Efficiently Ranking Hyphotheses in Machine Learning

NASA Technical Reports Server (NTRS)

Chien, Steve

1997-01-01

This paper considers the problem of learning the ranking of a set of alternatives based upon incomplete information (e.g. a limited number of observations). At each decision cycle, the system can output a complete ordering on the hypotheses or decide to gather additional information (e.g. observation) at some cost.

The impact of alternative trait-scaling hypotheses for the maximum photosynthetic carboxylation rate ( V cmax) on global gross primary production [The impact of alternative V cmax trait-scaling hypotheses on global gross primary production

DOE PAGES

Walker, Anthony P.; Quaife, Tristan; van Bodegom, Peter M.; ...

2017-06-23

Here, the maximum photosynthetic carboxylation rate (V cmax) is an influential plant trait that has multiple scaling hypotheses, which is a source of uncertainty in predictive understanding of global gross primary production (GPP). Four trait-scaling hypotheses (plant functional type, nutrient limitation, environmental filtering, and plant plasticity) with nine specific implementations were used to predict global V cmax distributions and their impact on global GPP in the Sheffield Dynamic Global Vegetation Model (SDGVM). Global GPP varied from 108.1 to 128.2 PgC yr –1, 65% of the range of a recent model intercomparison of global GPP. The variation in GPP propagated throughmore » to a 27% coefficient of variation in net biome productivity (NBP). All hypotheses produced global GPP that was highly correlated ( r = 0.85–0.91) with three proxies of global GPP. Plant functional type-based nutrient limitation, underpinned by a core SDGVM hypothesis that plant nitrogen (N) status is inversely related to increasing costs of N acquisition with increasing soil carbon, adequately reproduced global GPP distributions. Further improvement could be achieved with accurate representation of water sensitivity and agriculture in SDGVM. Mismatch between environmental filtering (the most data-driven hypothesis) and GPP suggested that greater effort is needed understand V cmax variation in the field, particularly in northern latitudes.« less

The impact of alternative trait-scaling hypotheses for the maximum photosynthetic carboxylation rate ( V cmax) on global gross primary production [The impact of alternative V cmax trait-scaling hypotheses on global gross primary production

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

Walker, Anthony P.; Quaife, Tristan; van Bodegom, Peter M.

Here, the maximum photosynthetic carboxylation rate (V cmax) is an influential plant trait that has multiple scaling hypotheses, which is a source of uncertainty in predictive understanding of global gross primary production (GPP). Four trait-scaling hypotheses (plant functional type, nutrient limitation, environmental filtering, and plant plasticity) with nine specific implementations were used to predict global V cmax distributions and their impact on global GPP in the Sheffield Dynamic Global Vegetation Model (SDGVM). Global GPP varied from 108.1 to 128.2 PgC yr –1, 65% of the range of a recent model intercomparison of global GPP. The variation in GPP propagated throughmore » to a 27% coefficient of variation in net biome productivity (NBP). All hypotheses produced global GPP that was highly correlated ( r = 0.85–0.91) with three proxies of global GPP. Plant functional type-based nutrient limitation, underpinned by a core SDGVM hypothesis that plant nitrogen (N) status is inversely related to increasing costs of N acquisition with increasing soil carbon, adequately reproduced global GPP distributions. Further improvement could be achieved with accurate representation of water sensitivity and agriculture in SDGVM. Mismatch between environmental filtering (the most data-driven hypothesis) and GPP suggested that greater effort is needed understand V cmax variation in the field, particularly in northern latitudes.« less

Assessing the Relationship between Campus Programs, Student Self-Efficacy, Stress, and Substance Abuse

ERIC Educational Resources Information Center

DiRamio, David; Payne, Ruthanna

2007-01-01

Student life educators continue searching for ways to assess campus programs. This is an exploratory study for an alternative assessment approach based on a hypothesized relationship between participation in campus activities, student self-efficacy, and student dispositions toward aspects of mental health and substance abuse. Focusing on the…

Titan Polar Landscape Evolution

NASA Technical Reports Server (NTRS)

Moore, Jeffrey M.

2016-01-01

With the ongoing Cassini-era observations and studies of Titan it is clear that the intensity and distribution of surface processes (particularly fluvial erosion by methane and Aeolian transport) has changed through time. Currently however, alternate hypotheses substantially differ among specific scenarios with respect to the effects of atmospheric evolution, seasonal changes, and endogenic processes. We have studied the evolution of Titan's polar region through a combination of analysis of imaging, elevation data, and geomorphic mapping, spatially explicit simulations of landform evolution, and quantitative comparison of the simulated landscapes with corresponding Titan morphology. We have quantitatively evaluated alternate scenarios for the landform evolution of Titan's polar terrain. The investigations have been guided by recent geomorphic mapping and topographic characterization of the polar regions that are used to frame hypotheses of process interactions, which have been evaluated using simulation modeling. Topographic information about Titan's polar region is be based on SAR-Topography and altimetry archived on PDS, SAR-based stereo radar-grammetry, radar-sounding lake depth measurements, and superposition relationships between geomorphologic map units, which we will use to create a generalized topographic map.

Testing Small Variance Priors Using Prior-Posterior Predictive p Values.

PubMed

Hoijtink, Herbert; van de Schoot, Rens

2017-04-03

Muthén and Asparouhov (2012) propose to evaluate model fit in structural equation models based on approximate (using small variance priors) instead of exact equality of (combinations of) parameters to zero. This is an important development that adequately addresses Cohen's (1994) The Earth is Round (p < .05), which stresses that point null-hypotheses are so precise that small and irrelevant differences from the null-hypothesis may lead to their rejection. It is tempting to evaluate small variance priors using readily available approaches like the posterior predictive p value and the DIC. However, as will be shown, both are not suited for the evaluation of models based on small variance priors. In this article, a well behaving alternative, the prior-posterior predictive p value, will be introduced. It will be shown that it is consistent, the distributions under the null and alternative hypotheses will be elaborated, and it will be applied to testing whether the difference between 2 means and the size of a correlation are relevantly different from zero. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Long-Lived Plasma Formations in the Atmosphere as an Alternative Energy Source

NASA Astrophysics Data System (ADS)

Dvornikov, M. S.; Mekhdieva, G. Sh.; Agamalieva, L. A.

2018-01-01

A model of a stable plasma formation, based on radial quantum oscillations of charged particles, is discussed. The given plasmoid is described with the help of the nonlinear Schrödinger equation. A new phenomenon of effective attraction between oscillating charged particles is considered within the framework of the proposed model. The possible existence of a composite plasma structure is also discussed. Hypotheses about using the obtained results to describe natural long-lived plasma formations which can serve as alternative energy sources are advanced.

How and when do expert emergency physicians generate and evaluate diagnostic hypotheses? A qualitative study using head-mounted video cued-recall interviews.

PubMed

Pelaccia, Thierry; Tardif, Jacques; Triby, Emmanuel; Ammirati, Christine; Bertrand, Catherine; Dory, Valérie; Charlin, Bernard

2014-12-01

The ability to make a diagnosis is a crucial skill in emergency medicine. Little is known about the way emergency physicians reach a diagnosis. This study aims to identify how and when, during the initial patient examination, emergency physicians generate and evaluate diagnostic hypotheses. We carried out a qualitative research project based on semistructured interviews with emergency physicians. The interviews concerned management of an emergency situation during routine medical practice. They were associated with viewing the video recording of emergency situations filmed in an "own-point-of-view" perspective. The emergency physicians generated an average of 5 diagnostic hypotheses. Most of these hypotheses were generated before meeting the patient or within the first 5 minutes of the meeting. The hypotheses were then rank ordered within the context of a verification procedure based on identifying key information. These tasks were usually accomplished without conscious effort. No hypothesis was completely confirmed or refuted until the results of investigations were available. The generation and rank ordering of diagnostic hypotheses is based on the activation of cognitive processes, enabling expert emergency physicians to process environmental information and link it to past experiences. The physicians seemed to strive to avoid the risk of error by remaining aware of the possibility of alternative hypotheses as long as they did not have the results of investigations. Understanding the diagnostic process used by emergency physicians provides interesting ideas for training residents in a specialty in which the prevalence of reasoning errors leading to incorrect diagnoses is high. Copyright © 2014 American College of Emergency Physicians. Published by Elsevier Inc. All rights reserved.

Using an Enhanced Conflict Map in the Classroom (Photoelectric Effect) Based on Lakatosian Heuristic Principle Strategies

ERIC Educational Resources Information Center

Oh, Jun-Young

2011-01-01

Researchers have shown that most students resist changes to their core beliefs by offering auxiliary hypotheses at the first sign of the development of conceptual change. Studies have viewed student reaction to discrepant events as an important clue in helping researchers understand not only the structure of alternative concepts (Niaz,…

Outsourcing the Gender Factory: Living Arrangements and Service Expenditures on Female and Male Tasks

ERIC Educational Resources Information Center

de Ruijter, Esther; Treas, Judith K.; Cohen, Philip N.

2005-01-01

Using data from the U.S. Consumer Expenditure Survey 1998, this study analyzes how much money different types of households spend for domestic services on "female" and "male" tasks. We test alternative hypotheses based on economic and sociological theories of gender differentiation. Contrary to arguments that marriage lowers the risk to one…

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution

PubMed Central

Kendall, Michelle; Colijn, Caroline

2016-01-01

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. Key words: phylogenetics, evolution, tree metrics, genetics, sequencing. PMID:27343287

Developing the research hypothesis.

PubMed

Toledo, Alexander H; Flikkema, Robert; Toledo-Pereyra, Luis H

2011-01-01

The research hypothesis is needed for a sound and well-developed research study. The research hypothesis contributes to the solution of the research problem. Types of research hypotheses include inductive and deductive, directional and non-directional, and null and alternative hypotheses. Rejecting the null hypothesis and accepting the alternative hypothesis is the basis for building a good research study. This work reviews the most important aspects of organizing and establishing an efficient and complete hypothesis.

What to expect from an evolutionary hypothesis for a human disease: The case of type 2 diabetes.

PubMed

Watve, Milind; Diwekar-Joshi, Manawa

2016-10-01

Evolutionary medicine has a promise to bring in a conceptual revolution in medicine. However, as yet the field does not have the same theoretical rigour as that of many other fields in evolutionary studies. We discuss here with reference to type 2 diabetes mellitus (T2DM) what role an evolutionary hypothesis should play in the development of thinking in medicine. Starting with the thrifty gene hypothesis, evolutionary thinking in T2DM has undergone several transitions, modifications and refinements of the thrift family of hypotheses. In addition alternative hypotheses independent of thrift are also suggested. However, most hypotheses look at partial pictures; make selective use of supportive data ignoring inconvenient truths. Most hypotheses look at a superficial picture and avoid getting into the intricacies of underlying molecular, neuronal and physiological processes. Very few hypotheses have suggested clinical implications and none of them have been tested with randomized clinical trials. In the meanwhile the concepts in the pathophysiology of T2DM are undergoing radical changes and evolutionary hypotheses need to take them into account. We suggest an approach and a set of criteria to evaluate the relative merits of the alternative hypotheses. A number of hypotheses are likely to fail when critically evaluated against these criteria. It is possible that more than one selective process are at work in the evolution of propensity to T2DM, but the intercompatibility of the alternative selective forces and their relative contribution needs to be examined. The approach we describe could potentially lead to a sound evolutionary theory that is clinically useful and testable by randomized controlled clinical trials. Copyright © 2016 Elsevier GmbH. All rights reserved.

How scientific experiments are designed: Problem solving in a knowledge-rich, error-rich environment

NASA Astrophysics Data System (ADS)

Baker, Lisa M.

While theory formation and the relation between theory and data has been investigated in many studies of scientific reasoning, researchers have focused less attention on reasoning about experimental design, even though the experimental design process makes up a large part of real-world scientists' reasoning. The goal of this thesis was to provide a cognitive account of the scientific experimental design process by analyzing experimental design as problem-solving behavior (Newell & Simon, 1972). Three specific issues were addressed: the effect of potential error on experimental design strategies, the role of prior knowledge in experimental design, and the effect of characteristics of the space of alternate hypotheses on alternate hypothesis testing. A two-pronged in vivo/in vitro research methodology was employed, in which transcripts of real-world scientific laboratory meetings were analyzed as well as undergraduate science and non-science majors' design of biology experiments in the psychology laboratory. It was found that scientists use a specific strategy to deal with the possibility of error in experimental findings: they include "known" control conditions in their experimental designs both to determine whether error is occurring and to identify sources of error. The known controls strategy had not been reported in earlier studies with science-like tasks, in which participants' responses to error had consisted of replicating experiments and discounting results. With respect to prior knowledge: scientists and undergraduate students drew on several types of knowledge when designing experiments, including theoretical knowledge, domain-specific knowledge of experimental techniques, and domain-general knowledge of experimental design strategies. Finally, undergraduate science students generated and tested alternates to their favored hypotheses when the space of alternate hypotheses was constrained and searchable. This result may help explain findings of confirmation bias in earlier studies using science-like tasks, in which characteristics of the alternate hypothesis space may have made it unfeasible for participants to generate and test alternate hypotheses. In general, scientists and science undergraduates were found to engage in a systematic experimental design process that responded to salient features of the problem environment, including the constant potential for experimental error, availability of alternate hypotheses, and access to both theoretical knowledge and knowledge of experimental techniques.

