evaluate occupational exposures in epidemiological studies. OBJECTIVE: The broad aim of the present study was to evaluate the contribution of an expert assessment performed by an occupational hygienist to the diagnosis of OA. The specific aim was to compare work-place exposures identified by an occupational hygienist and by chest physicians in subjects with positive SICs and subjects with asthma, but with a negative SIC. METHODS: SICs were performed in 120 cases: 67 were positive and 53 were negative. A clinician assessed occupational exposures to sensitizers during a routine clinical evaluation preceding the performance of the SIC. An expert assessment of occupational exposures was performed by an occupational hygienist blind to the result of the SIC. RESULTS: The occupational hygienist identified the causal agent in 96.7% of the 61 cases of positive SIC. In 33 (62.3%) cases of negative SICs, the occupational hygienist identified ≥1 sensitizing agent(s) that had not been identified by the clinician. CONCLUSION: The hygienist identified the causal agent in almost all subjects with OA. In contrast, the clinician failed to identify potential exposures to sensitizers in >60% of the negative SIC subjects, which may have resulted in some subjects being misdiagnosed as not having OA. PMID:26422401

Extended Neural Metastability in an Embodied Model of Sensorimotor Coupling

PubMed Central

Aguilera, Miguel; Bedia, Manuel G.; Barandiaran, Xabier E.

2016-01-01

The hypothesis that brain organization is based on mechanisms of metastable synchronization in neural assemblies has been popularized during the last decades of neuroscientific research. Nevertheless, the role of body and environment for understanding the functioning of metastable assemblies is frequently dismissed. The main goal of this paper is to investigate the contribution of sensorimotor coupling to neural and behavioral metastability using a minimal computational model of plastic neural ensembles embedded in a robotic agent in a behavioral preference task. Our hypothesis is that, under some conditions, the metastability of the system is not restricted to the brain but extends to the system composed by the interaction of brain, body and environment. We test this idea, comparing an agent in continuous interaction with its environment in a task demanding behavioral flexibility with an equivalent model from the point of view of “internalist neuroscience.” A statistical characterization of our model and tools from information theory allow us to show how (1) the bidirectional coupling between agent and environment brings the system closer to a regime of criticality and triggers the emergence of additional metastable states which are not found in the brain in isolation but extended to the whole system of sensorimotor interaction, (2) the synaptic plasticity of the agent is fundamental to sustain open structures in the neural controller of the agent flexibly engaging and disengaging different behavioral patterns that sustain sensorimotor metastable states, and (3) these extended metastable states emerge when the agent generates an asymmetrical circular loop of causal interaction with its environment, in which the agent responds to variability of the environment at fast timescales while acting over the environment at slow timescales, suggesting the constitution of the agent as an autonomous entity actively modulating its sensorimotor coupling with the world. We conclude with a reflection about how our results contribute in a more general way to current progress in neuroscientific research. PMID:27721746

Extended Neural Metastability in an Embodied Model of Sensorimotor Coupling.

PubMed

Aguilera, Miguel; Bedia, Manuel G; Barandiaran, Xabier E

2016-01-01

The hypothesis that brain organization is based on mechanisms of metastable synchronization in neural assemblies has been popularized during the last decades of neuroscientific research. Nevertheless, the role of body and environment for understanding the functioning of metastable assemblies is frequently dismissed. The main goal of this paper is to investigate the contribution of sensorimotor coupling to neural and behavioral metastability using a minimal computational model of plastic neural ensembles embedded in a robotic agent in a behavioral preference task. Our hypothesis is that, under some conditions, the metastability of the system is not restricted to the brain but extends to the system composed by the interaction of brain, body and environment. We test this idea, comparing an agent in continuous interaction with its environment in a task demanding behavioral flexibility with an equivalent model from the point of view of "internalist neuroscience." A statistical characterization of our model and tools from information theory allow us to show how (1) the bidirectional coupling between agent and environment brings the system closer to a regime of criticality and triggers the emergence of additional metastable states which are not found in the brain in isolation but extended to the whole system of sensorimotor interaction, (2) the synaptic plasticity of the agent is fundamental to sustain open structures in the neural controller of the agent flexibly engaging and disengaging different behavioral patterns that sustain sensorimotor metastable states, and (3) these extended metastable states emerge when the agent generates an asymmetrical circular loop of causal interaction with its environment, in which the agent responds to variability of the environment at fast timescales while acting over the environment at slow timescales, suggesting the constitution of the agent as an autonomous entity actively modulating its sensorimotor coupling with the world. We conclude with a reflection about how our results contribute in a more general way to current progress in neuroscientific research.

Phytophthora ramorum

USDA-ARS?s Scientific Manuscript database

Phytophthora ramorum is a recently emerged plant pathogen and causal agent of one of the most destructive and devastating diseases currently affecting US horticulture and forests. Formally described in 2001, P. ramorum is a filamentous, diploid protozoan that is one of 117 currently recognized Phyto...

Urbanism and Life Satisfaction among the Aged.

ERIC Educational Resources Information Center

Liang, Jersey; Warfel, Becky L.

1983-01-01

Examined the impact of urbanism on the causal mechanisms by which life satisfaction is determined using a causal model that incorporates urbanism as a polytomous variable. Urbanism was found to have indirect main effects as well as interaction effects on life satisfaction. (Author/JAC)

Papillomaviruses: a systematic review

PubMed Central

Araldi, Rodrigo Pinheiro; Assaf, Suely Muro Reis; de Carvalho, Rodrigo Franco; de Carvalho, Márcio Augusto Caldas Rocha; de Souza, Jacqueline Mazzuchelli; Magnelli, Roberta Fiusa; Módolo, Diego Grando; Roperto, Franco Peppino; Stocco, Rita de Cassia; Beçak, Willy

2017-01-01

Abstract In the last decades, a group of viruses has received great attention due to its relationship with cancer development and its wide distribution throughout the vertebrates: the papillomaviruses. In this article, we aim to review some of the most relevant reports concerning the use of bovines as an experimental model for studies related to papillomaviruses. Moreover, the obtained data contributes to the development of strategies against the clinical consequences of bovine papillomaviruses (BPV) that have led to drastic hazards to the herds. To overcome the problem, the vaccines that we have been developing involve recombinant DNA technology, aiming at prophylactic and therapeutic procedures. It is important to point out that these strategies can be used as models for innovative procedures against HPV, as this virus is the main causal agent of cervical cancer, the second most fatal cancer in women. PMID:28212457

Understanding the HPV integration and its progression to cervical cancer.

PubMed

Oyervides-Muñoz, Mariel Araceli; Pérez-Maya, Antonio Alí; Rodríguez-Gutiérrez, Hazyadee Frecia; Gómez-Macias, Gabriela Sofía; Fajardo-Ramírez, Oscar Raúl; Treviño, Víctor; Barrera-Saldaña, Hugo Alberto; Garza-Rodríguez, María Lourdes

2018-07-01

Cervical cancer is one of the main causes of female cancer death worldwide, and human papilloma virus (HPV) its causal agent. To investigate viral oncogenesis several studies have focused on the effects of HPV oncoproteins E6 and E7 and the mechanisms by which these proteins stimulate the cellular transformation process. However, phenomena such as the physical state of the viral genome (episomal or integrated) and the effects of this integration on cell proliferation contribute new clues to understand how HPV infection causes carcinogenesis. New molecular technologies are currently facilitating these discoveries. This paper reviews the tumor development process initiated by HPV, recent findings on the process of viral integration into the host genome, new methods to detect HPV integration, and derived associated effects. Copyright © 2018 Elsevier B.V. All rights reserved.

Severe Foot Lesions in Dairy Goats Associated with Digital Dermatitis Treponemes.

PubMed

Crosby-Durrani, H E; Clegg, S R; Singer, E; Angell, J W; Evans, N J; Carter, S D; Blundell, R J; Duncan, J S

2016-05-01

Treponeme-associated foot disease has been described in cattle with digital dermatitis and sheep with contagious ovine digital dermatitis. In this study, severe foot lesions in dairy goats associated with digital dermatitis treponemes (i.e. Treponema medium, Treponema phagedenis and Treponema pedis) were characterized macroscopically, radiographically and histologically. The main macroscopic foot lesion was of extensive solar ulceration with or without exophytic papilliform hyperkeratosis. Radiographically, the distal phalanx and distal sesamoid bones were severely damaged and remodelled. Histologically, the lesion was categorized as a chronic lymphoplasmacytic, suppurative and ulcerative pododermatitis. Immunohistochemistry identified the spirochaetal microorganisms located extracellularly in the superficial horn. Study limitations mean that the treponeme bacteria could not be considered the sole or causal agents in the cases described. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

A critical review of the epidemiology of Agent Orange or 2,3,7,8-tetrachlorodibenzo-p-dioxin and lymphoid malignancies.

PubMed

Chang, Ellen T; Boffetta, Paolo; Adami, Hans-Olov; Mandel, Jack S

2015-04-01

Establishing a causal relationship between 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and risk of specific lymphoid cancers, including non-Hodgkin lymphoma (NHL), Hodgkin lymphoma (HL), and multiple myeloma (MM), would be useful for risk assessment. This article systematically and critically reviews epidemiologic studies of the association between exposure to TCDD or TCDD-contaminated herbicides and risk of lymphoid malignancies. These include studies of military, industrial, accidental environmental, and general environmental exposure to Agent Orange or TCDD. Collectively, the epidemiologic evidence from industrial cohorts suggests a positive association with NHL mortality, but results are not consistent across other studies, a clear exposure-response gradient is not evident, and data are insufficient to conclude that the association is causal. Furthermore, available studies provide little information on NHL incidence or specific NHL subtypes. Epidemiologic studies do not show an association of TCDD exposure with HL, whereas the indication of a positive association with MM in a limited number of studies, but not others, remains to be confirmed in additional research. Exposure classification error and small numbers are important limitations of the available epidemiologic studies. Overall, a causal effect of TCDD on NHL, HL, MM, or subtypes of these lymphoid malignancies has not been established. Copyright © 2015 Elsevier Inc. All rights reserved.

Causal attribution for success and failure in mathematics among MDAB pre-diploma students

NASA Astrophysics Data System (ADS)

Maidinsah, Hamidah; Embong, Rokiah; Wahab, Zubaidah Abd

2014-07-01

The Program Mengubah Destini Anak Bangsa (MDAB) is a pre-diploma programme catering to SPM school leavers who do not meet the minimum requirement to enter any of UiTM diploma programmes. The study aims to evaluate the perceptions of MDAB students toward the main causal attribution factors underlying students' success and failure in mathematics. Research sample comprised of 482 students from five UiTM branch campuses. Research instrument used was a set of GALUS questionnaire consisting of 36 items based on the Weiner Attribution Theory. Four causal attributions factors for success and failures evaluated are ability, effort, question difficulty and environment. GALUS reliability index was 0.93. The research found that effort appears to be the main causal attribution factor in students' success and failure in mathematics, followed by environment, question difficulty and ability. High achiever students strongly agree that the ability factor influenced their success while low achiever students strongly agree that all attributing factors influenced their failures in mathematics.

A qualitative study evaluating causality attribution for serious adverse events during early phase oncology clinical trials.

PubMed

Mukherjee, Som D; Coombes, Megan E; Levine, Mitch; Cosby, Jarold; Kowaleski, Brenda; Arnold, Andrew

2011-10-01

In early phase oncology trials, novel targeted therapies are increasingly being tested in combination with traditional agents creating greater potential for enhanced and new toxicities. When a patient experiences a serious adverse event (SAE), investigators must determine whether the event is attributable to the investigational drug or not. This study seeks to understand the clinical reasoning, tools used and challenges faced by the researchers who assign causality to SAE's. Thirty-two semi-structured interviews were conducted with medical oncologists and trial coordinators at six Canadian academic cancer centres. Interviews were recorded and transcribed verbatim. Individual interview content analysis was followed by thematic analysis across the interview set. Our study found that causality assessment tends to be a rather complex process, often without complete clinical and investigational data at hand. Researchers described using a common processing strategy whereby they gather pertinent information, eliminate alternative explanations, and consider whether or not the study drug resulted in the SAE. Many of the interviewed participants voiced concern that causality assessments are often conducted quickly and tend to be highly subjective. Many participants were unable to identify any useful tools to help in assigning causality and welcomed more objectivity in the overall process. Attributing causality to SAE's is a complex process. Clinical trial researchers apply a logical system of reasoning, but feel that the current method of assigning causality could be improved. Based on these findings, future research involving the development of a new causality assessment tool specifically for use in early phase oncology clinical trials may be useful.

Importance of Footwear for Preventing Xerosis and Hyperkeratosis in Older People with Psychiatric Disorders Living in an Institution

PubMed Central

Marcos-Tejedor, Félix; Iglesias-Sánchez, María José

2018-01-01

Few studies have focused on the relation between the use and characteristics of footwear and the presence of foot lesions in people with psychiatric disorders. This work analyzes the influence of different footwear habits on the presence of deformities and ungueal and dermal pathologies of the foot of institutionalized people with psychiatric disorders compared to people without these disorders. A transversal and observational study was conducted on 107 participants, divided into two groups who have used different types of shoes throughout their lives. The control group comprised 63 autonomous people who mainly use leather footwear and a study group of 44 institutionalized people with intellectual disabilities and psychiatric disorders who mainly use textile footwear. There were significant differences between populations. The group with psychiatric disorders presented more xerosis and hyperkeratosis. Footwear with inappropriate characteristics is a possible causal agent of skin alterations. Wearing footwear with quality textile uppers, e.g., fabric or felt, could influence the appearance of these alterations. Leather footwear is recommended for institutionalized people to reduce symptoms of xerosis and improve their quality of life. PMID:29587357

Importance of Footwear for Preventing Xerosis and Hyperkeratosis in Older People with Psychiatric Disorders Living in an Institution.

PubMed

Pérez-Pico, Ana María; Marcos-Tejedor, Félix; Iglesias-Sánchez, María José; Acevedo, Raquel Mayordomo

2018-03-24

Few studies have focused on the relation between the use and characteristics of footwear and the presence of foot lesions in people with psychiatric disorders. This work analyzes the influence of different footwear habits on the presence of deformities and ungueal and dermal pathologies of the foot of institutionalized people with psychiatric disorders compared to people without these disorders. A transversal and observational study was conducted on 107 participants, divided into two groups who have used different types of shoes throughout their lives. The control group comprised 63 autonomous people who mainly use leather footwear and a study group of 44 institutionalized people with intellectual disabilities and psychiatric disorders who mainly use textile footwear. There were significant differences between populations. The group with psychiatric disorders presented more xerosis and hyperkeratosis. Footwear with inappropriate characteristics is a possible causal agent of skin alterations. Wearing footwear with quality textile uppers, e.g., fabric or felt, could influence the appearance of these alterations. Leather footwear is recommended for institutionalized people to reduce symptoms of xerosis and improve their quality of life.

Neurotoxicity of cancer chemotherapy☆

PubMed Central

Yang, Miyoung; Moon, Changjong

2013-01-01

There is accumulating clinical evidence that chemotherapeutic agents induce neurological side effects, including memory deficits and mood disorders, in cancer patients who have undergone chemotherapeutic treatments. This review focuses on chemotherapy-induced neurodegeneration and hippocampal dysfunctions and related mechanisms as measured by in vivo and in vitro approaches. These investigations are helpful in determining how best to further explore the causal mechanisms of chemotherapy-induced neurological side effects and in providing direction for the future development of novel optimized chemotherapeutic agents. PMID:25206457

Malignant Fibrous Histiocytoma of the Maxillary Sinus in a Spray Painter from an Automobile Repair Shop

PubMed Central

2013-01-01

Background We report a case of a spray painter who developed malignant fibrous histiocytoma (MFH) of the maxillary sinus following long-term exposure to chromium, nickel, and formaldehyde, implying that these agents are probable causal agents of MFH. Case report The patient developed right-sided prosopalgia that began twenty months ago. The symptom persisted despite medical treatment. After two months, he was diagnosed with MFH through imaging studies, surgery, and pathological microscopic findings at a university hospital in Seoul. His social, medical, and family history was unremarkable. The patient had worked for about 18 years at an automobile repair shop as a spray painter. During this period, he had been exposed to various occupational agents, such as hexavalent chromium, nickel, and formaldehyde, without appropriate personal protective equipment. He painted 6 days a week and worked for about 8 hours a day. Investigation of the patient’s work environment detected hexavalent chromium, chromate, nickel, and formaldehyde. Conclusions The study revealed that the patient had been exposed to hexavalent chromium, formaldehyde, and nickel compounds through sanding and spray painting. The association between paranasal cancer and exposure to the aforementioned occupational human carcinogens has been established. We suggest, in this case, the possibility that the paint spraying acted as a causal agent for paranasal cancer. PMID:24472378

The Born Rule and Free Will: why Libertarian Agent-Causal Free Will is not "antiscientific"

NASA Astrophysics Data System (ADS)

Kastner, Ruth E.

In the libertarian "agent causation" view of free will, free choices are attributable only to the choosing agent, as opposed to a specific cause or causes outside the agent. An often-repeated claim in the philosophical literature on free will is that agent causation necessarily implies lawlessness, and is therefore "antiscientific." That claim is critiqued and it is argued, on the contrary, that the volitional powers of a free agent need not be viewed as anomic, specifically with regard to the quantum statistical law (the Born Rule). Assumptions about the role and nature of causation, taken as bearing on volitional agency, are examined and found inadequate to the task. Finally, it is suggested that quantum theory may constitute precisely the sort of theory required for a nomic grounding of libertarian free will.

Transformation of the cucurbit powdery mildew pathogen Podosphaera xanthii by Agrobacterium tumefaciens.

PubMed

Martínez-Cruz, Jesús; Romero, Diego; de Vicente, Antonio; Pérez-García, Alejandro

2017-03-01

The obligate biotrophic fungal pathogen Podosphaera xanthii is the main causal agent of powdery mildew in cucurbit crops all over the world. A major limitation of molecular studies of powdery mildew fungi (Erysiphales) is their genetic intractability. In this work, we describe a robust method based on the promiscuous transformation ability of Agrobacterium tumefaciens for reliable transformation of P. xanthii. The A. tumefaciens-mediated transformation (ATMT) system yielded transformants of P. xanthii with diverse transferred DNA (T-DNA) constructs. Analysis of the resultant transformants showed the random integration of T-DNA into the P. xanthii genome. The integrations were maintained in successive generations in the presence of selection pressure. Transformation was found to be transient, because in the absence of selection agent, the introduced genetic markers were lost due to excision of T-DNA from the genome. The ATMT system represents a potent tool for genetic manipulation of P. xanthii and will likely be useful for studying other biotrophic fungi. We hope that this method will contribute to the development of detailed molecular studies of the intimate interaction established between powdery mildew fungi and their host plants. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Environmental agency in read-alouds

NASA Astrophysics Data System (ADS)

Oliveira, Alandeom W.; Rogers, Patterson; Quigley, Cassie F.; Samburskiy, Denis; Barss, Kimberly; Rivera, Seema

2015-06-01

Despite growing interest in helping students become agents of environmental change who can, through informed decision-making and action-taking, transform environmentally detrimental forms of human activity, science educators have reduced agency to rationality by overlooking sociocultural influences such as norms and values. We tackle this issue by examining how elementary teachers and students negotiate and attribute responsibility, credit, or blame for environmental events during three environmental read-alouds. Our verbal analysis and visual representation of meta-agentive discourse revealed varied patterns of agential attribution. First, humans were simultaneously attributed negative agentive roles (agents of endangerment and imbalance) and positive agentive roles (agents of prevention, mitigation, and balance). Second, while wolves at Yellowstone were constructed as intentional (human-like) agents when they crossed over into the human world to kill livestock in nearby farms, polar bears in the Arctic were denied any form of agential responsibility when they approached people's homes. Third, anthropogenic causation of global warming was constructed as distal and indirect chains of cause and effect (i.e., sophisticated sequences of ripple effects), whereas its mitigation and prevention assumed the form of simple and unidirectional causative links (direct and proximal causality). Fourth, the notion of balance of nature was repeatedly used as a justification for environmental conservation but its cause and dynamic nature remained unclear. And, fifth, while one teacher promoted environmental agency by encouraging students to experience positive emotions such as love of nature, freedom, and oneness with nature, the other teachers encouraged students to experience negative emotions such as self-blame and guilt. This study's main significance is that it highlights the need for environmental educators who set out to promote environmental agency to expand the focus of their instructional efforts beyond rational argumentation and reasoning. It also underscores the importance of increasing school teachers' awareness of implicit discursive messages in particular patterns of environmental agency attribution when discussing environmental issues with students and implementing pedagogical strategies centered on oral deliberation such as read-alouds.

Indicators of causal agency in physical interactions: the role of the prior context.

PubMed

Mayrhofer, Ralf; Waldmann, Michael R

2014-09-01

The question how agent and patient roles are assigned to causal participants has largely been neglected in the psychological literature on force dynamics. Inspired by the linguistic theory of Dowty (1991), we propose that agency attributions are based on a prototype concept of human intervention. We predicted that the number of criteria a participant in a causal interaction shares with this prototype determines the strength of agency intuitions. We showed in two experiments using versions of Michotte's (1963) launching scenarios that agency intuitions were moderated by manipulations of the context prior to the launching event. Altering features, such as relative movement, sequence of visibility, and self-propelled motion, tended to increase agency attributions to the participant that is normally viewed as patient in the standard scenario. Copyright © 2014 Elsevier B.V. All rights reserved.

Does Causality Matter More Now? Increase in the Proportion of Causal Language in English Texts.

PubMed

Iliev, Rumen; Axelrod, Robert

2016-05-01

The vast majority of the work on culture and cognition has focused on cross-cultural comparisons, largely ignoring the dynamic aspects of culture. In this article, we provide a diachronic analysis of causal cognition over time. We hypothesized that the increased role of education, science, and technology in Western societies should be accompanied by greater attention to causal connections. To test this hypothesis, we compared word frequencies in English texts from different time periods and found an increase in the use of causal language of about 40% over the past two centuries. The observed increase was not attributable to general language effects or to changing semantics of causal words. We also found that there was a consistent difference between the 19th and the 20th centuries, and that the increase happened mainly in the 20th century. © The Author(s) 2016.

Characterization of effectors from Fusarium graminearum

USDA-ARS?s Scientific Manuscript database

Fusarium graminearum is the causal agent of Fusarium head blight (FHB), which reduces crop yield and quality by producing various mycotoxins. Effectors play an important role in the pathogenesis of many bacterial and fungal pathogens. In this study, 26 effector candidates were selected for investiga...

Blueberry virus A

USDA-ARS?s Scientific Manuscript database

Leaf yellowing on highbush blueberry ‘Spartan’ prompted Isogai et al. to investigate whether a virus was the causal agent of the disorder. After double-stranded RNA extraction from symptomatic material they identified a single band of 17 Kb, indicative of virus infection. Shotgun cloning and sequenc...

ALIEN SPECIES: THEIR ROLE IN AMPHIBIAN POPULATION DECLINES AND RESTORATION

EPA Science Inventory

Alien species (also referred to as exotic, invasive, introduced, or normative species) have been implicated as causal agents in population declines of many amphibian species. Herein, we evaluate the relative contributions of alien species and other factors in adversely affecting ...

ECONOMIC GROWTH AND SALMON RECOVERY: AN IRRECONCILABLE CONFLICT?

EPA Science Inventory

Throughout the southern region of western North America, many wild salmon stocks have declined and some have disappeared. The decline was induced by an extensively studied and reasonably well understood combination of causal agents. The public appears to support reversing the d...

Etiology of bronze leaf disease of Populus

Treesearch

Jason A. Smith; R. A. Blanchette; M. E. Ostry; N. A. Anderson

2002-01-01

Bronze leaf disease is a potentially destructive disorder of the Populus section of the genus Populus. The causal agent has been reported to be Apioplagiostoma populi (anarnorph: Discula sp.). Based on etiological and symptomological studies, field observations of symptom development suggest that the pathogen...

UNRECOGNIZED OR POTENTIAL RISK FACTORS FOR CHILDHOOD CANCER

EPA Science Inventory

Traditional epidemiological studies suggest that the contribution of environmental agents to childhood cancer may be minor. However, epidemiological methods can only seldom identify causal factors associated with a relative risk of less than a factor of one and a half to two. App...

New Insights into Signed Path Coefficient Granger Causality Analysis.

PubMed

Zhang, Jian; Li, Chong; Jiang, Tianzi

2016-01-01

Granger causality analysis, as a time series analysis technique derived from econometrics, has been applied in an ever-increasing number of publications in the field of neuroscience, including fMRI, EEG/MEG, and fNIRS. The present study mainly focuses on the validity of "signed path coefficient Granger causality," a Granger-causality-derived analysis method that has been adopted by many fMRI researches in the last few years. This method generally estimates the causality effect among the time series by an order-1 autoregression, and defines a positive or negative coefficient as an "excitatory" or "inhibitory" influence. In the current work we conducted a series of computations from resting-state fMRI data and simulation experiments to illustrate the signed path coefficient method was flawed and untenable, due to the fact that the autoregressive coefficients were not always consistent with the real causal relationships and this would inevitablely lead to erroneous conclusions. Overall our findings suggested that the applicability of this kind of causality analysis was rather limited, hence researchers should be more cautious in applying the signed path coefficient Granger causality to fMRI data to avoid misinterpretation.

Systematic Review of the Exposure Assessment and Epidemiology of High-Frequency Voltage Transients

PubMed Central

de Vocht, Frank; Olsen, Robert G.

2016-01-01

Conclusions of epidemiological studies describing adverse health effects as a result of exposure to electromagnetic fields are not unanimous and often contradictory. It has been proposed that an explanation could be that high-frequency voltage transients [dirty electricity (DE)] which are superimposed on 50/60-Hz fields, but are generally not measured, are the real causal agent. DE has been linked to many different health and wellbeing effects, and on the basis of this, an industry selling measurement and filtering equipment is growing. We reviewed the available peer-reviewed evidence for DE as a causal agent for adverse human health effects. A literature search was performed in the Cochrane Library, PubMed, Web of Science, Google Scholar, and additional publications were obtained from reference lists and from the gray literature. This search resulted in 25 publications; 16 included primary epidemiological and/or exposure data. All studies were reviewed by both authors independently, and including a re-review of studies included in a review of data available up to July 31, 2009 by one of the authors. DE has been measured differently in different studies and comparison data are not available. There is no evidence for 50 Graham/Stetzer (GS) units as a safety threshold being anything more than arbitrary. The epidemiological evidence on human health effects of DE is primarily based on, often re-used, case descriptions. Quantitative evidence relies on self-reporting in non-blinded interventions, ecological associations, and one cross-sectional cohort study of cancer risk, which does not point to DE as the causal agent. The available evidence for DE as an exposure affecting human health at present does not stand up to scientific scrutiny. PMID:27066469

Investigating work-related neoplasia associated with solar radiation.

PubMed

Turner, S; Forman, S D; McNamee, R; Wilkinson, S M; Agius, R

2015-01-01

Both solar and non-solar exposures associated with occupation and work tasks have been reported as skin carcinogens. In the UK, there are well-established surveillance schemes providing relevant information, including when exposures took place, occupation, location of work and dates of symptom onset and diagnosis. To add to the evidence on work-related skin neoplasia, including causal agents, geographical exposure and time lag between exposure and diagnosis. This study investigated incident case reports of occupational skin disease originating from clinical specialists in dermatology reporting to a UK-wide surveillance scheme (EPIDERM) by analysing case reports of skin neoplasia from 1996 to 2012 in terms of diagnosis, employment, suspected causal agent and symptom onset. The suspected causal agent was 'sun/sunlight/ultraviolet light' in 99% of the reported work-related skin neoplasia cases. Most cases reported (91%) were in males, and the majority (62%) were aged over 65 at the time of reporting. More detailed information on exposure was available for 42% of the cases, with the median time from exposure to symptom onset ranging from 44 (melanoma) to 57 (squamous cell carcinoma) years. Irrespective of diagnostic category, the median duration of exposure to 'sun/sunlight/ultraviolet light' appeared longer where exposures occurred in the UK (range 39-51 years) rather than outside the UK (range 2.5-6.5 years). It is important to provide effective information about skin protection to workers exposed to solar radiation, especially to outdoor workers based outside the UK. © The Author 2014. Published by Oxford University Press on behalf of the Society of Occupational Medicine. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Embodied cognition and circular causality: on the role of constitutive autonomy in the reciprocal coupling of perception and action

PubMed Central

Vernon, David; Lowe, Robert; Thill, Serge; Ziemke, Tom

2015-01-01

The reciprocal coupling of perception and action in cognitive agents has been firmly established: perceptions guide action but so too do actions influence what is perceived. While much has been said on the implications of this for the agent's external behavior, less attention has been paid to what it means for the internal bodily mechanisms which underpin cognitive behavior. In this article, we wish to redress this by reasserting that the relationship between cognition, perception, and action involves a constitutive element as well as a behavioral element, emphasizing that the reciprocal link between perception and action in cognition merits a renewed focus on the system dynamics inherent in constitutive biological autonomy. Our argument centers on the idea that cognition, perception, and action are all dependent on processes focussed primarily on the maintenance of the agent's autonomy. These processes have an inherently circular nature—self-organizing, self-producing, and self-maintaining—and our goal is to explore these processes and suggest how they can explain the reciprocity of perception and action. Specifically, we argue that the reciprocal coupling is founded primarily on their endogenous roles in the constitutive autonomy of the agent and an associated circular causality of global and local processes of self-regulation, rather than being a mutual sensory-motor contingency that derives from exogenous behavior. Furthermore, the coupling occurs first and foremost via the internal milieu realized by the agent's organismic embodiment. Finally, we consider how homeostasis and the related concept of allostasis contribute to this circular self-regulation. PMID:26579043

Endemic pathogens may interfere with HLB

USDA-ARS?s Scientific Manuscript database

Since the first citrus tree was confirmed positive for Candidatus Liberibacter asiaticus (CLas), the causal agent of Huanglongbing (HLB) in 2012, trees continue to be found in urban areas of southern California that are also positive for CLas, demonstrating a slow spread of this disease. However, C...

Exploring Fusarium head blight disease control by RNA interference

USDA-ARS?s Scientific Manuscript database

RNA interference (RNAi) technology provides a novel tool to study gene function and plant protection strategies. Fusarium graminearum is the causal agent of Fusarium head blight (FHB), which reduces crop yield and quality by producing trichothecene mycotoxins including 3-acetyl deoxynivalenol (3-ADO...

Temporal Patterns of Airborne Pesticides in Alpine Lakes of the Sierra Nevada, California

EPA Science Inventory

Airborne agricultural pesticides are being transported many tens of kilometers to remote mountain areas, and have been implicated as a causal agent for recent, dramatic population declines of several amphibian species in such locations. Largely unmeasured, however, are the magnit...

The Causal Structure of Utility Conditionals

ERIC Educational Resources Information Center

Bonnefon, Jean-Francois; Sloman, Steven A.

2013-01-01

The psychology of reasoning is increasingly considering agents' values and preferences, achieving greater integration with judgment and decision making, social cognition, and moral reasoning. Some of this research investigates utility conditionals, ‘"if 'p' then 'q'’" statements where the realization of "p" or "q" or…

Hop powdery mildew control through alteration of spring pruning practices

USDA-ARS?s Scientific Manuscript database

Since 1997, Podosphaera macularis, the causal agent of hop powdery mildew, has become a recurrent threat to hops in the Pacific Northwest because of the potential to reduce cone yield and quality. Disease management practices often involve preventative fungicide applications, but alternative approac...

Barriers to movement and spread of Radopholus similis in anthurium

USDA-ARS?s Scientific Manuscript database

Radopholus similis, the causal agent of anthurium decline, is challenging to manage in anthurium cut flower production. Management can include preplant soil fumigation and the planting of nematode-free anthurium into the field. However, nematodes reinfect the newly planted anthurium quickly through ...

Growth sensitivity of Corynespora cassiicola to Thiophanate-methyl, Iprodione, and Fludioxonil

USDA-ARS?s Scientific Manuscript database

Corynespora cassiicola (Berk. & M.A. Curtis) C.T. Wei, causal agent of Corynespora leaf spot, can cause devastating epidemics in African violet (Saintpaulia ionantha H. Wendl.) production facilities. Because of phytotoxicity and visible residue issues with some fungicides such as chlorothalonil, pro...