Achievement goals, competition appraisals, and the psychological and emotional welfare of sport participants.

PubMed

Adie, James W; Duda, Joan L; Ntoumanis, Nikos

2008-06-01

Grounded in the 2x2 achievement goal framework (Elliot & McGregor, 2001), a model was tested examining the hypothesized relationships between approach and avoidance (mastery and performance) goals, challenge and threat appraisals of sport competition, and positive and negative indices of well-being (i.e., self-esteem, positive, and negative affect). A further aim was to determine the degree to which the cognitive appraisals mediated the relationship between the four achievement goals and the indicators of athletes' welfare. Finally, measurement and structural invariance was tested with respect to gender in the hypothesized model. An alternative model was also estimated specifying self-esteem as an antecedent of the four goals and cognitive appraisals. Four hundred and twenty-four team sport participants (Mage=24.25) responded to a multisection questionnaire. Structural equation modeling analyses provided support for the hypothesized model only. Challenge and threat appraisals partially mediated the relationships observed between mastery-based goals and the well-being indicators. Lastly, the hypothesized model was found to be invariant across gender.

Determination of spin and parity of the Higgs boson in the [Formula: see text] decay channel with the ATLAS detector.

PubMed

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Studies of the spin and parity quantum numbers of the Higgs boson in the [Formula: see text] final state are presented, based on proton-proton collision data collected by the ATLAS detector at the Large Hadron Collider, corresponding to an integrated luminosity of 20.3 fb[Formula: see text] at a centre-of-mass energy of [Formula: see text] TeV. The Standard Model spin-parity [Formula: see text] hypothesis is compared with alternative hypotheses for both spin and CP. The case where the observed resonance is a mixture of the Standard-Model-like Higgs boson and CP-even ([Formula: see text]) or CP-odd ([Formula: see text]) Higgs boson in scenarios beyond the Standard Model is also studied. The data are found to be consistent with the Standard Model prediction and limits are placed on alternative spin and CP hypotheses, including CP mixing in different scenarios.

Determination of spin and parity of the Higgs boson in the $$WW^*\\rightarrow e \

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2015-05-27

Research of the spin and parity quantum numbers of the Higgs boson in the WW* → eνμν final state are presented, based on proton–proton collision data collected by the ATLAS detector at the Large Hadron Collider, corresponding to an integrated luminosity of 20.3 fb –1 at a centre-of-mass energy of √s=8 TeV. The Standard Model spin-parity J CP=0 ++ hypothesis is compared with alternative hypotheses for both spin and CP. The case where the observed resonance is a mixture of the Standard-Model-like Higgs boson and CP-even (J CP=0 ++) or CP-odd (J CP=0 +–) Higgs boson in scenarios beyond themore » Standard Model is also studied. The data are found to be consistent with the Standard Model prediction and limits are placed on alternative spin and CP hypotheses, including CP mixing in different scenarios.« less

Determination of spin and parity of the Higgs boson in the $$WW^*\\rightarrow e \

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

Aad, G.; Abbott, B.; Abdallah, J.

Research of the spin and parity quantum numbers of the Higgs boson in the WW* → eνμν final state are presented, based on proton–proton collision data collected by the ATLAS detector at the Large Hadron Collider, corresponding to an integrated luminosity of 20.3 fb –1 at a centre-of-mass energy of √s=8 TeV. The Standard Model spin-parity J CP=0 ++ hypothesis is compared with alternative hypotheses for both spin and CP. The case where the observed resonance is a mixture of the Standard-Model-like Higgs boson and CP-even (J CP=0 ++) or CP-odd (J CP=0 +–) Higgs boson in scenarios beyond themore » Standard Model is also studied. The data are found to be consistent with the Standard Model prediction and limits are placed on alternative spin and CP hypotheses, including CP mixing in different scenarios.« less

Alternating gender incongruity: a new neuropsychiatric syndrome providing insight into the dynamic plasticity of brain-sex.

PubMed

Case, Laura K; Ramachandran, Vilayanur S

2012-05-01

Between the two extreme ends of human sexuality - male and female - lie a poorly understood and poorly studied spectrum of ambiguously defined sexual identities that are very much a part of the human condition but defy rigid classification. "Bigender" is a recently formed sub-category of transgenderism, describing individuals who experience a blending or alternation of gender states. While recognized nominally by the APA, no scientific work to our knowledge has addressed this fascinating condition, or proposed any physiological basis for it. In addition, the alternation aspect has not been proposed as a nosological entity distinct from blending. We present descriptive data suggesting that many bigender individuals experience an involuntary switching of gender states without any amnesia for either state. In addition, similar to transsexual individuals, the majority of bigender individuals experience phantom breasts or genitalia corresponding to the non-biologic gender when they are in a trans-gender state. Finally, our survey found decreased lateralization of handedness in the bigender community. These observations suggest a biologic basis of bigenderism and lead us to propose a novel gender condition, "alternating gender incongruity" (AGI). We hypothesize that AGI may be related to an unusual degree or depth of hemispheric switching and corresponding callosal suppression of sex appropriate body maps in parietal cortex- possibly the superior parietal lobule- and its reciprocal connections with the insula and hypothalamus. This is based on two lines of reasoning. First, bigender individuals in our survey sample reported an elevated rate of bipolar disorder, which has been linked to slowed hemispheric switching. We hypothesize that tracking the nasal cycle, rate of binocular rivalry, and other markers of hemispheric switching will reveal a physiological basis for AGI individuals' subjective reports of gender switches. Switching may also trigger hormonal cascades, which we are currently exploring. Second, we base our hypotheses on ancient and modern associations between the left and right hemispheres and the male and female genders. By providing a case of sharp brain-sex shifts within individuals, we believe that the study of AGI could prove illuminating to scientific understanding of gender, body representation, and the nature of self. Copyright © 2012 Elsevier Ltd. All rights reserved.

Habitat structure mediates predation risk for sedentary prey: Experimental tests of alternative hypotheses

USGS Publications Warehouse

Chalfoun, A.D.; Martin, T.E.

2009-01-01

Predation is an important and ubiquitous selective force that can shape habitat preferences of prey species, but tests of alternative mechanistic hypotheses of habitat influences on predation risk are lacking. 2. We studied predation risk at nest sites of a passerine bird and tested two hypotheses based on theories of predator foraging behaviour. The total-foliage hypothesis predicts that predation will decline in areas of greater overall vegetation density by impeding cues for detection by predators. The potential-prey-site hypothesis predicts that predation decreases where predators must search more unoccupied potential nest sites. 3. Both observational data and results from a habitat manipulation provided clear support for the potential-prey-site hypothesis and rejection of the total-foliage hypothesis. Birds chose nest patches containing both greater total foliage and potential nest site density (which were correlated in their abundance) than at random sites, yet only potential nest site density significantly influenced nest predation risk. 4. Our results therefore provided a clear and rare example of adaptive nest site selection that would have been missed had structural complexity or total vegetation density been considered alone. 5. Our results also demonstrated that interactions between predator foraging success and habitat structure can be more complex than simple impedance or occlusion by vegetation. ?? 2008 British Ecological Society.

Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges.

PubMed

Massatti, Rob; Knowles, L Lacey

2016-08-01

Deterministic processes may uniquely affect codistributed species' phylogeographic patterns such that discordant genetic variation among taxa is predicted. Yet, explicitly testing expectations of genomic discordance in a statistical framework remains challenging. Here, we construct spatially and temporally dynamic models to investigate the hypothesized effect of microhabitat preferences on the permeability of glaciated regions to gene flow in two closely related montane species. Utilizing environmental niche models from the Last Glacial Maximum and the present to inform demographic models of changes in habitat suitability over time, we evaluate the relative probabilities of two alternative models using approximate Bayesian computation (ABC) in which glaciated regions are either (i) permeable or (ii) a barrier to gene flow. Results based on the fit of the empirical data to data sets simulated using a spatially explicit coalescent under alternative models indicate that genomic data are consistent with predictions about the hypothesized role of microhabitat in generating discordant patterns of genetic variation among the taxa. Specifically, a model in which glaciated areas acted as a barrier was much more probable based on patterns of genomic variation in Carex nova, a wet-adapted species. However, in the dry-adapted Carex chalciolepis, the permeable model was more probable, although the difference in the support of the models was small. This work highlights how statistical inferences can be used to distinguish deterministic processes that are expected to result in discordant genomic patterns among species, including species-specific responses to climate change. © 2016 John Wiley & Sons Ltd.

Genetic Programming for Automatic Hydrological Modelling

NASA Astrophysics Data System (ADS)

Chadalawada, Jayashree; Babovic, Vladan

2017-04-01

One of the recent challenges for the hydrologic research community is the need for the development of coupled systems that involves the integration of hydrologic, atmospheric and socio-economic relationships. This poses a requirement for novel modelling frameworks that can accurately represent complex systems, given, the limited understanding of underlying processes, increasing volume of data and high levels of uncertainity. Each of the existing hydrological models vary in terms of conceptualization and process representation and is the best suited to capture the environmental dynamics of a particular hydrological system. Data driven approaches can be used in the integration of alternative process hypotheses in order to achieve a unified theory at catchment scale. The key steps in the implementation of integrated modelling framework that is influenced by prior understanding and data, include, choice of the technique for the induction of knowledge from data, identification of alternative structural hypotheses, definition of rules, constraints for meaningful, intelligent combination of model component hypotheses and definition of evaluation metrics. This study aims at defining a Genetic Programming based modelling framework that test different conceptual model constructs based on wide range of objective functions and evolves accurate and parsimonious models that capture dominant hydrological processes at catchment scale. In this paper, GP initializes the evolutionary process using the modelling decisions inspired from the Superflex framework [Fenicia et al., 2011] and automatically combines them into model structures that are scrutinized against observed data using statistical, hydrological and flow duration curve based performance metrics. The collaboration between data driven and physical, conceptual modelling paradigms improves the ability to model and manage hydrologic systems. Fenicia, F., D. Kavetski, and H. H. Savenije (2011), Elements of a flexible approach for conceptual hydrological modeling: 1. Motivation and theoretical development, Water Resources Research, 47(11).

Hypothesis testing and earthquake prediction.

PubMed

Jackson, D D

1996-04-30

Requirements for testing include advance specification of the conditional rate density (probability per unit time, area, and magnitude) or, alternatively, probabilities for specified intervals of time, space, and magnitude. Here I consider testing fully specified hypotheses, with no parameter adjustments or arbitrary decisions allowed during the test period. Because it may take decades to validate prediction methods, it is worthwhile to formulate testable hypotheses carefully in advance. Earthquake prediction generally implies that the probability will be temporarily higher than normal. Such a statement requires knowledge of "normal behavior"--that is, it requires a null hypothesis. Hypotheses can be tested in three ways: (i) by comparing the number of actual earth-quakes to the number predicted, (ii) by comparing the likelihood score of actual earthquakes to the predicted distribution, and (iii) by comparing the likelihood ratio to that of a null hypothesis. The first two tests are purely self-consistency tests, while the third is a direct comparison of two hypotheses. Predictions made without a statement of probability are very difficult to test, and any test must be based on the ratio of earthquakes in and out of the forecast regions.

Hypothesis testing and earthquake prediction.

PubMed Central

Jackson, D D

1996-01-01

Requirements for testing include advance specification of the conditional rate density (probability per unit time, area, and magnitude) or, alternatively, probabilities for specified intervals of time, space, and magnitude. Here I consider testing fully specified hypotheses, with no parameter adjustments or arbitrary decisions allowed during the test period. Because it may take decades to validate prediction methods, it is worthwhile to formulate testable hypotheses carefully in advance. Earthquake prediction generally implies that the probability will be temporarily higher than normal. Such a statement requires knowledge of "normal behavior"--that is, it requires a null hypothesis. Hypotheses can be tested in three ways: (i) by comparing the number of actual earth-quakes to the number predicted, (ii) by comparing the likelihood score of actual earthquakes to the predicted distribution, and (iii) by comparing the likelihood ratio to that of a null hypothesis. The first two tests are purely self-consistency tests, while the third is a direct comparison of two hypotheses. Predictions made without a statement of probability are very difficult to test, and any test must be based on the ratio of earthquakes in and out of the forecast regions. PMID:11607663

Why Current Statistics of Complementary Alternative Medicine Clinical Trials is Invalid.

PubMed

Pandolfi, Maurizio; Carreras, Giulia

2018-06-07

It is not sufficiently known that frequentist statistics cannot provide direct information on the probability that the research hypothesis tested is correct. The error resulting from this misunderstanding is compounded when the hypotheses under scrutiny have precarious scientific bases, which, generally, those of complementary alternative medicine (CAM) are. In such cases, it is mandatory to use inferential statistics, considering the prior probability that the hypothesis tested is true, such as the Bayesian statistics. The authors show that, under such circumstances, no real statistical significance can be achieved in CAM clinical trials. In this respect, CAM trials involving human material are also hardly defensible from an ethical viewpoint.

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.

PubMed

Kendall, Michelle; Colijn, Caroline

2016-10-01

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. phylogenetics, evolution, tree metrics, genetics, sequencing. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Awareness and Ethical Orientation of Alternatively Certified Prospective Teachers to Intention for Whistle Blowing

ERIC Educational Resources Information Center

Toker Gokce, Asiye

2013-01-01

This study inquires whistle blowing intentions of alternatively certified prospective teachers, investigating their moral reasoning to blow the whistle. Specifically three hypotheses were tested: Overall ethical awareness of the alternatively certified prospective teachers is high; the participants will identify reasons related to philosophical…

Regulatory design governing progression of population growth phases in bacteria.

PubMed

Martínez-Antonio, Agustino; Lomnitz, Jason G; Sandoval, Santiago; Aldana, Maximino; Savageau, Michael A

2012-01-01

It has long been noted that batch cultures inoculated with resting bacteria exhibit a progression of growth phases traditionally labeled lag, exponential, pre-stationary and stationary. However, a detailed molecular description of the mechanisms controlling the transitions between these phases is lacking. A core circuit, formed by a subset of regulatory interactions involving five global transcription factors (FIS, HNS, IHF, RpoS and GadX), has been identified by correlating information from the well- established transcriptional regulatory network of Escherichia coli and genome-wide expression data from cultures in these different growth phases. We propose a functional role for this circuit in controlling progression through these phases. Two alternative hypotheses for controlling the transition between the growth phases are first, a continuous graded adjustment to changing environmental conditions, and second, a discontinuous hysteretic switch at critical thresholds between growth phases. We formulate a simple mathematical model of the core circuit, consisting of differential equations based on the power-law formalism, and show by mathematical and computer-assisted analysis that there are critical conditions among the parameters of the model that can lead to hysteretic switch behavior, which--if validated experimentally--would suggest that the transitions between different growth phases might be analogous to cellular differentiation. Based on these provocative results, we propose experiments to test the alternative hypotheses.

Exploration of interaction zones of β-tubulin colchicine binding domain of helminths and binding mechanism of anthelmintics.

PubMed

Ranjan, Prabodh; Kumar, Sivakumar Prasanth; Kari, Vijayakrishna; Jha, Prakash Chandra

2017-06-01

Numerous studies postulated the possible modes of anthelmintic activity by targeting alternate or extended regions of colchicine binding domain of helminth β-tubulin. We present three interaction zones (zones vide -1 to -3) in the colchicine binding domain of Haemonchus contortus (a helminth) β-tubulin homology model and developed zone-wise structure-based pharmacophore models coupled with molecular docking technique to unveil the binding hypotheses. The resulted ten structure-based hypotheses were then refined to essential three point pharmacophore features that captured recurring and crucial non-covalent receptor contacts and proposed three characteristics necessary for optimal zone-2 binding: a conserved pair of H bond acceptor (HBA to form H bond with Asn226 residue) and an aliphatic moiety of molecule separated by 3.75±0.44Å. Further, an aliphatic or a heterocyclic group distant (11.75±1.14Å) to the conserved aliphatic site formed the third feature component in the zone-2 specific anthelmintic pharmacophore model. Alternatively, an additional HBA can be substituted as a third component to establish H bonding with Asn204. We discern that selective zone-2 anthelmintics can be designed effectively by closely adapting the pharmacophore feature patterns and its geometrical constraints. Copyright © 2017 Elsevier Ltd. All rights reserved.

Model-based confirmation of alternative substrates of mitochondrial electron transport chain.

PubMed

Kleessen, Sabrina; Araújo, Wagner L; Fernie, Alisdair R; Nikoloski, Zoran

2012-03-30

Discrimination of metabolic models based on high throughput metabolomics data, reflecting various internal and external perturbations, is essential for identifying the components that contribute to the emerging behavior of metabolic processes. Here, we investigate 12 different models of the mitochondrial electron transport chain (ETC) in Arabidopsis thaliana during dark-induced senescence in order to elucidate the alternative substrates to this metabolic pathway. Our findings demonstrate that the coupling of the proposed computational approach, based on dynamic flux balance analysis, with time-resolved metabolomics data results in model-based confirmations of the hypotheses that, during dark-induced senescence in Arabidopsis, (i) under conditions where the main substrate for the ETC are not fully available, isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase are able to donate electrons to the ETC, (ii) phytanoyl-CoA does not act even as an indirect substrate of the electron transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex, and (iii) the mitochondrial γ-aminobutyric acid transporter has functional significance in maintaining mitochondrial metabolism. Our study provides a basic framework for future in silico studies of alternative pathways in mitochondrial metabolism under extended darkness whereby the role of its components can be computationally discriminated based on available molecular profile data.

Bayesian models based on test statistics for multiple hypothesis testing problems.

PubMed

Ji, Yuan; Lu, Yiling; Mills, Gordon B

2008-04-01

We propose a Bayesian method for the problem of multiple hypothesis testing that is routinely encountered in bioinformatics research, such as the differential gene expression analysis. Our algorithm is based on modeling the distributions of test statistics under both null and alternative hypotheses. We substantially reduce the complexity of the process of defining posterior model probabilities by modeling the test statistics directly instead of modeling the full data. Computationally, we apply a Bayesian FDR approach to control the number of rejections of null hypotheses. To check if our model assumptions for the test statistics are valid for various bioinformatics experiments, we also propose a simple graphical model-assessment tool. Using extensive simulations, we demonstrate the performance of our models and the utility of the model-assessment tool. In the end, we apply the proposed methodology to an siRNA screening and a gene expression experiment.

Towards self-learning based hypotheses generation in biomedical text domain.

PubMed

Gopalakrishnan, Vishrawas; Jha, Kishlay; Xun, Guangxu; Ngo, Hung Q; Zhang, Aidong

2018-06-15

The overwhelming amount of research articles in the domain of bio-medicine might cause important connections to remain unnoticed. Literature Based Discovery is a sub-field within biomedical text mining that peruses these articles to formulate high confident hypotheses on possible connections between medical concepts. Although many alternate methodologies have been proposed over the last decade, they still suffer from scalability issues. The primary reason, apart from the dense inter-connections between biological concepts, is the absence of information on the factors that lead to the edge-formation. In this work, we formulate this problem as a collaborative filtering task and leverage a relatively new concept of word-vectors to learn and mimic the implicit edge-formation process. Along with single-class classifier, we prune the search-space of redundant and irrelevant hypotheses to increase the efficiency of the system and at the same time maintaining and in some cases even boosting the overall accuracy. We show that our proposed framework is able to prune up to 90% of the hypotheses while still retaining high recall in top-K results. This level of efficiency enables the discovery algorithm to look for higher-order hypotheses, something that was infeasible until now. Furthermore, the generic formulation allows our approach to be agile to perform both open and closed discovery. We also experimentally validate that the core data-structures upon which the system bases its decision has a high concordance with the opinion of the experts.This coupled with the ability to understand the edge formation process provides us with interpretable results without any manual intervention. The relevant JAVA codes are available at: https://github.com/vishrawas/Medline-Code_v2. Supplementary data are available at Bioinformatics online.

Evolutionary origin and early biogeography of otophysan fishes (Ostariophysi: Teleostei).

PubMed

Chen, Wei-Jen; Lavoué, Sébastien; Mayden, Richard L

2013-08-01

The biogeography of the mega-diverse, freshwater, and globally distributed Otophysi has received considerable attention. This attraction largely stems from assumptions as to their ancient origin, the clade being almost exclusively freshwater, and their suitability as to explanations of trans-oceanic distributions. Despite multiple hypotheses explaining present-day distributions, problems remain, precluding more parsimonious explanations. Underlying previous hypotheses are alternative phylogenies for Otophysi, uncertainties as to temporal diversification and assumptions integral to various explanations. We reexamine the origin and early diversification of this clade based on a comprehensive time-calibrated, molecular-based phylogenetic analysis and event-based approaches for ancestral range inference of lineages. Our results do not corroborate current phylogenetic classifications of otophysans. We demonstrate Siluriformes are never sister to Gymnotiformes and Characiformes are most likely nonmonophyletic. Divergence time estimates specify a split between Cypriniformes and Characiphysi with the fragmentation of Pangea. The early diversification of characiphysans either predated, or was contemporary with, the separation of Africa and South America, and involved a combination of within- and between-continental divergence events for these lineages. The intercontinental diversification of siluroids and characoids postdated major intercontinental tectonic fragmentations (<90 Mya). Post-tectonic drift dispersal events are hypothesized to account for their current distribution patterns. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

The Importance of Proving the Null

PubMed Central

Gallistel, C. R.

2010-01-01

Null hypotheses are simple, precise, and theoretically important. Conventional statistical analysis cannot support them; Bayesian analysis can. The challenge in a Bayesian analysis is to formulate a suitably vague alternative, because the vaguer the alternative is (the more it spreads out the unit mass of prior probability), the more the null is favored. A general solution is a sensitivity analysis: Compute the odds for or against the null as a function of the limit(s) on the vagueness of the alternative. If the odds on the null approach 1 from above as the hypothesized maximum size of the possible effect approaches 0, then the data favor the null over any vaguer alternative to it. The simple computations and the intuitive graphic representation of the analysis are illustrated by the analysis of diverse examples from the current literature. They pose 3 common experimental questions: (a) Are 2 means the same? (b) Is performance at chance? (c) Are factors additive? PMID:19348549

Student Adjustment to Higher Education: The Role of Alternative Educational Pathways in Coping with the Demands of Student Life

ERIC Educational Resources Information Center

Shankland, Rebecca; Genolini, Christophe; Franca, Lionel Riou; Guelfi, Julien-Daniel; Ionescu, Serban

2010-01-01

The present longitudinal study measured student adjustment to higher education, comparing 50 participants from alternative schools (Steiner, Montessori, New Schools) with 80 students from the traditional school system. We hypothesized that students from alternative schools adapt better, because of greater perceived social support, academic…

Formulating appropriate statistical hypotheses for treatment comparison in clinical trial design and analysis.

PubMed

Huang, Peng; Ou, Ai-hua; Piantadosi, Steven; Tan, Ming

2014-11-01

We discuss the problem of properly defining treatment superiority through the specification of hypotheses in clinical trials. The need to precisely define the notion of superiority in a one-sided hypothesis test problem has been well recognized by many authors. Ideally designed null and alternative hypotheses should correspond to a partition of all possible scenarios of underlying true probability models P={P(ω):ω∈Ω} such that the alternative hypothesis Ha={P(ω):ω∈Ωa} can be inferred upon the rejection of null hypothesis Ho={P(ω):ω∈Ω(o)} However, in many cases, tests are carried out and recommendations are made without a precise definition of superiority or a specification of alternative hypothesis. Moreover, in some applications, the union of probability models specified by the chosen null and alternative hypothesis does not constitute a completed model collection P (i.e., H(o)∪H(a) is smaller than P). This not only imposes a strong non-validated assumption of the underlying true models, but also leads to different superiority claims depending on which test is used instead of scientific plausibility. Different ways to partition P fro testing treatment superiority often have different implications on sample size, power, and significance in both efficacy and comparative effectiveness trial design. Such differences are often overlooked. We provide a theoretical framework for evaluating the statistical properties of different specification of superiority in typical hypothesis testing. This can help investigators to select proper hypotheses for treatment comparison inclinical trial design. Copyright © 2014 Elsevier Inc. All rights reserved.

The effects of ambivalent fertility desires on pregnancy risk in young women in Michigan, United States

PubMed Central

Miller, Warren B.; Barber, Jennifer S.; Gatny, Heather H.

2012-01-01

Many different definitions of the construct of motivational ambivalence have appeared in the literature on reproductive health. Using a theoretical framework in which motivational ambivalence is defined as an interaction between positive and negative pregnancy desires, we propose two hypotheses. The first is that positive and negative pregnancy desires independently predict the risk of an unplanned pregnancy. The second is that ambivalence and three related constructs that are also based on the interaction between positive and negative desires are each important predictors of pregnancy risk. We use weekly journal data collected from a U.S. sample of 1,003 women aged 18–19 years and conduct hazard model analysis to test our hypotheses. Using both dummy and continuous predictors, we report results that confirm both hypotheses. The proposed interaction framework has demonstrated validity, compares favorably with previously reported alternative approaches, and incorporates a set of constructs that have potential importance for further research directed at the prevention of unplanned pregnancy. PMID:23234316

Personal, Role, Structural, Alternative and Affective Correlates of Organizational Commitment.