Population dynamics of the felted beech scale and associated Neonectria species, causal agents of beech bark disease

Treesearch

Jeffrey Garnas; David Houston; Matthew Ayres; Celia Evans

2009-01-01

Biotic threats to tree growth, survival, or reproduction often arise from interactions among a suite of species, primarily insects and fungi, that function together to varying degrees to defeat host defenses, secure resources, and infect...

AIRBORNE PESTICIDES AND POPULATION DECLINES OF A CALIFORNIA ALPINE FROG

EPA Science Inventory

The mountain yellow-legged frog (Rana muscosa) has disappeared from most of its historic localities in the Sierra Nevada of California, and airborne pesticides from the Central Valley have been implicated as a causal agent. To determine the distribution and temporal variation of ...

Afternoon ascospore release in Claviceps purpurea optimizes perennial ryegrass infection

USDA-ARS?s Scientific Manuscript database

In Kentucky bluegrass, Claviceps purpurea, the causal agent of ergot, typically releases ascospores during the early morning hours, between about midnight and 10:00 a.m., corresponding to time of flowering, when the unfertilized ovaries are most susceptible for infection. During aeromycology studies...

Aspergillus section Flavi community structure in Zambia influences aflatoxin contamination of Maize and Groundnut

USDA-ARS?s Scientific Manuscript database

Aflatoxins are cancer-causing, immuno-suppressive mycotoxins that frequently contaminate important staples in Zambia including maize and groundnut. Several species within Aspergillus section Flavi have been implicated as causal agents of aflatoxin contamination in Africa. However, Aspergillus popula...

Detection of Spiroplasma citri by droplet digital PCR

USDA-ARS?s Scientific Manuscript database

Spiroplasmas are motile, helical bacteria belonging to the Class Mollicutes, a group of prokaryotics with no cell wall and phylogenetically related to Gram-positive bacteria. Spiroplasma citri is the first-cultured spiroplasma and causal agent of citrus stubborn disease (CSD). Detection of CSD is di...

Indole-3-acetic acid biosynthesis in Fusarium delphinoides strain GPK, a causal agent of Wilt in Chickpea.

PubMed

Kulkarni, Guruprasad B; Sanjeevkumar, S; Kirankumar, B; Santoshkumar, M; Karegoudar, T B

2013-02-01

Fusarium delphinoides (Ascomycota; Nectriaceae) is an indole-3-acetic acid (IAA) producing plant pathogen and a causal agent of wilt in chickpea. The IAA biosynthetic pathway in F. delphinoides strain GPK (FDG) was examined by analyzing metabolic intermediates and by feeding experiments. Gas chromatograph (GC) analysis of FDG culture filtrates showed the presence of metabolic intermediates of indole-3-pyruvic acid (IPyA), indole-3-acetamide (IAM), and tryptamine (TRA) pathways. The different IAA biosynthetic pathways were further confirmed by identifying the presence of different enzymes of these pathways. Substrate specificity study of aromatic amino acid aminotransferase revealed that the enzyme is highly specific for tryptophan (Trp) and α-ketoglutarate (α-kg) as amino group donor and acceptor, respectively. Furthermore, the concentration-dependent effect of exogenous IAA on fungal growth was established. Low concentration of exogenous IAA increases the fungal growth and at high concentration it decreases the growth of FDG.

Cognitive Modeling for Agent-Based Simulation of Child Maltreatment

NASA Astrophysics Data System (ADS)

Hu, Xiaolin; Puddy, Richard

This paper extends previous work to develop cognitive modeling for agent-based simulation of child maltreatment (CM). The developed model is inspired from parental efficacy, parenting stress, and the theory of planned behavior. It provides an explanatory, process-oriented model of CM and incorporates causality relationship and feedback loops from different factors in the social ecology in order for simulating the dynamics of CM. We describe the model and present simulation results to demonstrate the features of this model.

Whole-Genome Sequence of Pseudomonas fluorescens EK007-RG4, a Promising Biocontrol Agent against a Broad Range of Bacteria, Including the Fire Blight Bacterium Erwinia amylovora.

PubMed

Habibi, Roghayeh; Tarighi, Saeed; Behravan, Javad; Taheri, Parissa; Kjøller, Annelise Helene; Brejnrod, Asker; Madsen, Jonas Stenløkke; Sørensen, Søren Johannes

2017-03-30

Here, we report the first draft whole-genome sequence of Pseudomonas fluorescens strain EK007-RG4, which was isolated from the phylloplane of a pear tree. P. fluorescens EK007-RG4 displays strong antagonism against Erwinia amylovora , the causal agent for fire blight disease, in addition to several other pathogenic and non-pathogenic bacteria. Copyright © 2017 Habibi et al.

[Bovine herpesvirus 4 (BoHV-4): general aspects of the biology and status in Argentina].

PubMed

Morán, Pedro E; Pérez, Sandra E; Odeón, Anselmo C; Verna, Andrea E

2015-01-01

Bovine herpesvirus 4 (BoHV-4) has been isolated from cattle with respiratory infections, vulvovaginitis, mastitis, abortions, endometritis and from apparently healthy animals throughout the world. Although it has not yet been established as causal agent of a specific disease entity, it is primarily associated with reproductive disorders of cattle. This virus can infect a wide range of species, either in vivo or in vitro. Two groups of prototype strains were originated from the first isolates: the DN599-type strains (American group) and the Movar-type strains (European group). In Argentina, BoHV-4 was isolated and characterized in 2007 from vaginal discharge samples taken from cows that had aborted. So far, more than 40 isolates, mainly associated with aborting bovine females have been registered in our country. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Models for preclinical studies in aging-related disorders: One is not for all

PubMed Central

Santulli, Gaetano; Borras, Consuelo; Bousquet, Jean; Calzà, Laura; Cano, Antonio; Illario, Maddalena; Franceschi, Claudio; Liotta, Giuseppe; Maggio, Marcello; Molloy, William D.; Montuori, Nunzia; O’Caoimh, Rónán; Orfila, Francesc; Rauter, Amelia P.; Santoro, Aurelia; Iaccarino, Guido

2015-01-01

Preclinical studies are essentially based on animal models of a particular disease. The primary purpose of preclinical efficacy studies is to support generalization of treatment–effect relationships to human subjects. Researchers aim to demonstrate a causal relationship between an investigational agent and a disease-related phenotype in such models. Numerous factors can muddle reliable inferences about such cause-effect relationships, including biased outcome assessment due to experimenter expectations. For instance, responses in a particular inbred mouse might be specific to the strain, limiting generalizability. Selecting well-justified and widely acknowledged model systems represents the best start in designing preclinical studies, especially to overcome any potential bias related to the model itself. This is particularly true in the research that focuses on aging, which carries unique challenges, mainly attributable to the fact that our already long lifespan makes designing experiments that use people as subjects extremely difficult and largely impractical. PMID:27042427

Outward foreign direct investments and home country's economic growth

NASA Astrophysics Data System (ADS)

Ciesielska, Dorota; Kołtuniak, Marcin

2017-09-01

The study examines the time stability of the causality direction and cross-correlations between the home country's economic growth and pace of growth of its outward foreign direct investment (OFDI) stocks within the complex system of the Polish national economy. The research has been performed in order to verify, using both the time and frequency domains time series analyses, if economic agents' long term decisions on outward foreign direct investments, leading to cross-border value chains and production fragmentation processes, are of adaptive or predictive character. Consequently, the aim was to check if the home country's economic growth leads the internationalization processes of domestic enterprises, which stays in line with Dunning's Investment Development Path (IDP) paradigm, or if these complex processes, thanks to entrepreneurs' ability to formulate relevant rational expectations, precede the home country's economic growth, which would be supported with the introduction of the policy on reinforcing the internationalization processes of domestic enterprises. The presence of the unidirectional economic growth-led internationalization, consistent with the IDP concept's base assumptions, has been ascertained by the results of the short term Granger causality tests. Nevertheless, the results of the wavelet analyses, supported with the results of the econometric block exogeneity long term causality Wald tests, have revealed that in the long term the OFDI stocks' growth permanently precedes the home country's economic growth, which stays in the unequivocal contrast with the IDP paradigm's premises, as well as with the indicated above short term Granger causality tests' outcomes and indicates that economic agents' choices are not strictly of adaptive but also of predictive character, which influences the current state of knowledge on economic complex systems' characteristics. Such a result is of a great importance in the light of the existence of the significant and still unexploited internationalization potential of Polish enterprises.

Microbiological and biochemical origins of human axillary odour.

PubMed

James, A Gordon; Austin, Corrine J; Cox, Diana S; Taylor, David; Calvert, Ralph

2013-03-01

The generation of malodour on various sites of the human body is caused by the microbial biotransformation of odourless natural secretions into volatile odorous molecules. On the skin surface, distinctive odours emanate, in particular, from the underarm (axilla), where a large and permanent population of microorganisms thrives on secretions from the eccrine, apocrine and sebaceous glands. Traditional culture-based microbiological studies inform us that this resident microbiota consists mainly of Gram-positive bacteria of the genera Staphylococcus, Micrococcus, Corynebacterium and Propionibacterium. Among the molecular classes that have been implicated in axillary malodour are short- and medium-chain volatile fatty acids, 16-androstene steroids and, most recently, thioalcohols. Most of the available evidence suggests that members of the Corynebacterium genus are the primary causal agents of axillary odour, with the key malodour substrates believed to originate from the apocrine gland. In this article, we examine, in detail, the microbiology and biochemistry of malodour formation on axillary skin, focussing on precursor-product relationships, odour-forming enzymes and metabolic pathways and causal organisms. As well as reviewing the literature, some relevant new data are presented and considered alongside that already available in the public domain to reach an informed view on the current state-of-the-art, as well as future perspectives. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Toward Agent-Based Models of the Development And Evolution of Business Relations and Networks

NASA Astrophysics Data System (ADS)

Wilkinson, Ian F.; Marks, Robert E.; Young, Louise

Firms achieve competitive advantage in part through the development of cooperative relations with other firms and organisations. We describe a program of research designed to map and model the development of cooperative inter-firm relations, including the processes and paths by which firms may evolve from adversarial to more cooperative relations. Narrative-event-history methods will be used to develop stylised histories of the emergence of business relations in various contexts and to identify relevant causal mechanisms to be included in the agent-based models of relationship and network evolution. The relationship histories will provide the means of assuring the agent-based models developed.

Urbanism and life satisfaction among the aged.

PubMed

Liang, J; Warfel, B L

1983-01-01

This study examines the impact of urbanism on the causal mechanisms by which life satisfaction is determined. Although the links between the type of community and life satisfaction have been the foci of many studies, the findings are by no means conclusive. Some have found that the rural elderly express greater satisfaction, others have not. Such a discrepancy may be due to (a) the neglect of other variables, (b) a lack of explicit causal specifications, and (c) the failure to distinguish main effects from interaction effects. In this study a causal model that incorporates urbanism as a polytomous variable and its interaction effects has been proposed. The model was evaluated by using four data sets with sample sizes ranging from 961 to 3,996. Urbanism was found to have indirect main effects as well as interaction effects on life satisfaction.

Identifying Causal Variants at Loci with Multiple Signals of Association

PubMed Central

Hormozdiari, Farhad; Kostem, Emrah; Kang, Eun Yong; Pasaniuc, Bogdan; Eskin, Eleazar

2014-01-01

Although genome-wide association studies have successfully identified thousands of risk loci for complex traits, only a handful of the biologically causal variants, responsible for association at these loci, have been successfully identified. Current statistical methods for identifying causal variants at risk loci either use the strength of the association signal in an iterative conditioning framework or estimate probabilities for variants to be causal. A main drawback of existing methods is that they rely on the simplifying assumption of a single causal variant at each risk locus, which is typically invalid at many risk loci. In this work, we propose a new statistical framework that allows for the possibility of an arbitrary number of causal variants when estimating the posterior probability of a variant being causal. A direct benefit of our approach is that we predict a set of variants for each locus that under reasonable assumptions will contain all of the true causal variants with a high confidence level (e.g., 95%) even when the locus contains multiple causal variants. We use simulations to show that our approach provides 20–50% improvement in our ability to identify the causal variants compared to the existing methods at loci harboring multiple causal variants. We validate our approach using empirical data from an expression QTL study of CHI3L2 to identify new causal variants that affect gene expression at this locus. CAVIAR is publicly available online at http://genetics.cs.ucla.edu/caviar/. PMID:25104515

Identifying causal variants at loci with multiple signals of association.

PubMed

Hormozdiari, Farhad; Kostem, Emrah; Kang, Eun Yong; Pasaniuc, Bogdan; Eskin, Eleazar

2014-10-01

Although genome-wide association studies have successfully identified thousands of risk loci for complex traits, only a handful of the biologically causal variants, responsible for association at these loci, have been successfully identified. Current statistical methods for identifying causal variants at risk loci either use the strength of the association signal in an iterative conditioning framework or estimate probabilities for variants to be causal. A main drawback of existing methods is that they rely on the simplifying assumption of a single causal variant at each risk locus, which is typically invalid at many risk loci. In this work, we propose a new statistical framework that allows for the possibility of an arbitrary number of causal variants when estimating the posterior probability of a variant being causal. A direct benefit of our approach is that we predict a set of variants for each locus that under reasonable assumptions will contain all of the true causal variants with a high confidence level (e.g., 95%) even when the locus contains multiple causal variants. We use simulations to show that our approach provides 20-50% improvement in our ability to identify the causal variants compared to the existing methods at loci harboring multiple causal variants. We validate our approach using empirical data from an expression QTL study of CHI3L2 to identify new causal variants that affect gene expression at this locus. CAVIAR is publicly available online at http://genetics.cs.ucla.edu/caviar/. Copyright © 2014 by the Genetics Society of America.

Screening of bacteria for antagonistic activity against phytopathogens of avocados

USDA-ARS?s Scientific Manuscript database

Bacteria and fungi were isolated from the bark of the avocado tree (Persea americana) located in southern Florida. The bacterial strains were subsequently assayed for antagonism activity against Raffaelea lauricola, the causal agent of laurel wilt in avocados. The screen identified no isolates that ...

What causes flag smut of wheat?

USDA-ARS?s Scientific Manuscript database

The causal agent of flag smut of wheat is currently subject to strict quarantine regulations in many countries and is believed to have a wide host range on wild and cultivated grasses. This fungus has been classified as both Urocystis agropyri and Urocystis tritici. Urocystis agropyri was first desc...

Mating disruption of Homalodisca vitripennis (Germar) (Hemiptera: Cicadellidae) by playback of vibrational signals in vineyard trellis

USDA-ARS?s Scientific Manuscript database

BACKGROUND: Glassy-winged sharpshooter (GWSS), Homalodisca vitripennis (Germar) (Hemiptera: Cicadellidae), is an important vector of the bacterium Xylella fastidiosa, the causal agent of Pierce’s disease of grapevine. Area-wide applications of neonicotinoid insecticides have suppressed GWSS populati...

Pathogenicity variation in two west coast forest Phytophthoras, Phytophthora nemorosa and P. pseudosyringae, to bay laurel

Treesearch

R.E. Linzer; M. Garbelotto

2008-01-01

Two recently described pathogenic oomycetes, Phytophthora nemorosa and P. pseudosyringae, have overlapping host and geographic ranges in California and Oregon forests with P. ramorum, causal agent of ?sudden oak death? disease. Preliminary genetic evidence indicates P. nemorosa and P....

The Draft Genome Sequence of Mycosphaerella fijiensis, the Black Sigatoka Pathogen of Banana

USDA-ARS?s Scientific Manuscript database

Mycosphaerella fijiensis is a fungal pathogen of banana and the causal agent of the devastating Black Sigatoka or black leaf streak disease. Its control requires weekly fungicide applications when bananas are grown under disease-conducive conditions, which mostly represent precarious tropical enviro...

Cytology of infection of apple leaves by Diplocarpon mali

USDA-ARS?s Scientific Manuscript database

Diplocarpon mali, the causal agent of Marssonina leaf blotch of apple, causes severe defoliation during the growing season. Little information is available on the mode of infection and infection process. In this study, the infection strategies of D. mali in apple leaves were investigated using fluor...

Genetic recombination in Venturia effusa, causal agent of pecan scab

USDA-ARS?s Scientific Manuscript database

Venturia effusa causes pecan scab, the most prevalent disease of pecan in the southeastern USA. Mating type idiomorphs were recently characterized and the sexual stage was subsequently produced in vitro. To investigate sexual reproduction and recombination of traits in V. effusa, select isolates wer...

AFLP fingerprinting for identification of infra-species groups of Rhizoctonia solani and Waitea circinata

USDA-ARS?s Scientific Manuscript database

Patch diseases caused by Thanatephorus cucumeris and Waitea circinata varieties (anamorphs: Rhizoctonia species) pose a serious threat to successful maintenance of several important turfgrass species. Reliance on field symptoms to identify Rhizoctonia causal agents can be difficult and misleading. D...

Surveys for Pathogens of Monoecious Hydrilla in 2013

DTIC Science & Technology

2014-10-01

formulated as a mycoherbicide. Species in the genera Fusarium and Verticillium are best known as vascular wilt pathogens of vegetables, flowers , field...attacks only bananas (Agrios 2005). The causal agents of most Verticillium wilts are V. albo- atrum and V. dahlia. Although both species have been reported

Characterization of physiological and molecular processes associated with potato response to Zebra chip disease

USDA-ARS?s Scientific Manuscript database

Transcriptional analyses were applied to identify molecular mechanisms associated with the response of leaf and root potato tissues to ‘Ca. Liberibacter solanacearum’ (Lso) infection, causal agent of zebra chip disease (ZC). Lso infection affected several host processes including defense response-, ...

Distribution and severity of alder phytophthora in Alaska

Treesearch

G.C. Adams; M. Catal; L. Trummer

2010-01-01

In Alaska, an unprecedented dieback and mortality of Alnus incana ssp. tenuifolia has occurred which stimulated an effort to determine causal agents of the disease. In Europe, similar dieback and mortality of Alnus incana and Alnus glutinosa has been attributed to root rot by a spectrum...

Evidence for sexual reproduction in Fusicladium effusum

USDA-ARS?s Scientific Manuscript database

Fusicladium effusum is the causal agent of pecan scab, the most prevalent and often catastrophic disease of pecan in the southeastern USA. Despite earlier efforts to determine a sexual stage, reproduction in F. effusum has been observed only by asexually produced conidia. However, the degree and dis...

Pseudomonas blight discovered on raspberry in Watsonville

USDA-ARS?s Scientific Manuscript database

In the winter (February) of 2013, a field of raspberries in Watsonville was discovered to be infected with Pseudomonas syringae, the causal agent of Pseudomonas blight disease. This was the first documentation of this disease on raspberry in our region. The infection of raspberry plants is manifeste...

The phloem-sap feeding mealybug (Ferrisia virgata) carries 'Candidatus Liberibacter asiaticus' populations without transmitting disease

USDA-ARS?s Scientific Manuscript database

Candidatus Liberibacter asiaticus (Las) is the primary causal agent of huanglongbing (HLB), the most devastating disease of citrus worldwide. Currently the known insect vectors of the HLB-associated bacteria are three species of psyllids, Diaphorina citri (Hemiptera: Sternorrhyncha: Psyllidae), Trio...

Propagation of Homalodisca Coagulata Virus-01 via Homalodisca Vitripennis cell culture

USDA-ARS?s Scientific Manuscript database

The glassy-winged sharpshooter (Homalodisca vitripennis) is a highly vagile and polyphagous insect found throughout the southwestern United States. These insects are the predominant vectors of Xylella fastidiosa, a xylem-limited bacterium that is the causal agent of Pierce's disease (PD) of grapevin...

Inhibition of Ophiognomonia clavigignenti-juglandacearum by Juglans species bark extracts

Treesearch

M.J. Moore; M.E. Ostry; A.D. Hegeman; A.C. Martin

2015-01-01

A rapid and reliable technique is needed for identifying butternut trees (Juglans cinerea) with resistance to butternut canker. We investigated the potential of a bark extract bioassay to detect levels of resistance to Ophiognomonia clavigignenti-juglandacearum (Oc-j), the causal agent of butternut canker....

AFLPs detect low genetic diversity for Phytophthora nemorosa and P. pseudosyringae in the US and Europe

Treesearch

Rachel E. Linzer; David M. Rizzo; Santa Olga Cacciola; Matteo Garbelotto

2009-01-01

In California and Oregon, two recently described oomycete forest pathogens, Phytophthora nemorosa and P. pseudosyringae, overlap in their host and geographic ranges with the virulent P. ramorum, causal agent of "sudden oak death." Epidemiological observations, namely broader geographic...

Occurrence of fludioxonil resistance in penicillium digitatum from citrus in California

USDA-ARS?s Scientific Manuscript database

Penicillium digitatum is the causal agent of green mold, the most important postharvest disease of citrus (Citrus spp.). Fludioxonil is marketed as either a solo product or in combination with azoxystrobin for control of green mold and other postharvest diseases. Baseline sensitivity to fludioxonil ...

ROADSIDE AMMONIA MEASUREMENTS USING OPTICAL REMOTE SENSING INSTRUMENTS

EPA Science Inventory

Fine particles less than 2.5 microns in diameter have been identified as a causal agent of excess mortality and other undesirable health impacts. A large part of these airborne particles, generally more than one-half, are formed in the atmosphere by reactions of ammonia with acid...

New Insights into Signed Path Coefficient Granger Causality Analysis

PubMed Central

Zhang, Jian; Li, Chong; Jiang, Tianzi

2016-01-01

Granger causality analysis, as a time series analysis technique derived from econometrics, has been applied in an ever-increasing number of publications in the field of neuroscience, including fMRI, EEG/MEG, and fNIRS. The present study mainly focuses on the validity of “signed path coefficient Granger causality,” a Granger-causality-derived analysis method that has been adopted by many fMRI researches in the last few years. This method generally estimates the causality effect among the time series by an order-1 autoregression, and defines a positive or negative coefficient as an “excitatory” or “inhibitory” influence. In the current work we conducted a series of computations from resting-state fMRI data and simulation experiments to illustrate the signed path coefficient method was flawed and untenable, due to the fact that the autoregressive coefficients were not always consistent with the real causal relationships and this would inevitablely lead to erroneous conclusions. Overall our findings suggested that the applicability of this kind of causality analysis was rather limited, hence researchers should be more cautious in applying the signed path coefficient Granger causality to fMRI data to avoid misinterpretation. PMID:27833547

The gut microbiota and obesity: from correlation to causality.

PubMed

Zhao, Liping

2013-09-01

The gut microbiota has been linked with chronic diseases such as obesity in humans. However, the demonstration of causality between constituents of the microbiota and specific diseases remains an important challenge in the field. In this Opinion article, using Koch's postulates as a conceptual framework, I explore the chain of causation from alterations in the gut microbiota, particularly of the endotoxin-producing members, to the development of obesity in both rodents and humans. I then propose a strategy for identifying the causative agents of obesity in the human microbiota through a combination of microbiome-wide association studies, mechanistic analysis of host responses and the reproduction of diseases in gnotobiotic animals.

Asthma, hypersensitivity pneumonitis and other respiratory diseases caused by metalworking fluids.

PubMed

Rosenman, Kenneth D

2009-04-01

To highlight advances in understanding the respiratory disease associated with metal machining, a common work process involving approximately 1.2 million workers in the USA. Recent studies emphasize that work-related asthma and hypersensitivity pneumonitis continue to be caused by exposure to metalworking fluid. Identification of an individual patient indicates the need for follow-up investigations at the work site to prevent additional disease and/or identify additional effected individuals. Identification of the causal agent for hypersensitivity pneumonitis has centered on microbial contamination of metalworking fluids with a number of studies focusing on Mycobacterium immunogenum. Both asthma and hypersensitivity pneumonitis occur among workers exposed to metalworking fluid. The incidence of these diseases among such workers is unknown. Outbreaks of these conditions continue to be identified among metal machinists. Whether these are true outbreaks associated with some breakdown in workplace controls or, rather the recognition of ongoing endemic disease that is typically misdiagnosed as pneumonia or common adult onset asthma, needs further evaluation. Further work to elucidate the specific causal agent(s) is necessary to affect effective workplace controls. Treating an identified individual case as an index case with a follow-up workplace investigation will only be possible if practicing physicians interact with public health authorities to report newly diagnosed cases.

Identification of acute toxicants in New Bedford Harbor sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, K.T.; McKinney, R.A.; Kuhn, A.

1997-03-01

New Bedford Harbor (NBH) is a marine Superfund site contaminated with high concentrations of polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs) and metals. Experiments were conducted to determine the causal toxic agent(s) in pore waters from New Bedford Harbor sediments to amphipods and mysid shrimp. Chemical manipulations to characterize toxicity revealed that pore-water toxicity was organic in nature. Fractionation and subsequent mass spectral identification of peaks in the toxic fraction indicated that PCBs. PAHs, and unknown compounds were present. Comparisons of PAH LC50s and PAH concentrations in this fraction indicated that the toxicity was not due to PAHs because themore » PAH concentrations were much lower than the reported PAH LC50s. One unknown peak was positively identified as bis(2-ethylhexyl) phthalate, and the other tentatively identified as pyrazole. Toxicity tests and comparison of toxicity in the blank and toxic fractions eliminated the two unknowns as toxic causal agents. The authors determined the range of PCB LC50s to fall between 10 and 110 ppb for Mysidopsis bahia and Ampelisca abdita. Concentrations of PCBs for the toxic fractions ranged from 12 to 27 ppb. This range falls within the observed PCB LC50s for M. bahia and A. abdita. Based upon these PCB concentrations, they concluded that PCBs were the acute toxic agents in NBH pore waters. Other compounds in the toxic fractions, or compounds that coeluted and were undistinguished from PCBs had minor contributions to the measured toxicity.« less

Divalent Copper as a Major Triggering Agent in Alzheimer's Disease.

PubMed

Brewer, George J

2015-01-01

Alzheimer's disease (AD) is at epidemic proportions in developed countries, with a steady increase in the early 1900 s, and then exploding over the last 50 years. This epidemiology points to something causative in the environment of developed countries. This paper will review the considerable evidence that that something could be inorganic copper ingestion. The epidemic parallels closely the spread of copper plumbing, with copper leached from the plumbing into drinking water being a main causal feature, aided by the increasingly common use of supplement pills containing copper. Inorganic copper is divalent copper, or copper-2, while we now know that organic copper, or copper in foods, is primarily monovalent copper, or copper-1. The intestinal transport system, Ctr1, absorbs copper-1 and the copper moves to the liver, where it is put into safe channels. Copper-2 is not absorbed by Ctr1, and some of it bypasses the liver and goes directly into the blood, where it appears to be exquisitely toxic to brain cognition. Thus, while aggregation of amyloid-β has been postulated to be the cause of AD under current dogma, the great increase in prevalence over the last century appears to be due to ingestion of copper-2, which may be causing the aggregation, and/or increasing the oxidant toxicity of the aggregates. An alternative hypothesis proposes that oxidant stress is the primary injuring agent, and under this hypothesis, copper-2 accumulation in the brain may be a causal factor of the oxidant injury. Thus, irrespective of which hypothesis is correct, AD can be classified, at least in part, as a copper-2 toxicity disease. It is relatively easy to avoid copper-2 ingestion, as discussed in this review. If most people begin avoiding copper-2 ingestion, perhaps the epidemic of this serious disease can be aborted.

Emergence of white pine needle damage in the northeastern United States is associated with changes in pathogen pressure in response to climate change.

PubMed

Wyka, Stephen A; Smith, Cheryl; Munck, Isabel A; Rock, Barrett N; Ziniti, Beth L; Broders, Kirk

2017-01-01

The defoliation of the eastern white pine (Pinus strobus) across the northeastern United States is an escalating concern threatening the ecological health of northern forests and economic vitality of the region's lumber industry. First documented in the spring of 2010 affecting 24 328 hectares in the state of Maine, white pine needle damage (WPND) has continued to spread and is now well established in all New England states. While causal agents of WPND are known, current research is lacking in both sampling distribution and the specific environmental factor(s) that affect the development and spread of this disease complex. This study aims to construct a more detailed distribution map of the four primary causal agents within the region, as well as utilize long-term WPND monitoring plots and data collected from land-based weather stations to develop a climatic model to predict the severity of defoliation events in the proceeding year. Sampling results showed a greater distribution of WPND than previously reported. WPND was generally found in forest stands that compromised >50% eastern white pine by basal area. No single species, nor a specific combination of species had a dominating presence in particular states or regions, thus supporting the disease complex theory that WPND is neither caused by an individual species nor by a specific combination of species. In addition, regional weather data confirmed the trend of increasing temperature and precipitation observed in this region with the previous year's May, June, and July rainfall being the best predictor of defoliation events in the following year. Climatic models were developed to aid land managers in predicting disease severity and accordingly adjust their management decisions. Our results clearly demonstrate the role changing climate patterns have on the health of eastern white pine in the northeastern United States. © 2016 John Wiley & Sons Ltd.

CROSS REACTIVITY IN ALLERGIC ASTHMA-LIKE RESPONSES BETWEEN MOLD AND HOUSE DUST MITE IN MICE

EPA Science Inventory

Molds are ubiquitous in the environment and exposures to molds contribute to various human diseases including allergic asthma. Some mold allergens have been implicated as the causal agent for allergic asthma. Western blot analysis demonstrated IgE-binding cross-reactivity among m...

Identifying a new causal agent of mosaic in Louisiana sugarcane

USDA-ARS?s Scientific Manuscript database

Sugarcane mosaic virus (SCMV) is a pathogen of economic concern that infects maize, sorghum, and sugarcane worldwide. It is a member of the genus Potyvirus in the family Potyviridae and contains a linear, positive sense ssRNA genome 10 kb long. It is transmitted non-persistently via aphids and ...

Draft Genome Sequence of Cercospora arachidicola, Cause of Early Leaf Spot in Peanut

USDA-ARS?s Scientific Manuscript database

Cercospora arachidicola and Cercosporidium personatum, causal agents of early and late leaf spot, respectively, are important fungal pathogens of peanut. Leaf spot disease is a major contributor to the economic losses experienced by peanut farmers and the industry. Though peanut germplasms with so...

Genome-wide identification of genes regulated by the Rcs Phosphorelay system in Erwinia amylovora

USDA-ARS?s Scientific Manuscript database

The exopolysaccharide amylovoran is one of the major pathgenicity factors in Erwinia amylovora, the causal agent of fire blight of apples and pears. We have previously demonstrated that the RcsBCD phosphorelay system is essential for virulence by controlling amylovoran biosynthesis. We have also fou...

Genotyping of the Valencia peanut core collection with a molecular marker associated with Sclerotinia blight resistance

USDA-ARS?s Scientific Manuscript database

Cultivated peanut, the second most economically important legume crop throughout the United States and the third most important oilseed in the world, is consistently threatened by various diseases and pests. Sclerotinia blight, (causal agents Sclerotinia sclerotiorum (S. sclerotiorum) and Sclerotin...

Diversity, virulence and 2,4-diacetylphloroglucinol sensitivity of Gaeumannomyces graminis var. tritici isolates from Washington State.

USDA-ARS?s Scientific Manuscript database

Populations of 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas fluorescens buildup in soils that have undergone continuous wheat or barley monoculture, resulting in take-all decline (TAD). We tested whether Gaeumannomyces graminis var. tritici (Ggt) isolates (causal agent of take-all) in mon...

PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions

USDA-ARS?s Scientific Manuscript database

Penicillium expansum, the causal agent of blue mold, is one of the most prevalent postharvest pathogens infecting a wide range of crops after harvest. In response, crops have evolved various defense systems to protect themselves against this and other pathogens. Penicillium-crop interaction is a m...

Sequence diversity of wheat mosaic virus isolates

USDA-ARS?s Scientific Manuscript database

High Plains disease of wheat and maize emerged in the United States in 1993 and its distribution has expanded in subsequent years. Wheat mosaic virus (WMoV), transmitted by eriophyid wheat curl mites (Aceria tosichella) is the causal agent of disease. WMoV and other members of the genus Emaravirus...

Spatio-temporal dynamics of Fusarium head blight and Trichothecene toxin types in Canada

USDA-ARS?s Scientific Manuscript database

In many parts of the world Fusarium graminearum is the primary causal agent of Fusarium head blight (FHB), a disease of cereal crops that adversely affects crop yield, food safety, and animal health. We previously demonstrated population structure associated with differences in trichothecene toxin t...

Incidence-severity relationships for scab on foliage and fruit of pecan

USDA-ARS?s Scientific Manuscript database

Venturia effusa is the causal agent of pecan scab, the most prevalent disease of pecan in the southeastern US. Venturia effusa is currently only known to reproduce asexually, yet the genetic diversity among populations of pecan scab suggest it is a sexually reproducing pathogen. Analysis of the mati...