DTIC Science & Technology

1982-01-01

relationships (p. 79). Farrell and Rusbult (1981) seek to integrate the commitment literature through a model based on the social psychological exchange theory...permits testing a number of the components of the Farrell and Rusbult model . Hypotheses Drawing on the recent reviews and conceptual developments of... Climate Questionnalre (OCQ), (Porter et al., 1974) and the short version of the Job Diagnostic Survey (JDS), (Hackman and Oldham, 1975). The JDS scales

Alternatives to Goodman and Kruskal's Lambda.

ERIC Educational Resources Information Center

Stavig, Gordon R.

1979-01-01

Lambda and kappa coefficients of nominal scale association are developed for research hypotheses that involve predictions of modality, agreement, or some theoretically specified configuration. The proposed new coefficient is offered as an alternative to Goodman and Kruskal's lambda. (Author/CTM)

Thinking Evolutionarily About Obesity

PubMed Central

Genné-Bacon, Elizabeth A.

2014-01-01

Obesity, diabetes, and metabolic syndrome are growing worldwide health concerns, yet their causes are not fully understood. Research into the etiology of the obesity epidemic is highly influenced by our understanding of the evolutionary roots of metabolic control. For half a century, the thrifty gene hypothesis, which argues that obesity is an evolutionary adaptation for surviving periods of famine, has dominated the thinking on this topic. Obesity researchers are often not aware that there is, in fact, limited evidence to support the thrifty gene hypothesis and that alternative hypotheses have been suggested. This review presents evidence for and against the thrifty gene hypothesis and introduces readers to additional hypotheses for the evolutionary origins of the obesity epidemic. Because these alternate hypotheses imply significantly different strategies for research and clinical management of obesity, their consideration is critical to halting the spread of this epidemic. PMID:24910556

Consider the alternative: The effects of causal knowledge on representing and using alternative hypotheses in judgments under uncertainty.

PubMed

Hayes, Brett K; Hawkins, Guy E; Newell, Ben R

2016-05-01

Four experiments examined the locus of impact of causal knowledge on consideration of alternative hypotheses in judgments under uncertainty. Two possible loci were examined; overcoming neglect of the alternative when developing a representation of a judgment problem and improving utilization of statistics associated with the alternative hypothesis. In Experiment 1, participants could search for information about the various components of Bayes's rule in a diagnostic problem. A majority failed to spontaneously search for information about an alternative hypothesis, but this bias was reduced when a specific alternative hypothesis was mentioned before search. No change in search patterns was found when a generic alternative cause was mentioned. Experiments 2a and 2b broadly replicated these patterns when participants rated or made binary judgments about the relevance of each of the Bayesian components. In contrast, Experiment 3 showed that when participants were given the likelihood of the data given a focal hypothesis p(D|H) and an alternative hypothesis p(D|¬H), they gave estimates of p(H|D) that were consistent with Bayesian principles. Additional causal knowledge had relatively little impact on such judgments. These results show that causal knowledge primarily affects neglect of the alternative hypothesis at the initial stage of problem representation. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Bayesian networks for evaluation of evidence from forensic entomology.

PubMed

Andersson, M Gunnar; Sundström, Anders; Lindström, Anders

2013-09-01

In the aftermath of a CBRN incident, there is an urgent need to reconstruct events in order to bring the perpetrators to court and to take preventive actions for the future. The challenge is to discriminate, based on available information, between alternative scenarios. Forensic interpretation is used to evaluate to what extent results from the forensic investigation favor the prosecutors' or the defendants' arguments, using the framework of Bayesian hypothesis testing. Recently, several new scientific disciplines have been used in a forensic context. In the AniBioThreat project, the framework was applied to veterinary forensic pathology, tracing of pathogenic microorganisms, and forensic entomology. Forensic entomology is an important tool for estimating the postmortem interval in, for example, homicide investigations as a complement to more traditional methods. In this article we demonstrate the applicability of the Bayesian framework for evaluating entomological evidence in a forensic investigation through the analysis of a hypothetical scenario involving suspect movement of carcasses from a clandestine laboratory. Probabilities of different findings under the alternative hypotheses were estimated using a combination of statistical analysis of data, expert knowledge, and simulation, and entomological findings are used to update the beliefs about the prosecutors' and defendants' hypotheses and to calculate the value of evidence. The Bayesian framework proved useful for evaluating complex hypotheses using findings from several insect species, accounting for uncertainty about development rate, temperature, and precolonization. The applicability of the forensic statistic approach to evaluating forensic results from a CBRN incident is discussed.

Transformation based endorsement systems

NASA Technical Reports Server (NTRS)

Sudkamp, Thomas

1988-01-01

Evidential reasoning techniques classically represent support for a hypothesis by a numeric value or an evidential interval. The combination of support is performed by an arithmetic rule which often requires restrictions to be placed on the set of possibilities. These assumptions usually require the hypotheses to be exhausitive and mutually exclusive. Endorsement based classification systems represent support for the alternatives symbolically rather than numerically. A framework for constructing endorsement systems is presented in which transformations are defined to generate and update the knowledge base. The interaction of the knowledge base and transformations produces a non-monotonic reasoning system. Two endorsement based reasoning systems are presented to demonstrate the flexibility of the transformational approach for reasoning with ambiguous and inconsistent information.

Alternative Policy Instruments. CPRE Joint Note Series.

ERIC Educational Resources Information Center

McDonnell, Lorraine M.; Elmore, Richard F.

This publication builds a conceptual framework that categorizes alternative policy instruments for educational reform into actions. It defines four categories of policy instruments and hypothesizes how each will operate in addressing different policy problems in different political and organizational contexts. Subsequent research will assess…

Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain

PubMed Central

Kleessen, Sabrina; Araújo, Wagner L.; Fernie, Alisdair R.; Nikoloski, Zoran

2012-01-01

Discrimination of metabolic models based on high throughput metabolomics data, reflecting various internal and external perturbations, is essential for identifying the components that contribute to the emerging behavior of metabolic processes. Here, we investigate 12 different models of the mitochondrial electron transport chain (ETC) in Arabidopsis thaliana during dark-induced senescence in order to elucidate the alternative substrates to this metabolic pathway. Our findings demonstrate that the coupling of the proposed computational approach, based on dynamic flux balance analysis, with time-resolved metabolomics data results in model-based confirmations of the hypotheses that, during dark-induced senescence in Arabidopsis, (i) under conditions where the main substrate for the ETC are not fully available, isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase are able to donate electrons to the ETC, (ii) phytanoyl-CoA does not act even as an indirect substrate of the electron transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex, and (iii) the mitochondrial γ-aminobutyric acid transporter has functional significance in maintaining mitochondrial metabolism. Our study provides a basic framework for future in silico studies of alternative pathways in mitochondrial metabolism under extended darkness whereby the role of its components can be computationally discriminated based on available molecular profile data. PMID:22334689

Deficiency in the Opioid Hypotheses of Self-Injurious Behavior.

ERIC Educational Resources Information Center

King, Bryan H.; And Others

1991-01-01

This commentary critiques two papers by Curt Sandman, pointing out interpretive problems in models explaining self-injurious behavior in terms of opioids. Withdrawal effects are emphasized as an alternative to hypotheses asserting congenital opioid excess as a cause of sensory depression or an addiction to a relative excess of opioid activity in…

Elementary School Children's Ability to Distinguish Hypothetical Beliefs From Statements of Preference

ERIC Educational Resources Information Center

Diakidoy, Irene-Anna N.; Ioannides, Christos

2004-01-01

The authors examined students' understanding of hypotheses as beliefs that can be empirically verified. Thirty second graders and 30 sixth graders considered cases of disagreement about foods and colors that reflected either alternative hypotheses or different preferences. Their task was to decide whether the validity of each expressed belief…

Comparison of Alternate and Original Items on the Montreal Cognitive Assessment.

PubMed

Lebedeva, Elena; Huang, Mei; Koski, Lisa

2016-03-01

The Montreal Cognitive Assessment (MoCA) is a screening tool for mild cognitive impairment (MCI) in elderly individuals. We hypothesized that measurement error when using the new alternate MoCA versions to monitor change over time could be related to the use of items that are not of comparable difficulty to their corresponding originals of similar content. The objective of this study was to compare the difficulty of the alternate MoCA items to the original ones. Five selected items from alternate versions of the MoCA were included with items from the original MoCA administered adaptively to geriatric outpatients (N = 78). Rasch analysis was used to estimate the difficulty level of the items. None of the five items from the alternate versions matched the difficulty level of their corresponding original items. This study demonstrates the potential benefits of a Rasch analysis-based approach for selecting items during the process of development of parallel forms. The results suggest that better match of the items from different MoCA forms by their difficulty would result in higher sensitivity to changes in cognitive function over time.

The epistemological function of Hill's criteria.

PubMed

Bird, Alexander

2011-10-01

This article outlines an epistemological framework for understanding how Hill's criteria may aid us in establishing a causal hypothesis (A causes B) in an observational study. We consider Hill's criteria in turn with respect to their ability or otherwise to exclude alternative hypotheses (B causes A; there is a common cause of A and B; there is no causal connection between A and B). We may classify Hill's criteria according to which of the alternative hypotheses they are able to exclude, and also on the basis of whether they relate to (a) evidence from within observational study or (b) evidence independent of that study. It is noted that no criterion is able to exclude the common cause hypothesis in a systematic way. Observational studies are typically weaker than experimental studies, since the latter can systematically exclude competing hypotheses, whereas observational studies lack a systematic way of ruling out the common cause hypothesis. Copyright © 2011 Elsevier Inc. All rights reserved.

Life history of the most complete fossil primate skeleton: exploring growth models for Darwinius

PubMed Central

López-Torres, Sergi; Schillaci, Michael A.; Silcox, Mary T.

2015-01-01

Darwinius is an adapoid primate from the Eocene of Germany, and its only known specimen represents the most complete fossil primate ever found. Its describers hypothesized a close relationship to Anthropoidea, and using a Saimiri model estimated its age at death. This study reconstructs the ancestral permanent dental eruption sequences for basal Euprimates, Haplorhini, Anthropoidea, and stem and crown Strepsirrhini. The results show that the ancestral sequences for the basal euprimate, haplorhine and stem strepsirrhine are identical, and similar to that of Darwinius. However, Darwinius differs from anthropoids by exhibiting early development of the lower third molars relative to the lower third and fourth premolars. The eruption of the lower second premolar marks the point of interruption of the sequence in Darwinius. The anthropoid Saimiri as a model is therefore problematic because it exhibits a delayed eruption of P2. Here, an alternative strepsirrhine model based on Eulemur and Varecia is presented. Our proposed model shows an older age at death than previously suggested (1.05–1.14 years), while the range for adult weight is entirely below the range proposed previously. This alternative model is more consistent with hypotheses supporting a stronger relationship between adapoids and strepsirrhines. PMID:26473056

Energy, economic growth, and equity in the United States

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

Kannan, N.P.

1979-01-01

Decades of economic growth in the United States, although improving the lot of many, have failed to solve the problem of poverty. Islands of acute poverty persist amidst affluence even today, invalidating the conventional wisdom that a growing economy lifts everyone. For better or for worse, economic growth has been mainly dependent upon energy to solve the problem of poverty, and the insidious energy crisis that confronts us today threatens this economic growth and the dream of an equitable society. For this reason it is important to consider all the potential consequences of energy policies that are designed to helpmore » achieve energy self-sufficiency. In this study alternate energy policies are identified and compared for their relative degrees of potential trade-offs. The evaluation of the policies is carried out with the aid of two computer simulation models, ECONOMY1 and FOSSIL1, which are designed to capture the interactions between the energy sector and the rest of the economy of the United States. The study proposes an alternate set of hypotheses that emphasize the dynamics of social conflict over the distributive shares in the economy. The ECONOMY1 model is based on these hypotheses. 103 references, 79 figures, 16 tables.« less

The importance of proving the null.

PubMed

Gallistel, C R

2009-04-01

Null hypotheses are simple, precise, and theoretically important. Conventional statistical analysis cannot support them; Bayesian analysis can. The challenge in a Bayesian analysis is to formulate a suitably vague alternative, because the vaguer the alternative is (the more it spreads out the unit mass of prior probability), the more the null is favored. A general solution is a sensitivity analysis: Compute the odds for or against the null as a function of the limit(s) on the vagueness of the alternative. If the odds on the null approach 1 from above as the hypothesized maximum size of the possible effect approaches 0, then the data favor the null over any vaguer alternative to it. The simple computations and the intuitive graphic representation of the analysis are illustrated by the analysis of diverse examples from the current literature. They pose 3 common experimental questions: (a) Are 2 means the same? (b) Is performance at chance? (c) Are factors additive? (c) 2009 APA, all rights reserved

On selecting evidence to test hypotheses: A theory of selection tasks.