Evidence for sexual reproduction in Venturia effusa, causal agent of pecan scab

USDA-ARS?s Scientific Manuscript database

Pecan scab caused by Venturia effusa is widespread across southwest USA and epidemics can result in catastrophic yield loss. Venturia effusa reproduces asexually during the active phase of the disease cycle (spring through summer) with no evidence of a sexual cycle. Yet, genetic diversity among popu...

Sporulation capacity and longevity of Puccinia horiana teliospores in infected chrysanthemum leaves

USDA-ARS?s Scientific Manuscript database

PUCCINIA HORIANA is a quarantine-significant fungal pathogen and causal agent of Chrysanthemum white rust, first discovered in the U.S. in 1977. The disease was eradicated and for many years successfully controlled by fungicides and strict regulatory measures. However, recently Chrysanthemum white r...

Climate-host mapping of Phytophthora ramorum, causal agent of sudden oak death

Treesearch

Glenn Fowler; Roger Magarey; Manuel Colunga

2006-01-01

Phytophthora ramorum infection was modeled using the NAPPFAST system for the conterminous United States. Parameters used to model P. ramorum infection were: leaf wetness, minimum temperature, optimum temperature and maximum temperature over a specified number of accumulated days. The model was used to create maps showing the...

RNAi-mediated down-regulation of a melanin polyketide synthase (pks1) gene in the fungus Slafractonia leguminicola

USDA-ARS?s Scientific Manuscript database

The fungus Slafractonia leguminicola, the causal agent of blackpatch disease of legumes produces two mycotoxins slaframine and swainsonine, causing slobbers’ symptoms and locoism of grazing animals, respectively. The genetics of this important fungus is poorly understood. This work aimed to develop ...

Evaluation of wild Juglans species for crown gall resistance

USDA-ARS?s Scientific Manuscript database

Paradox, the most widely used rootstock in CA walnut production, is highly susceptible to the causal agent of crown gall (CG) Agrobacterium tumefaciens. The bacterial pathogen induces the formation of large tumors around the crown of the tree resulting in a reduction in both vigor and yield. If left...

Clonal Propagation of walnut rootstock genotypes for genetic improvement 2010

USDA-ARS?s Scientific Manuscript database

The soilborne bacterium Agrobacterium tumefaciens is the causal agent of crown gall disease of walnut. Large tumors located near the crown of the tree are hallmark symptoms induced by the bacterial pathogen. Untreated tumors can have an adverse effect on tree health resulting in reduced nut yield an...

Development of orange rust of sugarcane in Louisiana

USDA-ARS?s Scientific Manuscript database

Orange rust of sugarcane was observed for the first time in the Americas in 2007 in Florida. Urediniospores of Puccinia kuehnii, the causal agent of orange rust, were collected in aerial traps located in Louisiana in 2010; however, the first observation of disease symptoms in the state was not made ...

Anaerobic soil disinfestation reduces survival and infectivity of Phytophthora nicotianae chlamydospores in pepper

USDA-ARS?s Scientific Manuscript database

Phytophthora nicotianae is the principal causal agent of root and crown rot disease of pepper plants in Extremadura (western Spain), a spring-summer crop in this region. Preplant soil treatment by anaerobic soil disinfestation (ASD) may effectively control plant pathogens in many crop production sys...

Determining yield loss caused by brown rust in production fields of sugarcane

USDA-ARS?s Scientific Manuscript database

Infections of Puccinia melanocephala, the causal agent of brown rust, appear on Louisiana sugarcane in the spring. Disease expression is usually limited to 2 to 3 months until temperatures exceed those favorable for spore production. The affected sugarcane is harvested 4 to 6 months after rust sympt...

Does infection by southern root-knot nematode influence development of Phytophthora blight in pepper?

USDA-ARS?s Scientific Manuscript database

The southern root-knot nematode, Meloidogyne incognita, and Phytophthora capsici, the causal agent of Phytophthora blight, are both important pathogens of pepper (Capsicum annuum L.) in the U.S. and worldwide. Although there is significant information in the literature about the responses of pepper...

Childhood Asthma and Environmental Exposures at Swimming Pools: State of the Science and Research Recommendations

EPA Science Inventory

Recent studies have explored the potential for swimming pool disinfection byproducts (DBPs) which are respiratory irritants to cause asthma in young children. While these studies raise concerns, gaps still exist in our knowledge regarding the exact causal agents and mechanisms f...

A qPCR assay for detection and quantification of Verticillium dahliae in spinach seed.

USDA-ARS?s Scientific Manuscript database

The fungus Verticillium dahliae is the causal agent of Verticillium wilt of lettuce and other specialty crops in the Salinas Valley of California. Spinach, another major specialty crop in California, is not affected by Verticillium wilt in commercial production. However, spinach seed infected with ...

Chitin degradation and metabolism by virulent Aeromonas hydropila

USDA-ARS?s Scientific Manuscript database

Aeromonas hydrophila is the causal agent of motile Aeromonas septicemia (MAS) in catfish and other warm-water fishes. Severe outbreak of MAS caused by virulent A. hydrophila (vAh) was reported in 2009 in the Southeastern United States; the disease has since resulted in loss of millions of pounds of ...

Expression of a synthetic rust fungal virus cDNA in yeast

USDA-ARS?s Scientific Manuscript database

Mycoviruses are viruses that infect fungi. Recently, mycovirus-like RNAs were sequenced from the fungus Phakopsora pachyrhizi, the causal agent of soybean rust. One of the RNAs appeared to represent a novel mycovirus and was designated Phakopsora pachyrhizi virus 2383 (PpV2383). The genome of PpV...

The role of somatic recombination in natural populations of the root pathogen Armillaria mellea

USDA-ARS?s Scientific Manuscript database

Fungi have evolved various mechanisms of shuffling genetic material, which can occur in the absence of fruiting and meiosis. In the homobasidiomycete Armillaria (causal agent of Armillaria root disease), the predominant vegetative stage is diploid. Diploid and haploid mycelia can fuse and undergo ka...

A genome survey of Moniliophthora perniciosa gives new insights into Witches’ Broom Disease of cacao

USDA-ARS?s Scientific Manuscript database

Background: The basidiomycete fungus Moniliophthora perniciosa is the causal agent of Witches’ Broom Disease (WBD) in cacao (Theobroma cacao). It is a hemibiotrophic pathogen that colonizes the apoplast of cacao’s meristematic tissues as a biotrophic pathogen, switching to a saprotrophic lifestyle d...

Pseudoperonospora cubensis and P. humuli detection using species-specific probes and high definition melt curve analysis

USDA-ARS?s Scientific Manuscript database

Three assays were developed for molecular differentiation of Pseudoperonospora cubensis and P. humuli, causal agents of cucurbit and hop downy mildew, respectively, for detection of airborne sporangia and diagnosis of symptomatic leaf tissue. The assays were based on previously identified single nuc...

Design of a candidate vibrational signal for mating disruption against the glassy-winged sharpshooter, Homalodisca Vitripennis

USDA-ARS?s Scientific Manuscript database

The glassy-winged sharpshooter (GWSS), Homalodisca vitripennis, is an important pest of grapevines due to its ability to transmit Xylella fastidiosa, the causal agent of Pierce’s disease. GWSS mating communication is based on vibrational signals; therefore, vibrational mating disruption could be an ...

Population structure of Geosmithia morbida, the causal agent of thousand cankers disease of walnut trees in the United States

Treesearch

Marcelo M. Zerillo; Jorge Ibarra Caballero; Keith Woeste; Andrew D. Graves; Colleen Hartel; Jay W. Pscheidt; Jadelys Tonos; Kirk Broders; Whitney Cranshaw; Steven J. Seybold; Ned Tisserat

2014-01-01

The ascomycete Geosmithia morbida and the walnut twig beetle Pityophthorus juglandis are associated with thousand cankers disease of Juglans (walnut) and Pterocarya (wingnut). The disease was first reported in the western United States (USA) on several Juglans species, but...

Choosing Among Causal Agents in a Dynamic Environment

DTIC Science & Technology

2009-07-30

Participants in a video game environment were required to make a series of decisions in which they must identify which of three targets was causing a...was higher but not when prior video game experience was controlled for. In contrast, women observed their targets for much longer before making a

Distribution of Phytophthora ramorum, P. nemorosa, and P.pseudosyringae in native coastal California forest communities

Treesearch

S.K. Murphy; A.C. Wickland; S.C. Lynch; C.E. Jensen; P.E. Maloney; D.M. Rizzo

2008-01-01

Phytophthora ramorum, causal agent of sudden oak death, is well established over approximately 450 km of native forest along the California coast. In the course of research on this invasive exotic pathogen, two other putatively exotic aerial Phytophthora species, P. nemorosa and P. pseudosyringae...

Evaluating Hawaii-Grown Papaya for Resistance to Internal Yellowing Disease Caused by Enterobacter cloacae

USDA-ARS?s Scientific Manuscript database

Papaya (Carica papaya L.) cultivars and breeding lines were evaluated for resistance to Enterobacter cloacae (Jordan) Hormaeche & Edwards, the bacterial causal agent of internal yellowing disease (IY), using a range of concentrations of the bacterium. Linear regression analysis was performed and IY ...

Sharka epidemiology and worldwide management strategies: learning lessons to optimize disease control in perennial plants

USDA-ARS?s Scientific Manuscript database

Many plant epidemics that cause major economic losses cannot be controlled with pesticides. Among them, sharka epidemics severely affect prunus trees worldwide. Its causal agent, Plum pox virus (PPV;, genus Potyvirus), has been classified as a quarantine pathogen in numerous countries. As a result, ...

The DinJ/RelE toxin-antitoxin system suppresses virulence in Xylella fastidiosa

USDA-ARS?s Scientific Manuscript database

Xylella fastidiosa, the causal agent of a number agriculturally important plant diseases, encodes multiple toxin-antitoxin (TA) systems. TA modules consist of a toxin protein co-expressed with a specific antitoxin, and are often acquired through horizontal gene transfer. Antitoxin molecules (RNA or ...

Natural infection of Sorghum bicolor germplasm by Sugarcane yellow leaf virus in Florida

USDA-ARS?s Scientific Manuscript database

Sugarcane yellow leaf virus (SCYLV), the causal agent of sugarcane yellow leaf, is vectored by the aphid Melanaphis sacchari. Although sugarcane is the primary host of SCYLV, two new natural hosts were recently identified in Florida: the weed Columbus grass (Sorghum almum) and grain sorghum (Sorghum...

Effect of sulfuryl fluoride on the pinewood nematode in pine wood

Treesearch

L. David Dwinell; E. Thoms; S. Prabhakaran

2003-01-01

The pinewood nematode (PUTN) (Bursaphelenchus xylophilus), the causal agent of pine wilt disease, has been intercepted in pine chips, unseasoned pine lumber, and wood packing material (WPM). Likewise, the PWN's insect vectors, Monochamus spp. (pine sawyers), have been found in pallets, crates and dunnage. The PWN, which is...

Geosmithia morbida, the causal agent of thousand cankers disease, found in Indiana

Treesearch

Matthew Ginzel; Jennifer Juzwik

2014-01-01

Thousand Cankers Disease (TCD) is caused by a fungus (Geosmithia morbida) that is vectored by a bark beetle, the walnut twig beetle (WTB), Pityophthorus juglandis (Coleoptera: Curculionidae: Scolytinae). The disease was first recognized in 2008 and has caused the widespread death of walnut trees (Juglans sp.)...

Climate-Host Mapping of Phytophthora ramorum, causal agent of sudden oak death

Treesearch

Roger Magarey; Glenn Fowler; Manuel Colunga; Bill Smith; Ross Meentemeyer

2008-01-01

We modeled Phytophthora ramorum infection using the North Carolina State University- Animal and Plant Health Inspection Service Plant Pest Forecasting System (NAPPFAST) for the conterminous United States. Our infection model is based on a temperature-moisture response function. The model parameters were: leaf wetness, minimum temperature, optimum...

Chlorate poisoning in beef cattle

PubMed Central

Blakley, Barry R.; Fraser, Lorrie M.; Waldner, Cheryl

2007-01-01

A disease syndrome characterized by hemolysis, methemoglobinemia, methemoglobinuria, and death was observed in a herd of purebred Limousin beef cattle grazing on pasture in November in Alberta. Improper disposal of the nonselective herbicide, sodium chlorate, was identified as the causal agent. Highly variable blood methemoglobin levels reflected differences in herbicide consumption. PMID:17987970

Timing and Methodology of Application of Azoxystrobin to Control Rhizoctonia Solani in Sugarbeet

USDA-ARS?s Scientific Manuscript database

Rhizoctonia solani AG 2-2 is the causal agent of Rhizoctonia root and crown rot of sugar beet (Beta vulgaris) in North Dakota and Minnesota. This disease is a major limiting factor to sugar beet production. Management strategies currently include using partially resistant cultivars and fungicides. ...

Multimodal cues drive host-plant assessment in Asian citrus psyllid (Diaphorina citri)

USDA-ARS?s Scientific Manuscript database

Asian citrus psyllid (Diaphorina citri) transmits the causal agent of Huanglongbing, a devastating disease of citrus trees. In this study, we measured behavioral responses of D. citri to combinations of visual, olfactory, and gustatory stimuli in test arenas. Stimuli were presented to the psyllids ...

The virally encoded killer proteins from Ustilago maydis

USDA-ARS?s Scientific Manuscript database

Several strains of Ustilago maydis, a causal agent of corn smut disease, exhibit a 'killer' phenotype that is due to persistent infection by double-stranded RNA Totiviruses. These viruses produce potent killer proteins that are secreted by the host. This is a rare example of virus/host symbiosis in ...

RNA-mediated Gene Silencing in the Cereal Fungal Pathogen Cochliobolus sativus

USDA-ARS?s Scientific Manuscript database

Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is the causal agent of spot blotch, common root rot and black point in barley and wheat. However, little is known about the mechanisms underlying the pathogenicity and virulence of the pathogen. In this study, we developed a high-throughput RNA-...

ANALYSIS OF LOW-LEVEL PESTICIDES FROM HIGH-ELEVATION LAKE WATERS BY LARGE-VOLUME INJECTION GCMS

EPA Science Inventory

Pesticides are among the factors being proposed as causal agents for amphibian population declines in the Sierra Nevada range of California, USA. We hypothesize that agricultural pesticides applied in the San Joaquin Valley west of the mountains are volatilized or eroded, transpo...

A multi-agent intelligent environment for medical knowledge.

PubMed

Vicari, Rosa M; Flores, Cecilia D; Silvestre, André M; Seixas, Louise J; Ladeira, Marcelo; Coelho, Helder

2003-03-01

AMPLIA is a multi-agent intelligent learning environment designed to support training of diagnostic reasoning and modelling of domains with complex and uncertain knowledge. AMPLIA focuses on the medical area. It is a system that deals with uncertainty under the Bayesian network approach, where learner-modelling tasks will consist of creating a Bayesian network for a problem the system will present. The construction of a network involves qualitative and quantitative aspects. The qualitative part concerns the network topology, that is, causal relations among the domain variables. After it is ready, the quantitative part is specified. It is composed of the distribution of conditional probability of the variables represented. A negotiation process (managed by an intelligent MediatorAgent) will treat the differences of topology and probability distribution between the model the learner built and the one built-in in the system. That negotiation process occurs between the agents that represent the expert knowledge domain (DomainAgent) and the agent that represents the learner knowledge (LearnerAgent).

Characteristics of diarrheagenic Escherichia coli among children under 5 years of age with acute diarrhea: a hospital based study.

PubMed

Zhou, Yu; Zhu, Xuhui; Hou, Hongyan; Lu, Yanfang; Yu, Jing; Mao, Lie; Mao, Liyan; Sun, Ziyong

2018-02-01

Diarrhea is the leading infectious cause of childhood morbidity and mortality. Among bacterial agents, diarrheagenic Escherichia coli (DEC) is the major causal agent of childhood diarrhea in developing countries, particularly in children under the age of 5 years. Here, we performed a hospital-based prospective study to explore the pathotype distribution, epidemiological characteristics and antibiotic resistance patterns of DEC from < 5-year-old diarrheal children. Between August 2015 and September 2016, 684 stool samples were collected from children (< 5 years old) with acute diarrhea. All samples were cultured and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and biochemical tests. PCR was used for subtyping, and enteropathogenic E. coli (EPEC) isolates were identified simultaneously with serology. Furthermore, antimicrobial sensitivity tests and sequencing of antibiotic resistance-related genes were conducted. DEC strains were identified in 7.9% of the 684 stool samples. Among them, the most commonly detected pathotype was EPEC (50.0% of DEC), of which 77.8% were classified as atypical EPEC (aEPEC). Age and seasonal distribution revealed that DEC tended to infect younger children and to occur in summer/autumn periods. Multidrug-resistant DEC isolates were 66.7%; resistance rates to ampicillin, co-trimoxazole, cefazolin, cefuroxime, cefotaxime, and ciprofloxacin were ≥ 50%. Among 5 carbapenem-resistant DEC, 60.0% were positive for carbapenemase genes (2 blaNDM-1 and 1 blaKPC-2). Among 30 cephalosporin-resistant DEC, 93.3% were positive for extended-spectrum β-lactamase (ESBL) genes, with blaTEM-1 and blaCTX-M-55 being the most common types. However, no gyrA or gyrB genes were detected in 16 quinolone-resistant isolates. Notably, aEPEC, which has not received much attention before, also exhibited high rates of drug resistance (81.0%, 66.7%, and 14.3% for ampicillin, co-trimoxazole , and carbapenem resistance, respectively). EPEC was the most frequent DEC pathotype in acute diarrheal children, with aEPEC emerging as a dominant diarrheal agent in central China. Most DEC strains were multidrug-resistant, making even ciprofloxacin unsuitable for empiric treatment against DEC infection. Among carbapenem-resistant DEC strains, those harboring blaNDM-1 and blaKPC-2 were the main causal agents. blaTEM-1 and blaCTX-M-55 were the major genetic determinants associated with high levels of cephalosporin resistance.

On the causal structure between CO2 and global temperature

PubMed Central

Stips, Adolf; Macias, Diego; Coughlan, Clare; Garcia-Gorriz, Elisa; Liang, X. San

2016-01-01

We use a newly developed technique that is based on the information flow concept to investigate the causal structure between the global radiative forcing and the annual global mean surface temperature anomalies (GMTA) since 1850. Our study unambiguously shows one-way causality between the total Greenhouse Gases and GMTA. Specifically, it is confirmed that the former, especially CO2, are the main causal drivers of the recent warming. A significant but smaller information flow comes from aerosol direct and indirect forcing, and on short time periods, volcanic forcings. In contrast the causality contribution from natural forcings (solar irradiance and volcanic forcing) to the long term trend is not significant. The spatial explicit analysis reveals that the anthropogenic forcing fingerprint is significantly regionally varying in both hemispheres. On paleoclimate time scales, however, the cause-effect direction is reversed: temperature changes cause subsequent CO2/CH4 changes. PMID:26900086

Addressing the translational dilemma: dynamic knowledge representation of inflammation using agent-based modeling.

PubMed

An, Gary; Christley, Scott

2012-01-01

Given the panoply of system-level diseases that result from disordered inflammation, such as sepsis, atherosclerosis, cancer, and autoimmune disorders, understanding and characterizing the inflammatory response is a key target of biomedical research. Untangling the complex behavioral configurations associated with a process as ubiquitous as inflammation represents a prototype of the translational dilemma: the ability to translate mechanistic knowledge into effective therapeutics. A critical failure point in the current research environment is a throughput bottleneck at the level of evaluating hypotheses of mechanistic causality; these hypotheses represent the key step toward the application of knowledge for therapy development and design. Addressing the translational dilemma will require utilizing the ever-increasing power of computers and computational modeling to increase the efficiency of the scientific method in the identification and evaluation of hypotheses of mechanistic causality. More specifically, development needs to focus on facilitating the ability of non-computer trained biomedical researchers to utilize and instantiate their knowledge in dynamic computational models. This is termed "dynamic knowledge representation." Agent-based modeling is an object-oriented, discrete-event, rule-based simulation method that is well suited for biomedical dynamic knowledge representation. Agent-based modeling has been used in the study of inflammation at multiple scales. The ability of agent-based modeling to encompass multiple scales of biological process as well as spatial considerations, coupled with an intuitive modeling paradigm, suggest that this modeling framework is well suited for addressing the translational dilemma. This review describes agent-based modeling, gives examples of its applications in the study of inflammation, and introduces a proposed general expansion of the use of modeling and simulation to augment the generation and evaluation of knowledge by the biomedical research community at large.

Foodborne Salmonella-caused outbreaks in Catalonia (Spain), 1990 to 2003.

PubMed

Domínguez, Angela; Torner, Nuria; Ruiz, Laura; Martínez, Ana; Bartolomé, Rosa; Sulleiro, Elena; Teixidó, Angel; Plasencia, Antoni

2007-01-01

In most developed countries, nontyphoid Salmonella is an important cause of sporadic cases and outbreaks of foodborne gastroenteritis. The aim of this study was to investigate the trend of foodborne Salmonella-caused outbreaks and number of cases, hospitalizations, and deaths and compare them with those caused by other infectious agents. The study was carried out in Catalonia, a region in northeastern Spain with a population of 6.5 million inhabitants, in 2002. All information on reported outbreaks of foodborne disease from 1990 to 2003 was reviewed. For each outbreak, the following variables were collected: year; setting (household, restaurant, school, hospital, nursing home, and others); number of cases, hospitalizations, and deaths; causal agent; and food vehicle involved. Of 1652 reported outbreaks, 1078 had a known causal agent. Among them, 871 (80.8%) were caused by Salmonella, with 14,695 cases, 1534 hospitalizations, and 4 deaths. The rate of hospitalization was higher in outbreaks due to Salmonella than in those caused by other infectious agents (rate ratio, 2.54; 95% confidence interval, 2.20 to 2.94). Forty-eight percent of Salmonella-caused outbreaks were eggborne, compared with 5.3% of those caused by other infectious agents (rate ratio, 1.40; 95% confidence interval, 1.33 to 1.48). The annual number of cases in household outbreaks of eggborne Salmonella rose over time (R2 = 0.82), but the number of outbreaks produced in other settings did not. Eggborne outbreaks caused by Salmonella in households are a major cause of disease, and increased preventive efforts are necessary, especially consumer education and awareness of the risk of eating food containing raw or slightly cooked eggs.

Causal Inference in Educational Effectiveness Research: A Comparison of Three Methods to Investigate Effects of Homework on Student Achievement

ERIC Educational Resources Information Center

Gustafsson, Jan-Eric

2013-01-01

In educational effectiveness research, it frequently has proven difficult to make credible inferences about cause and effect relations. The article first identifies the main categories of threats to valid causal inference from observational data, and discusses designs and analytic approaches which protect against them. With the use of data from 22…

Assessing Causality in the Relationship between Adolescents' Risky Sexual Online Behavior and Their Perceptions of This Behavior

ERIC Educational Resources Information Center

Baumgartner, Susanne E.; Valkenburg, Patti M.; Peter, Jochen

2010-01-01

The main aim of this study was to investigate the causal nature of the relationship between adolescents' risky sexual behavior on the internet and their perceptions of this behavior. Engagement in the following online behaviors was assessed: searching online for someone to talk about sex, searching online for someone to have sex, sending intimate…

Causality analysis in business performance measurement system using system dynamics methodology

NASA Astrophysics Data System (ADS)

Yusof, Zainuridah; Yusoff, Wan Fadzilah Wan; Maarof, Faridah

2014-07-01

One of the main components of the Balanced Scorecard (BSC) that differentiates it from any other performance measurement system (PMS) is the Strategy Map with its unidirectional causality feature. Despite its apparent popularity, criticisms on the causality have been rigorously discussed by earlier researchers. In seeking empirical evidence of causality, propositions based on the service profit chain theory were developed and tested using the econometrics analysis, Granger causality test on the 45 data points. However, the insufficiency of well-established causality models was found as only 40% of the causal linkages were supported by the data. Expert knowledge was suggested to be used in the situations of insufficiency of historical data. The Delphi method was selected and conducted in obtaining the consensus of the causality existence among the 15 selected expert persons by utilizing 3 rounds of questionnaires. Study revealed that only 20% of the propositions were not supported. The existences of bidirectional causality which demonstrate significant dynamic environmental complexity through interaction among measures were obtained from both methods. With that, a computer modeling and simulation using System Dynamics (SD) methodology was develop as an experimental platform to identify how policies impacting the business performance in such environments. The reproduction, sensitivity and extreme condition tests were conducted onto developed SD model to ensure their capability in mimic the reality, robustness and validity for causality analysis platform. This study applied a theoretical service management model within the BSC domain to a practical situation using SD methodology where very limited work has been done.

Does partial Granger causality really eliminate the influence of exogenous inputs and latent variables?

PubMed

Roelstraete, Bjorn; Rosseel, Yves

2012-04-30

Partial Granger causality was introduced by Guo et al. (2008) who showed that it could better eliminate the influence of latent variables and exogenous inputs than conditional G-causality. In the recent literature we can find some reviews and applications of this type of Granger causality (e.g. Smith et al., 2011; Bressler and Seth, 2010; Barrett et al., 2010). These articles apparently do not take into account a serious flaw in the original work on partial G-causality, being the negative F values that were reported and even proven to be plausible. In our opinion, this undermines the credibility of the obtained results and thus the validity of the approach. Our study is aimed to further validate partial G-causality and to find an answer why negative partial Granger causality estimates were reported. Time series were simulated from the same toy model as used in the original paper and partial and conditional causal measures were compared in the presence of confounding variables. Inference was done parametrically and using non-parametric block bootstrapping. We counter the proof that partial Granger F values can be negative, but the main conclusion of the original article remains. In the presence of unknown latent and exogenous influences, it appears that partial G-causality will better eliminate their influence than conditional G-causality, at least when non-parametric inference is used. Copyright © 2012 Elsevier B.V. All rights reserved.

Prevalence of Rotavirus Genogroup A and Norovirus Genogroup II in Bassaseachic Falls National Park Surface Waters in Chihuahua, Mexico.

PubMed

Delgado-Gardea, Ma Carmen E; Tamez-Guerra, Patricia; Gomez-Flores, Ricardo; Mendieta-Mendoza, Aurora; Zavala-Díaz de la Serna, Francisco Javier; Contreras-Cordero, Juan Francisco; Erosa-de la Vega, Gilberto; Pérez-Recoder, María Concepción; Sánchez-Ramírez, Blanca; González-Horta, Carmen; Infante-Ramírez, Rocío

2017-05-05

In areas lacking potable water treatment, drinking contaminated water may represent a public health threat. In addition to enteropathogenic bacteria and parasites, fecal contamination in water environments is associated with the transmission of enteric viruses and other causal agents of infectious disease. Rotavirus and norovirus are the main enteric viral agents responsible for diarrheic outbreaks. The aim of the present study was to detect seasonal variation of rotavirus and norovirus in the surface water at Bassaseachic Falls National Park during 2013. Rivers and streams within and nearby this park were sampled once in each season during 2013. Viral concentration was carried out by a handmade filtration equipment, using a commercial electropositive membrane coupled with the virus absortion elution technique (VIRADEL©). Detection of rotavirus and norovirus was performed by SYBR Green reverse transcription-real time polymerase chain reaction (SYBR GREEN© RT-qPCR) analyses. Norovirus genogroup II was detected in samples collected in June and October 2013. In the case of rotavirus, genogroup A was detected in March and June. The presence of rotavirus and norovirus was related to viral acute diarrhea in children less than five years of age, who were inhabiting the sampled areas. This may indicates that the contaminated water was potentially a risk factor for regional diarrheic outbreaks.

[Laboratory diagnosis of lymphocytic meningitis].

PubMed

Marí, José María Navarro; Ruiz, Mercedes Pérez; Anza, Diego Vicente

2010-01-01

Lymphocytic meningitis, mainly those with an acute and benign course, are caused by viruses. In our area, the most commonly involved agents are enteroviruses, herpes simplex, varicella zoster and Toscana viruses. Nucleic acids amplification techniques (NAAT) are the methods of choice to diagnose viral meningitis from cerebrospinal fluid (CSF) samples. They are more rapid and sensitive, and indeed, they are not influenced by the viability of the virus in the clinical specimen as traditional methods are. The development of commercial equipments, the degree of automation, and the use of real-time polymerase chain reaction (PCR) systems are the most important premises to choose the molecular method in each laboratory. Recently, commercial kits of real-time PCR are available for the detection of enteroviruses and herpesviruses, which are the most frequently viruses involved in meningitis. Although NAAT from the clinical sample have replaced cell culture for diagnostic purposes, the combination of both methods remain useful. When the detection of the causal agent from the CSF sample is not possible, other specimens (pharyngeal exudates, stools) or serological methods can be used. Serology is the reference method for meningitis caused by West Nile virus and lymphocytic choriomeningitis virus, which are less frequently detected in our area. 2010 Elsevier España S.L. All rights reserved.

The Agent Brain: A Review of Non-invasive Brain Stimulation Studies on Sensing Agency.

PubMed

Crivelli, Davide; Balconi, Michela

2017-01-01

According to philosophy of mind and neuroscientific models, the sense of agency can be defined as the sense that I am the one that is generating an action and causing its effects. Such ability to sense ourselves as causal agents is critical for the definition of intentional behavior and is a primary root for human interaction skills. The present mini-review aims at discussing evidences from non-invasive brain stimulation (NIBS) studies targeting functional correlates of different aspects of agency and evidences on the way stimulation techniques affect such core feature of human subjective experience. Clinical and brain imaging studies helped in defining a neural network mediating agency-related processes, which includes the dorsolateral prefrontal cortex (dlPFC), the cingulate cortex (CC), the supplementary and pre-supplementary motor areas (SMA and pre-SMA), the posterior parietal cortex (PPC) and its inferior regions and the cerebellum. However, while the plurality of those structures mirrors the complexity of the phenomenon, their actual roles with respect to different components of the experience of agency have been primarily explored via correlational techniques, without a clear evidence about their causal significance with respect to the integration of sensorimotor information, intentionalization, and action monitoring processes. Therefore, insights into the specific causal role of different cortical structures can be specified by using NIBS techniques, in order to provide improved understanding into the bases of our ability vs. inability to properly act in complex social contexts.

Vertical Distribution and Daily Flight Periodicity of Ambrosia Beetles (Coleoptera: Curculionidae) in Florida Avocado Orchards Affected by Laurel Wilt

USDA-ARS?s Scientific Manuscript database

Ambrosia beetles have emerged as significant pests of avocado (Persea americana Miller) due to their association with pathogenic fungal symbionts, most notably Raffaelea lauricola, the causal agent of laurel wilt. We evaluated the interaction of ambrosia beetles with host avocado trees by documentin...

The effects of Zebra Chip disease development and bacterial titer on biochemical properties in relation to the time of infection

USDA-ARS?s Scientific Manuscript database

Potato tuber biochemical responses to ‘Candidatus’ Liberibacter solanacearum (Lso), the causal agent of Zebra chip disease, were evaluated both within infected tubers and across different infection dates. Tuber biochemistry also was related to symptom severity and bacterial titer. Symptom severity w...

EPG waveforms of blue green sharpshooter: impedance and voltage level effects on stylet probing

USDA-ARS?s Scientific Manuscript database

Blue-green sharpshooter (BGSS), Graphocephala atropunctata, is a native California vector of Xylella fastidiosa (Xf) a foregut-borne bacterium that is the causal agent of Pierce’s disease in grapevines. A 3rd-generation, AC-DC electropenetrograph (EPG) was used to record probing behaviors of adult B...

Clarireedia: A new fungal genus comprising four pathogenic species responsible for dollar spot disease of turfgrass

USDA-ARS?s Scientific Manuscript database

Dollar spot is one of the most destructive and economically important fungal diseases of amenity turfgrasses. The causal agent was first described in 1937 as the ascomycete Sclerotinia homoeocarpa. However, the genus-level taxonomic placement of this fungus has been the subject of an ongoing debate ...

Collateral damage: fire and Phytophthora ramorum interact to increase mortality in coast redwood

Treesearch

Margaret R. Metz; J. Morgan Varner; Kerri M. Frangioso; Ross K. Meentemeyer; David M. Rizzo

2013-01-01

Invading species can alter ecosystems by impacting the frequency, severity, and consequences of endemic disturbance regimes (Mack and D'Antonio 1998). Phytophthora ramorum, the causal agent of the emergent disease sudden oak death (SOD), is an invasive pathogen causing widespread tree mortality in coastal forests of California and Oregon. In...

Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages

PubMed Central

Esplin, Ian N. D.; Berg, Jordan A.; Sharma, Ruchira; Allen, Robert C.; Arens, Daniel K.; Ashcroft, Cody R.; Bairett, Shannon R.; Beatty, Nolan J.; Bickmore, Madeline; Bloomfield, Travis J.; Brady, T. Scott; Bybee, Rachel N.; Carter, John L.; Choi, Minsey C.; Duncan, Steven; Fajardo, Christopher P.; Foy, Brayden B.; Fuhriman, David A.; Gibby, Paul D.; Grossarth, Savannah E.; Harbaugh, Kala; Harris, Natalie; Hilton, Jared A.; Hurst, Emily; Hyde, Jonathan R.; Ingersoll, Kayleigh; Jacobson, Caitlin M.; James, Brady D.; Jarvis, Todd M.; Jaen-Anieves, Daniella; Jensen, Garrett L.; Knabe, Bradley K.; Kruger, Jared L.; Merrill, Bryan D.; Pape, Jenny A.; Payne Anderson, Ashley M.; Payne, David E.; Peck, Malia D.; Pollock, Samuel V.; Putnam, Micah J.; Ransom, Ethan K.; Ririe, Devin B.; Robinson, David M.; Rogers, Spencer L.; Russell, Kerri A.; Schoenhals, Jonathan E.; Shurtleff, Christopher A.; Simister, Austin R.; Smith, Hunter G.; Stephenson, Michael B.; Staley, Lyndsay A.; Stettler, Jason M.; Stratton, Mallorie L.; Tateoka, Olivia B.; Tatlow, P. J.; Taylor, Alexander S.; Thompson, Suzanne E.; Townsend, Michelle H.; Thurgood, Trever L.; Usher, Brittian K.; Whitley, Kiara V.; Ward, Andrew T.; Ward, Megan E. H.; Webb, Charles J.; Wienclaw, Trevor M.; Williamson, Taryn L.; Wells, Michael J.; Wright, Cole K.; Breakwell, Donald P.; Hope, Sandra

2017-01-01

ABSTRACT Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages. PMID:29146842

Vertical distribution and daily flight periodicity of ambrosia beetles associated with laurel wilt affected avocado orchards.

USDA-ARS?s Scientific Manuscript database

Recently, ambrosia beetles have emerged as significant pests of avocado (Persea americana Mill.; Lauraceae) due to their association with fungal pathogens, in particular, the causal agent of laurel wilt disease, Raffaelea lauricola. The objective of this study was to provide insights into the intera...

Armillaria root disease in the western USA

Treesearch

John Hanna; Sara Ashiglar; Anna Case; Mary Lou Fairweather; Chris Hoffman; Mee-Sook Kim; Helen Maffei; Robert Mathiasen; Geral McDonald; Erik Nelson; Amy Ross-Davis; John Shaw; Ned Klopfenstein

2012-01-01

Armillaria species display diverse ecological behaviors from beneficial saprobe to virulent pathogen. Armillaria solidipes, a causal agent of Armillaria root disease (ARD), is a virulent primary pathogen with a broad host range. ARD is responsible for reduced forest productivity as a result of direct tree mortality and non-lethal cryptic infections that impact growth....

Identification of genes differentially expressed during interaction of resistant and susceptible apple cultivars (Malus x domestica) with Erwinia amylovora

USDA-ARS?s Scientific Manuscript database

The necrogenic enterobacterium, Erwinia amylovora is the causal agent of the fire blight (FB) disease in many Rosaceae species, including apple and pear. During the infection process, the bacteria induce an oxidative stress response with kinetics similar to those induced in an incompatible bacteria-...

Horizontal transmission of "Candidatus Liberibacter solanacearum" by Bactericera cockerelli (Hemiptera: Triozidae) on Convolvulus and Ipomoea (Solanales: Convolvulaceae)

USDA-ARS?s Scientific Manuscript database

“Candidatus Liberibacter solanacearum” (Proteobacteria) is an important pathogen of solanaceous crops (Solanales: Solanaceae) in North America and New Zealand, and is the putative causal agent of zebra chip disease of potato. This phloem-limited pathogen is transmitted to potato and other Solanaceo...

Differential apple transcriptomic responses to penicillium expansum (pathogen) and penicillium digitatum (non-host pathogen) infection

USDA-ARS?s Scientific Manuscript database

Penicillium expansum is the causal agent of blue mould of pome fruits and is responsible for important economical losses during postharvest handling in all producing countries. Although control of this pathogen can be achieved by using chemical fungicides, the appearance of resistant strains and in...

Using hierarchical clustering of secreted protein families to classify and rank candidate effectors of rust fungi

USDA-ARS?s Scientific Manuscript database

Rust fungi are obligate biotrophic pathogens causing considerable damage on crop plants. P. graminis f. sp. tritici, the causal agent of wheat stem rust, and M. larici-populina, the poplar rust pathogen, have strong deleterious impact on wheat and poplar wood production, respectively. The recently r...

Recent change in the nomenclature of Phellinus pini: What is Porodaedalea?

Treesearch

Jessie A. Glaeser; Karen K. Nakasone

2010-01-01

The white-rot genus Phellinus contains many important forest pathogens and saprotrophs, including those that produce heartrot, saprot, and root-rot or butt-rot. One of the most notorious species is Phellinus pini, the causal agent of "red ring decay" or "white fleck," which primarily affects older stands of...

Using classification tree analysis to predict oak wilt distribution in Minnesota and Texas

Treesearch

Marla c. Downing; Vernon L. Thomas; Jennifer Juzwik; David N. Appel; Robin M. Reich; Kim Camilli

2008-01-01

We developed a methodology and compared results for predicting the potential distribution of Ceratocystis fagacearum (causal agent of oak wilt), in both Anoka County, MN, and Fort Hood, TX. The Potential Distribution of Oak Wilt (PDOW) utilizes a binary classification tree statistical technique that incorporates: geographical information systems (GIS...

Phytophthora megakarya, a causal agent of black pod rot in Africa

USDA-ARS?s Scientific Manuscript database

In most parts of the world where Theobroma cacao is grown, Phytophthora palmivora is the major concern for causing black pod rot (BPR). Phytophthora megakarya, on the other hand, occurs only in Africa, but represents a major threat to cacao production, the countries of West Africa being the largest ...

Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum

USDA-ARS?s Scientific Manuscript database

The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability of colonizing woody tissue combined with the secretion of phytotoxic compounds is thought to underlie its...

DNA fingerprinting and anastomosis grouping reveal similar genetic diversity in Rhizoctonia species infecting turfgrasses in the transition zone of USA

USDA-ARS?s Scientific Manuscript database

Rhizoctonia blight (sensu lato) is a common and serious disease of many turfgrass species. The most widespread causal agent, R. solani, consists of several genetically different subpopulations. Though hyphal anastomosis reactions have been used to group Rhizoctonia species, they are time consuming a...

Prevalance of aflatoxin contamination in maize and groundnut in Ghana: Population structure, distribution, and toxigenicity of the causal agents

USDA-ARS?s Scientific Manuscript database

Aflatoxin contamination in maize and groundnut is perennial in Ghana with substantial health and economic burden on the population. The present study examined for the first time the prevalence of aflatoxin contamination in maize and groundnut in major producing regions across three agroecological zo...

Draft genome sequence of Venturia carpophila, the causal agent of peach scab

USDA-ARS?s Scientific Manuscript database

Venturia carpophila causes peach scab, a disease that renders peach fruit unmarketable. We report a high-quality draft genome sequence (36.9 Mb) of V. carpophila from an isolate collected from a peach tree in central Georgia in the United States. The genome sequence described will be a useful resour...

A mineral seed coating for control of seedling diseases of alfalfa suitable for organic production systems

USDA-ARS?s Scientific Manuscript database

Most alfalfa seed is treated with the systemic fungicide mefenoxam (Apron XL) for control of soilborne seedling diseases. However, Apron XL does not have activity against Aphanomyces euteiches, the causal agent of Aphanomyces root rot (ARR), which is an important component of the alfalfa root rot co...

Association of ‘Candidatus Liberibacter asiaticus’, the causal agent of citrus huanglongbing in Murraya paniculata and Diaphorina citri in Thailand

USDA-ARS?s Scientific Manuscript database

Orange jasmine, Murraya paniculata, is a preferred alternative host for the Asian citrus psyllid, the primary vector of citrus Huanglongbing (HLB) disease caused by ‘Candidatus Liberibacter asiaticus’ (Las). M. paniculata plant samples and psyllids on the Murraya plants from ten diverse geographical...

Candidatus Liberibacter asiaticus is present in orange jasmine and Asian citrus psyllid reared from jasmine at low titers

USDA-ARS?s Scientific Manuscript database

Orange jasmine, Murraya paniculata, is a common horticultural plant in Florida, and an alternate host of the Asian citrus psyllid, Diaphorina citri Kuwayama. Orange jasmine has also been reported to harbor the bacteria Candidatus Liberibacter asiaticus, the causal agent of huanglongbing disease. We ...

Discovery of uncharacterized sugarcane viruses by next generation sequencing technology: the case of Ramu stunt

USDA-ARS?s Scientific Manuscript database

Ramu stunt disease of sugarcane was first reported in Papua New Guinea in the mid 1980's. The disease can reduce sugarcane yields significantly and causes severe stunting and mortality in highly susceptible cultivars. The causal agent of Ramu stunt has been investigated but its characterization has ...

Field screening of sugarcane varieties for sugarcane yellow leaf in Louisiana

USDA-ARS?s Scientific Manuscript database

The causal agent of sugarcane yellow leaf is the Sugarcane yellow leaf virus (SCYLV), a member of Luteoviridae family. As with other luteoviruses, SCYLV is only transmitted by specific aphids in a circulative, non-propagative manner. In Louisiana, the primary vector of SCYLV is believed to be the su...

Reference assembly and annotation of the Pyrenophora teres f. teres isolate 0-1

USDA-ARS?s Scientific Manuscript database

Pyrenophora teres f. teres, the causal agent of net form net blotch (NFNB) of barley, has become a prevalent pathogen in barley growing regions of the world. Typical yield losses due to NFNB range from 10-40%, however, complete loss has been observed on susceptible barley lines where environmental c...

Population biology of Verticillium dahliae isolates from lettuce in the Sallinas Valley of Californis.

USDA-ARS?s Scientific Manuscript database

Verticillium dahliae is a soil borne fungus and the primary causal agent of Verticillium wilt, which affects many crops worldwide. Many crops grown in the Salinas Valley (SV) of California, including strawberry and lettuce (Lactuca sativa), are susceptible to V. dahliae and severe outbreaks are comm...

Assessment of soybean breeding lines for resistance to Phomopsis seed decay from field trials in Stoneville, Mississippi

USDA-ARS?s Scientific Manuscript database

Phomopsis seed decay (PSD) is one of the most important seed diseases in soybean. A fungal pathogen, Phomopsis longicolla (syn. Diaporthe longicolla), is the primary causal agent of PSD. Planting PSD-resistant soybean cultivars is the most effective strategy to manage this disease. However, few comm...

Evaluating soybean breeding lines developed from differenct sources of resistance to phomopsis seed decay

USDA-ARS?s Scientific Manuscript database

Phomopsis seed decay (PSD) causes poor soybean seed quality worldwide. The primary causal agent of PSD is Phomopsis longicolla (syn. Diaporthe longicolla). Breeding for PSD-resistance is the most effective long-term strategy to control this disease. To develop soybean lines with resistance to PSD, m...

Incidence of 'Candidatus Liberibacter asiaticus' in a Florida population of Asian citrus psyllid

USDA-ARS?s Scientific Manuscript database

A study was conducted to assess the incidence of a bacterium ‘Candidatus Liberibacter asiaticus’ in a Florida population of Asian citrus psyllid (ACP), Diaphorina citri. The bacterium is the presumed causal agent of Asiatic huanglongbing, a serious citrus disease also known as citrus greening or yel...

A Qualitative Synthesis of the Flynn Effect

ERIC Educational Resources Information Center

Ceci, Stephen J.; Williams, Wendy M.

2016-01-01

Clark et al. focus on the likely drivers of the Flynn effect (sociocultural, educational, technological), and imply that it is not a single causal agent driving the upward climb in IQ scores but perhaps multiple causes with different onsets. Given, the authors' conception of intelligence in terms of underlying attentional and cognitive resources…

The mating type idiomorphs of Fusicladium effusum: identification, frequency and spatial distribution in the southeastern USA

USDA-ARS?s Scientific Manuscript database

Fusicladium effusum is the causal agent of pecan scab, the most prevalent disease of pecan (Carya illinoinensis) in the southeastern USA. Infection by the pathogen can result in serious and even catastrophic yield loss when conditions are favorable for an epidemic. Despite earlier efforts to determi...

Assessment of spore presence for Cercospora beticola as demonstrated by sentinel beets

USDA-ARS?s Scientific Manuscript database

Cercospora beticola, the causal agent of Cercospora leaf spot (CLS) in Beta vulgaris (sugar, table, and leaf beet), is an important pathogen globally. Disease forecasting models are widely used to aid in CLS management for sugar beet. Most models rely on weather data to predict infection periods but...

Plasmolysis and vital staining reveal viable oospores of Peronospora effusa in spinach seed lots

USDA-ARS?s Scientific Manuscript database

Production of oospores by Peronospora effusa, the causal agent of downy mildew on spinach (Spinacia oleracea), was reported on spinach seed over three decades ago. In view of the rapid proliferation of new races of P. effusa worldwide, seed borne transmission has been suspected but methods to test ...

Association mapping utilizing diverse barley lines reveals net form net blotch seedling resistance/susceptibility loci

USDA-ARS?s Scientific Manuscript database

Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the causal agent of the economically important foliar disease net form net blotch (NFNB) of barley. The deployment of effective and durable resistance against P. teres f. teres has been hindered by the complexity of quantitative resist...

Development of practical diagnostic methods for monitoring rice bacterial panicle blight disease and evaluation of rice germplasm for resistance

USDA-ARS?s Scientific Manuscript database

A study was initiated to understand Burkholderia glumae, the major causal agent for bacterial panicle blight disease of rice; to develop practical diagnostic methods for monitoring the disease; and to evaluate rice germplasm for resistance. Burkholderia glumae was frequently isolated from infected p...

Development of practical diagnostic methods for monitoring rice bacterial panicle blight disease and evaluation of rice germplasm for resistance

USDA-ARS?s Scientific Manuscript database

A study was initiated to understand Burkholderia glumae (major causal agent for bacterial panicle blight disease of rice) to develop practical diagnostic methods for monitoring the disease; and to evaluate rice germplasm for resistance. B. glumae was frequently isolated from symptomatic panicles on...

Severe outbreak of bacterial panicle blight across Texas Rice Belt in 2010

USDA-ARS?s Scientific Manuscript database

Bacterial panicle blight symptoms have been observed in rice fields in Texas for many years, but it was not until 1996 that Burkholderia glumae was identified as the causal agent. Although it is generally considered a minor disease, there have been years where significant losses to yield and milling...

Biocuration and improvement of the Diaphorina citri draft genome assembly with long reads, optical maps and long-range scaffolding

USDA-ARS?s Scientific Manuscript database

The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for the citrus greening or Huanglongbing disease which threatens citrus industry worldwide. This vector is the primary target of approaches to stop th...

Spatial Patterns of Airborne Pesticides in the Alpine Habitat of a Declining Calfornia Amphibian, The Mountain Yellow-Legged Frog

EPA Science Inventory

The mountain yellow-legged frog complex (Rana muscosa complex) has disappeared from most of its historic localities in the Sierra Nevada of California, and airborne pesticides from the Central Valley have been implicated as a causal agent. To determine the distributions and conce...

Spatial Patterns of Airborne Pesticides in the Alpine Habitat of a Declining California Amphibian, The Mountain Yellow-Legged Frog

EPA Science Inventory

The mountain yellow-legged frog complex (Rana muscosa complex) has disappeared from most of its historic localities in the Sierra Nevada of California, and airborne pesticides from the Central Valley have been implicated as a causal agent. To determine the distributions and conce...

'HoneySweet' plum - a valuable genetically engineered fruit-tree cultivar and germplasm resource

USDA-ARS?s Scientific Manuscript database

‘HoneySweet’ is a plum variety developed through genetic engineering to be highly resistant to plum pox potyvirus (PPV), the causal agent of sharka disease, that threatens stone-fruit industries world-wide and most specifically, in Europe. Field testing for over 15 years in Europe has demonstrated ...

The DinJ/RelE toxin-antitoxin system suppresses bacterial proliferation and virulence of Xylella fastidiosa in grapevine

USDA-ARS?s Scientific Manuscript database

Xylella fastidiosa, the causal agent of Pierce’s disease of grapes, is a slow-growing, xylem-limited, bacterial pathogen. Disease progression is characterized by systemic spread of the bacterium through xylem vessel networks, causing leaf scorching symptoms, senescence, and vine decline. It appears ...

First report of Sugarcane yellow leaf virus infecting Columbus Grass (Sorghum almum) in Florida

USDA-ARS?s Scientific Manuscript database

Sugarcane yellow leaf virus (SCYLV) [genus Polerovirus, family Luteoviridae] is the causal agent of sugarcane yellow leaf disease. SCYLV is widespread in Florida where sugarcane was the only known natural host of this virus. During spring 2015, we collected (leaves or stalks) and tested several gras...

Host phenology and leaf effects on susceptibility of California bay laurel to Phytophthora ramorum

Treesearch

Steven F. Johnston; Michael F. Cohen; Tamas Torok; Ross K. Meentemeyer; Nathan E. Rank

2016-01-01

Spread of the plant pathogen Phytophthora ramorum, causal agent of the forest disease sudden oak death, is driven by a few competent hosts that support spore production from foliar lesions. The relationship between traits of a principal foliar host, California bay laurel (Umbellularia californica), and susceptibility to

Identification of putative plant pathogenic determinants from a draft genome sequence of an opportunistic klebsiella pneumoniae strain

USDA-ARS?s Scientific Manuscript database

Klebsiella pneumoniae has been known historically as a causal agent of bacterial pneumonia. More recently, K. pneumoniaerepresentatives have been shown to have a broad ecological distribution and are recognized nitrogen-fixers. Previously, we demonstrated the capacity of K. pneumoniae strain Kp 5-1R...

Temporal epidemiology of sudden oak death in Oregon

Treesearch

Ebba K. Peterson; Everett M. Hansen; Alan Kanaskie

2015-01-01

An effort to eradicate Phytophthora ramorum, causal agent of sudden oak death, has been underway since its discovery in Oregon forests. Using an information-theoretical approach, we sought to model yearly variation in the size of newly infested areas and dispersal distance. Maximum dispersal distances were best modeled by spring and winter...

Polymorphic SSR markers for Plasmopara obducens (Peronosporaceae), the newly emergent downy mildew pathogen of Impatiens (Balsaminaceae)

USDA-ARS?s Scientific Manuscript database

Premise of the study: Microsatellite markers were developed for Plasmopara obducens, the causal agent of the newly emergent downy mildew disease of Impatiens walleriana. Methods and Results: A 151.2 Mb draft genome assembly was generated from P. obducens using Illumina technology and mined to identi...

Quantitative trait loci for resistance to two fungal pathogens in Quercus robur

Treesearch

Cécile Robin; Amira Mougou-Hamdane; Jean-Marc Gion; Antoine Kremer; Marie-Laure Desprez-Loustau

2012-01-01

Powdery mildew, caused by Erysiphe alphitoides (Ascomycete), is the most frequent disease of oaks, which are also known to be host plants for Phytophthora cinnamomi (Oomycete), the causal agent of ink disease. Components of genetic resistance to these two pathogens, infecting either leaves or root and collar, were...

Candidatus Liberibacter solanacearum' development in Russet Norkotah under commercial storage conditions

USDA-ARS?s Scientific Manuscript database

‘Candidatus Liberibacter solanacearum’ (Lso) is the causal agent of zebra chip (ZC) disease in potato. Following the recent appearance of ZC in the Pacific Northwest region of the US, where waves of the vector arrive towards late-summer and early fall and tubers are stored for future marketing, emph...

Identification of two new races of Diplocarpon rosae Wolf, the causal agent of rose black spot disease

USDA-ARS?s Scientific Manuscript database

The fungal pathogen, Diplocarpon rosae Wolf, infects only roses (Rosa spp.) and leads to rose black spot disease. Rose black spot is the most problematic disease of outdoor grown roses worldwide, due to the potential for rapid leaf yellowing and defoliation. Plants repeatedly defoliated from black ...

Characterization and in Plant Detection of Bacteria that Cause Bacterial Panicle Blight Disease of Rice

USDA-ARS?s Scientific Manuscript database

Burkholderia glumae (BPB) presumably induces a grain rot symptom of rice that is threatening to production in most southern rice producing states of the USA. The present study was to determine the causal agent of BPB, virulence based on hypersensitive reactions on tobacco leaves, and distribution o...

Isolation and identification of bacteria causing blackleg and soft rot of potato

USDA-ARS?s Scientific Manuscript database

Both Dickeya and Pectobacterium spp. are important causal agents of blackleg and soft rot of potato. To understand the outbreak of blackleg in the Northeastern U.S. in 2015, samples were collected from symptomatic plants, dormant tubers, and surface water in 2016 and 2017. Diseased plant samples wer...

Population genetic structure, gene flow and recombination of Cochliobolus miyabeanus on cultivated wildrice (Zizania palustris)

USDA-ARS?s Scientific Manuscript database

Cochliobolus miyabeanus (Bipolaris oryzae) is the causal agent of fungal brown spot (FBS) in wildrice (Zizania palustris), an aquatic grass endemic to Minnesota, Wisconsin, Michigan, and parts of Canada. Grain yield losses can reach up to 74% when the disease starts at the boot stage and continues u...

Anthracnose disease of switchgrass caused by the novel fungal species Colletotrichum navitas.

PubMed

Crouch, Jo Anne; Beirn, Lisa A; Cortese, Laura M; Bonos, Stacy A; Clarke, Bruce B

2009-12-01

In recent years perennial grasses such as the native tallgrass prairie plant Panicum virgatum (switchgrass) have taken on a new role in the North American landscape as a plant-based source of renewable energy. Because switchgrass is a native plant, it has been suggested that disease problems will be minimal, but little research in this area has been conducted. Recently, outbreaks of switchgrass anthracnose disease have been reported from the northeastern United States. Incidences of switchgrass anthracnose are known in North America since 1886 through herbarium specimens and disease reports, but the causal agent of this disease has never been experimentally determined or taxonomically evaluated. In the present work, we evaluate the causal agent of switchgrass anthracnose, a new species we describe as Colletotrichum navitas (navitas=Latin for energy). Multilocus molecular phylogenetics and morphological characters show C. navitas is a novel species in the falcate-spored graminicolous group of the genus Colletotrichum; it is most closely related to the corn anthracnose pathogen Colletotrichum graminicola. We present a formal description and illustrations for C. navitas and provide experimental confirmation that this organism is responsible for switchgrass anthracnose disease.

New hosts of Myrothecium SPP. In brazil and a preliminary In Vitro assay of fungicides

PubMed Central

Quezado Duval, A.M.; Henz, G.P.; Paz-Lima, M.L.; Medeiros, A.R.; Miranda, B.E.C.; Pfenning, L.H.; Reis, A.

2010-01-01

Myrothecium roridum and M. verrucaria are two plant pathogenic species causing foliar spots in a large number of cultivated plants. This paper aims to study the causal agents of foliar spots in vegetable crops (sweet pepper, tomato, cucumber), ornamental plants (Spathiphyllum, Solidago canadensis, Anthurium, Dieffenbachia) and a solanaceous weed plant (Nicandra physalodes). Most of the isolates were identified as M. roridum; only the isolate ‘Myr-02’ from S. canadensis was identified as M. verrucaria. All the isolates were pathogenic to their original plant hosts and also to some other plants. Some fungicides were tested in vitro against an isolate of M. roridum and the mycelial growth recorded after seven days. Fungicides with quartenary ammonium, Tebuconzole and copper were highly effective in inhibiting the mycelial growth of M. roridum. This paper confirms the first record of M. roridum causing leaf spots in sweet pepper, tomato, Spathiphyllum, Anthurium, Dieffenbachia and N. physalodes. We also report M. roridum as causal agent of cucumber fruit rot and also M. verrucaria in tango plants. PMID:24031487

Rapid discrimination of the causal agents of urinary tract infection using ToF-SIMS with chemometric cluster analysis

NASA Astrophysics Data System (ADS)

Fletcher, John S.; Henderson, Alexander; Jarvis, Roger M.; Lockyer, Nicholas P.; Vickerman, John C.; Goodacre, Royston

2006-07-01

Advances in time of flight secondary ion mass spectrometry (ToF-SIMS) have enabled this technique to become a powerful tool for the analysis of biological samples. Such samples are often very complex and as a result full interpretation of the acquired data can be extremely difficult. To simplify the interpretation of these information rich data, the use of chemometric techniques is becoming widespread in the ToF-SIMS community. Here we discuss the application of principal components-discriminant function analysis (PC-DFA) to the separation and classification of a number of bacterial samples that are known to be major causal agents of urinary tract infection. A large data set has been generated using three biological replicates of each isolate and three machine replicates were acquired from each biological replicate. Ordination plots generated using the PC-DFA are presented demonstrating strain level discrimination of the bacteria. The results are discussed in terms of biological differences between certain species and with reference to FT-IR, Raman spectroscopy and pyrolysis mass spectrometric studies of similar samples.

Morality is real, objective, and natural.

PubMed

Shermer, Michael

2016-11-01

To make the case that morality is real, objective, and natural, it will be argued, first, that morals exist in human nature as part of our evolutionary heritage; that morality involves how we think and act toward other moral agents in terms of whether our thoughts and actions are right or wrong with regard to their survival and flourishing; and that moral progress is real, quantifiable, and the result of our improved understanding of causality in the social and moral sciences in the same manner as our understanding of causality has progressed in the physical and biological sciences. A moral starting point is the survival and flourishing of sentient beings. © 2016 New York Academy of Sciences.

[A study of relation between hopelessness and causal attribution in school-aged children].

PubMed

Sakurai, S

1989-12-01

This study was conducted to investigate the relation between hopelessness and causal attribution in Japanese school-aged children. In Study 1, the Japanese edition of hopelessness scale for children developed by Kazdin, French, Unis, Esveldt-Dawsan, and Sherick (1983) was constructed. Seventeen original items were translated into Japanese and they were administrated to 405 fifth- and sixth-graders. All of the items could be included to the Japanese edition of hopelessness scale. The reliability and validity was examined. In Study 2, the relation between hopelessness and causal attribution in children were investigated. The causal attribution questionnaire developed by Higuchi, Kambare, and Otsuka (1983) and the hopelessness scale developed by Study 1 were administered to 188 sixth-graders. Children with high scores in hopelessness scale significantly attributed negative events to much more effort factor than children with low scores. It supports neither the reformulated learned helplessness model nor the causal attribution theory of achievement motivation. It was explained mainly from points of self-serving attribution, cultural difference, and social desirability. Some questions were discussed for developing studies on depression and causal attribution in Japan.

Development and Inter-Rater Reliability of the Liverpool Adverse Drug Reaction Causality Assessment Tool

PubMed Central

Gallagher, Ruairi M.; Kirkham, Jamie J.; Mason, Jennifer R.; Bird, Kim A.; Williamson, Paula R.; Nunn, Anthony J.; Turner, Mark A.; Smyth, Rosalind L.; Pirmohamed, Munir

2011-01-01

Aim To develop and test a new adverse drug reaction (ADR) causality assessment tool (CAT). Methods A comparison between seven assessors of a new CAT, formulated by an expert focus group, compared with the Naranjo CAT in 80 cases from a prospective observational study and 37 published ADR case reports (819 causality assessments in total). Main Outcome Measures Utilisation of causality categories, measure of disagreements, inter-rater reliability (IRR). Results The Liverpool ADR CAT, using 40 cases from an observational study, showed causality categories of 1 unlikely, 62 possible, 92 probable and 125 definite (1, 62, 92, 125) and ‘moderate’ IRR (kappa 0.48), compared to Naranjo (0, 100, 172, 8) with ‘moderate’ IRR (kappa 0.45). In a further 40 cases, the Liverpool tool (0, 66, 81, 133) showed ‘good’ IRR (kappa 0.6) while Naranjo (1, 90, 185, 4) remained ‘moderate’. Conclusion The Liverpool tool assigns the full range of causality categories and shows good IRR. Further assessment by different investigators in different settings is needed to fully assess the utility of this tool. PMID:22194808

Causal Inference Regarding Infectious Aetiology of Chronic Conditions: A Systematic Review

PubMed Central

Orrskog, Sofia; Medin, Emma; Tsolova, Svetla; Semenza, Jan C.

2013-01-01

Background The global burden of disease has shifted from communicable diseases in children to chronic diseases in adults. This epidemiologic shift varies greatly by region, but in Europe, chronic conditions account for 86% of all deaths, 77% of the disease burden, and up to 80% of health care expenditures. A number of risk factors have been implicated in chronic diseases, such as exposure to infectious agents. A number of associations have been well established while others remain uncertain. Methods and Findings We assessed the body of evidence regarding the infectious aetiology of chronic diseases in the peer-reviewed literature over the last decade. Causality was assessed with three different criteria: First, the total number of associations documented in the literature between each infectious agent and chronic condition; second, the epidemiologic study design (quality of the study); third, evidence for the number of Hill's criteria and Koch's postulates that linked the pathogen with the chronic condition. We identified 3136 publications, of which 148 were included in the analysis. There were a total of 75 different infectious agents and 122 chronic conditions. The evidence was strong for five pathogens, based on study type, strength and number of associations; they accounted for 60% of the associations documented in the literature. They were human immunodeficiency virus, hepatitis C virus, Helicobacter pylori, hepatitis B virus, and Chlamydia pneumoniae and were collectively implicated in the aetiology of 37 different chronic conditions. Other pathogens examined were only associated with very few chronic conditions (≤3) and when applying the three different criteria of evidence the strength of the causality was weak. Conclusions Prevention and treatment of these five pathogens lend themselves as effective public health intervention entry points. By concentrating research efforts on these promising areas, the human, economic, and societal burden arising from chronic conditions can be reduced. PMID:23935899

Development of infectious cDNA clones of citrus yellow vein clearing virus using a novel and rapid strategy.

PubMed

Cui, Tian Tian; Bin, Yu; Yan, Jian Hong; Mei, Peng Ying; Li, Zhong An; Zhou, Chang Yong; Song, Zhen

2018-05-04

Yellow vein clearing disease (YVCD) causes significant economic losses in lemon and other species of citrus. Usually, citrus yellow vein clearing virus (CYVCV) is considered to be the causal agent of YVCD. However, mixed infection of CYVCV and Indian citrus ringspot virus (ICRSV) or other pathogens is often detected in citrus plants with YVCD. In this study, we re-examined the causal agent of YVCD to fulfill Koch's postulates. First, the full-length genome of CYVCV isolate AY (CYVCV-AY) was amplified by long-distance RT-PCR from a Eureka lemon [Citrus limon (L) Brum. f.] tree with typical YVCD symptoms. The genomic cDNAs were then cloned into a ternary Yeast-Escherichia coli-Agrobacterium tumefaciens shuttle vector, pCY, using transformation-associated recombination (TAR) strategy, and 15 full-length cDNA clones of CYVCV-AY were obtained. Subsequently, four of these clones were selected randomly and inoculated on Jincheng [C. sinensis (L) Osbeck] seedlings through Agrobacterium-mediated vacuum-infiltration, and it was found that 80 to 100% of inoculated plants were infected with CYVCV by RT-PCR at 20 to 40 days post inoculation (dpi) and by direct tissue blot immunoassay at 60 dpi. The progeny of CYVCV-AY from cDNA clones caused typical symptoms of YVCD such as yellow vein clearing, leaf distortion, and chlorosis, which were the same as that elicited by wild-type virus. Finally, the regeneration of CYVCV-AY genome was confirmed by long-distance RT-PCR in lemon trees inoculated with the infectious cDNA clone. These results proved that CYVCV was the primary causal agent of YVCD. This is the first report on the development of infectious cDNA clones of CYVCV, which lays the foundation for further studies on viral gene functions and virus-host interactions.

Comparison of the White-Nose Syndrome Agent Pseudogymnoascus destructans to Cave-Dwelling Relatives Suggests Reduced Saprotrophic Enzyme Activity

PubMed Central

Reynolds, Hannah T.; Barton, Hazel A.