PubMed

Ragni, Marco; Kola, Ilir; Johnson-Laird, Philip N

2018-05-21

How individuals choose evidence to test hypotheses is a long-standing puzzle. According to an algorithmic theory that we present, it is based on dual processes: individuals' intuitions depending on mental models of the hypothesis yield selections of evidence matching instances of the hypothesis, but their deliberations yield selections of potential counterexamples to the hypothesis. The results of 228 experiments using Wason's selection task corroborated the theory's predictions. Participants made dependent choices of items of evidence: the selections in 99 experiments were significantly more redundant (using Shannon's measure) than those of 10,000 simulations of each experiment based on independent selections. Participants tended to select evidence corresponding to instances of hypotheses, or to its counterexamples, or to both. Given certain contents, instructions, or framings of the task, they were more likely to select potential counterexamples to the hypothesis. When participants received feedback about their selections in the "repeated" selection task, they switched from selections of instances of the hypothesis to selection of potential counterexamples. These results eliminated most of the 15 alternative theories of selecting evidence. In a meta-analysis, the model theory yielded a better fit of the results of 228 experiments than the one remaining theory based on reasoning rather than meaning. We discuss the implications of the model theory for hypothesis testing and for a well-known paradox of confirmation. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Challenges Facing Evidence-Based Prevention: Incorporating an Abductive Theory of Method.

PubMed

Mason, W Alex; Cogua-Lopez, Jasney; Fleming, Charles B; Scheier, Lawrence M

2018-06-01

Current systems used to determine whether prevention programs are "evidence-based" rely on the logic of deductive reasoning. This reliance has fostered implementation of strategies with explicitly stated evaluation criteria used to gauge program validity and suitability for dissemination. Frequently, investigators resort to the randomized controlled trial (RCT) combined with null hypothesis significance testing (NHST) as a means to rule out competing hypotheses and determine whether an intervention works. The RCT design has achieved success across numerous disciplines but is not without limitations. We outline several issues that question allegiance to the RCT, NHST, and the hypothetico-deductive method of scientific inquiry. We also discuss three challenges to the status of program evaluation including reproducibility, generalizability, and credibility of findings. As an alternative, we posit that extending current program evaluation criteria with principles drawn from an abductive theory of method (ATOM) can strengthen our ability to address these challenges and advance studies of drug prevention. Abductive reasoning involves working from observed phenomena to the generation of alternative explanations for the phenomena and comparing the alternatives to select the best possible explanation. We conclude that an ATOM can help increase the influence and impact of evidence-based prevention for population benefit.

Towards a Lakatosian Analysis of the Piagetian and Alternative Conceptions Research Programs.

ERIC Educational Resources Information Center

Gilbert, John K.; Swift, David J.

1985-01-01

Lakatos's methodology of scientific research programs is summarized and discussed for Piagetian schools and alternative conceptions movement. Commonalities/differences between these two rival programs are presented along with fundamental assumptions, auxiliary hypotheses, and research policy. Suggests that research findings should not be merely…

Species trees for the tree swallows (Genus Tachycineta): an alternative phylogenetic hypothesis to the mitochondrial gene tree.

PubMed

Dor, Roi; Carling, Matthew D; Lovette, Irby J; Sheldon, Frederick H; Winkler, David W

2012-10-01

The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group. Copyright © 2012 Elsevier Inc. All rights reserved.

F-actin-based Ca signaling-a critical comparison with the current concept of Ca signaling.

PubMed

Lange, Klaus; Gartzke, Joachim

2006-11-01

A short comparative survey on the current idea of Ca signaling and the alternative concept of F-actin-based Ca signaling is given. The two hypotheses differ in one central aspect, the mechanism of Ca storage. The current theory rests on the assumption of Ca-accumulating endoplasmic/sarcoplasmic reticulum-derived vesicles equipped with an ATP-dependent Ca pump and IP3- or ryanodine-sensitive channel-receptors for Ca-release. The alternative hypothesis proceeds from the idea of Ca storage at the high-affinity binding sites of actin filaments. Cellular sites of F-actin-based Ca storage are microvilli and the submembrane cytoskeleton. Several specific features of Ca signaling such as store-channel coupling, quantal Ca release, spiking and oscillations, biphasic and "phasic" uptake kinetics, and Ca-induced Ca release (CICR), which are not adequately described by the current concept, are inherent properties of the F-actin system and its dynamic state of treadmilling. Copyright 2006 Wiley-Liss, Inc.

Differentiation without distancing. explaining bi-polarization of opinions without negative influence.

PubMed

Mäs, Michael; Flache, Andreas

2013-01-01

Explanations of opinion bi-polarization hinge on the assumption of negative influence, individuals' striving to amplify differences to disliked others. However, empirical evidence for negative influence is inconclusive, which motivated us to search for an alternative explanation. Here, we demonstrate that bi-polarization can be explained without negative influence, drawing on theories that emphasize the communication of arguments as central mechanism of influence. Due to homophily, actors interact mainly with others whose arguments will intensify existing tendencies for or against the issue at stake. We develop an agent-based model of this theory and compare its implications to those of existing social-influence models, deriving testable hypotheses about the conditions of bi-polarization. Hypotheses were tested with a group-discussion experiment (N = 96). Results demonstrate that argument exchange can entail bi-polarization even when there is no negative influence.

The Importance of Proving the Null

ERIC Educational Resources Information Center

Gallistel, C. R.

2009-01-01

Null hypotheses are simple, precise, and theoretically important. Conventional statistical analysis cannot support them; Bayesian analysis can. The challenge in a Bayesian analysis is to formulate a suitably vague alternative, because the vaguer the alternative is (the more it spreads out the unit mass of prior probability), the more the null is…

Neural basis of major depressive disorder: Beyond monoamine hypothesis.

PubMed

Boku, Shuken; Nakagawa, Shin; Toda, Hiroyuki; Hishimoto, Akitoyo

2018-01-01

The monoamine hypothesis has been accepted as the most common hypothesis of major depressive disorder (MDD) for a long period because of its simplicity and understandability. Actually, most currently used antidepressants have been considered to act based on the monoamine hypothesis. However, an important problem of the monoamine hypothesis has been pointed out as follows: it fails to explain the latency of response to antidepressants. In addition, many patients with MDD have remained refractory to currently used antidepressants. Therefore, monoamine-alternate hypotheses are required to explain the latency of response to antidepressants. Such hypotheses have been expected to contribute to identifying hopeful new therapeutic targets for MDD. Past studies have revealed that the volume of the hippocampus is decreased in patients with MDD, which is likely caused by the failure of the hypothalamic-pituitary-adrenal axis and following elevation of glucocorticoids. Two hypotheses have been proposed to explain the volume of the hippocampus: (i) the neuroplasticity hypothesis; and (ii) the neurogenesis hypothesis. The neuroplasticity hypothesis explains how the hippocampal volume is decreased by the morphological changes of hippocampal neurons, such as the shortening length of dendrites and the decreased number and density of spines. The neurogenesis hypothesis explains how the hippocampal volume is decreased by the decrease of neurogenesis in the hippocampal dentate gyrus. These hypotheses are able to explain the latency of response to antidepressants. In this review, we first overview how the neuroplasticity and neurogenesis hypotheses have been developed. We then describe the details of these hypotheses. © 2017 The Authors. Psychiatry and Clinical Neurosciences © 2017 Japanese Society of Psychiatry and Neurology.

A more powerful test based on ratio distribution for retention noninferiority hypothesis.

PubMed

Deng, Ling; Chen, Gang

2013-03-11

Rothmann et al. ( 2003 ) proposed a method for the statistical inference of fraction retention noninferiority (NI) hypothesis. A fraction retention hypothesis is defined as a ratio of the new treatment effect verse the control effect in the context of a time to event endpoint. One of the major concerns using this method in the design of an NI trial is that with a limited sample size, the power of the study is usually very low. This makes an NI trial not applicable particularly when using time to event endpoint. To improve power, Wang et al. ( 2006 ) proposed a ratio test based on asymptotic normality theory. Under a strong assumption (equal variance of the NI test statistic under null and alternative hypotheses), the sample size using Wang's test was much smaller than that using Rothmann's test. However, in practice, the assumption of equal variance is generally questionable for an NI trial design. This assumption is removed in the ratio test proposed in this article, which is derived directly from a Cauchy-like ratio distribution. In addition, using this method, the fundamental assumption used in Rothmann's test, that the observed control effect is always positive, that is, the observed hazard ratio for placebo over the control is greater than 1, is no longer necessary. Without assuming equal variance under null and alternative hypotheses, the sample size required for an NI trial can be significantly reduced if using the proposed ratio test for a fraction retention NI hypothesis.

La Grippe and World War I: conflict participation and pandemic confrontation.

PubMed

Steele, B J; Collins, C D

2009-01-01

This paper assesses whether a nation-state's participation in conflict influences its ability to confront global pandemic or disease. Two alternative hypotheses are proposed. First, increased levels of conflict participation lead to increased abilities of states to confront pandemics. A second and alternative hypothesis is that increased conflict participation decreases the ability of states to confront pandemics. The hypotheses are tested through the ultimate case of war and pandemic: the 1918 Influenza pandemic (Spanish Flu or 'La Grippe') that killed 20-100 million people worldwide. Using simple correlation and case illustrations, we test these hypotheses with special focus upon the ability of the participant countries to confront the pandemic. The findings suggest, in a limited and varied fashion, that while neutral countries enjoyed the lowest levels of pandemic deaths, of the participant countries greater levels of conflict participation correlate with lower levels of pandemic deaths. The paper concludes with some propositions regarding the relationship between the current 'war on terror' and prospective pandemics such as avian flu.

Psychosocial job factors and biological cardiovascular risk factors in Mexican workers.

PubMed

Garcia-Rojas, Isabel Judith; Choi, BongKyoo; Krause, Niklas

2015-03-01

Psychosocial job factors (PJF) have been implicated in the development of cardiovascular disease. The paucity of data from developing economies including Mexico hampers the development of worksite intervention efforts in those regions. This cross-sectional study of 2,330 Mexican workers assessed PJF (job strain [JS], social support [SS], and job insecurity [JI]) and biological cardiovascular disease risk factors [CVDRF] by questionnaire and on-site physical examinations. Alternative formulations of the JS scales were developed based on factor analysis and literature review. Associations between both traditional and alternative job factor scales with CVDRF were examined in multiple regression models, adjusting for physical workload, and socio-demographic factors. Alternative formulations of the job demand and control scales resulted in substantial changes in effect sizes or statistical significance when compared with the original scales. JS and JI showed hypothesized associations with most CVDRF, but they were inversely associated with diastolic blood pressure and some adiposity measures. SS was mainly protective against CVDRF. Among Mexican workers, alternative PJF scales predicted health outcomes better than traditional scales, and psychosocial stressors were associated with most CVDRF. © 2015 Wiley Periodicals, Inc.

Assessment of student learning associated with tree thinking in an undergraduate introductory organismal biology course.

PubMed

Smith, James J; Cheruvelil, Kendra Spence; Auvenshine, Stacie

2013-01-01

Phylogenetic trees provide visual representations of ancestor-descendant relationships, a core concept of evolutionary theory. We introduced "tree thinking" into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted of designing and implementing a set of experiences to help students learn to read, interpret, and manipulate phylogenetic trees, with a particular emphasis on using data to evaluate alternative phylogenetic hypotheses (trees). To assess the outcomes of these learning experiences, we designed and implemented a Phylogeny Assessment Tool (PhAT), an open-ended response instrument that asked students to: 1) map characters on phylogenetic trees; 2) apply an objective criterion to decide which of two trees (alternative hypotheses) is "better"; and 3) demonstrate understanding of phylogenetic trees as depictions of ancestor-descendant relationships. A pre-post test design was used with the PhAT to collect data from students in two consecutive Fall semesters. Students in both semesters made significant gains in their abilities to map characters onto phylogenetic trees and to choose between two alternative hypotheses of relationship (trees) by applying the principle of parsimony (Occam's razor). However, learning gains were much lower in the area of student interpretation of phylogenetic trees as representations of ancestor-descendant relationships.

Assessment of Student Learning Associated with Tree Thinking in an Undergraduate Introductory Organismal Biology Course

PubMed Central

Smith, James J.; Cheruvelil, Kendra Spence; Auvenshine, Stacie

2013-01-01

Phylogenetic trees provide visual representations of ancestor–descendant relationships, a core concept of evolutionary theory. We introduced “tree thinking” into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted of designing and implementing a set of experiences to help students learn to read, interpret, and manipulate phylogenetic trees, with a particular emphasis on using data to evaluate alternative phylogenetic hypotheses (trees). To assess the outcomes of these learning experiences, we designed and implemented a Phylogeny Assessment Tool (PhAT), an open-ended response instrument that asked students to: 1) map characters on phylogenetic trees; 2) apply an objective criterion to decide which of two trees (alternative hypotheses) is “better”; and 3) demonstrate understanding of phylogenetic trees as depictions of ancestor–descendant relationships. A pre–post test design was used with the PhAT to collect data from students in two consecutive Fall semesters. Students in both semesters made significant gains in their abilities to map characters onto phylogenetic trees and to choose between two alternative hypotheses of relationship (trees) by applying the principle of parsimony (Occam's razor). However, learning gains were much lower in the area of student interpretation of phylogenetic trees as representations of ancestor–descendant relationships. PMID:24006401

Comparison of Alternate and Original Items on the Montreal Cognitive Assessment

PubMed Central

Lebedeva, Elena; Huang, Mei; Koski, Lisa

2016-01-01

Background The Montreal Cognitive Assessment (MoCA) is a screening tool for mild cognitive impairment (MCI) in elderly individuals. We hypothesized that measurement error when using the new alternate MoCA versions to monitor change over time could be related to the use of items that are not of comparable difficulty to their corresponding originals of similar content. The objective of this study was to compare the difficulty of the alternate MoCA items to the original ones. Methods Five selected items from alternate versions of the MoCA were included with items from the original MoCA administered adaptively to geriatric outpatients (N = 78). Rasch analysis was used to estimate the difficulty level of the items. Results None of the five items from the alternate versions matched the difficulty level of their corresponding original items. Conclusions This study demonstrates the potential benefits of a Rasch analysis-based approach for selecting items during the process of development of parallel forms. The results suggest that better match of the items from different MoCA forms by their difficulty would result in higher sensitivity to changes in cognitive function over time. PMID:27076861

The role of propriospinal neuronal network in transmitting the alternating muscular activities of flexor and extensor in parkinsonian tremor.

PubMed

Hao, M; He, X; Lan, N

2012-01-01

It has been shown that normal cyclic movement of human arm and resting limb tremor in Parkinson's disease (PD) are associated with the oscillatory neuronal activities in different cerebral networks, which are transmitted to the antagonistic muscles via the same spinal pathway. There are mono-synaptic and multi-synaptic corticospinal pathways for conveying motor commands. This study investigates the plausible role of propriospinal neuronal (PN) network in the C3-C4 levels in multi-synaptic transmission of cortical commands for oscillatory movements. A PN network model is constructed based on known neurophysiological connections, and is hypothesized to achieve the conversion of cortical oscillations into alternating antagonistic muscle bursts. Simulations performed with a virtual arm (VA) model indicate that without the PN network, the alternating bursts of antagonistic muscle EMG could not be reliably generated, whereas with the PN network, the alternating pattern of bursts were naturally displayed in the three pairs of antagonist muscles. Thus, it is suggested that oscillations in the primary motor cortex (M1) of single and double tremor frequencies are processed at the PN network to compute the alternating burst pattern in the flexor and extensor muscles.

Classification image analysis: estimation and statistical inference for two-alternative forced-choice experiments

NASA Technical Reports Server (NTRS)

Abbey, Craig K.; Eckstein, Miguel P.

2002-01-01

We consider estimation and statistical hypothesis testing on classification images obtained from the two-alternative forced-choice experimental paradigm. We begin with a probabilistic model of task performance for simple forced-choice detection and discrimination tasks. Particular attention is paid to general linear filter models because these models lead to a direct interpretation of the classification image as an estimate of the filter weights. We then describe an estimation procedure for obtaining classification images from observer data. A number of statistical tests are presented for testing various hypotheses from classification images based on some more compact set of features derived from them. As an example of how the methods we describe can be used, we present a case study investigating detection of a Gaussian bump profile.

An Alternative Study of Transfer of Learning in Clinical Evaluation.

ERIC Educational Resources Information Center

Patel, Vimla; Cranton, Patricia A.

The use of an alternative methodology to study transfer of learning in clinical instruction during medical school was investigated. The environment in which clinical instruction takes place was examined, after which hypotheses were proposed and tested in a quasi-experimental design. The first phase of the study, an ethnographic analysis of the…

Relationship between mediation analysis and the structured life course approach

PubMed Central

Howe, Laura D; Smith, Andrew D; Macdonald-Wallis, Corrie; Anderson, Emma L; Galobardes, Bruna; Lawlor, Debbie A; Ben-Shlomo, Yoav; Hardy, Rebecca; Cooper, Rachel; Tilling, Kate; Fraser, Abigail

2016-01-01

Abstract Many questions in life course epidemiology involve mediation and/or interaction because of the long latency period between exposures and outcomes. In this paper, we explore how mediation analysis (based on counterfactual theory and implemented using conventional regression approaches) links with a structured approach to selecting life course hypotheses. Using theory and simulated data, we show how the alternative life course hypotheses assessed in the structured life course approach correspond to different combinations of mediation and interaction parameters. For example, an early life critical period model corresponds to a direct effect of the early life exposure, but no indirect effect via the mediator and no interaction between the early life exposure and the mediator. We also compare these methods using an illustrative real-data example using data on parental occupational social class (early life exposure), own adult occupational social class (mediator) and physical capability (outcome). PMID:27681097

Differentiation without Distancing. Explaining Bi-Polarization of Opinions without Negative Influence

PubMed Central

Mäs, Michael; Flache, Andreas

2013-01-01

Explanations of opinion bi-polarization hinge on the assumption of negative influence, individuals’ striving to amplify differences to disliked others. However, empirical evidence for negative influence is inconclusive, which motivated us to search for an alternative explanation. Here, we demonstrate that bi-polarization can be explained without negative influence, drawing on theories that emphasize the communication of arguments as central mechanism of influence. Due to homophily, actors interact mainly with others whose arguments will intensify existing tendencies for or against the issue at stake. We develop an agent-based model of this theory and compare its implications to those of existing social-influence models, deriving testable hypotheses about the conditions of bi-polarization. Hypotheses were tested with a group-discussion experiment (N = 96). Results demonstrate that argument exchange can entail bi-polarization even when there is no negative influence. PMID:24312164

Organizational culture and organizational effectiveness: a meta-analytic investigation of the competing values framework's theoretical suppositions.

PubMed

Hartnell, Chad A; Ou, Amy Yi; Kinicki, Angelo

2011-07-01

We apply Quinn and Rohrbaugh's (1983) competing values framework (CVF) as an organizing taxonomy to meta-analytically test hypotheses about the relationship between 3 culture types and 3 major indices of organizational effectiveness (employee attitudes, operational performance [i.e., innovation and product and service quality], and financial performance). The paper also tests theoretical suppositions undergirding the CVF by investigating the framework's nomological validity and proposed internal structure (i.e., interrelationships among culture types). Results based on data from 84 empirical studies with 94 independent samples indicate that clan, adhocracy, and market cultures are differentially and positively associated with the effectiveness criteria, though not always as hypothesized. The findings provide mixed support for the CVF's nomological validity and fail to support aspects of the CVF's proposed internal structure. We propose an alternative theoretical approach to the CVF and delineate directions for future research.

Fourier power, subjective distance, and object categories all provide plausible models of BOLD responses in scene-selective visual areas

PubMed Central

Lescroart, Mark D.; Stansbury, Dustin E.; Gallant, Jack L.

2015-01-01

Perception of natural visual scenes activates several functional areas in the human brain, including the Parahippocampal Place Area (PPA), Retrosplenial Complex (RSC), and the Occipital Place Area (OPA). It is currently unclear what specific scene-related features are represented in these areas. Previous studies have suggested that PPA, RSC, and/or OPA might represent at least three qualitatively different classes of features: (1) 2D features related to Fourier power; (2) 3D spatial features such as the distance to objects in a scene; or (3) abstract features such as the categories of objects in a scene. To determine which of these hypotheses best describes the visual representation in scene-selective areas, we applied voxel-wise modeling (VM) to BOLD fMRI responses elicited by a set of 1386 images of natural scenes. VM provides an efficient method for testing competing hypotheses by comparing predictions of brain activity based on encoding models that instantiate each hypothesis. Here we evaluated three different encoding models that instantiate each of the three hypotheses listed above. We used linear regression to fit each encoding model to the fMRI data recorded from each voxel, and we evaluated each fit model by estimating the amount of variance it predicted in a withheld portion of the data set. We found that voxel-wise models based on Fourier power or the subjective distance to objects in each scene predicted much of the variance predicted by a model based on object categories. Furthermore, the response variance explained by these three models is largely shared, and the individual models explain little unique variance in responses. Based on an evaluation of previous studies and the data we present here, we conclude that there is currently no good basis to favor any one of the three alternative hypotheses about visual representation in scene-selective areas. We offer suggestions for further studies that may help resolve this issue. PMID:26594164

A systems approach to the physiology of weightlessness

NASA Technical Reports Server (NTRS)

White, Ronald J.; Leonard, Joel I.; Rummel, John A.; Leach, Carolyn S.

1991-01-01

A general systems approach to conducting and analyzing research on the human adaptation to weightlessness is presented. The research is aimed at clarifying the role that each of the major components of the human system plays following the transition to and from space. The approach utilizes a variety of mathematical models in order to pose and test alternative hypotheses concerned with the adaptation process. Certain aspects of the problem of fluid and electrolyte shifts in weightlessnes are considered, and an integrated hypothesis based on numerical simulation studies and experimental data is presented.

Testing Alternative Hypotheses Regarding the Association Between Behavioral Inhibition and Language Development in Toddlerhood

PubMed Central

Watts, Ashley K. Smith; Patel, Deepika; Corley, Robin P.; Friedman, Naomi P.; Hewitt, John K.; Robinson, JoAnn L.; Rhee, Soo H.

2014-01-01

Studies have reported an inverse association between language development and behavioral inhibition or shyness across childhood, but the direction of this association is unclear. The present study tested alternative hypotheses regarding this association in a large sample of toddlers. Data on behavioral inhibition and expressive and receptive language abilities were collected from 816 twins at ages 14, 20, and 24 months. Growth and regression models were fit to the data to assess the longitudinal associations between behavioral inhibition and language development from 14 to 24 months. Overall, there were significant associations between behavioral inhibition and expressive language, and minimal associations with receptive language, indicating that the association is better explained by reticence to respond rather than deficient language development. PMID:24499266

Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks.

PubMed

Rumschinski, Philipp; Borchers, Steffen; Bosio, Sandro; Weismantel, Robert; Findeisen, Rolf

2010-05-25

Mathematical modeling and analysis have become, for the study of biological and cellular processes, an important complement to experimental research. However, the structural and quantitative knowledge available for such processes is frequently limited, and measurements are often subject to inherent and possibly large uncertainties. This results in competing model hypotheses, whose kinetic parameters may not be experimentally determinable. Discriminating among these alternatives and estimating their kinetic parameters is crucial to improve the understanding of the considered process, and to benefit from the analytical tools at hand. In this work we present a set-based framework that allows to discriminate between competing model hypotheses and to provide guaranteed outer estimates on the model parameters that are consistent with the (possibly sparse and uncertain) experimental measurements. This is obtained by means of exact proofs of model invalidity that exploit the polynomial/rational structure of biochemical reaction networks, and by making use of an efficient strategy to balance solution accuracy and computational effort. The practicability of our approach is illustrated with two case studies. The first study shows that our approach allows to conclusively rule out wrong model hypotheses. The second study focuses on parameter estimation, and shows that the proposed method allows to evaluate the global influence of measurement sparsity, uncertainty, and prior knowledge on the parameter estimates. This can help in designing further experiments leading to improved parameter estimates.

Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks

PubMed Central

2010-01-01

Background Mathematical modeling and analysis have become, for the study of biological and cellular processes, an important complement to experimental research. However, the structural and quantitative knowledge available for such processes is frequently limited, and measurements are often subject to inherent and possibly large uncertainties. This results in competing model hypotheses, whose kinetic parameters may not be experimentally determinable. Discriminating among these alternatives and estimating their kinetic parameters is crucial to improve the understanding of the considered process, and to benefit from the analytical tools at hand. Results In this work we present a set-based framework that allows to discriminate between competing model hypotheses and to provide guaranteed outer estimates on the model parameters that are consistent with the (possibly sparse and uncertain) experimental measurements. This is obtained by means of exact proofs of model invalidity that exploit the polynomial/rational structure of biochemical reaction networks, and by making use of an efficient strategy to balance solution accuracy and computational effort. Conclusions The practicability of our approach is illustrated with two case studies. The first study shows that our approach allows to conclusively rule out wrong model hypotheses. The second study focuses on parameter estimation, and shows that the proposed method allows to evaluate the global influence of measurement sparsity, uncertainty, and prior knowledge on the parameter estimates. This can help in designing further experiments leading to improved parameter estimates. PMID:20500862

A Lakatosian Conceptual Change Teaching Strategy Based on Student Ability to Build Models with Varying Degrees of Conceptual Understanding of Chemical Equilibrium

NASA Astrophysics Data System (ADS)

Niaz, M.