2014-01-01

White-nose Syndrome (WNS) is an emerging infectious mycosis that has impacted multiple species of North American bats since its initial discovery in 2006, yet the physiology of the causal agent, the psychrophilic fungus Pseudogymnoascus destructans ( = Geomyces destructans), is not well understood. We investigated the ability of P. destructans to secrete enzymes that could permit environmental growth or affect pathogenesis and compared enzyme activity across several Pseudogymnoascus species isolated from both hibernating bats and cave sediments. We found that P. destructans produced enzymes that could be beneficial in either a pathogenic or saprotrophic context, such as lipases, hemolysins, and urease, as well as chitinase and cellulases, which could aid in saprotrophic growth. The WNS pathogen showed significantly lower activity for urease and endoglucanase compared to con-generic species (Pseudogymnoascus), which may indicate a shift in selective pressure to the detriment of P. destructans’ saprotrophic ability. Based on the positive function of multiple saprotrophic enzymes, the causal agent of White-nose Syndrome shows potential for environmental growth on a variety of substrates found in caves, albeit at a reduced level compared to environmental strains. Our data suggest that if P. destructans emerged as an opportunistic infection from an environmental source, co-evolution with its host may have led to a reduced capacity for saprotrophic growth. PMID:24466096

Comparison of the white-nose syndrome agent Pseudogymnoascus destructans to cave-dwelling relatives suggests reduced saprotrophic enzyme activity.

PubMed

Reynolds, Hannah T; Barton, Hazel A

2014-01-01

White-nose Syndrome (WNS) is an emerging infectious mycosis that has impacted multiple species of North American bats since its initial discovery in 2006, yet the physiology of the causal agent, the psychrophilic fungus Pseudogymnoascus destructans ( = Geomyces destructans), is not well understood. We investigated the ability of P. destructans to secrete enzymes that could permit environmental growth or affect pathogenesis and compared enzyme activity across several Pseudogymnoascus species isolated from both hibernating bats and cave sediments. We found that P. destructans produced enzymes that could be beneficial in either a pathogenic or saprotrophic context, such as lipases, hemolysins, and urease, as well as chitinase and cellulases, which could aid in saprotrophic growth. The WNS pathogen showed significantly lower activity for urease and endoglucanase compared to con-generic species (Pseudogymnoascus), which may indicate a shift in selective pressure to the detriment of P. destructans' saprotrophic ability. Based on the positive function of multiple saprotrophic enzymes, the causal agent of White-nose Syndrome shows potential for environmental growth on a variety of substrates found in caves, albeit at a reduced level compared to environmental strains. Our data suggest that if P. destructans emerged as an opportunistic infection from an environmental source, co-evolution with its host may have led to a reduced capacity for saprotrophic growth.

Cladosporium cladosporioides and Cladosporium pseudocladosporioides as potential new fungal antagonists of Puccinia horiana Henn., the causal agent of chrysanthemum white rust.

PubMed

Torres, David Eduardo; Rojas-Martínez, Reyna Isabel; Zavaleta-Mejía, Emma; Guevara-Fefer, Patricia; Márquez-Guzmán, G Judith; Pérez-Martínez, Carolina

2017-01-01

Puccinia horiana Hennings, the causal agent of chrysanthemum white rust, is a worldwide quarantine organism and one of the most important fungal pathogens of Chrysanthemum × morifolium cultivars, which are used for cut flowers and as potted plants in commercial production regions of the world. It was previously reported to be controlled by Lecanicillium lecanii, Cladosporium sphaerospermum, C. uredinicola and Aphanocladium album, due to their antagonistic and hyperparasitic effects. We report novel antagonist species on Puccinia horiana. Fungi isolated from rust pustules in a commercial greenhouse from Villa Guerrero, México, were identified as Cladosporium cladosporioides and Cladosporium pseudocladosporioides based upon molecular analysis and morphological characters. The antagonism of C. cladosporioides and C. pseudocladosporioides on chrysanthemum white rust was studied using light and electron microscopy in vitro at the host/parasite interface. Cladosporium cladosporioides and C. pseudocladosporioides grew towards the white rust teliospores and colonized the sporogenous cells, but no direct penetration of teliospores was observed; however, the structure and cytoplasm of teliospores were altered. The two Cladosporium spp. were able to grow on media containing laminarin, but not when chitin was used as the sole carbon source; these results suggest that they are able to produce glucanases. Results from the study indicate that both Cladosporium species had potential as biological control agents of chrysanthemum white rust.

Cladosporium cladosporioides and Cladosporium pseudocladosporioides as potential new fungal antagonists of Puccinia horiana Henn., the causal agent of chrysanthemum white rust

PubMed Central

Guevara-Fefer, Patricia; Márquez-Guzmán, G. Judith; Pérez-Martínez, Carolina

2017-01-01

Puccinia horiana Hennings, the causal agent of chrysanthemum white rust, is a worldwide quarantine organism and one of the most important fungal pathogens of Chrysanthemum × morifolium cultivars, which are used for cut flowers and as potted plants in commercial production regions of the world. It was previously reported to be controlled by Lecanicillium lecanii, Cladosporium sphaerospermum, C. uredinicola and Aphanocladium album, due to their antagonistic and hyperparasitic effects. We report novel antagonist species on Puccinia horiana. Fungi isolated from rust pustules in a commercial greenhouse from Villa Guerrero, México, were identified as Cladosporium cladosporioides and Cladosporium pseudocladosporioides based upon molecular analysis and morphological characters. The antagonism of C. cladosporioides and C. pseudocladosporioides on chrysanthemum white rust was studied using light and electron microscopy in vitro at the host/parasite interface. Cladosporium cladosporioides and C. pseudocladosporioides grew towards the white rust teliospores and colonized the sporogenous cells, but no direct penetration of teliospores was observed; however, the structure and cytoplasm of teliospores were altered. The two Cladosporium spp. were able to grow on media containing laminarin, but not when chitin was used as the sole carbon source; these results suggest that they are able to produce glucanases. Results from the study indicate that both Cladosporium species had potential as biological control agents of chrysanthemum white rust. PMID:28141830

Quantum Interactive Dualism: An Alternative to Materialism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stapp, Henry P

2005-06-01

Materialism rest implicitly upon the general conception of nature promoted by Galileo and Newton during the seventeenth century. It features the causal closure of the physical: The course of physically described events for all time is fixed by laws that refer exclusively to the physically describeable features of nature, and initial conditions on these feature. No reference to subjective thoughts or feeling of human beings enter. That simple conception of nature was found during the first quarter of the twentieth century to be apparently incompatible with the empirical facts. The founders of quantum theory created a new fundamental physical theory,more » quantum theory, which introduced crucially into the causal structure certain conscious choices made by human agents about how they will act. These conscious human choices are ''free'' in the sense that they are not fixed by the known laws. But they can influence the course of physically described events. Thus the principle of the causal closure of the physical fails. Applications in psycho-neuro-dynamics are described.« less

GMC oxidoreductase, a highly expressed protein in a potent biocontrol agent Fusarium oxysporum Cong:1-2, is dispensable for biocontrol activity.

PubMed

Kawabe, Masato; Okabe Onokubo, Akiko; Arimoto, Yutaka; Yoshida, Takanobu; Azegami, Koji; Teraoka, Tohru; Arie, Tsutomu

2011-01-01

A spontaneous non-pathogenic variant (Cong:1-2) derived from Fusarium oxysporum f. sp. conglutinans (Cong: 1-1), a causal agent of cabbage yellows, carries biocontrol activity for cabbage yellows. We found a GMC oxidoreductase (ODX1) among the proteins expressed much more in Cong:1-2 than Cong:1-1 by 2D-DIGE comparison. GMC oxidoreductases have been reported to be involved in biocontrol activity of several plant pathogenic fungi. The gene encoding ODX1 in Cong:1-2 was cloned, and targeted disruption of the gene in Cong:1-2 did not affect its biocontrol activity, suggesting that GMC oxidoreductase is dispensable for biocontrol activity in the fungal biocontrol agent.

Misconceived causal explanations for emergent processes.

PubMed

Chi, Michelene T H; Roscoe, Rod D; Slotta, James D; Roy, Marguerite; Chase, Catherine C

2012-01-01

Studies exploring how students learn and understand science processes such as diffusion and natural selection typically find that students provide misconceived explanations of how the patterns of such processes arise (such as why giraffes' necks get longer over generations, or how ink dropped into water appears to "flow"). Instead of explaining the patterns of these processes as emerging from the collective interactions of all the agents (e.g., both the water and the ink molecules), students often explain the pattern as being caused by controlling agents with intentional goals, as well as express a variety of many other misconceived notions. In this article, we provide a hypothesis for what constitutes a misconceived explanation; why misconceived explanations are so prevalent, robust, and resistant to instruction; and offer one approach of how they may be overcome. In particular, we hypothesize that students misunderstand many science processes because they rely on a generalized version of narrative schemas and scripts (referred to here as a Direct-causal Schema) to interpret them. For science processes that are sequential and stage-like, such as cycles of moon, circulation of blood, stages of mitosis, and photosynthesis, a Direct-causal Schema is adequate for correct understanding. However, for science processes that are non-sequential (or emergent), such as diffusion, natural selection, osmosis, and heat flow, using a Direct Schema to understand these processes will lead to robust misconceptions. Instead, a different type of general schema may be required to interpret non-sequential processes, which we refer to as an Emergent-causal Schema. We propose that students lack this Emergent Schema and teaching it to them may help them learn and understand emergent kinds of science processes such as diffusion. Our study found that directly teaching students this Emergent Schema led to increased learning of the process of diffusion. This article presents a fine-grained characterization of each type of Schema, our instructional intervention, the successes we have achieved, and the lessons we have learned. Copyright © 2011 Cognitive Science Society, Inc.

Species-Specific Detection and Identification of Fusarium Species Complex, the Causal Agent of Sugarcane Pokkah Boeng in China

PubMed Central

Que, Youxiong; Wang, Jihua; Comstock, Jack C.; Wei, Jinjin; McCord, Per H.; Chen, Baoshan; Chen, Rukai; Zhang, Muqing

2014-01-01

Background Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. Methods A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological observation, pathogenicity test, and phylogenetic analysis based on the fungus-conserved rDNA-ITS. Species-specific TaqMan real-time PCR and conventional PCR methods were developed for rapid and accurate detection of the causal agent of sugarcane pokkah boeng. The specificity and sensitivity of PCR assay were also evaluated on a total of 84 isolates of Fusarium from China and several isolates from other fungal pathogens of Sporisorium scitamineum and Phoma sp. and sugarcane endophyte of Acremonium sp. Result Two Fusarium species (F. verticillioides and F. proliferatum) that caused sugarcane pokahh boeng were identified by morphological observation, pathogenicity test, and phylogenetic analysis. Species-specific TaqMan PCR and conventional PCR were designed and optimized to target their rDNA-ITS regions. The sensitivity of the TaqMan PCR was approximately 10 pg of fungal DNA input, which was 1,000-fold over conventional PCR, and successfully detected pokkah boeng in the field-grown sugarcane. Conclusions/Significance This study was the first to identify two species, F. verticillioides and F. proliferatum, that were causal pathogens of sugarcane pokkah boeng in China. It also described the development of a species-specific PCR assay to detect and confirm these pathogens in sugarcane plants from mainland China. This method will be very useful for a broad range of research endeavors as well as the regulatory response and management of sugarcane pokkah boeng. PMID:25141192

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.

[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.

The dorsomedial prefrontal cortex plays a causal role in mediating in-group advantage in emotion recognition: A TMS study.

PubMed

Gamond, L; Cattaneo, Z

2016-12-01

Consistent evidence suggests that emotional facial expressions are better recognized when the expresser and the perceiver belong to the same social group (in-group advantage). In this study, we used transcranial magnetic stimulation (TMS) to investigate the possible causal involvement of the dorsomedial prefrontal cortex (dmPFC) and of the right temporo-parietal junction (TPJ), two main nodes of the mentalizing neural network, in mediating the in-group advantage in emotion recognition. Participants performed an emotion discrimination task in a minimal (blue/green) group paradigm. We found that interfering with activity in the dmPFC significantly interfered with the effect of minimal group-membership on emotion recognition, reducing participants' ability to discriminate emotions expressed by in-group members. In turn, rTPJ mainly affected emotion discrimination per se, irrespective of group membership. Overall, our results point to a causal role of the dmPFC in mediating the in-group advantage in emotion recognition, favoring intragroup communication. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development and evaluation of a TaqMan Real-Time PCR assay for Fusarium oxysporum f. sp. spinaciae

USDA-ARS?s Scientific Manuscript database

Fusarium oxysporum f. sp. spinaciae, causal agent of spinach Fusarium wilt, is an important soilborne pathogen in many areas of the world where spinach is grown. The pathogen is persistent in acid soils of maritime western Oregon and Washington, the only region of the USA suitable for commercial spi...

Species identification of the causal agent of Eutypa dieback of grapevine in northeastern American and southeastern Canadian vineyards

USDA-ARS?s Scientific Manuscript database

Eutypa dieback of Vitis (grape) is caused by the Ascomycete fungus Eutypa lata. The pathogen infects grapevine through wounds, and cause wood canker and dieback symptoms. E. lata has been identified in all major grape production areas in the world. The first report of Eutypa dieback from northeaster...

Invasive Blackberry Species in Oregon, USA: Their Identity and Susceptibility to Rust Disease, and Implications for Biological Control

USDA-ARS?s Scientific Manuscript database

Two of five species of European blackberry (Rubus fruticosus L. Aggregate) along the West Coast of the United States are invasive, and they are also similar in appearance. Biological control by Phragmidium violaceum, causal agent of a rust disease, was under consideration when rust-diseased blackber...

Identification of environmental factors related to Claviceps purpurea ascospore production in perennial ryegrass seed fields and development of predictive models

USDA-ARS?s Scientific Manuscript database

Claviceps purpurea, the causal agent of ergot of perennial ryegrass seed crops, overwinters as sclerotia in the soil and releases airborne ascospores in the spring that infect flower ovaries and replace seed with sclerotia. Burkard spore traps were used to quantify the dispersal phenology and concen...

The Effect of Contextualized Conversational Feedback in a Complex Open-Ended Learning Environment

ERIC Educational Resources Information Center

Segedy, James R.; Kinnebrew, John S.; Biswas, Gautam

2013-01-01

Betty's Brain is an open-ended learning environment in which students learn about science topics by teaching a virtual agent named Betty through the construction of a visual causal map that represents the relevant science phenomena. The task is complex, and success requires the use of metacognitive strategies that support knowledge acquisition,…

Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages.

PubMed

Esplin, Ian N D; Berg, Jordan A; Sharma, Ruchira; Allen, Robert C; Arens, Daniel K; Ashcroft, Cody R; Bairett, Shannon R; Beatty, Nolan J; Bickmore, Madeline; Bloomfield, Travis J; Brady, T Scott; Bybee, Rachel N; Carter, John L; Choi, Minsey C; Duncan, Steven; Fajardo, Christopher P; Foy, Brayden B; Fuhriman, David A; Gibby, Paul D; Grossarth, Savannah E; Harbaugh, Kala; Harris, Natalie; Hilton, Jared A; Hurst, Emily; Hyde, Jonathan R; Ingersoll, Kayleigh; Jacobson, Caitlin M; James, Brady D; Jarvis, Todd M; Jaen-Anieves, Daniella; Jensen, Garrett L; Knabe, Bradley K; Kruger, Jared L; Merrill, Bryan D; Pape, Jenny A; Payne Anderson, Ashley M; Payne, David E; Peck, Malia D; Pollock, Samuel V; Putnam, Micah J; Ransom, Ethan K; Ririe, Devin B; Robinson, David M; Rogers, Spencer L; Russell, Kerri A; Schoenhals, Jonathan E; Shurtleff, Christopher A; Simister, Austin R; Smith, Hunter G; Stephenson, Michael B; Staley, Lyndsay A; Stettler, Jason M; Stratton, Mallorie L; Tateoka, Olivia B; Tatlow, P J; Taylor, Alexander S; Thompson, Suzanne E; Townsend, Michelle H; Thurgood, Trever L; Usher, Brittian K; Whitley, Kiara V; Ward, Andrew T; Ward, Megan E H; Webb, Charles J; Wienclaw, Trevor M; Williamson, Taryn L; Wells, Michael J; Wright, Cole K; Breakwell, Donald P; Hope, Sandra; Grose, Julianne H

2017-11-16

Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages. Copyright © 2017 Esplin et al.

Surveying and monitoring sudden oak death in southwest Oregon forests

Treesearch

Ellen Michaels Goheen; Alan Kanaskie; Mike McWilliams; Everett Hansen; Wendy Sutton; Nancy Osterbauer

2006-01-01

Phytophthora ramorum, the causal agent of sudden oak death, was first discovered in Oregon in July 2001 by aerial survey (Goheen and others 2002). Alerted to the situation in California and experienced in aerial tree mortality surveys, cooperators from the USDA Forest Service and the Oregon Department of Forestry planned a pilot survey for P...

Management of foliar infection of Rhododendron by Phytophthora ramorum with film forming polymers and surfactants

Treesearch

Ebba K. Peterson; Eric Larson

2017-01-01

Phytophthora ramorum, causal agent of sudden oak death (SOD) and ramorum leaf blight, remains a persistent problem of regulatory concern within the horticultural industry. Damages to nurseries have been realized as a result of enforced quarantine and sanitation efforts designed to prevent the spread and establishment of this invasive pathogen....

First report of anthracnose fruit rot of blueberry caused by Colletotrichum fioriniae in New Jersey

USDA-ARS?s Scientific Manuscript database

Anthracnose fruit rot is the most important disease of blueberry in New Jersey. Most fungicide applications in New Jersey and other blueberry growing regions is for the control of this disease. The causal agent of this disease has been reported to be Colletotrichum acutatum and other species in the ...

First report of hop stunt viroid from sweet cherry with dapple apple fruit symptoms in China

USDA-ARS?s Scientific Manuscript database

Hop stunt viroid (HSVd), the type member of the genus Hostuviroid, family Pospiviroidae, was first described from hops with stunt disease in Japan. HSVd has a wide host range that includes hop, cucumber, citrus, grapevine, plum, pear, peach, apricot and almond and is the causal agent of serious dis...

Repeated Challenge Studies: A Comparison of Union-Intersection Testing with Linear Modeling.

ERIC Educational Resources Information Center

Levine, Richard A.; Ohman, Pamela A.

1997-01-01

Challenge studies can be used to see whether there is a causal relationship between an agent of interest and a response. An approach based on union-intersection testing is presented that allows researchers to examine observations on a single subject and test the hypothesis of interest. An application using psychological data is presented. (SLD)

Screening Gulf Coast forest species for susceptibility to Phytophthora ramorum

Treesearch

Jason Preuett; Daniel Collins; Douglas Luster; Timothy Widmer

2013-01-01

Phytophthora ramorum, the causal agent of sudden oak death in California oak woodlands, poses a threat to woody plants in the rest of the United States, including the Gulf Coast area, which is regarded as a high-risk location. Several plant species native to Gulf Coast forests were tested for susceptibility to P. ramorum,...

The effects of Phytophthora ramorum stem inoculation on aspects of tanoak physiology and xylem function in saplings and seedlings

Treesearch

Elizabeth Stamm

2012-01-01

Phytophthora ramorum, an oomycete plant pathogen, is the causal agent of sudden oak death, a serious disease of Fagaceous trees in California and Oregon over the last decade. Tanoak (Notholithocarpus densiflorus) is one of the most susceptible host species, but the cause of host mortality is poorly understood....

Diversity of Diaporthe species associated with wood cankers of fruit and nut crops in northern California

USDA-ARS?s Scientific Manuscript database

Diaporthe ampelina, causal agent of Phomopsis cane and leaf spot of grapevine (Vitis vinifera L.), is also frequently isolated from grapevine wood, causing Phomopsis dieback. In California, Diaporthe species cause a wide range of symptoms not only on grape, but also other fruit and nut crops. To bet...

Detection of cucumber green mottle mosaic virus-infected watermelon seeds using short wave infrared (SWIR) hyperspectral imaging system

USDA-ARS?s Scientific Manuscript database

The cucurbit diseases caused by cucumber green mottle mosaic virus (CGMMV) have led to a serious problem to growers and seed producers because it is difficult to prevent spreading through causal agent of seeds. Conventional detection methods for infected seed such as a biological, serological, and m...

Neofusicoccum parvum colonization of the grapevine woody stem triggers asynchronous host responses at the site of infection and in the leaves

USDA-ARS?s Scientific Manuscript database

Grapevine trunk diseases cause important economic losses in vineyards worldwide. Neofusicoccum parvum, one of the most aggressive causal agents of the trunk disease Botryosphaeria dieback, colonizes cells and tissues of the grapevine wood, leading to the formation of an internal canker. Symptoms the...

‘US Furr’ and ‘US Furr-ST’ Mandarin

USDA-ARS?s Scientific Manuscript database

This document marks the official release of ‘US Furr’, a hybrid of ‘Clementine’ x ‘Murcott’, and ‘US Furr-ST’, an irradiated variant of ‘US Furr’ with apparent field tolerance to citrus scab (causal agent Elsinoe fawcetti Bitanc. and Jenk.). The hybridization creating ‘US Furr’ and ultimately ‘US Fu...

Through the Looking Glass: No Wonderland Yet! (The Reciprocal Relationship between Methodology and Models of Reality).

ERIC Educational Resources Information Center

Unger, Rhoda Kesler

1983-01-01

Discusses the relationship between conceptual frameworks and methodology in psychology. Argues that models of reality influence research in terms of question selection, causal factors hypothesized, and interpretation of data. Considers the position and role of women as objects and agents of research using a sociology of knowledge perspective.…

Real-time PCR and spore trap-based detection of the downy mildew pathogen, Peronospora effusa

USDA-ARS?s Scientific Manuscript database

Peronospora effusa is an obligate pathogen and the causal agent of downy mildew on spinach. The pathogen can be dispersed by splashing rain and wind, and may overwinter as oospores. Outbreaks of downy mildew on spinach are common in the cool climate of central coastal California, including the Sal...

Comparison of nine PCR primer sets designed to detect Pantoea stewartii subsp. stewartii in maize

USDA-ARS?s Scientific Manuscript database

Pantoea stewartii subsp. stewartii, the causal agent of Stewart's bacterial wilt of maize, is a major quarantine pest in maize seed. Verifying freedom from P. stewartii remains a significant hurdle in exporting corn seed from the U.S. Several PCR primer sets have been developed and suggested as bein...

Use of culture filtrates of Ceratocystis ulmi as a bioassay to screen for disease tolerant Ulmus americana

Treesearch

Paula M. Pijut; Subash C. Domir; R. Daniel Lineberger; Lawrence R. Schreiber

1990-01-01

Callus cultures of elm (Ulmus americana L.) derived from Dutch elm disease susceptible, intermediate-resistant, and resistant genotypes were exposed to the culture filtrates of three pathogenic isolates of Ceratocystis ulmi, the causal agent of Dutch elm disease. Callus fresh weights, cell viability, and reactions of stem cuttings...

Large scale field inoculation and scoring of maize southern leaf blight and other maize foliar fungal diseases

USDA-ARS?s Scientific Manuscript database

Field-grown maize is inoculated with Cochliobolus heterostrophus, causal agent of Southern Leaf Blight disease, by dropping sorghum grains infested with the fungus into the whorl of each maize plant at an early stage of growth. The initial lesions produce secondary inoculum that is dispersed by wind...

Population subdivision of Fusarium graminearum from barley and wheat in the upper Midwestern United States at the turn of the century

USDA-ARS?s Scientific Manuscript database

Fusarium graminearum, the causal agent of Fusarium head blight (FHB) in wheat and barley, is one of the most economically destructive pathogens of these grains worldwide. Recent population genetic studies of the pathogen obtained from wheat in North America supported population subdivision in part c...

Attributing causal agents to nationwide maps of forest disturbance

Treesearch

Gretchen G. Moisen; Todd A. Schroeder; Karen Schleeweis; Chris Toney; Warren B. Cohen; Samuel N. Goward

2012-01-01

Currently in its third phase, the North American Forest Dynamics (NAFD) project has launched nationwide processing of historic Landsat data to provide a comprehensive annual, wall-to-wall analysis of U.S. disturbance history over the last 30+ years. Because understanding the cause of disturbance is important to quantifying carbon dynamics, work is underway to attribute...

Adoption and validation of Ribonucleotide Reductase (RNR)-based real-time assays for detection of HLB ‘Candidatus Liberibacter asiaticus’ (CLas)

USDA-ARS?s Scientific Manuscript database

Huanglongbing (HLB), aka Citrus Greening, is a well-known destructive disease that threatens the multi-billion dollar citrus industry in the United States and citrus production in other countries around the world. The presumptive causal agent of HLB, ‘Candidatus Liberibacter asiaticus' (CLas), is of...

Diurnal patterns in flight activity and effects of light on host finding behavior of the Asian citrus psyllid

USDA-ARS?s Scientific Manuscript database

The Asian citrus psyllid (ACP), Diaphorina citri (Hemiptera: Psyllidae), is an invasive pest of citrus in the United States. The psyllid feeds and reproduces primarily on new flush growth of citrus and other rutaceous plants. Because it vectors the bacterial causal agents of the deadly citrus green...

Standardizing the Nomenclature for Clonal Lineages of the Sudden Oak Death Pathogen, Phytophthora ramorum

USDA-ARS?s Scientific Manuscript database

Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight, is known to exist as three distinct clonal lineages based on a range of molecular marker systems. However, in the recent literature there exists no consensus on naming of lineages. Here we name clonal lineages of P. ramor...

Development and validation of polymorphic microsatellite loci for the NA2 lineage of Phytophthora ramorum from whole genome sequence data

USDA-ARS?s Scientific Manuscript database

Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only tw...

Use of microsatellite markers derived from whole genome sequence data for identifying polymorphism in Phytophthora ramorum

Treesearch

Kelly Ivors; Matteo Garbelotto; Ineke De Vries; Peter Bonants

2006-01-01

Investigating the population genetics of Phytophthora ramorum, the causal agent of sudden oak death (SOD), is critical to understanding the biology and epidemiology of this important phytopathogen. Raw sequence data (445,000 reads) of P. ramorum was provided by the Joint Genome Institute. Our objective was to develop and utilize...

Evaluations and modifications of semi-selective media for improved isolation of Agrobacterium tumefaciens biovar 1 from cultivated walnut

USDA-ARS?s Scientific Manuscript database

Agrobacterium tumefaciens, the causal agent of crown gall of walnut, is an aerobic, Gram negative bacterium belonging to the family Rhizobiaceae. Like many in this group, A. tumefaciens is a common inhabitant of soil and plant host tissue. Isolation from these complex environments is difficult even ...

Detection by next generation sequencing of a multi-segmented viral genome from sugarcane associated with Ramu stunt disease

USDA-ARS?s Scientific Manuscript database

Ramu stunt disease of sugarcane was first reported in Papua New Guinea in the mid 1980's. The disease can reduce sugarcane yields significantly and causes severe stunting and mortality in highly susceptible cultivars. The causal agent of Ramu stunt has been investigated but its characterization has ...

Spread, genetic variation and methods for the detection of Puccinia kuehnii, the causal agent of sugarcane orange rust.

USDA-ARS?s Scientific Manuscript database

Sugarcane is susceptible to infection by two rust pathogens, Puccinia melanocephala and P. kuehnii, causing brown and orange rust, respectively. Orange rust of sugarcane was first reported in the Western hemisphere in Florida in July 2007. The pathogen was found to be distributed widely throughout t...

Phytophthora betacei, a new species within Phytophthora clade 1c causing late blight on Solanum betaceum in Colombia

USDA-ARS?s Scientific Manuscript database

Over the past few years, symptoms akin to late blight disease have been reported on a variety of crop plants in South America. Despite the economic importance of these crops, the causal agents of the diseases belonging to the genus Phytophthora have not been completely characterized. In this study, ...

Characterization of a recombinant Cathepsin B-Like cysteine peptidase from Diaphorina citri Kuwayama (Hemiptera: Liviidae): A putative target control of citrus huanglongbing

USDA-ARS?s Scientific Manuscript database

Huanglongbing (HLB) is one of the most destructive disease affecting citrus plants. The causal agent is associated with the phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas) spread by the Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae). Among the control strategies for H...

Ft. Collins sugar beet germplasm evaluated for rhizomania and storage rot resistance in Idaho, 2015

USDA-ARS?s Scientific Manuscript database

Fifty-seven sugar beet (Beta vulgaris L.) lines from the USDA-ARS Ft. Collins sugar beet program and four check cultivars were screened for resistance to Beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania, and storage rot. The rhizomania evaluation was conducted at the USDA-ARS...

De novo assembly and transcriptome characterization of an Armillaria solidipes mycelial fan

Treesearch

Amy L. Ross-Davis; Jane E. Stewart; John W. Hanna; Mee-Sook Kim; Rich C. Cronn; Hardeep S. Rai; Bryce A. Richardson; Geral I. McDonald; Ned B. Klopfenstein

2012-01-01

Armillaria (Fr.) Staude is a widely distributed fungal genus comprising approximately 40 species (Volk and Burdsall 1995) that display diverse ecological behaviors ranging from beneficial saprobe to virulent pathogen. Armillaria solidipes (formerly A. ostoyae; Burdsall and Volk 2008; pending vote to conserve A. ostoyae; Redhead et al. 2011), one of the causal agents of...

De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease

Treesearch

Taruna A. Schuelke; Anthony Westbrook; Kirk Broders; Keith Woeste; Matthew D. MacManes

2016-01-01

Geosmithia morbida is a filamentous ascomycete that causes thousand cankers disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated. G. morbida is one of two...

Competition studies of QoI resistant and sensitive Cercospora sojina isolates the causal agent of frogeye leaf spot

USDA-ARS?s Scientific Manuscript database

Frogeye leaf spot (FLS), caused by Cercospora sojina, is a yearly foliar disease in Tennessee and causes substantial economic losses if not properly managed. Quinone outside inhibitor (QoI) fungicides are often used to manage FLS, but C. sojina isolates have developed resistance to this class of fun...

Identification of Teosinte (Zea mays ssp. parviglumis) alleles for resistance to southern leaf blight in near isogenic maize lines

USDA-ARS?s Scientific Manuscript database

Southern Leaf Blight [(SLB), causal agent Cochliobolus heterostrophus race O] is an important fungal disease of maize in the United States. Teosinte (Zea mays ssp. parviglumis), the wild progenitor of maize, offers a novel source of resistance alleles that may have been lost during domestication. T...

Identification of alleles conferring resistance to gray leaf spot in maize derived from its wild progenitor species teosinte (Zea mays ssp. parviglumis)

USDA-ARS?s Scientific Manuscript database

Gray Leaf Spot [(GLS), causal agent Cercospora zeae-maydis and Cercospora zeina] is an important maize disease in the United States. Current control methods for GLS include using resistant cultivars, crop rotation, chemical applications, and conventional tillage to reduce inoculum levels. Teosinte ...

Virulence differences in blumeria graminis f. sp. tritici from the central and eastern United States

USDA-ARS?s Scientific Manuscript database

Wheat powdery mildew is a disease of international importance that occurs across a wide geographic area in the USA. A virulence survey of Blumeria graminis f. sp. tritici, the causal agent, was conducted by sampling 36 wheat fields in 15 U.S. states in the years 2013 and 2014. Using a hierarchical...

An emergent disease causes directional changes in forest species composition in coastal California

Treesearch

Margaret Metz; Kerri Frangioso; Allison Wickland; Ross Meentemeyer; David Rizzo

2012-01-01

Non-native forest pathogens can cause dramatic and long-lasting changes to the composition of forests, and these changes may have cascading impacts on community interactions and ecosystem functioning. Phytophthora ramorum, the causal agent of the emergent forest disease sudden oak death (SOD), has a wide host range, but mortality is concentrated in...

Eucalypt powdery mildew caused by Podosphaera pannosa in Brazil

Treesearch

Natalia R. Fonseca; Lucio M. S. Guimaraes; Raul P. Pires; Ned B. Klopfenstein; Acelino C. Alfenas

2017-01-01

Eucalypt powdery mildew is an important disease in greenhouses and clonal hedges of Eucalyptus spp. in Brazil, which can cause leaf and shoot distortion, shoot discoloration, and growth reduction that results in production losses. Because reliable information regarding the causal agent of the disease is lacking, this study used ITS and 28S rDNA sequencing and...

Development of single chain variable fragment (scFv) antibodies against surface proteins of ‘Ca. Liberibacter asiaticus’

USDA-ARS?s Scientific Manuscript database

‘Ca. Liberibacter asiaticus’ is the causal agent of citrus huanglongbing, the most serious disease of citrus worldwide. We have developed and applied immunization and affinity screening methods to develop a primary library of recombinant single chain variable fragment (scFv) antibodies in an M13 vec...

Transcriptome analysis of a Ustilago maydis ust1 deletion mutant uncovers involvement of laccase and polyketide synthase genes in spore development

USDA-ARS?s Scientific Manuscript database

Ustilago maydis, causal agent of corn smut disease, is a dimorphic fungus alternating between a saprobic budding haploid, and an obligate pathogenic filamentous dikaryon. Maize responds to U. maydis colonization by producing tumorous structures, and only within these does the fungus sporulate, produ...

Thousand cankers pathway assessment: movement of Geosmithia sp. and Pityophthorus juglandis Blackman from the western into the eastern United States

Treesearch

Leslie Newton; Glenn Fowler; Alison Neeley; Robert Schall; Yu Takeuchi; Scott. Pfister

2011-01-01

A newly recognized fungal canker disease of walnut, identified by state cooperators, may threaten the native range of eastern black walnut, Juglans nigra. The causal agent is a Geosmithia fungus (proposed name Geosmithia morbida) and the only known vector is the walnut twig beetle, Pityophthorus...

Spatial relationship between Phytophthora ramorum and roads or streams in Oregon tanoak forests

Treesearch

Ebba Peterson; Everett Hansen; Alan Kanaskie

2014-01-01

The pathogen, Phytophthora ramorum, causal agent of sudden oak death (SOD) of oaks and tanoaks, continues to expand its range within Oregon despite an effort to eradicate it from native forests. With its early detection and prompt removal of infected hosts, the Oregon SOD eradication program has produced a landscape distribution of disease...

First report of Leptosphaeria maculans and Leptosphaeria biglobosa, causal agents of blackleg, on canola in Washington State

USDA-ARS?s Scientific Manuscript database

Blackleg, caused by Leptosphaeria maculans, is endemic in the Canadian prairies and the Midwestern and southern USA (Roger Rimmer et al. 2007). The canola production region of the Pacific Northwest USA was considered free of blackleg until 2011, when L. maculans was found in canola fields in norther...

Functional roles of FgLaeA in controlling secondary metabolism, sexual development, and virulence in Fusarium graminearum

USDA-ARS?s Scientific Manuscript database

Fusarium graminearum, the causal agent of Fusarium head blight in cereal crops, produces mycotoxins such as trichothecenes and zearalenone in infected plants. Here, we focused on the function of FgLaeA in F. graminearum, a homolog of Aspergillus nidulans LaeA encoding the global regulator for both s...

Killer yeasts inhibit the growth of the phytopathogen Moniliophthora perniciosa, the causal agent of Witches’ Broom disease

PubMed Central

de Souza Cabral, Anderson; de Carvalho, Patricia Maria Barroso; Pinotti, Tatiana; Hagler, Allen Norton; Mendonça-Hagler, Leda Cristina Santana; Macrae, Andrew

2009-01-01

Fruit and soil yeasts isolated from the Amazon, Atlantic Rainforests and an organic farm were screened for killer activity against yeasts. Killer yeasts were then tested against the phytopathogen Moniliophthora perniciosa (syn. Crinipellis perniciosa) and a Dipodascus capitatus strain and a Candida sp strain inhibited its growth. PMID:24031327

Population genetic structure and mycotoxin potential of the wheat crown rot and head blight pathogen Fusarium culmorum in Algeria

USDA-ARS?s Scientific Manuscript database

Surveys for crown rot (FCR) and head blight (FHB) of Algerian wheat conducted during 2014 and 2015 revealed that Fusarium culmorum strains producing 3-acetyl-deoxynivalenol (3ADON) or nivalenol (NIV) were the primary causal agents of these important diseases. Morphological identification of the isol...

Host ranges of Penicillium species causing blue mold of bulb crops in Washington State and Idaho

USDA-ARS?s Scientific Manuscript database

First reported from the Pacific Northwest (PNW) of U.S.A. as causal agents of blue mold on edible and/or ornamental bulbs are Penicillium albocoremium (from Tulipa sp.; pathogenic on Allium sativum, A. cepa, A. stipitatum, Iris hollandica and Tulipa sp.), P. crustosum (from Narcissus; pathogenic on ...

Resistance among U.S. wheat Triticum aestivum cultivars to the wheat pathotype of Magnaporthe oryzae

USDA-ARS?s Scientific Manuscript database

Magnaporthe oryzae is the causal agent of blast on several graminaceous plants. The M. oryzae population causing wheat blast has not been found outside South America. U.S. wheat production is at risk to this pathogen if introduced and established. Proactive testing of US wheat cultivars for their re...

Characterization and correlation of EPG waveforms of Bactericera cockerelli (Hemiptera: Triozidae): variability in waveform appearance in relation to applied signal

USDA-ARS?s Scientific Manuscript database

The potato psyllid, Bactericera cockerelli, was recently shown to be a vector of “Candidatus Liberibacter solanacearum” (Lso), a phloem-limited bacterium that is the putative causal agent of “Zebra Chip” in potato and unnamed diseases in other solanaceous species. Despite its importance, very little...

Applying survival analysis to a large-scale forest inventory for assessment of tree mortality in Minnesota

Treesearch

C.W. Woodall; P.L. Grambsch; W. Thomas

2005-01-01

Tree mortality has traditionally been assessed in forest inventories through summaries of mortality by location, species, and causal agents. Although these methods have historically constituted the majority of tree mortality summarizations, they have had limited use in assessing mortality trends and dynamics. This study proposed a novel method of applying survival...

Simultaneous detection of four causal agents of tobacco bushy top disease by a multiplex one-step RT-PCR

USDA-ARS?s Scientific Manuscript database

Tobacco bushy top disease is a complex disease caused by mixed infection of Tobacco bushy top virus (TBTV), Tobacco vein distorting virus (TVDV), satellite RNA of TBTV (Sat-TBTV) and Tobacco vein distorting virus associate RNA (TVDVaRNA). A one-tube multiplex reverse transcription-PCR (RT-PCR) assay...

The aphid Melanaphis sacchari and the weed Sorghum almum – Partners in crime

USDA-ARS?s Scientific Manuscript database

Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf disease of sugarcane, is widespread in Florida and vectored by the aphid Melanaphis sacchari. Sugarcane was the only known natural host of SCYLV in the USA until 2015 when a new natural host was found for this virus in Florida: Sor...

Temperature, Moisture, and Fungicide Effects in Managing Rhizoctonia Root and Crown Rot of Sugar Beet

USDA-ARS?s Scientific Manuscript database

Rhizoctonia solani AG-2-2 is the causal agent of Rhizoctonia root and crown rot in sugar beet. To assess the capacity at which other anastomosis groups (AGs) are able to infect sugar beet, 15 AGs and subgroups were tested for pathogenicity on resistant (FC708 CMS) and susceptible (Monohikari) seedl...

Host resistance to Botrytis bunch rot in Vitis spp. and its correlation with Botrytis leaf spot

USDA-ARS?s Scientific Manuscript database

Botrytis cinerea, the causal agent of Botrytis bunch rot, is the number one postharvest disease of fresh grapes in the U.S. Fungicide applications are used to manage the disease, but resistant isolates are common and postharvest losses occur annually. Host resistance is needed for long-term manageme...

Evaluation of host resistance to Botrytis bunch rot in Vitis spp. and its correlation with Botrytis leaf spot

USDA-ARS?s Scientific Manuscript database

Botrytis cinerea, the causal agent of Botrytis bunch rot and gray mold, is the number one postharvest disease of fresh grapes in the United States. Fungicide applications are used to manage the disease, but fungicide-resistant isolates are common and postharvest losses occur annually. Host resistanc...

TEMPORAL AND SPATIAL PATTERNS OF AIRBORNE PESTICIDES IN THE ALPINE ENVIRONMENT OF A DECLINING CALIFORNIA AMPHIBIAN, THE MOUNTAIN YELLOW-LEGGED FROG

EPA Science Inventory

The mountain yellow-legged frog (Rana muscosa) has disappeared from most of its historic localities in the Sierra Nevada of California, and airborne pesticides from the Central Valley have been implicated as a causal agent. To determine the distribution and temporal variation of...

Tobacco carcinogen (NNK) induces both lung cancer and non-alcoholic steatohepatitis and hepatocellular carcinomas in ferrets which can be attenuated by lycopene supplementation

USDA-ARS?s Scientific Manuscript database

Early epidemiologic studies have reported that tobacco smoking, which is causally associated with liver cancer, is an independent risk factor for non-alcoholic fatty liver diseases (NAFLD). Lycopene from tomatoes has been shown to be a potential preventive agent against NAFLD and hepatocellular carc...

Population Genetic Structure of Cochliobolus miyabeanus on Cultivated Wild Rice (Zizania palustris L.) in Minnesota

USDA-ARS?s Scientific Manuscript database

Cochliobolus miyabeanus (Bipolaris oryzae) is the causal agent of fungal brown spot (FBS) in wild rice (Zizania palustris L.), an aquatic grass, endemic in Minnesota, Wisconsin, and parts of Canada. Grain yield losses can reach up to 74% when the disease starts at the boot stage and continues until ...

Identification and distribution of the mating-type idiomorphs in populations of Podosphaera macularis and development of chasmothecia of the fungus

USDA-ARS?s Scientific Manuscript database

Podosphaera macularis, the causal agent of hop powdery mildew, is known to produce cleistothecia (syn. chasmothecia) in eastern North America and Europe. Ascocarps have not yet been reported from the Pacific Northwestern region of North America. Reasons for the apparent absence of cleistothecia in t...

Species diversity and toxigenic potential of Fusarium graminearum complex isolates from maize fields in northwest Argentina

USDA-ARS?s Scientific Manuscript database

Members of the Fusarium graminearum species complex (Fg complex) are the causal agents of ear rot in maize and Fusarium head blight of wheat and other small grain cereals. The potential of these pathogens to contaminate cereals with trichothecene mycotoxins is a health risk for both humans and anima...

Explaining the Third Reich: Swedish Students' Causal Reasoning about the Nazi Seizure of Power in Germany

ERIC Educational Resources Information Center

Wendell, Joakim

2018-01-01

The topic of this study is how Swedish students aged 15-16 use causal reasoning in history when given a high-stakes task about explaining a historically significant event, the rise of the Nazi regime in Germany. The study is based on student texts from the Swedish national test in history. The student texts are mainly analysed with regards to how…

FPGA design for constrained energy minimization

NASA Astrophysics Data System (ADS)

Wang, Jianwei; Chang, Chein-I.; Cao, Mang

2004-02-01

The Constrained Energy Minimization (CEM) has been widely used for hyperspectral detection and classification. The feasibility of implementing the CEM as a real-time processing algorithm in systolic arrays has been also demonstrated. The main challenge of realizing the CEM in hardware architecture in the computation of the inverse of the data correlation matrix performed in the CEM, which requires a complete set of data samples. In order to cope with this problem, the data correlation matrix must be calculated in a causal manner which only needs data samples up to the sample at the time it is processed. This paper presents a Field Programmable Gate Arrays (FPGA) design of such a causal CEM. The main feature of the proposed FPGA design is to use the Coordinate Rotation DIgital Computer (CORDIC) algorithm that can convert a Givens rotation of a vector to a set of shift-add operations. As a result, the CORDIC algorithm can be easily implemented in hardware architecture, therefore in FPGA. Since the computation of the inverse of the data correlction involves a series of Givens rotations, the utility of the CORDIC algorithm allows the causal CEM to perform real-time processing in FPGA. In this paper, an FPGA implementation of the causal CEM will be studied and its detailed architecture will be also described.

Dynamics and causalities of atmospheric and oceanic data identified by complex networks and Granger causality analysis

NASA Astrophysics Data System (ADS)

Charakopoulos, A. K.; Katsouli, G. A.; Karakasidis, T. E.

2018-04-01

Understanding the underlying processes and extracting detailed characteristics of spatiotemporal dynamics of ocean and atmosphere as well as their interaction is of significant interest and has not been well thoroughly established. The purpose of this study was to examine the performance of two main additional methodologies for the identification of spatiotemporal underlying dynamic characteristics and patterns among atmospheric and oceanic variables from Seawatch buoys from Aegean and Ionian Sea, provided by the Hellenic Center for Marine Research (HCMR). The first approach involves the estimation of cross correlation analysis in an attempt to investigate time-lagged relationships, and further in order to identify the direction of interactions between the variables we performed the Granger causality method. According to the second approach the time series are converted into complex networks and then the main topological network properties such as degree distribution, average path length, diameter, modularity and clustering coefficient are evaluated. Our results show that the proposed analysis of complex network analysis of time series can lead to the extraction of hidden spatiotemporal characteristics. Also our findings indicate high level of positive and negative correlations and causalities among variables, both from the same buoy and also between buoys from different stations, which cannot be determined from the use of simple statistical measures.

[Poisoning with household cleaning products in a city in Northeast Brazil].

PubMed

Fook, Sayonara Maria Lia; Azevedo, Esthefanye Fernandes de; Costa, Monalisa Maciel; Feitosa, Itavielly Layany França; Bragagnoli, Gerson; Mariz, Saulo Rios

2013-05-01

This study analyzes toxic exposures to household cleaning products based on data from the Center for Notification and Treatment of Poisoning (CEATOX) in Campina Grande, Paraíba State, Brazil, from 2007 to 2010. The data were collected from the reporting forms from the Information System on Notifiable Diseases (SINAN), analyzed with SPSS (Version 17). Chemical identification was performed in urine samples using high-resolution chromatography techniques (GC-MS and HPLC-UV). Six hundred and sixty cases of poisoning were reported, with pesticides as the principal causal agents (42.2%). Poisoning with household cleaning products occurred mainly in children (30.1%) and/or females (55.21%) who were exposed to the product accidentally (55.4%) by the oral route (82%). These data indicate that poisoning with household cleaning products in Campina Grande should be treated with specific prevention and control measures, including evaluation of ease of access to pesticides, in order to reach the goals set by the Brazilian National Health Plan for 2012-2015.

The causal agents of witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae.

PubMed

Aime, M C; Phillips-Mora, W

2005-01-01

The two most devastating diseases of cacao (Theobroma cacao)--the source of chocolate--in tropical America are caused by the fungi Crinipellis perniciosa (witches' broom disease) and Moniliophthora roreri (frosty pod rot or moniliasis disease). Despite the agricultural, socio-economic and environmental impact of these fungi, most aspects of their life cycles are unknown, and the phylogenetic relationships of M. roreri have yet to be conclusively established. In this paper, extensive phylogenetic analyses of five nuclear gene regions (28S rDNA, 18S rDNA, ITS, RPB1, and EF1-alpha) confirm that C. perniciosa and M. roreri are sister taxa that belong in the Marasmiaceae (euagarics). Furthermore, these taxa form part of a separate and distinct lineage within the family. This lineage includes the biotrophic fungi Moniliophthora perniciosa comb. nov. and M. roreri, as well as one undescribed endophytic species. The sister genera to Moniliophthora are Marasmius, Crinipellis and Chaetocalathus, which consist mainly of saprotrophic litter fungi.

Bovine Papillomavirus in Brazil: Detection of Coinfection of Unusual Types by a PCR-RFLP Method

PubMed Central

Carvalho, R. F.; Sakata, S. T.; Giovanni, D. N. S.; Mori, E.; Brandão, P. E.; Richtzenhain, L. J.; Pozzi, C. R.; Arcaro, J. R. P.; Miranda, M. S.; Mazzuchelli-de-Souza, J.; Melo, T. C.; Comenale, G.; Assaf, S. L. M. R.; Beçak, W.; Stocco, R. C.

2013-01-01

Bovine papillomavirus (BPV) is recognized as a causal agent of benign and malignant tumors in cattle. Thirteen types of BPV are currently characterized and classified into three distinct genera, associated with different pathological outcomes. The described BPV types as well as other putative ones have been demonstrated by molecular biology methods, mainly by the employment of degenerated PCR primers. Specifically, divergences in the nucleotide sequence of the L1 gene are useful for the identification and classification of new papillomavirus types. On the present work, a method based on the PCR-RFLP technique and DNA sequencing was evaluated as a screening tool, allowing for the detection of two relatively rare types of BPV in lesions samples from a six-year-old Holstein dairy cow, chronically affected with cutaneous papillomatosis. These findings point to the dissemination of BPVs with unclear pathogenic potential, since two relatively rare, new described BPV types, which were first characterized in Japan, were also detected in Brazil. PMID:23865043

In vivo and in vitro control of Leishmania mexicana due to garlic-induced NO production.

PubMed

Gamboa-León, M R; Aranda-González, I; Mut-Martín, M; García-Miss, M R; Dumonteil, E

2007-11-01

Leishmania mexicana is the main causal agent of cutaneous leishmaniasis in the Yucatán peninsula in Mexico. Control of this disease is associated with a Th1-type immune response and garlic extract has been reported as a Th1 immunomodulator in BALB/c mice infected with Leishmania major. In this study, we investigated the effect of garlic extracts on L. mexicana infection in vivo and in vitro. Garlic extract reduced footpad lesions in L. mexicana-infected BALB/c mice by inducing IFN-gamma production from T cells. In vitro, garlic extract reduced macrophage infection through induction of nitric oxide (NO) production. Garlic extract may thus act on both T cells and macrophages to stimulate IFN-gamma production and NO synthesis for parasite killing. A 10- to 14-kDa fraction was identified as responsible for the in vitro effect of the whole extract and may lead to the identification of novel immunomodulating drugs and therapeutic alternatives for the treatment of leishmaniasis.

Fungicide Sensitivity and Characterization of Cobweb Disease on a Pleurotus eryngii Mushroom Crop Caused by Cladobotryum mycophilum

PubMed Central

Kim, Min Keun; Seuk, Su Won; Lee, Young Han; Kim, Hye Ran; Cho, Kye Man

2014-01-01

In 2009–2010, unusual symptoms were observed on Pleurotus eryngii grown in mushroom farms in Gyeongnam Province, Republic of Korea. One of the main symptoms was a cobweb-like growth of fungal mycelia over the surface of the mushroom. The colonies on the surface rapidly overwhelmed the mushrooms and developed several spores within 3–4 days. The colonized surface turned pale brown or yellow. The fruit body eventually turned dark brown and became rancid. Koch’s postulates were completed by spraying and spotting using isolated strains. The phylogenetic tree obtained from the internal transcribed spacer sequence analysis showed that the isolated fungal pathogen corresponded to Cladobotryum mycophilum (99.5%). In the fungicide sensitivity tests, the ED50 values for the isolate with respect to benomyl and carbendazim were from 0.29 to 0.31 ppm. Benzimidazole fungicides were most effective against C. mycophilum, a causal agent of cobweb disease in P. eryngii. PMID:25288989

Reliability of Causality Assessment for Drug, Herbal and Dietary Supplement Hepatoxicity in the Drug-Induced Liver Injury Network (DILIN)

PubMed Central

Hayashi, Paul H.; Barnhart, Huiman X.; Fontana, Robert J.; Chalasani, Naga; Davern, Timothy J.; Talwalkar, Jayant A.; Reddy, K. Rajender; Stolz, Andrew A.; Hoofnagle, Jay H.; Rockey, Don C.

2014-01-01

Background Due to the lack of objective tests to diagnose drug induced liver injury (DILI), causality assessment is a matter of debate. Expert opinion is often used in research and industry but its test-retest reliability is unknown. Aims To determine the test-retest reliability of the expert opinion process used by the Drug-Induced Liver Injury Network (DILIN) Methods Three DILIN hepatologists adjudicate suspected hepatotoxicity cases to 1 of 5 categories representing levels of likelihood of DILI. Adjudication is based on retrospective assessment of gathered case data that includes prospective follow-up information. One hundred randomly selected DILIN cases were re-assessed using the same processes for initial assessment but by 3 different reviewers in 92% of cases. Results The median time between assessments was 938 days (range: 140–2352). Thirty-one cases involved >1 agent. Weighted kappa statistics for overall case and individual agent category agreement were 0.60 (95% CI: 0.50–0.71) and 0.60 (0.52–0.68), respectively. Overall case adjudications were within one category of each other 93% of the time, while 5% differed by 2 categories and 2% differed by 3 categories. Fourteen-percent crossed the 50% threshold of likelihood due to competing diagnoses or atypical timing between drug exposure and injury. Conclusions The DILIN expert opinion causality assessment method has moderate inter-observer reliability but very good agreement within 1 category. A small but important proportion of cases could not be reliably diagnosed as ≥ 50% likely to be DILI. PMID:24661785

Rational expectations, psychology and inductive learning via moving thresholds

NASA Astrophysics Data System (ADS)

Lamba, H.; Seaman, T.

2008-06-01

This paper modifies a previously introduced class of heterogeneous agent models in a way that allows for the inclusion of different types of agent motivations and behaviours in a consistent manner. The agents operate within a highly simplified environment where they are only able to be long or short one unit of the asset. The price of the asset is influenced by both an external information stream and the demand of the agents. The current strategy of each agent is defined by a pair of moving thresholds straddling the current price. When the price crosses either of the thresholds for a particular agent, that agent switches position and a new pair of thresholds is generated. The threshold dynamics can mimic different sources of investor motivation, running the gamut from purely rational information-processing, through rational (but often undesirable) behaviour induced by perverse incentives and moral hazards, to purely psychological effects. The simplest model of this kind precisely conforms to the Efficient Market Hypothesis (EMH) and this allows causal relationships to be established between actions at the agent level and violations of EMH price statistics at the global level. In particular, the effects of herding behaviour and perverse incentives are examined.

Myalgic encephalomyelitis, chronic fatigue syndrome: An infectious disease.

PubMed

Underhill, R A

2015-12-01

The etiology of myalgic encephalomyelitis also known as chronic fatigue syndrome or ME/CFS has not been established. Controversies exist over whether it is an organic disease or a psychological disorder and even the existence of ME/CFS as a disease entity is sometimes denied. Suggested causal hypotheses have included psychosomatic disorders, infectious agents, immune dysfunctions, autoimmunity, metabolic disturbances, toxins and inherited genetic factors. Clinical, immunological and epidemiological evidence supports the hypothesis that: ME/CFS is an infectious disease; the causal pathogen persists in patients; the pathogen can be transmitted by casual contact; host factors determine susceptibility to the illness; and there is a population of healthy carriers, who may be able to shed the pathogen. ME/CFS is endemic globally as sporadic cases and occasional cluster outbreaks (epidemics). Cluster outbreaks imply an infectious agent. An abrupt flu-like onset resembling an infectious illness occurs in outbreak patients and many sporadic patients. Immune responses in sporadic patients resemble immune responses in other infectious diseases. Contagion is shown by finding secondary cases in outbreaks, and suggested by a higher prevalence of ME/CFS in sporadic patients' genetically unrelated close contacts (spouses/partners) than the community. Abortive cases, sub-clinical cases, and carrier state individuals were found in outbreaks. The chronic phase of ME/CFS does not appear to be particularly infective. Some healthy patient-contacts show immune responses similar to patients' immune responses, suggesting exposure to the same antigen (a pathogen). The chronicity of symptoms and of immune system changes and the occurrence of secondary cases suggest persistence of a causal pathogen. Risk factors which predispose to developing ME/CFS are: a close family member with ME/CFS; inherited genetic factors; female gender; age; rest/activity; previous exposure to stress or toxins; various infectious diseases preceding the onset of ME/CFS; and occupational exposure of health care professionals. The hypothesis implies that ME/CFS patients should not donate blood or tissue and usual precautions should be taken when handling patients' blood and tissue. No known pathogen has been shown to cause ME/CFS. Confirmation of the hypothesis requires identification of a causal pathogen. Research should focus on a search for unknown and known pathogens. Finding a causal pathogen could assist with diagnosis; help find a biomarker; enable the development of anti-microbial treatments; suggest preventive measures; explain pathophysiological findings; and reassure patients about the validity of their symptoms.

Virulence and SSR marker segregation in a Puccinia striiformis f. sp. tritici population produced by selfing a Chinese isolate on Berberis shensiana

USDA-ARS?s Scientific Manuscript database

Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust, is highly variable. The fungal pathogen produces new races overcoming resistance in wheat cultivars. A recently identified race, V26 with virulence to Yr26 and many other stripe rust resistance genes, has a high potent...

Conserved and distinct functions of the "stunted" (StuA)-Homolog Ust1 during cell differentiation in the corn smut fungus Ustilago maydis

USDA-ARS?s Scientific Manuscript database

Ustilago maydis, causal agent of corn smut, is a model for obligate fungal plant pathogens because, although it can proliferate saprobically in its yeast form, the infectious filamentous form is absolutely dependent on the host to complete its life cycle. Maize responds to U. maydis colonization by...

Mla- and Rom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus

USDA-ARS?s Scientific Manuscript database

Barley Mla (Mildew resistance locus a) confers allele-specific interactions with natural variants of the ascomycete fungus, Blumeria graminis f. sp. hordei (Bgh), causal agent of powdery mildew disease. Significant reprogramming of host gene expression occurs upon infection by this obligate biotrop...

When More of A Doesn't Result in More of B: Physics Experiments with a Surprising Outcome

ERIC Educational Resources Information Center

Tsakmaki, Paraskevi; Koumaras, Panagiotis

2016-01-01

Science education research has shown that students use causal reasoning, particularly the model "agent--instrument--object," to explain or predict the outcome of many natural situations. Students' reasoning seems to be based on a small set of few intuitive rules. One of these rules quantitatively correlates the outcome of an experiment…

D.B.H. and Survival Analysis: A New Methodology for Assessing Forest Inventory Mortality

Treesearch

Christopher W. Woodall; Patricia L. Grambsch; William Thomas

2005-01-01

Tree mortality has typically been assessed in Forest Inventory and Analysis (FIA) studies through summaries of mortality by location, species, and causal agents. Although these methods have historically been used for most of FIA's tree mortality analyses, they are inadequate for robust assessment of mortality trends and dynamics. To offer a new method of analyzing...

Complete Genome Sequence of Biocontrol Strain Pseudomonas fluorescens LBUM223

PubMed Central

Roquigny, Roxane; Arseneault, Tanya; Gadkar, Vijay J.; Novinscak, Amy

2015-01-01

Pseudomonas fluorescens LBUM223 is a plant growth-promoting rhizobacterium (PGPR) with biocontrol activity against various plant pathogens. It produces the antimicrobial metabolite phenazine-1-carboxylic acid, which is involved in the biocontrol of Streptomyces scabies, the causal agent of common scab of potato. Here, we report the complete genome sequence of P. fluorescens LBUM223. PMID:25953163

Association of Enterobacter cloacae and other bacteria with onion bulb rot in the Columbia Basin of Washington and Oregon, USA

USDA-ARS?s Scientific Manuscript database

Approximately 1.6 million metric tons of onion bulbs are produced annually in the Pacific Northwest USA. Bulb decay can be a major problem and is caused by a variety of plant pathogens. Onion bulbs exhibiting symptoms of bacterial rot were sampled to determine the causal agents. Enterobacter cloacae...

PCR-based identification of cacao black pod causal agents and identification of biological factors possibly contributing to Phytophthora megakarya's field dominance in West Africa

USDA-ARS?s Scientific Manuscript database

Among the Phytophthora species that cause black pod of cacao, P. megakarya is the most virulent, posing a serious threat to cacao production in Africa. Correct identification of the species causing the black pod and understanding the virulence factors involved are important for developing sustainabl...

Sentinel plant monitoring of Phytophthora ramorum at a research nursery over a six-year-period indicates limited aerial pathogen spread

Treesearch

Tomas Pastalka; Karen Suslow; Wolfgang Schweigkofler

2017-01-01

The National Ornamentals Research Site at Dominican University of California (NORS-DUC) is a research nursery that was established in 2009 to study invasive plant pathogens like Phytophthora ramorum, causal agent of sudden oak death and ramorum blight. In order to fulfill federal and state regulations, the possible...

Production and Characterization of an Avian Ricin Antitoxin

DTIC Science & Technology

1992-01-15

naturally -occurring plant and/or bacterial toxins as biological threat agents, effective antitoxins are needed for either piophylactic or causal...system, an avian antitoxin against the potent phytotoxin , ricin. will be developed and evaluated. The production of therapeutic antibodies in avian...Dynatech). PolyacrylmIde gel electrophoresis (PAGE): Acrylamide gels were prepared according to methods described by Laemmli ( Nature . 227. 1970) and

Detection of Jasmine virus H and characterization of a second pelarspovirus infecting star jasmine (Jasminum multiflorum) and angelwing jasmine (J. nitidum) plants displaying virus-like symptoms

USDA-ARS?s Scientific Manuscript database

Star jasmine (Jasminum multiflorum) plants growing in Hawaii expressing a diverse array of virus-like foliar symptoms were examined for the presence of a causal agent. Symptomatic tissues collected from three locations on the island of Oahu, Hawaii consistently harbored double-stranded (ds)RNAs app...

Migration patterns of the emerging plant pathogen Phytophthora ramorum on the West Coast of the United States of America

Treesearch

S. Prospero; N.J. Grünwald; L.M. Winton; E.M. Hansen

2009-01-01

Phytophthora ramorum (oomycetes) is the causal agent of sudden oak death and ramorum blight on trees, shrubs, and woody ornamentals in the forests of coastal California and southwestern Oregon and in nurseries of California, Oregon, and Washington. In this study, we investigated the genetic structure of P. ramorum on the West...

An expedited method to isolate DNA for PCR from Magnaporthe oryzae stored on filter paper

USDA-ARS?s Scientific Manuscript database

The fungus Magnaporthe oryzae is the causal agent for a wide range of cereal diseases. For long-term preservation, the fungus is grown and stored desiccated on filter papers at -20° C. Inoculated filter papers were cut into pieces from 0.5-1 cm diameter prior to storage. In the present study, a quic...

Analysis of molecular variability among the isolated of Verticillium dahliae from diverse host species based on florescene-based amplified fragment length polymorphism.

USDA-ARS?s Scientific Manuscript database

Verticillium dahliae is a soil borne fungus and the primary causal agent of Verticillium wilt, which affects many crops worldwide. Many crops grown in the Salinas Valley (SV) of California, including strawberry and lettuce (Lactuca sativa), are susceptible to V. dahliae and severe outbreaks are comm...

Modeling the potential distribution of white pine blister rust in the central Rocky Mountains.

Treesearch

Holly S. J. Kearns; William R. Jacobi

2006-01-01

Cronartium ribicola (J. C. Fischer ex Rabh.), the causal agent of white pine blister rust (WPBR), was introduced to western North America via infected nursery stock imported from France to Point Grey near Vancouver, British Columbia (Mielke 1943). Primary infection of white pines occurs on the needles where fungal spores land, enter through stomata,...

EPG waveform library for Graphocephala atropunctata (Hemiptera: Cicadellidae): Effect of input resistor and voltage levels on waveform appearance and probing behaviors

USDA-ARS?s Scientific Manuscript database

Graphocephala atropunctata is a vector of Xylella fastidiosa (Xf), the causal agent of Pierce’s disease of grapevines. A 3rd-generation, AC-DC electropenetrograph (EPG) was used to record stylet probing and ingestion behaviors of adult G. atropunctata on healthy grapevines. This study presents a com...

VdCYC8, encoding CYC8 glucose repression mediator protein, is required for microsclerotia formation and full virulence in Verticillium dahliae

USDA-ARS?s Scientific Manuscript database

Verticillium dahliae is the primary causal agent for Verticillium wilt disease on a diverse array of economically important crops, including cotton. In previous research, we screened a T-DNA insertional mutant library of the highly virulent isolate Vd080 derived from cotton. In this study, the targ...

Local genetic diversity of Xanthomonas citri subsp. citri in citrus orchards in northwest Paraná state, Brazil

USDA-ARS?s Scientific Manuscript database

Xanthomonas citri subsp. citri, causal agent of Asiatic citrus canker, is an important pathogen of citrus in Brazil and elsewhere. The genetic diversity of X. citri subsp. citri pathtype ‘A’ has not been studied in Brazil at a local scale (up to 300 km). A total of 40 isolates were collected from le...

Identification, transmission and genomic characterization of a new member of the family Caulimoviridae causing a flower distortion disease of Rudbeckia hirta

USDA-ARS?s Scientific Manuscript database

A disease of Rudbeckia hirta (Black-eyed Susan), characterized by severe flower deformation, was observed in Minnesota during 20010-2016. A previously undescribed virus, named Rudbeckia flower distortion virus (RuFDV), was determined to be the causal agent of the disease. Symptoms induced by RuFDV i...