The main objective of this study is to construct a Lakatosian teaching strategy that can facilitate conceptual change in students'' understanding of chemical equilibrium. The strategy is based on the premise that cognitive conflicts must have been engendered by the students themselves in trying to cope with different problem solving strategies. Results obtained (based on Venezuelan freshman students) show that the performance of the experimental group of students was generally better (especially on the immediate post tests) than that of the control group. It is concluded that a conceptual change teaching strategy must take into consideration the following aspects: a) core beliefs of the students in the topic (cf. ''hard core'', Lakatos 1970); b) exploration of the relationship between core beliefs and student alternative conceptions (misconceptions); c) cognitive complexity of the core belief can be broken down into a series of related and probing questions; d) students resist changes in their core beliefs by postulating ''auxiliary hypotheses'' in order to resolve their contradictions; e) students'' responses based on their alternative conceptions must be considered not as wrong, but rather as models, perhaps in the same sense as used by scientists to break the complexity of a problem; and f) students'' misconceptions be considered as alternative conceptions (theories) that compete with the present scientific theories and at times recapitulate theories scientists held in the past.

Cognitive influences on risk-seeking by rhesus macaques

PubMed Central

Hayden, Benjamin Y.; Heilbronner, Sarah R.; Nair, Amrita C.; Platt, Michael L.

2009-01-01

Humans and other animals are idiosyncratically sensitive to risk, either preferring or avoiding options having the same value but differing in uncertainty. Many explanations for risk sensitivity rely on the non-linear shape of a hypothesized utility curve. Because such models do not place any importance on uncertainty per se, utility curve-based accounts predict indifference between risky and riskless options that offer the same distribution of rewards. Here we show that monkeys strongly prefer uncertain gambles to alternating rewards with the same payoffs, demonstrating that uncertainty itself contributes to the appeal of risky options. Based on prior observations, we hypothesized that the appeal of the risky option is enhanced by the salience of the potential jackpot. To test this, we subtly manipulated payoffs in a second gambling task. We found that monkeys are more sensitive to small changes in the size of the large reward than to equivalent changes in the size of the small reward, indicating that they attend preferentially to the jackpots. Together, these results challenge utility curve-based accounts of risk sensitivity, and suggest that psychological factors, such as outcome salience and uncertainty itself, contribute to risky decision-making. PMID:19844596

An Alternative Evaluation: Online Puzzle as a Course-End Activity

ERIC Educational Resources Information Center

Genç, Zülfü; Aydemir, Emrah

2015-01-01

Purpose: The purpose of this study is to determine whether the use of online puzzles in the instructional process has an effect on student achievement and learning retention. This study examined students ' perception and experiences on use of puzzle as an alternative evaluation tool. To achieve this aim, the following hypotheses were tested: using…

A study of drop-off recycling in Norman, Oklahoma: Behavior of recyclers and nonrecyclers

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

Sims, J.L.; Everett, J.W.

The reality of growing negative public opinion to new landfills prompted a newfound popularity for recycling programs as an alternative to traditional waste management in municipalities. The purpose of this research is to examine the behavioral and attitudinal differences between recyclers and nonrecyclers. These differences were tested statistically based on recycling behavior data gathered through two independent questionnaire surveys, one administered through utility bill statements, the other administered directly by the first author. Data were collected on: contact with the recycling organization, demographics, participation, convenience, incentives, ideological agreement, and assessment rationale. Seven hypotheses were tested, addressing most aspects of themore » Environmental Collective Action model (ECA), first proposed by the second author in 1994. The surveys were administered to City of Norman, Oklahoma residents. Norman operates several drop-off centers within the city limits. The results of the analysis indicate that individuals do make the decision to participate based on the principles outlined in the model of participation. All seven hypotheses are supported by the data in both surveys.« less

Terrestrial N Cycling And C Storage: Some Insights From A Process-based Land Surface Model

NASA Astrophysics Data System (ADS)

Zaehle, S.; Friend, A. D.; Friedlingstein, P.

2008-12-01

We present results of a new land surface model, O-CN, which includes a process-based coupling between the terrestrial cycling of energy, water, carbon, and nitrogen. The model represents the controls of the terrestrial nitrogen (N) cycling on carbon (C) pools and fluxes through photosynthesis, respiration, changes in allocation, and soil organic matter decomposition, and explicitly accounts for N leaching and gaseous losses. O-CN has been shown to give realistic results in comparison to observations at a wide range of scales, including in situ flux measurements, productivity databases, and atmospheric CO2 concentration data. O-CN is run for three free air carbon dioxide enrichment (FACE) sites (Duke, Oak Ridge, Aspen), and reproduces observed magnitudes of changes in net primary productivity, foliage area and foliage N content. Several alternative hypotheses concerning the control of N on vegetation growth and decomposition, including effects of diluting foliage N concentrations, down-regulation of photosynthesis and respiration, acclimation of C allocation patterns and biological N fixation, are tested with respect to their effect on long- term C sequestration estimate. Differences in initial N availability, small transient changes in N inputs and the assumed plasticity of C:N stoichiometry can lead to substantial differences in the simulated long-term changes in productivity and C sequestration. We discuss the capacity of observations obtained at FACE sites to evaluate these alternative hypotheses, and investigate implications of a transient versus instantaneous increase in atmospheric carbon dioxide for the magnitude of the simulated limiting effect of N on C cycling. Finally, we re-examine earlier model-based assessments of the terrestrial C sequestration potential using a global transient O-CN simulation driven by increases in atmospheric CO2, N deposition and climatic changes over the 21st century.

The levels of analysis revisited

PubMed Central

MacDougall-Shackleton, Scott A.

2011-01-01

The term levels of analysis has been used in several ways: to distinguish between ultimate and proximate levels, to categorize different kinds of research questions and to differentiate levels of reductionism. Because questions regarding ultimate function and proximate mechanisms are logically distinct, I suggest that distinguishing between these two levels is the best use of the term. Integrating across levels in research has potential risks, but many benefits. Consideration at one level can help generate novel hypotheses at the other, define categories of behaviour and set criteria that must be addressed. Taking an adaptationist stance thus strengthens research on proximate mechanisms. Similarly, it is critical for researchers studying adaptation and function to have detailed knowledge of proximate mechanisms that may constrain or modulate evolutionary processes. Despite the benefits of integrating across ultimate and proximate levels, failure to clearly identify levels of analysis, and whether or not hypotheses are exclusive alternatives, can create false debates. Such non-alternative hypotheses may occur between or within levels, and are not limited to integrative approaches. In this review, I survey different uses of the term levels of analysis and the benefits of integration, and highlight examples of false debate within and between levels. The best integrative biology reciprocally uses ultimate and proximate hypotheses to generate a more complete understanding of behaviour. PMID:21690126

The impact of alternative trait-scaling hypotheses for the maximum photosynthetic carboxylation rate (Vcmax ) on global gross primary production.

PubMed

Walker, Anthony P; Quaife, Tristan; van Bodegom, Peter M; De Kauwe, Martin G; Keenan, Trevor F; Joiner, Joanna; Lomas, Mark R; MacBean, Natasha; Xu, Chongang; Yang, Xiaojuan; Woodward, F Ian

2017-09-01

The maximum photosynthetic carboxylation rate (V cmax ) is an influential plant trait that has multiple scaling hypotheses, which is a source of uncertainty in predictive understanding of global gross primary production (GPP). Four trait-scaling hypotheses (plant functional type, nutrient limitation, environmental filtering, and plant plasticity) with nine specific implementations were used to predict global V cmax distributions and their impact on global GPP in the Sheffield Dynamic Global Vegetation Model (SDGVM). Global GPP varied from 108.1 to 128.2 PgC yr -1 , 65% of the range of a recent model intercomparison of global GPP. The variation in GPP propagated through to a 27% coefficient of variation in net biome productivity (NBP). All hypotheses produced global GPP that was highly correlated (r = 0.85-0.91) with three proxies of global GPP. Plant functional type-based nutrient limitation, underpinned by a core SDGVM hypothesis that plant nitrogen (N) status is inversely related to increasing costs of N acquisition with increasing soil carbon, adequately reproduced global GPP distributions. Further improvement could be achieved with accurate representation of water sensitivity and agriculture in SDGVM. Mismatch between environmental filtering (the most data-driven hypothesis) and GPP suggested that greater effort is needed understand V cmax variation in the field, particularly in northern latitudes. © 2017 UT-Battelle LLC. New Phytologist © 2017 New Phytologist Trust.

The Impact of Alternative Trait-Scaling Hypotheses for the Maximum Photosynthetic Carboxylation Rate (V (sub cmax)) on Global Gross Primary Production

NASA Technical Reports Server (NTRS)

Walker, Anthony P.; Quaife, Tristan; Van Bodegom, Peter M.; De Kauwe, Martin G.; Keenan, Trevor F.; Joiner, Joanna; Lomas, Mark R.; MacBean, Natasha; Xu, Chongang; Yang, Xiaojuan;

Experiment data report for Semiscale Mod-1 Test S-05-1 (alternate ECC injection test)

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

Feldman, E. M.; Patton, Jr., M. L.; Sackett, K. E.

Recorded test data are presented for Test S-05-1 of the Semiscale Mod-1 alternate ECC injection test series. These tests are among several Semiscale Mod-1 experiments conducted to investigate the thermal and hydraulic phenomena accompanying a hypothesized loss-of-coolant accident in a pressurized water reactor (PWR) system. Test S-05-1 was conducted from initial conditions of 2263 psia and 544/sup 0/F to investigate the response of the Semiscale Mod-1 system to a depressurization and reflood transient following a simulated double-ended offset shear of the cold leg broken loop piping. During the test, cooling water was injected into the vessel lower plenum to simulatemore » emergency core coolant injection in a PWR, with the flow rate based on system volume scaling.« less

Skipping of Chinese characters does not rely on word-based processing.

PubMed

Lin, Nan; Angele, Bernhard; Hua, Huimin; Shen, Wei; Zhou, Junyi; Li, Xingshan

2018-02-01

Previous eye-movement studies have indicated that people tend to skip extremely high-frequency words in sentence reading, such as "the" in English and "/de" in Chinese. Two alternative hypotheses have been proposed to explain how this frequent skipping happens in Chinese reading: one assumes that skipping happens when the preview has been fully identified at the word level (word-based skipping); the other assumes that skipping happens whenever the preview character is easy to identify regardless of whether lexical processing has been completed or not (character-based skipping). Using the gaze-contingent display change paradigm, we examined the two hypotheses by substituting the preview of the third character of a four-character Chinese word with the high-frequency Chinese character "/de", which should disrupt the ongoing word-level processing. The character-based skipping hypothesis predicts that this manipulation will enhance the skipping probability of the target character (i.e., the third character of the target word), because the character "/de" has much higher character frequency than the original character. The word-based skipping hypothesis instead predicts a reduction of the skipping probability of the target character because the presence of the character "/de" is lexically infelicitous at word level. The results supported the character-based skipping hypothesis, indicating that in Chinese reading the decision of skipping a character can be made before integrating it into a word.

Valid randomization-based p-values for partially post hoc subgroup analyses.

PubMed

Lee, Joseph J; Rubin, Donald B

2015-10-30

By 'partially post-hoc' subgroup analyses, we mean analyses that compare existing data from a randomized experiment-from which a subgroup specification is derived-to new, subgroup-only experimental data. We describe a motivating example in which partially post hoc subgroup analyses instigated statistical debate about a medical device's efficacy. We clarify the source of such analyses' invalidity and then propose a randomization-based approach for generating valid posterior predictive p-values for such partially post hoc subgroups. Lastly, we investigate the approach's operating characteristics in a simple illustrative setting through a series of simulations, showing that it can have desirable properties under both null and alternative hypotheses. Copyright © 2015 John Wiley & Sons, Ltd.

Trends in Extreme Rainfall Frequency in the Contiguous United States: Attribution to Climate Change and Climate Variability Modes

NASA Astrophysics Data System (ADS)

Armal, S.; Devineni, N.; Khanbilvardi, R.