Fitness and competition studies of QoI resistant and sensitive Cercospora sojina isolates, the causal agent of frogeye leaf spot

USDA-ARS?s Scientific Manuscript database

Frogeye leaf spot (FLS), caused by Cercospora sojina, is a yearly foliar disease of soybean in Tennessee and causes substantial economic losses if not properly managed. Quinone outside inhibitor (QoI) fungicides are often used to manage FLS, but C. sojina isolates have developed resistance to this c...

Causal Perception of Action-and-Reaction Sequences in 8- to 10-Month-Olds

ERIC Educational Resources Information Center

Schlottmann, Anne; Surian, Luca; Ray, Elizabeth D.

2009-01-01

Four experiments with 202 8- to 10-month-old infants studied their sensitivity to causation-at-a-distance in schematic events seen as goal-directed action and reaction by adults and whether this depends on attributes associated with animate agents. In Experiment 1, a red square moved toward a blue square without making contact; in "reaction"…

Virulence of Rhizoctonia solani AG2-2 isolates on sugar beet (Beta vulgaris) in response to low temperature

USDA-ARS?s Scientific Manuscript database

Rhizoctonia solani AG2-2 is not only the causal agent of Rhizoctonia root and crown rot in sugar beet (Beta vulgaris) but it can also cause a seedling damping-off. Significant losses can occur in all regions where sugar beets are grown. One recommendation for managing seedling losses to R. solani is...

Signalling requirements for Erwinia amylovora-induced disease resistance, callose deposition and cell growth in the non-host Arabidopsis thaliana

USDA-ARS?s Scientific Manuscript database

Erwinia amylovora is the causal agent of the fire blight disease in some plants of the Rosaceae family. The nonhost plant Arabidopsis serves as a powerful system to dissect mechanisms of resistance to E. amylovora. Although not yet known to mount gene-for-gene resistance to E. amylovora, we found ...

Genetic maps of stem rust resistance gene Sr35 in diploid and hexaploid wheat

USDA-ARS?s Scientific Manuscript database

Puccinia graminis f. sp. tritici is the causal agent of stem rust of wheat. A new race designated TTKSK (also known as Ug99) has recently spread through East Africa, Yemen and on to Iran. TTKSK and its variants (TTKST and TTTSK) are virulent to most of the stem rust resistance genes currently deploy...

Plant water stress effects on stylet probing behaviors of Homalodisca vitripennis (Hemiptera: Cicadellidae) associated with acquisition and inoculation of the bacterium Xylella fastidiosa

USDA-ARS?s Scientific Manuscript database

The glassy-winged sharpshooter, Homalodisca vitripennis, is a xylem fluid-ingesting leafhopper that transmits Xylella fastidiosa, the causal agent of several plant diseases in the Americas. While the role of plant water stress on the population density and dispersal of H. vitripennis has been studie...

Evaluation of Human Papilloma Virus Communicative Education Strategies: A Pilot Screening Study for Cervical Cancer

ERIC Educational Resources Information Center

Barrera-Clavijo, Lizeth K.; Wiesner-Ceballos, Carolina; Rincón-Martínez, Lina M.

2016-01-01

Background: High-risk human papilloma virus (HR-HPV) is highly prevalent in sexually active men and women; HR-HPV has been classified as a sexually transmitted infection (STI) and as a necessary, but not sufficient, causal agent for cervical cancer. Women who test positive for HPV often experience serious psychosocial consequences such as fear,…

Does Fusarium-caused seed mortality contribute to Bromus tectorum stand failure in the Great Basin?

Treesearch

S. E. Meyer; J.-L. Franke; O. W. Baughman; J. Beckstead; B. Geary

2014-01-01

Bromus tectorum (cheatgrass, downy brome) is an important invader in western North America, dominating millions of hectares of former semi-arid shrubland. Stand failure or 'die-off' is relatively common in monocultures of this annual grass. The study reported here investigated whether soil-borne pathogens could be causal agents in die-offs. Soils from two die...

Quick detection of Leifsonia xyli subsp. xyli by PCR and necleotide sequence analysis of PCR amplicons from Chinese Leifsonia xyli subsp. xyli isolates

USDA-ARS?s Scientific Manuscript database

A quick polymerase chain reaction (PCR) assay was developed for the detection of Leifsonia xyli subsp. xyli (Lxx), the bacterial causal agent of ratoon stunting disease (RSD) of sugarcane, in crude juice samples from stalks. After removal of abiotic impurities and large molecular weight microorgani...

De novo assembly and phasing of dikaryotic genomes from two isolates of Puccini coronata f. sp. avenae, the causal agent of oat crown rust

Treesearch

Marisa E. Miller; Ying Zhang; Vahid Omidvar; Jana Sperschneider; Benjamin Schwessinger; Castle Raley; Jonathan M. Palmer; Diana Garnica; Narayana Upadhyaya; John Rathjen; Jennifer M. Taylor; Robert F. Park; Peter N. Dodds; Cory D. Hirsch; Shahryar F. Kianian; Melania Figueroa

2018-01-01

Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting...

Influence of host resistance on the genetic structure of the white pine blister rust fungus in the western United States

Treesearch

B. A. Richardson; N. B. Klopfenstein; P. J. Zambino; G. I. McDonald; B. W. Geils; L. M. Carris

2008-01-01

Cronartium ribicola, the causal agent of white pine blister rust, has been devastating to five-needled white pines in North America since its introduction nearly a century ago. However, dynamic and complex interactions occur among C. ribicola, five-needled white pines, and the environment. To examine potential evolutionary...

Chapter 4: Genetic Identification of Fungi Involved in Wood Decay

Treesearch

Grant Kirker

2014-01-01

Wood decay is a complex process that involves contributions from molds, bacteria, decay fungi, and often insects. The first step in the accurate diagnosis of decay is identification of the causal agents, but wood decay in the strictest sense (white and brown rot) is caused by cryptic fungal species that are very difficult to identify using traditional methods. Genetic...

Using sigmoidal curve-fitting in a real- time PCR detection assay to determine detection thresholds

Treesearch

Pedro Uribe; Frank N. Martin

2008-01-01

Phytophthora ramorum, the causal agent of sudden oak death (SOD) is a quarantine pathogen that has forced the implementation of extraordinary measures to track and contain the movement of infected nursery stock both within and outside of the three western states of California, Oregon and Washington. Federal guidelines in the United States for...

Dietary Levels of Pure Flavonoids Improve Spatial Memory Performance and Increase Hippocampal Brain-Derived Neurotrophic Factor

PubMed Central

Rendeiro, Catarina; Vauzour, David; Rattray, Marcus; Waffo-Téguo, Pierre; Mérillon, Jean Michel; Butler, Laurie T.; Williams, Claire M.; Spencer, Jeremy P. E.

2013-01-01

Evidence suggests that flavonoid-rich foods are capable of inducing improvements in memory and cognition in animals and humans. However, there is a lack of clarity concerning whether flavonoids are the causal agents in inducing such behavioral responses. Here we show that supplementation with pure anthocyanins or pure flavanols for 6 weeks, at levels similar to that found in blueberry (2% w/w), results in an enhancement of spatial memory in 18 month old rats. Pure flavanols and pure anthocyanins were observed to induce significant improvements in spatial working memory (p = 0.002 and p = 0.006 respectively), to a similar extent to that following blueberry supplementation (p = 0.002). These behavioral changes were paralleled by increases in hippocampal brain-derived neurotrophic factor (R = 0.46, p<0.01), suggesting a common mechanism for the enhancement of memory. However, unlike protein levels of BDNF, the regional enhancement of BDNF mRNA expression in the hippocampus appeared to be predominantly enhanced by anthocyanins. Our data support the claim that flavonoids are likely causal agents in mediating the cognitive effects of flavonoid-rich foods. PMID:23723987

The kuru infectious agent is a unique geographic isolate distinct from Creutzfeldt–Jakob disease and scrapie agents

PubMed Central

Manuelidis, Laura; Chakrabarty, Trisha; Miyazawa, Kohtaro; Nduom, Nana-Aba; Emmerling, Kaitlin

2009-01-01

Human sporadic Creutzfeldt–Jakob disease (sCJD), endemic sheep scrapie, and epidemic bovine spongiform encephalopathy (BSE) are caused by a related group of infectious agents. The new U.K. BSE agent spread to many species, including humans, and clarifying the origin, specificity, virulence, and diversity of these agents is critical, particularly because infected humans do not develop disease for many years. As with viruses, transmissible spongiform encephalopathy (TSE) agents can adapt to new species and become more virulent yet maintain fundamentally unique and stable identities. To make agent differences manifest, one must keep the host genotype constant. Many TSE agents have revealed their independent identities in normal mice. We transmitted primate kuru, a TSE once epidemic in New Guinea, to mice expressing normal and ≈8-fold higher levels of murine prion protein (PrP). High levels of murine PrP did not prevent infection but instead shortened incubation time, as would be expected for a viral receptor. Sporadic CJD and BSE agents and representative scrapie agents were clearly different from kuru in incubation time, brain neuropathology, and lymphoreticular involvement. Many TSE agents can infect monotypic cultured GT1 cells, and unlike sporadic CJD isolates, kuru rapidly and stably infected these cells. The geographic independence of the kuru agent provides additional reasons to explore causal environmental pathogens in these infectious neurodegenerative diseases. PMID:19633190

Characterization of a novel single-stranded RNA mycovirus related to invertebrate viruses from the plant pathogen Verticillium dahliae.

PubMed

Cañizares, M Carmen; López-Escudero, Francisco J; Pérez-Artés, Encarnación; García-Pedrajas, María D

2018-03-01

Fungal viruses, also known as mycoviruses, are widespread in all major groups of fungi. Mycoviruses from plant pathogens can reduce the virulence of their host fungus and have therefore potential as biological control agents. This has spurred the identification of novel mycoviruses in plant pathogens, research which is greatly contributing to our understanding of these organisms. In this work, we report the characterization of a novel monopartite mycovirus from Verticillium dahliae, the main causal agent of Verticillium wilt. This novel mycovirus, which we termed Verticillium dahliae RNA virus 1 (VdRV1), was identified in three different isolates of V. dahliae collected in olive growing areas of the Guadalquivir valley, southern Spain. We determined that the VdRV1 genome is a positive (+) single-stranded (ss) RNA, 2631 nucleotides in length, containing two open reading frames. VdRV1 showed few similarities with known mycoviruses, only with a group of unassigned (+) ssRNA mycoviruses which are related to plant viruses classified within the family Tombusviridae. However, phylogenetic analysis revealed that VdRV1 and the unassigned (+) ssRNA mycoviruses have a closer relationship with recently reported invertebrate viruses. This result indicates that as more viral sequences become available, the relationships of mycoviruses with viruses from other hosts should be reexamined. Additionally, the work supports the hypothesis of a heterogeneous origin for mycoviruses.

Prevalence of Rotavirus Genogroup A and Norovirus Genogroup II in Bassaseachic Falls National Park Surface Waters in Chihuahua, Mexico

PubMed Central

Delgado-Gardea, Ma. Carmen E.; Tamez-Guerra, Patricia; Gomez-Flores, Ricardo; Mendieta-Mendoza, Aurora; Zavala-Díaz de la Serna, Francisco Javier; Contreras-Cordero, Juan Francisco; Erosa-de la Vega, Gilberto; Pérez-Recoder, María Concepción; Sánchez-Ramírez, Blanca; González-Horta, Carmen; Infante-Ramírez, Rocío

2017-01-01

In areas lacking potable water treatment, drinking contaminated water may represent a public health threat. In addition to enteropathogenic bacteria and parasites, fecal contamination in water environments is associated with the transmission of enteric viruses and other causal agents of infectious disease. Rotavirus and norovirus are the main enteric viral agents responsible for diarrheic outbreaks. The aim of the present study was to detect seasonal variation of rotavirus and norovirus in the surface water at Bassaseachic Falls National Park during 2013. Rivers and streams within and nearby this park were sampled once in each season during 2013. Viral concentration was carried out by a handmade filtration equipment, using a commercial electropositive membrane coupled with the virus absortion elution technique (VIRADEL©). Detection of rotavirus and norovirus was performed by SYBR Green reverse transcription-real time polymerase chain reaction (SYBR GREEN© RT-qPCR) analyses. Norovirus genogroup II was detected in samples collected in June and October 2013. In the case of rotavirus, genogroup A was detected in March and June. The presence of rotavirus and norovirus was related to viral acute diarrhea in children less than five years of age, who were inhabiting the sampled areas. This may indicates that the contaminated water was potentially a risk factor for regional diarrheic outbreaks. PMID:28475152

[Acting out and psychoactive substances: alcohol, drugs, illicit substances].

PubMed

Gillet, C; Polard, E; Mauduit, N; Allain, H

2001-01-01

In humans, some psychotropic agents (alcohol, drugs, illicit substances) have been suggested to play a role in the occurrence of major behavioural disorders, mainly due to the suppression of psychomotor inhibition. Behavioural disinhibition is a physiological mechanism which allows humans to behave appropriately according to a given environmental situation. The behavioural disinhibition induced by either therapeutic dosage or misuse involves the loss of restraint over certain types of social behaviour and may increase the risk of auto or hetero-aggression and acting out. The increased use of psychotropic agents in recent years and the occurrence of unwanted effects are worrying and must be detected and evaluated. The objective of the present study was to establish a causal relationship between psychoactive substance use and occurrence of major behavioural disorders, such as paradoxical rage reactions and suicidal behaviour, based on a literature analysis. It consisted of reviewing reports of drug-induced violent reactions in healthy volunteers and demonstrating, where possible, a cause-effect relationship. Patients with schizophrenia and psychopathic personalities were not included in our study since psychiatric comorbidity could influence behavioural responses. Psychotropic agents included drugs, licit and illicit substances already associated with violence in the past. Many reports used the "Go/No Go test" to evaluate the disinhibiting effect of psychotropic substances; this allows the "cognitive mapping" of drugs. The results suggest that only alcohol, antidepressants, benzodiazepines and cocaïne are related to aggressive behaviour. The best known precipitant of behavioural disinhibition is alcohol, which induces aggressive behaviour. However, there are large differences between individuals, and attentional mechanisms are now recognised as being important in mediating the effects of alcohol. Suicidal tendency as an adverse antidepressant reaction is rare, especially with atypical antidepressants. However, the risk of acting out exists and the responsibility of antidepressant agents in the genesis of suicidal tendencies is now established. The disinhibiting effects of benzodiazepines are well-known and proven by clinical trials. It's a "model" of acting out, and the causal relationship is undeniable. That cocaïne is related to violent behaviour is demonstrated by its pharmacological actions on CNS. The chronic use of cocaïne induces "a limbic dyscontrol syndrome" based on the altered activity of limbic structures. On the contrary, we could not demonstrate a causal relationship between aggression and either cannabis, ecstasy or phencyclidine. Cannabis abusers look particularly for euphoria and relaxing effects. Aggression as an adverse cannabis reaction is very rare and occurs in most cases in association with other drugs and in predisposed individuals. Ecstasy use may lead to long-term alterations of neuronal function in the human CNS and cause psychiatric disorders. However, there is insufficient information about long-term use of ecstasy to estimate its role in the occurrence of behavioural disorders. Clinical and forensic assumptions about phencyclidine and violence were not warranted. However, the substance-effect relationships can be criticized in the case of alcohol, antidepressants, benzodiazepines and cocaïne. In fact, individual, social and psychiatric factors exert an influence on behaviour that is superior to the pharmacological effect of psychotropic agents. The most important parameter in drug-induced behavioural disinhibition is dosage, but mode of administration is also important. In addition, polysubstance abuse is very common. Substances may be taken simultaneously and alcohol is frequently combined with drugs. The combinations of substances result in multiple interactions, and very little is known about the effects of these interactions on violence in humans. Co-occurrence of substance abuse and other mental disorders is also very frequent. Multiple substance abuse should be avoided, because potential interactions between two or more drugs are more likely to cause violent behaviour. In the future, a specific treatment of these deleterious phenomena will have to be considered in order to reduce drug-induced iatrogenic behavioural disorders.

Genetic causal beliefs about obesity, self-efficacy for weight control, and obesity-related behaviours in a middle-aged female cohort

PubMed Central

Knerr, Sarah; Bowen, Deborah J.; Beresford, Shirley A.A.; Wang, Catharine

2015-01-01

Objective Obesity is a heritable condition with well-established risk-reducing behaviours. Studies have shown that beliefs about the causes of obesity are associated with diet and exercise behaviour. Identifying mechanisms linking causal beliefs and behaviours is important for obesity prevention and control. Design Cross-sectional multi-level regression analyses of self-efficacy for weight control as a possible mediator of obesity attributions (diet, physical activity, genetic) and preventive behaviours in 487 non-Hispanic White women from South King County, Washington. Main Outcome Measures Self-reported daily fruit and vegetable intake and weekly leisure-time physical activity. Results Diet causal beliefs were positively associated with fruit and vegetable intake, with self-efficacy for weight control partially accounting for this association. Self-efficacy for weight control also indirectly linked physical activity attributions and physical activity behaviour. Relationships between genetic causal beliefs, self-efficacy for weight control, and obesity-related behaviours differed by obesity status. Self-efficacy for weight control contributed to negative associations between genetic causal attributions and obesity-related behaviours in non-obese, but not obese, women. Conclusion Self-efficacy is an important construct to include in studies of genetic causal beliefs and behavioural self-regulation. Theoretical and longitudinal work is needed to clarify the causal nature of these relationships and other mediating and moderating factors. PMID:26542069

[Characterization of Campylobacter jejuni samples coming form poultry meat and feces].

PubMed

Gutiérrez, Sindy; Orellana, Daniel; Martínez, Claudio; García Mena, Verónica

2017-12-01

Background Campylobacter jejuni is one of the main causal agents of food borne diseases. Infections with this pathogen are mainly caused by chicken meat consumption. Aim To characterize antibiotic resistance and virulence factors in C. jejuni strains obtained from chicken meat and poultry feces in Central Chile. Material and Methods The presence of C. jejuni in 30 meat and 40 feces samples from poultry was studied. From these samples, we obtained 40 strains which were characterized at the molecular level for the presence of 16 genes involved in virulence using PCR. In parallel, antibiotic resistance for ciprofloxacin, nalidixic acid, tetracycline, erythromycin, azithromycin, chloramphenicol y ampicillin was analyzed. Results Twenty and 63% of feces and chicken meat samples were positive for C. jejuni, respectively. Moreover, a high percentage of strains showed antibiotic resistance, where 27% of strains were resistant to all tested antibiotics, except for azithromycin. Finally, 10% of the strains coming from feces contained 14 out of 16 virulence genes evaluated. Only 23% of the strains did not contain any of these genes. Conclusions A high percentage of feces and chicken meat samples are contaminated with C. jejuni. Moreover, these strains show a high genetic and phenotypic diversity represented by their antibiotic resistance profiles and the presence of virulence factors.

Cancer risk and the complexity of the interactions between environmental and host factors: HENVINET interactive diagrams as simple tools for exploring and understanding the scientific evidence.

PubMed

Merlo, Domenico F; Filiberti, Rosangela; Kobernus, Michael; Bartonova, Alena; Gamulin, Marija; Ferencic, Zeljko; Dusinska, Maria; Fucic, Aleksandra

2012-06-28

Development of graphical/visual presentations of cancer etiology caused by environmental stressors is a process that requires combining the complex biological interactions between xenobiotics in living and occupational environment with genes (gene-environment interaction) and genomic and non-genomic based disease specific mechanisms in living organisms. Traditionally, presentation of causal relationships includes the statistical association between exposure to one xenobiotic and the disease corrected for the effect of potential confounders. Within the FP6 project HENVINET, we aimed at considering together all known agents and mechanisms involved in development of selected cancer types. Selection of cancer types for causal diagrams was based on the corpus of available data and reported relative risk (RR). In constructing causal diagrams the complexity of the interactions between xenobiotics was considered a priority in the interpretation of cancer risk. Additionally, gene-environment interactions were incorporated such as polymorphisms in genes for repair and for phase I and II enzymes involved in metabolism of xenobiotics and their elimination. Information on possible age or gender susceptibility is also included. Diagrams are user friendly thanks to multistep access to information packages and the possibility of referring to related literature and a glossary of terms. Diagrams cover both chemical and physical agents (ionizing and non-ionizing radiation) and provide basic information on the strength of the association between type of exposure and cancer risk reported by human studies and supported by mechanistic studies. Causal diagrams developed within HENVINET project represent a valuable source of information for professionals working in the field of environmental health and epidemiology, and as educational material for students. Cancer risk results from a complex interaction of environmental exposures with inherited gene polymorphisms, genetic burden collected during development and non genomic capacity of response to environmental insults. In order to adopt effective preventive measures and the associated regulatory actions, a comprehensive investigation of cancer etiology is crucial. Variations and fluctuations of cancer incidence in human populations do not necessarily reflect environmental pollution policies or population distribution of polymorphisms of genes known to be associated with increased cancer risk. Tools which may be used in such a comprehensive research, including molecular biology applied to field studies, require a methodological shift from the reductionism that has been used until recently as a basic axiom in interpretation of data. The complexity of the interactions between cells, genes and the environment, i.e. the resonance of the living matter with the environment, can be synthesized by systems biology. Within the HENVINET project such philosophy was followed in order to develop interactive causal diagrams for the investigation of cancers with possible etiology in environmental exposure. Causal diagrams represent integrated knowledge and seed tool for their future development and development of similar diagrams for other environmentally related diseases such as asthma or sterility. In this paper development and application of causal diagrams for cancer are presented and discussed.

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 outcomes for each party, these correlations form a polytope whose facets define causal inequalities. The case of quantum correlations in this paradigm is captured by the process matrix formalism. We investigate the link between causality and the closely related notion of causal separability of quantum processes, which we here define rigorously in analogy with the link between Bell locality and separability of quantum states. We show that causality and causal separability are not equivalent in general by giving an example of a physically admissible tripartite quantum process that is causal but not causally separable. We also show that there are causally separable quantum processes that become non-causal if extended by supplying the parties with entangled ancillas. This motivates the concepts of extensibly causal and extensibly causally separable (ECS) processes, for which the respective property remains invariant under extension. We characterize the class of ECS quantum processes in the tripartite case via simple conditions on the form of the process matrix. We show that the processes realizable by classically controlled quantum circuits are ECS and conjecture that the reverse also holds.

Causal illusions in children when the outcome is frequent

PubMed Central

2017-01-01

Causal illusions occur when people perceive a causal relation between two events that are actually unrelated. One factor that has been shown to promote these mistaken beliefs is the outcome probability. Thus, people tend to overestimate the strength of a causal relation when the potential consequence (i.e. the outcome) occurs with a high probability (outcome-density bias). Given that children and adults differ in several important features involved in causal judgment, including prior knowledge and basic cognitive skills, developmental studies can be considered an outstanding approach to detect and further explore the psychological processes and mechanisms underlying this bias. However, the outcome density bias has been mainly explored in adulthood, and no previous evidence for this bias has been reported in children. Thus, the purpose of this study was to extend outcome-density bias research to childhood. In two experiments, children between 6 and 8 years old were exposed to two similar setups, both showing a non-contingent relation between the potential cause and the outcome. These two scenarios differed only in the probability of the outcome, which could either be high or low. Children judged the relation between the two events to be stronger in the high probability of the outcome setting, revealing that, like adults, they develop causal illusions when the outcome is frequent. PMID:28898294

The impact of pretend play on children's development: a review of the evidence.

PubMed

Lillard, Angeline S; Lerner, Matthew D; Hopkins, Emily J; Dore, Rebecca A; Smith, Eric D; Palmquist, Carolyn M

2013-01-01

Pretend play has been claimed to be crucial to children's healthy development. Here we examine evidence for this position versus 2 alternatives: Pretend play is 1 of many routes to positive developments (equifinality), and pretend play is an epiphenomenon of other factors that drive development. Evidence from several domains is considered. For language, narrative, and emotion regulation, the research conducted to date is consistent with all 3 positions but insufficient to draw conclusions. For executive function and social skills, existing research leans against the crucial causal position but is insufficient to differentiate the other 2. For reasoning, equifinality is definitely supported, ruling out a crucially causal position but still leaving open the possibility that pretend play is epiphenomenal. For problem solving, there is no compelling evidence that pretend play helps or is even a correlate. For creativity, intelligence, conservation, and theory of mind, inconsistent correlational results from sound studies and nonreplication with masked experimenters are problematic for a causal position, and some good studies favor an epiphenomenon position in which child, adult, and environment characteristics that go along with play are the true causal agents. We end by considering epiphenomenalism more deeply and discussing implications for preschool settings and further research in this domain. Our take-away message is that existing evidence does not support strong causal claims about the unique importance of pretend play for development and that much more and better research is essential for clarifying its possible role. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Investigating Causality Between Interacting Brain Areas with Multivariate Autoregressive Models of MEG Sensor Data

PubMed Central

Michalareas, George; Schoffelen, Jan-Mathijs; Paterson, Gavin; Gross, Joachim

2013-01-01

Abstract In this work, we investigate the feasibility to estimating causal interactions between brain regions based on multivariate autoregressive models (MAR models) fitted to magnetoencephalographic (MEG) sensor measurements. We first demonstrate the theoretical feasibility of estimating source level causal interactions after projection of the sensor-level model coefficients onto the locations of the neural sources. Next, we show with simulated MEG data that causality, as measured by partial directed coherence (PDC), can be correctly reconstructed if the locations of the interacting brain areas are known. We further demonstrate, if a very large number of brain voxels is considered as potential activation sources, that PDC as a measure to reconstruct causal interactions is less accurate. In such case the MAR model coefficients alone contain meaningful causality information. The proposed method overcomes the problems of model nonrobustness and large computation times encountered during causality analysis by existing methods. These methods first project MEG sensor time-series onto a large number of brain locations after which the MAR model is built on this large number of source-level time-series. Instead, through this work, we demonstrate that by building the MAR model on the sensor-level and then projecting only the MAR coefficients in source space, the true casual pathways are recovered even when a very large number of locations are considered as sources. The main contribution of this work is that by this methodology entire brain causality maps can be efficiently derived without any a priori selection of regions of interest. Hum Brain Mapp, 2013. © 2012 Wiley Periodicals, Inc. PMID:22328419

Phytophthora species in tanoak trees, canopy-drip, soil, and streams in the sudden oak death epidemic area of south-western Oregon, USA

Treesearch

Paul Reeser; Wendy Sutton; Everett Hansen.

2011-01-01

Various Phytophthora species were recovered from tanoak trees, tanoak canopy drip, soils, and streams, which were sampled as part of a larger survey and management effort aimed at limiting the spread of Phytophthora ramorum Werres, De Cock & Man in't Veld (the causal agent of sudden oak death) in an epidemic area...

Effects of Temperature and Drought Stress on Physiological Processes Associated With Oak Decline

Treesearch

Theodor D. Leininger

1998-01-01

Oak decline is a term used to describe a sequence of events (decline syndrome) which is typically triggered by anabioticstress and subsequently involves other biotic and abiotic factors that cause the progressive deterioration and eventual death of a tree. Decline diseases lack a single causal agent, and in that way are different from diseases caused by one pathogen or...

Draft genome sequence of the fungus associated with oak-wilt mortality in South Korea, Raffaelea quercus-mongolicae KACC44405

Treesearch

Jongbum Jeon; Ki-Tae Kim; Hyeunjeong Song; Gir-Won Lee; Kyeongchae Cheong; Hyunbin Kim; Gobong Choi; Yong-Hwan Lee; Jane E. Stewart; Ned B. Klopfenstein; Mee-Sook Kim

2017-01-01

The fungus Raffaelea quercus-mongolicae is the causal agent of Korean oak wilt, a disease associated with mass mortality of oak trees (e.g., Quercus spp.). The fungus is vectored and dispersed by the ambrosia beetle, Platypus koryoensis. Here, we present the 27.0-Mb draft genome sequence of R. quercus-mongolicae strain KACC44405.

The Brachypodium-Puccinia graminis system: Solving a puzzle to uncover the underlying mechanisms of non-host resistance and plant immunity

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon is regarded as non-host to the causal agent of stem rust in wheat and barley, P. graminis f. sp. tritici (Pgt), and a near-host to the pathogens of forage grasses, P. graminis f. sp. lolii (Pgl) and P. graminis f. sp. phlei-pratensis (Pgp). Given the devastating effect of ste...

Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod induce similar reactions when infecting pods of a susceptible cacao genotype

USDA-ARS?s Scientific Manuscript database

Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) cause black pod rot of Theobroma cacao. Of these two clade 4 species; Pmeg is more virulent and is displacing Ppal on cacao in many cacao production areas in Africa. To understand the advantages Pmeg has over Ppal, we compared symptom...

New relationships among the sudden oak death pathogen, bark and ambrosia beetles, and fungi colonizing coast live oaks

Treesearch

Nadir Erbilgin; Brice A. McPherson; Pierluigi Bonello; David L. Wood; Andrew J. Nelson

2008-01-01

Sudden oak death (SOD) has had devastating effects on several oak species in many California coastal forests. Phytophthora ramorum has been identified as the primary causal agent of sudden oak death. While the pathogen may be capable of killing mature trees, it is likely that in nature opportunistic organisms play significant roles in the decline and...

Draft Genome Sequence of the Phytopathogenic Fungus Ganoderma boninense, the Causal Agent of Basal Stem Rot Disease on Oil Palm

PubMed Central

Tanjung, Zulfikar Achmad; Aditama, Redi; Buana, Rika Fithri Nurani; Pratomo, Antonius Dony Madu; Tryono, Reno; Liwang, Tony

2018-01-01

ABSTRACT Ganoderma boninense is the dominant fungal pathogen of basal stem rot (BSR) disease on Elaeis guineensis. We sequenced the nuclear genome of mycelia using both Illumina and Pacific Biosciences platforms for assembly of scaffolds. The draft genome comprised 79.24 Mb, 495 scaffolds, and 26,226 predicted coding sequences. PMID:29700132

Characterization of resistance genes to rice blast fungus Magnaporthe oryzae in a “Green Revolution” rice variety

USDA-ARS?s Scientific Manuscript database

The indica rice variety Dee Geo Woo Gen (DGWG) was the source of the semi-dwarf gene (SD1) which played an important role in the Green Revolution. In the present study, resistance (R) genes to the U.S. race (isolate) IB54 of Magnaporthe oryzae, causal agent of rice blast disease, was investigated. T...

Draft Genome Sequence of Xanthomonas arboricola pv. pruni Strain Xap33, Causal Agent of Bacterial Spot Disease on Almond

PubMed Central

Garita-Cambronero, J.; Sena-Vélez, M.; Palacio-Bielsa, A.

2014-01-01

We report the annotated genome sequence of Xanthomonas arboricola pv. pruni strain Xap33, isolated from almond leaves showing bacterial spot disease symptoms in Spain. The availability of this genome sequence will aid our understanding of the infection mechanism of this bacterium as well as its relationship to other species of the same genus. PMID:24903863

De novo assembly and phasing of dikaryotic genomes from two isolates of Puccinia coronata f. sp. avenae, the causal agent of oat crown rust

USDA-ARS?s Scientific Manuscript database

Oat crown rust, caused by the fungus Puccinia coronata f. sp. avenae (Pca), is a devastating disease that impacts worldwide oat production. For much of its life cycle Pca is dikaryotic with two separate haploid nuclei that may vary in virulence genotypes, which highlights the importance of understan...

Geographical variation in seasonality and life history of pine sawyer beetles Monochamus spp: its relationship with phoresy by the pinewood nematode Bursaphelenchus xylophilus.

Treesearch

Carla S. Pimentel; Matthew P. Ayres; Vallery Erich; Chris Young; Douglas Streett

2014-01-01

Bursaphelenchus xylophilus (Steiner & Buhrer) (Nematoda: Aphelenchoididae), the pinewood nematode and the causal agent of the pine wilt disease, is a globally important invasive pathogen of pine forests. It is phoretic in woodborer beetles of the genus Monochamus (Megerle) (Coleoptera, Cerambycidae) and has been able to exploit novel indigenous species of...

Transcriptome of an Armillaria root disease pathogen reveals candidate genes involved in host substrate utilization at the host­-pathogen interface

Treesearch

A. L. Ross-Davis; J. E. Stewart; J. W. Hanna; M.-S. Kim; B. J. Knaus; R. Cronn; H. Rai; B. A. Richardson; G. I. McDonald; N. B. Klopfenstein

2013-01-01

Armillaria species display diverse ecological roles ranging from beneficial saprobe to virulent pathogen. Armillaria solidipes (formerly A. ostoyae), a causal agent of Armillaria root disease, is a virulent primary pathogen with a broad host range of woody plants across the Northern Hemisphere. This white-rot pathogen grows between trees as rhizomorphs and attacks...

Standardizing the nomenclature for clonal lineages of the sudden oak death pathogen, Phytophthora ramorum

Treesearch

N.J. Grünwald; E.M. Goss; K. Ivors; M. Garbelotto; F.N. Martin; S. Prospero; E. Hansen; P.J.M. Bonants; R.C. Hamelin; G. Chastagner; S. Werres; D.M. Rizzo; G. Abad; P. Beales; G.J. Bilodeau; C.L. Blomquist; C. Brasier; S.C. Brière; A. Chandelier; J.M. Davidson; S. Denman; M. Elliott; S.J. Frankel; E.M. Goheen; H. de Gruyter; K. Heungens; D. James; A. Kanaskie; M.G. McWilliams; W. Man in ' t Veld; E. Moralejo; N.K. Osterbauer; M.E. Palm; J.L. Parke; A.M. Perez Sierra; S.F. Shamoun; N. Shishkoff; P.W. Tooley; A.M. Vettraino; J. Webber; T.L. Widmer

2009-01-01

Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight, is known to exist as three distinct clonal lineages which can only be distinguished by performing molecular marker-based analyses. However, in the recent literature there exists no consensus on naming of these lineages. Here we propose a system for naming clonal lineages of P. ramorum based...

Coupling Spore Traps and Quantitative PCR Assays for Detection of Cercospora sojina, the Causal Agent of Soybean Frogeye Leaf Spot

USDA-ARS?s Scientific Manuscript database

Frogeye leaf spot (FLS), caused by Cercospora sojina Hara, is a common disease of soybean. Significant yield losses (10–60%) have been attributed to FLS. We present a novel trapping approach using Vaseline coated slides placed at a 45° angle within a passive, wind-vane spore trap used in combination...

Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases

USDA-ARS?s Scientific Manuscript database

Background: Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of Theobroma cacao, the source of chocolate and is one of the most destructive diseases of cacao in the Americas. This Basidiomycete only infects cacao pods and has an extended biotrophic phase lasting up to sixty ...

Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms

USDA-ARS?s Scientific Manuscript database

Phytophthora megakarya (Pmeg) and P. palmivora (Ppal) are closely related species causing black pod rot of cacao. While Ppal is a cosmopolitan plant pathogen, cacao is the only known host of importance for Pmeg. Pmeg is more virulent on cacao than Ppal. Therefore, we have sequenced both the Pmeg and...

Protocols to test the activity of antimicrobial peptides against the honey bee pathogen Paenibacillus larvae.

PubMed

Khilnani, Jasmin C; Wing, Helen J

2015-10-01

Paenibacillus larvae is the causal agent of the honey bee disease American Foulbrood. Two enhanced protocols that allow the activity of antimicrobial peptides to be tested against P. larvae are presented. Proof of principle experiments demonstrate that the honey bee antimicrobial peptide defensin 1 is active in both assays. Copyright © 2015 Elsevier B.V. All rights reserved.

Genetic analysis of virulence in the Pyrenophora teres f. teres population BB25 x FGOH04Ptt021

USDA-ARS?s Scientific Manuscript database

Pyrenophora teres f. teres is the causal agent of net form net blotch (NFNB) of barley. In order to map the genetics of avirulence/virulence in P. teres f. teres, a fungal population was developed using P. teres f. teres isolates BB25 (Denmark) and FGOH04Ptt-21 (North Dakota, USA) due to these two i...

Notice of Release of FC1018, FC1019, FC1020 and FC1022 Multigerm Sugarbeet Germplasms with Multiple Disease Resistance

USDA-ARS?s Scientific Manuscript database

FC1018 (PI 658059) has excellent resistance to root-rotting strains (AG-2-2) of Rhizoctonia solani Kühn and carries the Rz1 gene, which confers resistance to some strains of Beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania. FC1018 has shown a moderate tolerance to cercospora ...

Draft Genome Sequence of the Phytopathogenic Fungus Fusarium euwallaceae, the Causal Agent of Fusarium Dieback

PubMed Central

Sánchez-Rangel, Diana; Hernández-Domínguez, Eric; Pérez-Torres, Claudia-Anahí; Ortiz-Castro, Randy; Villafán, Emanuel; Alonso-Sánchez, Alexandro; Rodríguez-Haas, Benjamín; López-Buenfil, Abel; García-Avila, Clemente; Ramírez-Pool, José-Abrahán

2017-01-01

ABSTRACT Here, we report the genome of Fusarium euwallaceae strain HFEW-16-IV-019, an isolate obtained from Kuroshio shot hole borer (a Euwallacea sp.). These beetles were collected in Tijuana, Mexico, from elm trees showing typical symptoms of Fusarium dieback. The final assembly consists of 287 scaffolds spanning 48,274,071 bp and 13,777 genes. PMID:28860245

Japanese oak wilt as a newly emerged forest pest in Japan: why does a symbiotic ambrosia fungus kill host trees?

Treesearch

Naoto Kamata; Koujiro Esaki; Kenryu Kato; Hisahito Oana; Yutaka Igeta; Ryotaro Komura

2007-01-01

Japanese oak wilt (JOW) has been known since the 1930s, but in the last 15 years epidemics have intensified and spread to the island's western coastal areas. The symbiotic ambrosia fungus Raffaelea quercivora is the causal agent of oak dieback, and is vectored by Platypus quercivorus (Murayama). This is the first example of an...

Control of Rhizoctonia foliar blight in forest seedling nurseries: A 3-year study

Treesearch

Tom E. Starkey; Scott A. Enebak; Ken McQuage; Kevin Barfield

2013-01-01

Laboratory and field trials have shown Proline® (prothioconazole) to be efficacious against the causal agent of Rhizoctonia foliar blight on loblolly pine (Pinus taeda). A biweekly application of Proline ® at 5 fl oz/ac in nursery field tests significantly reduced Rhizoctonia foliar blight on loblolly pine when compared to applications of Abound ® azoxystrobin (24 fl...

Tracking population loss in Cornus florida since discovery of Discula destructiva, causal agent of dogwood anthracnose, in eastern North America

Treesearch

William E. Jones; William D. Smith; Daniel B. Twardus

2012-01-01

The purpose of this evaluation monitoring project was to document the losses of flowering dogwood, Cornus florida (L.), an important ornamental and wildlife tree that grows across much of Eastern North America. The project was prompted in 2001 by the apparent abundance of flowering dogwoods along roadsides in the Morgantown, WV, area, despite a...

New report of Lolium multiflorum and Rumex crispus as weed hosts of epiphytic populations of Psuedomonas sp., causal agent of yellow bud in onion in Geogia, USA

USDA-ARS?s Scientific Manuscript database

Yellow bud, an emerging bacterial disease of onion (Allium cepa L.), has been spreading throughout the Vidalia onion-growing region in Georgia since 2007. Symptoms of yellow bud include intense chlorosis in emerging leaves and severe blight in the older leaves leading to stand loss and reduced bulb ...

Quantum physics in neuroscience and psychology: A neurophysicalmodel of the mind/brain interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwartz, Jeffrey M.; Stapp, Henry P.; Beauregard, Mario

Neuropsychological research on the neural basis of behavior generally posits that brain mechanisms will ultimately suffice to explain all psychologically described phenomena. This assumption stems from the idea that the brain is made up entirely of material particles and fields, and that all causal mechanisms relevant to neuroscience can therefore be formulated solely in terms of properties of these elements. Thus terms having intrinsic mentalistic and/or experiential content (e.g., ''feeling,'' ''knowing,'' and ''effort'') are not included as primary causal factors. This theoretical restriction is motivated primarily by ideas about the natural world that have been known to be fundamentally incorrectmore » for more than three quarters of a century. Contemporary basic physical theory differs profoundly from classical physics on the important matter of how the consciousness of human agents enters into the structure of empirical phenomena. The new principles contradict the older idea that local mechanical processes alone can account for the structure of all observed empirical data. Contemporary physical theory brings directly and irreducibly into the overall causal structure certain psychologically described choices made by human agents about how they will act. This key development in basic physical theory is applicable to neuroscience, and it provides neuroscientists and psychologists with an alternative conceptual framework for describing neural processes. Indeed, due to certain structural features of ion channels critical to synaptic function, contemporary physical theory must in principle be used when analyzing human brain dynamics. The new framework, unlike its classical-physics-based predecessor is erected directly upon, and is compatible with, the prevailing principles of physics, and is able to represent more adequately than classical concepts the neuroplastic mechanisms relevant to the growing number of empirical studies of the capacity of directed attention and mental effort to systematically alter brain function.« less

Quantum physics in neuroscience and psychology: a neurophysical model of mind–brain interaction

PubMed Central

Schwartz, Jeffrey M; Stapp, Henry P; Beauregard, Mario

2005-01-01

Neuropsychological research on the neural basis of behaviour generally posits that brain mechanisms will ultimately suffice to explain all psychologically described phenomena. This assumption stems from the idea that the brain is made up entirely of material particles and fields, and that all causal mechanisms relevant to neuroscience can therefore be formulated solely in terms of properties of these elements. Thus, terms having intrinsic mentalistic and/or experiential content (e.g. ‘feeling’, ‘knowing’ and ‘effort’) are not included as primary causal factors. This theoretical restriction is motivated primarily by ideas about the natural world that have been known to be fundamentally incorrect for more than three-quarters of a century. Contemporary basic physical theory differs profoundly from classic physics on the important matter of how the consciousness of human agents enters into the structure of empirical phenomena. The new principles contradict the older idea that local mechanical processes alone can account for the structure of all observed empirical data. Contemporary physical theory brings directly and irreducibly into the overall causal structure certain psychologically described choices made by human agents about how they will act. This key development in basic physical theory is applicable to neuroscience, and it provides neuroscientists and psychologists with an alternative conceptual framework for describing neural processes. Indeed, owing to certain structural features of ion channels critical to synaptic function, contemporary physical theory must in principle be used when analysing human brain dynamics. The new framework, unlike its classic-physics-based predecessor, is erected directly upon, and is compatible with, the prevailing principles of physics. It is able to represent more adequately than classic concepts the neuroplastic mechanisms relevant to the growing number of empirical studies of the capacity of directed attention and mental effort to systematically alter brain function. PMID:16147524

Characterization of Streptomyces spp. isolated from the rhizosphere of oil palm and evaluation of their ability to suppress basal stem rot disease in oil palm seedlings when applied as powder formulations in a glasshouse trial.

PubMed

Shariffah-Muzaimah, S A; Idris, A S; Madihah, A Z; Dzolkhifli, O; Kamaruzzaman, S; Maizatul-Suriza, M

2017-12-18

Ganoderma boninense, the main causal agent of oil palm (Elaeis guineensis) basal stem rot (BSR), severely reduces oil palm yields around the world. To reduce reliance on fungicide applications to control BSR, we are investigating the efficacy of alternative control methods, such as the application of biological control agents. In this study, we used four Streptomyces-like actinomycetes (isolates AGA43, AGA48, AGA347 and AGA506) that had been isolated from the oil palm rhizosphere and screened for antagonism towards G. boninense in a previous study. The aim of this study was to characterize these four isolates and then to assess their ability to suppress BSR in oil palm seedlings when applied individually to the soil in a vermiculite powder formulation. Analysis of partial 16S rRNA gene sequences (512 bp) revealed that the isolates exhibited a very high level of sequence similarity (> 98%) with GenBank reference sequences. Isolates AGA347 and AGA506 showed 99% similarity with Streptomyces hygroscopicus subsp. hygroscopicus and Streptomyces ahygroscopicus, respectively. Isolates AGA43 and AGA48 also belonged to the Streptomyces genus. The most effective formulation, AGA347, reduced BSR in seedlings by 73.1%. Formulations using the known antifungal producer Streptomyces noursei, AGA043, AGA048 or AGA506 reduced BSR by 47.4, 30.1, 54.8 and 44.1%, respectively. This glasshouse trial indicates that these Streptomyces spp. show promise as potential biological control agents against Ganoderma in oil palm. Further investigations are needed to determine the mechanism of antagonism and to increase the shelf life of Streptomyces formulations.

Supporting shared hypothesis testing in the biomedical domain.

PubMed

Agibetov, Asan; Jiménez-Ruiz, Ernesto; Ondrésik, Marta; Solimando, Alessandro; Banerjee, Imon; Guerrini, Giovanna; Catalano, Chiara E; Oliveira, Joaquim M; Patanè, Giuseppe; Reis, Rui L; Spagnuolo, Michela

2018-02-08

Pathogenesis of inflammatory diseases can be tracked by studying the causality relationships among the factors contributing to its development. We could, for instance, hypothesize on the connections of the pathogenesis outcomes to the observed conditions. And to prove such causal hypotheses we would need to have the full understanding of the causal relationships, and we would have to provide all the necessary evidences to support our claims. In practice, however, we might not possess all the background knowledge on the causality relationships, and we might be unable to collect all the evidence to prove our hypotheses. In this work we propose a methodology for the translation of biological knowledge on causality relationships of biological processes and their effects on conditions to a computational framework for hypothesis testing. The methodology consists of two main points: hypothesis graph construction from the formalization of the background knowledge on causality relationships, and confidence measurement in a causality hypothesis as a normalized weighted path computation in the hypothesis graph. In this framework, we can simulate collection of evidences and assess confidence in a causality hypothesis by measuring it proportionally to the amount of available knowledge and collected evidences. We evaluate our methodology on a hypothesis graph that represents both contributing factors which may cause cartilage degradation and the factors which might be caused by the cartilage degradation during osteoarthritis. Hypothesis graph construction has proven to be robust to the addition of potentially contradictory information on the simultaneously positive and negative effects. The obtained confidence measures for the specific causality hypotheses have been validated by our domain experts, and, correspond closely to their subjective assessments of confidences in investigated hypotheses. Overall, our methodology for a shared hypothesis testing framework exhibits important properties that researchers will find useful in literature review for their experimental studies, planning and prioritizing evidence collection acquisition procedures, and testing their hypotheses with different depths of knowledge on causal dependencies of biological processes and their effects on the observed conditions.

Detecting switching and intermittent causalities in time series

NASA Astrophysics Data System (ADS)

Zanin, Massimiliano; Papo, David

2017-04-01

During the last decade, complex network representations have emerged as a powerful instrument for describing the cross-talk between different brain regions both at rest and as subjects are carrying out cognitive tasks, in healthy brains and neurological pathologies. The transient nature of such cross-talk has nevertheless by and large been neglected, mainly due to the inherent limitations of some metrics, e.g., causality ones, which require a long time series in order to yield statistically significant results. Here, we present a methodology to account for intermittent causal coupling in neural activity, based on the identification of non-overlapping windows within the original time series in which the causality is strongest. The result is a less coarse-grained assessment of the time-varying properties of brain interactions, which can be used to create a high temporal resolution time-varying network. We apply the proposed methodology to the analysis of the brain activity of control subjects and alcoholic patients performing an image recognition task. Our results show that short-lived, intermittent, local-scale causality is better at discriminating both groups than global network metrics. These results highlight the importance of the transient nature of brain activity, at least under some pathological conditions.

Causal analysis of self-sustaining processes in the logarithmic layer of wall-bounded turbulence

NASA Astrophysics Data System (ADS)

Bae, H. J.; Encinar, M. P.; Lozano-Durán, A.

2018-04-01

Despite the large amount of information provided by direct numerical simulations of turbulent flows, their underlying dynamics remain elusive even in the most simple and canonical configurations. Most common approaches to investigate the turbulence phenomena do not provide a clear causal inference between events, which is essential to determine the dynamics of self-sustaining processes. In the present work, we examine the causal interactions between streaks, rolls and mean shear in the logarithmic layer of a minimal turbulent channel flow. Causality between structures is assessed in a non-intrusive manner by transfer entropy, i.e., how much the uncertainty of one structure is reduced by knowing the past states of the others. We choose to represent streaks by the first Fourier modes of the streamwise velocity, while rolls are defined by the wall-normal and spanwise velocity modes. The results show that the process is mainly unidirectional rather than cyclic, and that the log-layer motions are sustained by extracting energy from the mean shear which controls the dynamics and time-scales. The well-known lift-up effect is also identified, but shown to be of secondary importance in the causal network between shear, streaks and rolls.

Causal analysis of self-sustaining processes in the log-layer of wall-bounded turbulence

NASA Astrophysics Data System (ADS)

Lozano-Duran, Adrian; Bae, Hyunji Jane

2017-11-01

Despite the large amount of information provided by direct numerical simulations of turbulent flows, the underlying dynamics remain elusive even in the most simple and canonical configurations. Most standard methods used to investigate turbulence do not provide a clear causal inference between events, which is necessary to determine this dynamics, particularly in self-sustaning processes. In the present work, we examine the causal interactions between streaks and rolls in the logarithmic layer of minimal turbulent channel flow. Causality between structures is assessed in a non-intrusive manner by transfer entropy, i.e., how much the uncertainty of one structure is reduced by knowing the past states of the others. Streaks are represented by the first Fourier modes of the streamwise velocity, while rolls are defined by the wall-normal and spanwise velocities. The results show that the process is mainly unidirectional rather than cyclic, and that the log-layer motions are sustained by extracting energy from the mean shear, which controls the dynamics and time-scales. The well-known lift-up effect is shown to be not a key ingredient in the causal network between shear, streaks and rolls. Funded by ERC Coturb Madrid Summer Program.

Doxycycline for Malaria Chemoprophylaxis and Treatment: Report from the CDC Expert Meeting on Malaria Chemoprophylaxis

PubMed Central

Tan, Kathrine R.; Magill, Alan J.; Parise, Monica E.; Arguin, Paul M.

2011-01-01

Doxycycline, a synthetically derived tetracycline, is a partially efficacious causal prophylactic (liver stage of Plasmodium) drug and a slow acting blood schizontocidal agent highly effective for the prevention of malaria. When used in conjunction with a fast acting schizontocidal agent, it is also highly effective for malaria treatment. Doxycycline is especially useful as a prophylaxis in areas with chloroquine and multidrug-resistant Plasmodium falciparum malaria. Although not recommended for pregnant women and children < 8 years of age, severe adverse events are rarely reported for doxycycline. This report examines the evidence behind current recommendations for the use of doxycycline for malaria and summarizes the available literature on its safety and tolerability. PMID:21460003

Variation in reactive oxygen species concentration among lettuce types and modulation of their production via PPO during E. coli O157:H7 colonization of injured lettuce leaves(Abstract)

USDA-ARS?s Scientific Manuscript database

Minimally processed leafy vegetables are the biggest culprits in produce-linked outbreaks of foodborne illness and E. coli O157:H7 (EcO157) is the predominant causal agent of these epidemics. Harvesting and processing cause plant lesions thus creating new niches for opportunistic colonization of lea...

Patterns of Phakopsora pachyrhizi spore deposition detected in North America rain and their use to calibrate IAMS soybean rust forecasts in 2007

USDA-ARS?s Scientific Manuscript database

In 2007, rain was assayed for Phakopsora pachyrhizi spores (the causal agent of Asian soybean rust) at 75 National Atmospheric Deposition Program sites in the US and at 12 sites in Canada using two types of rain collectors. A nested real-time PCR assay was used to detect P. pachyrhizi DNA in the fil...

Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3-Genes, Genomes, Genetics.

USDA-ARS?s Scientific Manuscript database

Pyrenophora tritici-repentis is a necrotrophic fungal pathogen and causal agent of tan spot disease of wheat, which has increased significantly over the last few decades. Pathogenicity by this fungus is due to host-selective toxins. These toxins are recognized by their host plant in a genotype-speci...

Sensitivity of Rhizoctonia isolates from the Inland Pacific Northwest of the United States to phenazine-1-carboxylic acid and biological control by phenazine-producing Pseudomonas spp

USDA-ARS?s Scientific Manuscript database

Rhizoctonia solani AG-8, AG-2-1, and R. oryzae, causal agents of Rhizoctonia root rot and bare patch, are ubiquitous in cereal-based cropping systems of the Columbia Plateau of the Inland Pacific Northwest, yet the severity of this disease differs throughout the region. R. solani AG-8 is most common...

Draft Genome Sequence of the Phytopathogenic Fungus Ganoderma boninense, the Causal Agent of Basal Stem Rot Disease on Oil Palm.

PubMed

Utomo, Condro; Tanjung, Zulfikar Achmad; Aditama, Redi; Buana, Rika Fithri Nurani; Pratomo, Antonius Dony Madu; Tryono, Reno; Liwang, Tony

2018-04-26

Ganoderma boninense is the dominant fungal pathogen of basal stem rot (BSR) disease on Elaeis guineensis We sequenced the nuclear genome of mycelia using both Illumina and Pacific Biosciences platforms for assembly of scaffolds. The draft genome comprised 79.24 Mb, 495 scaffolds, and 26,226 predicted coding sequences. Copyright © 2018 Utomo et al.

Draft Genome Sequence of Two Strains of Xanthomonas arboricola Isolated from Prunus persica Which Are Dissimilar to Strains That Cause Bacterial Spot Disease on Prunus spp.

PubMed Central

Garita-Cambronero, Jerson; Palacio-Bielsa, Ana; López, María M.

2016-01-01

The draft genome sequences of two strains of Xanthomonas arboricola, isolated from asymptomatic peach trees in Spain, are reported here. These strains are avirulent and do not belong to the same phylogroup as X. arboricola pv. pruni, a causal agent of bacterial spot disease of stone fruits and almonds. PMID:27609931

A genomic map enriched for markers linked to Avr1 in Cronartium quercuum f.sp. fusiforme

Treesearch

Thomas L Kubisiak; Claire L Anderson; Henry V Amerson; Jason A Smith; John M Davis; C Dana Nelson

2011-01-01

A novel approach is presented to map avirulence gene Avr1 in the basidiomycete Cronartium quercuum f.sp. fusiforme, the causal agent of fusiform rust disease in pines. DNA markers tightly linked to resistance gene Fr1 in loblolly pine tree 10-5 were used to classify 10-5 seedling progeny as either resistant or susceptible. A single dikaryotic isolate (P2) heterozygous...

Inoculation of Malus genotypes with a set of Erwinia amylovora strains indicates a gene-for-gene relationship between the effector gene eop1 and both Malus floribunda 821 and Malus 'Evereste'

USDA-ARS?s Scientific Manuscript database

The Gram-negative bacterium Erwinia amylovora (Burrill) Winslow. et al., causal agent of fire blight disease in pome fruit trees, encodes a type three secretion system (T3SS) that functions to translocate effector proteins into plant cells that collectively function to suppress host defenses and ena...

Measuring the wildland firefighting safety culture change - an analysis of entrapment rates from 1994 to 2013

Treesearch

Bob Loveless; Adam Hernandez

2015-01-01

The tragic fatality events of the mid-1990s and subsequent studies led to a concentrated effort to increase safety in the US federal wildland firefighter community beginning in 2000. Addressing human factors (HF) as a causal agent in accidents was a major focal point for this cultural change. To examine the effectiveness of this change, we hypothesized a decline in...

Complete Genome Sequence of EtG, the First Phage Sequenced from Erwinia tracheiphila.

PubMed

Andrade-Domínguez, Andrés; Kolter, Roberto; Shapiro, Lori R

2018-02-22

Erwinia tracheiphila is the causal agent of bacterial wilt of cucurbits. Here, we report the genome sequence of the temperate phage EtG, which was isolated from an E. tracheiphila -infected cucumber plant. Phage EtG has a linear 30,413-bp double-stranded DNA genome with cohesive ends and 45 predicted open reading frames. Copyright © 2018 Andrade-Domínguez et al.

Draft Genome Sequence of the Phytopathogenic Fungus Fusarium euwallaceae, the Causal Agent of Fusarium Dieback.

PubMed

Ibarra-Laclette, Enrique; Sánchez-Rangel, Diana; Hernández-Domínguez, Eric; Pérez-Torres, Claudia-Anahí; Ortiz-Castro, Randy; Villafán, Emanuel; Alonso-Sánchez, Alexandro; Rodríguez-Haas, Benjamín; López-Buenfil, Abel; García-Avila, Clemente; Ramírez-Pool, José-Abrahán

2017-08-31

Here, we report the genome of Fusarium euwallaceae strain HFEW-16-IV-019, an isolate obtained from Kuroshio shot hole borer (a Euwallacea sp.). These beetles were collected in Tijuana, Mexico, from elm trees showing typical symptoms of Fusarium dieback. The final assembly consists of 287 scaffolds spanning 48,274,071 bp and 13,777 genes. Copyright © 2017 Ibarra-Laclette et al.

Humanoid infers Archimedes' principle: understanding physical relations and object affordances through cumulative learning experiences

PubMed Central

2016-01-01

Emerging studies indicate that several species such as corvids, apes and children solve ‘The Crow and the Pitcher’ task (from Aesop's Fables) in diverse conditions. Hidden beneath this fascinating paradigm is a fundamental question: by cumulatively interacting with different objects, how can an agent abstract the underlying cause–effect relations to predict and creatively exploit potential affordances of novel objects in the context of sought goals? Re-enacting this Aesop's Fable task on a humanoid within an open-ended ‘learning–prediction–abstraction’ loop, we address this problem and (i) present a brain-guided neural framework that emulates rapid one-shot encoding of ongoing experiences into a long-term memory and (ii) propose four task-agnostic learning rules (elimination, growth, uncertainty and status quo) that correlate predictions from remembered past experiences with the unfolding present situation to gradually abstract the underlying causal relations. Driven by the proposed architecture, the ensuing robot behaviours illustrated causal learning and anticipation similar to natural agents. Results further demonstrate that by cumulatively interacting with few objects, the predictions of the robot in case of novel objects converge close to the physical law, i.e. the Archimedes principle: this being independent of both the objects explored during learning and the order of their cumulative exploration. PMID:27466440

Bradford Hill's criteria, emerging zoonoses, and One Health.

PubMed

Asokan, G V; Asokan, Vanitha

2016-09-01

Zoonoses constitute more than 60% of infectious diseases and 75% of emerging infectious diseases. Inappropriate overemphasis of specialization of disciplines has ignored public health. Identifying the causes of disease and determining how exposures are related to outcomes in "emerging zoonoses" affecting multiple species are considered to be the hallmarks of public health research and practice that compels the adoption of "One Health". The interactions within and among populations of vertebrates in the causation and transmissions of emerging zoonotic diseases are inherently dynamic, interdependent, and systems based. Disease causality theories have moved from one or several agents causing disease in a single species, to one infectious agent causing disease in multiple species-emerging zoonoses. Identification of the causative pathogen components or structures, elucidating the mechanisms of species specificity, and understanding the natural conditions of emergence would facilitate better derivation of the causal mechanism. Good quality evidence on causation in emerging zoonoses affecting multiple species makes a strong recommendation under the One Health approach for disease prevention and control from diagnostic tests, treatment, antimicrobial resistance, preventive vaccines, and evidence informed health policies. In the tenets of One Health, alliances work best when the legitimate interests of the different partners combine to prevent and control emerging zoonoses. Copyright © 2015 Ministry of Health, Saudi Arabia. Published by Elsevier Ltd. All rights reserved.

Optimal vaccine stockpile design for an eradicated disease: application to polio.

PubMed

Tebbens, Radboud J Duintjer; Pallansch, Mark A; Alexander, James P; Thompson, Kimberly M

2010-06-11

Eradication of a disease promises significant health and financial benefits. Preserving those benefits, hopefully in perpetuity, requires preparing for the possibility that the causal agent could re-emerge (unintentionally or intentionally). In the case of a vaccine-preventable disease, creation and planning for the use of a vaccine stockpile becomes a primary concern. Doing so requires consideration of the dynamics at different levels, including the stockpile supply chain and transmission of the causal agent. This paper develops a mathematical framework for determining the optimal management of a vaccine stockpile over time. We apply the framework to the polio vaccine stockpile for the post-eradication era and present examples of solutions to one possible framing of the optimization problem. We use the framework to discuss issues relevant to the development and use of the polio vaccine stockpile, including capacity constraints, production and filling delays, risks associated with the stockpile, dynamics and uncertainty of vaccine needs, issues of funding, location, and serotype dependent behavior, and the implications of likely changes over time that might occur. This framework serves as a helpful context for discussions and analyses related to the process of designing and maintaining a stockpile for an eradicated disease. (c) 2010 Elsevier Ltd. All rights reserved.

Drug-induced liver injury: present and future

PubMed Central

Suk, Ki Tae

2012-01-01

Liver injury due to prescription and nonprescription medications is a growing medical, scientific, and public health problem. Worldwide, the estimated annual incidence rate of drug-induced liver injury (DILI) is 13.9-24.0 per 100,000 inhabitants. DILI is one of the leading causes of acute liver failure in the US. In Korea, the annual extrapolated incidence of cases hospitalized at university hospital is 12/100,000 persons/year. Most cases of DILI are the result of idiosyncratic metabolic responses or unexpected reactions to medication. There is marked geographic variation in relevant agents; antibiotics, anticonvulsants, and psychotropic drugs are the most common offending agents in the West, whereas in Asia, 'herbs' and 'health foods or dietary supplements' are more common. Different medical circumstances also cause discrepancy in definition and classification of DILI between West and Asia. In the concern of causality assessment, the application of the Roussel Uclaf Causality Assessment Method (RUCAM) scale frequently undercounts the cases caused by 'herbs' due to a lack of previous information and incompatible time criteria. Therefore, a more objective and reproducible tool that could be used for the diagnosis of DILI caused by 'herbs' is needed in Asia. In addition, a reporting system similar to the Drug-Induced Liver Injury Network (DILIN) in the US should be established as soon as possible in Asia. PMID:23091804

Humanoid infers Archimedes' principle: understanding physical relations and object affordances through cumulative learning experiences.

PubMed

Bhat, Ajaz Ahmad; Mohan, Vishwanathan; Sandini, Giulio; Morasso, Pietro

2016-07-01

Emerging studies indicate that several species such as corvids, apes and children solve 'The Crow and the Pitcher' task (from Aesop's Fables) in diverse conditions. Hidden beneath this fascinating paradigm is a fundamental question: by cumulatively interacting with different objects, how can an agent abstract the underlying cause-effect relations to predict and creatively exploit potential affordances of novel objects in the context of sought goals? Re-enacting this Aesop's Fable task on a humanoid within an open-ended 'learning-prediction-abstraction' loop, we address this problem and (i) present a brain-guided neural framework that emulates rapid one-shot encoding of ongoing experiences into a long-term memory and (ii) propose four task-agnostic learning rules (elimination, growth, uncertainty and status quo) that correlate predictions from remembered past experiences with the unfolding present situation to gradually abstract the underlying causal relations. Driven by the proposed architecture, the ensuing robot behaviours illustrated causal learning and anticipation similar to natural agents. Results further demonstrate that by cumulatively interacting with few objects, the predictions of the robot in case of novel objects converge close to the physical law, i.e. the Archimedes principle: this being independent of both the objects explored during learning and the order of their cumulative exploration. © 2016 The Author(s).

Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

PubMed Central

Lang, Jillian M.; Langlois, Paul; Nguyen, Marian Hanna R.; Triplett, Lindsay R.; Purdie, Laura; Holton, Timothy A.; Djikeng, Appolinaire; Vera Cruz, Casiana M.; Verdier, Valérie

2014-01-01

Molecular diagnostics for crop diseases can enhance food security by enabling the rapid identification of threatening pathogens and providing critical information for the deployment of disease management strategies. Loop-mediated isothermal amplification (LAMP) is a PCR-based tool that allows the rapid, highly specific amplification of target DNA sequences at a single temperature and is thus ideal for field-level diagnosis of plant diseases. We developed primers highly specific for two globally important rice pathogens, Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB) disease, and X. oryzae pv. oryzicola, the causal agent of bacterial leaf streak disease (BLS), for use in reliable, sensitive LAMP assays. In addition to pathovar distinction, two assays that differentiate X. oryzae pv. oryzae by African or Asian lineage were developed. Using these LAMP primer sets, the presence of each pathogen was detected from DNA and bacterial cells, as well as leaf and seed samples. Thresholds of detection for all assays were consistently 104 to 105 CFU ml−1, while genomic DNA thresholds were between 1 pg and 10 fg. Use of the unique sequences combined with the LAMP assay provides a sensitive, accurate, rapid, simple, and inexpensive protocol to detect both BB and BLS pathogens. PMID:24837384