2017-12-01

This study presents a systematic analysis for identifying and attributing trends in the annual frequency of extreme rainfall events across the contiguous United States to climate change and climate variability modes. A Bayesian multilevel model is developed for 1,244 stations simultaneously to test the null hypothesis of no trend and verify two alternate hypotheses: Trend can be attributed to changes in global surface temperature anomalies, or to a combination of cyclical climate modes with varying quasi-periodicities and global surface temperature anomalies. The Bayesian multilevel model provides the opportunity to pool information across stations and reduce the parameter estimation uncertainty, hence identifying the trends better. The choice of the best alternate hypotheses is made based on Watanabe-Akaike Information Criterion, a Bayesian pointwise predictive accuracy measure. Statistically significant time trends are observed in 742 of the 1,244 stations. Trends in 409 of these stations can be attributed to changes in global surface temperature anomalies. These stations are predominantly found in the Southeast and Northeast climate regions. The trends in 274 of these stations can be attributed to the El Nino Southern Oscillations, North Atlantic Oscillation, Pacific Decadal Oscillation and Atlantic Multi-Decadal Oscillation along with changes in global surface temperature anomalies. These stations are mainly found in the Northwest, West and Southwest climate regions.

Comparison of Fertility Trends Estimated Alternatively from Birth Histories and Own Children. Papers of the East-West Population Institute, No. 94.

ERIC Educational Resources Information Center

Retherford, Robert D.; Alam, Iqbal

Fertility trends estimated alternately from birth histories and own children method are compared for eight developing countries in which the World Fertility Survey was conducted. Principle hypotheses are that fertility trends estimated by the two approaches suffer from similar errors in the reporting of women's and children's ages, and that these…

[General aspects of homeopathy].

PubMed

Avello L, Marcia; Avendaño O, Cristian; Mennickent C, Sigrid

2009-01-01

Homeopathic medicine is a type of therapy that appeared in Europe at the end of the eighteenth century. At the present time, it is widely accepted in developed countries as a form of alternative medicine. In Chile, health regulation includes homeopathy as pharmaceutical products and homeopathy is also considered a form of complementary medicine, that is well accepted by the public. The scientific rationale of homeopathy is based on an empiric type of thought that goes from the general to the particular. The symptoms that are valued are those that are particular to each sick individual. It uses diluted solutions of plants, minerals, animals and even venoms. There are basically two hypotheses to explain its mechanisms of action: The "immunological memory" and the "memory of water" or the transmission of electromagnetic information of the water. There still is needed to perform new studies to scientifically assess homeopathy and its usefulness, as an accepted alternative therapy.

Fight the power: the limits of empiricism and the costs of positivistic rigor.

PubMed

Indick, William

2002-01-01

A summary of the influence of positivistic philosophy and empiricism on the field of psychology is followed by a critique of the empirical method. The dialectic process is advocated as an alternative method of inquiry. The main advantage of the dialectic method is that it is open to any logical argument, including empirical hypotheses, but unlike empiricism, it does not automatically reject arguments that are not based on observable data. Evolutionary and moral psychology are discussed as examples of important fields of study that could benefit from types of arguments that frequently do not conform to the empirical standards of systematic observation and falsifiability of hypotheses. A dialectic method is shown to be a suitable perspective for those fields of research, because it allows for logical arguments that are not empirical and because it fosters a functionalist perspective, which is indispensable for both evolutionary and moral theories. It is suggested that all psychologists may gain from adopting a dialectic approach, rather than restricting themselves to empirical arguments alone.

Migrating songbirds tested in computer-controlled Emlen funnels use stellar cues for a time-independent compass.

PubMed

Mouritsen, H; Larsen, O N

2001-11-01

This paper investigates how young pied flycatchers, Ficedula hypoleuca, and blackcaps, Sylvia atricapilla, interpret and use celestial cues. In order to record these data, we developed a computer-controlled version of the Emlen funnel, which enabled us to make detailed temporal analyses. First, we showed that the birds use a star compass. Then, we tested the birds under a stationary planetarium sky, which simulated the star pattern of the local sky at 02:35 h for 11 consecutive hours of the night, and compared the birds' directional choices as a function of time with the predictions from five alternative stellar orientation hypotheses. The results supported the hypothesis suggesting that birds use a time-independent star compass based on learned geometrical star configurations to pinpoint the rotational point of the starry sky (north). In contrast, neither hypotheses suggesting that birds use the stars for establishing their global position and then perform true star navigation nor those suggesting the use of a time-compensated star compass were supported.

A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar.

PubMed

Brown, Jason L; Cameron, Alison; Yoder, Anne D; Vences, Miguel

2014-10-09

Pattern and process are inextricably linked in biogeographic analyses, though we can observe pattern, we must infer process. Inferences of process are often based on ad hoc comparisons using a single spatial predictor. Here, we present an alternative approach that uses mixed-spatial models to measure the predictive potential of combinations of hypotheses. Biodiversity patterns are estimated from 8,362 occurrence records from 745 species of Malagasy amphibians and reptiles. By incorporating 18 spatially explicit predictions of 12 major biogeographic hypotheses, we show that mixed models greatly improve our ability to explain the observed biodiversity patterns. We conclude that patterns are influenced by a combination of diversification processes rather than by a single predominant mechanism. A 'one-size-fits-all' model does not exist. By developing a novel method for examining and synthesizing spatial parameters such as species richness, endemism and community similarity, we demonstrate the potential of these analyses for understanding the diversification history of Madagascar's biota.

Relationship between mediation analysis and the structured life course approach.

PubMed

Howe, Laura D; Smith, Andrew D; Macdonald-Wallis, Corrie; Anderson, Emma L; Galobardes, Bruna; Lawlor, Debbie A; Ben-Shlomo, Yoav; Hardy, Rebecca; Cooper, Rachel; Tilling, Kate; Fraser, Abigail

2016-08-01

Many questions in life course epidemiology involve mediation and/or interaction because of the long latency period between exposures and outcomes. In this paper, we explore how mediation analysis (based on counterfactual theory and implemented using conventional regression approaches) links with a structured approach to selecting life course hypotheses. Using theory and simulated data, we show how the alternative life course hypotheses assessed in the structured life course approach correspond to different combinations of mediation and interaction parameters. For example, an early life critical period model corresponds to a direct effect of the early life exposure, but no indirect effect via the mediator and no interaction between the early life exposure and the mediator. We also compare these methods using an illustrative real-data example using data on parental occupational social class (early life exposure), own adult occupational social class (mediator) and physical capability (outcome). © The Author 2016. Published by Oxford University Press on behalf of the International Epidemiological Association.

Gastral drumming: a nest-based food-recruitment signal in a social wasp

NASA Astrophysics Data System (ADS)

Taylor, Benjamin J.; Jeanne, Robert L.

2018-04-01

Many social insect species produce signals that either recruit foragers to a specific food source or simply activate more nestmates to become foragers. Both are means of enhancing resource exploitation by increasing the number of individuals devoted to gathering profitable resources. Gastral drumming (GD) has been documented in several species of yellowjackets and hornets (Vespidae: Vespinae). It has been hypothesized that it is a hunger signal, but there is little empirical evidence to support this claim. An alternative hypothesis is that GD recruits workers to forage for food. Here, we report the results of a test between the hunger-signal and food-recruitment hypotheses in the German yellowjacket wasp, Vespula germanica. We show that the rate of performance of GD decreased when colonies were deprived of food and increased when supplemental food was provided. Playback of GD caused increased rates of (1) movement in the nest, (2) trophallaxis, and (3) worker departures from the nest. Together, these results support the conclusion that GD is not a hunger signal as previously asserted but instead is a nest-based food-recruitment signal, the first to be reported for a social wasp.

Gastral drumming: a nest-based food-recruitment signal in a social wasp.

PubMed

Taylor, Benjamin J; Jeanne, Robert L

2018-03-21

Many social insect species produce signals that either recruit foragers to a specific food source or simply activate more nestmates to become foragers. Both are means of enhancing resource exploitation by increasing the number of individuals devoted to gathering profitable resources. Gastral drumming (GD) has been documented in several species of yellowjackets and hornets (Vespidae: Vespinae). It has been hypothesized that it is a hunger signal, but there is little empirical evidence to support this claim. An alternative hypothesis is that GD recruits workers to forage for food. Here, we report the results of a test between the hunger-signal and food-recruitment hypotheses in the German yellowjacket wasp, Vespula germanica. We show that the rate of performance of GD decreased when colonies were deprived of food and increased when supplemental food was provided. Playback of GD caused increased rates of (1) movement in the nest, (2) trophallaxis, and (3) worker departures from the nest. Together, these results support the conclusion that GD is not a hunger signal as previously asserted but instead is a nest-based food-recruitment signal, the first to be reported for a social wasp.

A versatile test for equality of two survival functions based on weighted differences of Kaplan-Meier curves.

PubMed

Uno, Hajime; Tian, Lu; Claggett, Brian; Wei, L J

2015-12-10

With censored event time observations, the logrank test is the most popular tool for testing the equality of two underlying survival distributions. Although this test is asymptotically distribution free, it may not be powerful when the proportional hazards assumption is violated. Various other novel testing procedures have been proposed, which generally are derived by assuming a class of specific alternative hypotheses with respect to the hazard functions. The test considered by Pepe and Fleming (1989) is based on a linear combination of weighted differences of the two Kaplan-Meier curves over time and is a natural tool to assess the difference of two survival functions directly. In this article, we take a similar approach but choose weights that are proportional to the observed standardized difference of the estimated survival curves at each time point. The new proposal automatically makes weighting adjustments empirically. The new test statistic is aimed at a one-sided general alternative hypothesis and is distributed with a short right tail under the null hypothesis but with a heavy tail under the alternative. The results from extensive numerical studies demonstrate that the new procedure performs well under various general alternatives with a caution of a minor inflation of the type I error rate when the sample size is small or the number of observed events is small. The survival data from a recent cancer comparative study are utilized for illustrating the implementation of the process. Copyright © 2015 John Wiley & Sons, Ltd.

Skeletal heterochrony is associated with the anatomical specializations of snakes among squamate reptiles.

PubMed

Werneburg, Ingmar; Sánchez-Villagra, Marcelo R

2015-01-01

Snakes possess a derived anatomy, characterized by limb reduction and reorganization of the skull and internal organs. To understand the origin of snakes from an ontogenetic point of view, we conducted comprehensive investigations on the timing of skeletal elements, based on published and new data, and reconstructed the evolution of the ossification sequence among squamates. We included for the first time Varanus, a critical taxon in phylogenetic context. There is comprehensive delay in the onset of ossification of most skeletal elements in snakes when compared to reference developmental events through evolution. We hypothesize that progressing deceleration accompanied limb reduction and reorganization of the snake skull. Molecular and morphological studies have suggested close relationship of snakes to either amphisbaenians, scincids, geckos, iguanids, or varanids. Likewise, alternative hypotheses on habitat for stem snakes have been postulated. Our comprehensive heterochrony analyses detected developmental shifts in ossification for each hypothesis of snake origin. Moreover, we show that reconstruction of ancestral developmental sequences is a valuable tool to understand ontogenetic mechanisms associated with major evolutionary changes and test homology hypotheses. The "supratemporal" of snakes could be homolog to squamosal of other squamates, which starts ossification early to become relatively large in snakes. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Size-Energy Relationships in Ecological Communities

PubMed Central

Sewall, Brent J.; Freestone, Amy L.; Hawes, Joseph E.; Andriamanarina, Ernest

2013-01-01

Hypotheses that relate body size to energy use are of particular interest in community ecology and macroecology because of their potential to facilitate quantitative predictions about species interactions and to clarify complex ecological patterns. One prominent size-energy hypothesis, the energetic equivalence hypothesis, proposes that energy use from shared, limiting resources by populations or size classes of foragers will be independent of body size. Alternative hypotheses propose that energy use will increase with body size, decrease with body size, or peak at an intermediate body size. Despite extensive study, however, size-energy hypotheses remain controversial, due to a lack of directly-measured data on energy use, a tendency to confound distinct scaling relationships, and insufficient attention to the ecological contexts in which predicted relationships are likely to occur. Our goal, therefore, was to directly evaluate size-energy hypotheses while clarifying how results would differ with alternate methods and assumptions. We comprehensively tested size-energy hypotheses in a vertebrate frugivore guild in a tropical forest in Madagascar. Our test of size-energy hypotheses, which is the first to examine energy intake directly, was consistent with the energetic equivalence hypothesis. This finding corresponds with predictions of metabolic theory and models of energy distribution in ecological communities, which imply that body size does not confer an advantage in competition for energy among populations or size classes of foragers. This result was robust to different assumptions about energy regulation. Our results from direct energy measurement, however, contrasted with those obtained with conventional methods of indirect inference from size-density relationships, suggesting that size-density relationships do not provide an appropriate proxy for size-energy relationships as has commonly been assumed. Our research also provides insights into mechanisms underlying local size-energy relationships and has important implications for predicting species interactions and for understanding the structure and dynamics of ecological communities. PMID:23950873

Adaptationism--how to carry out an exaptationist program.

PubMed

Andrews, Paul W; Gangestad, Steven W; Matthews, Dan

2002-08-01

Adaptationism is a research strategy that seeks to identify adaptations and the specific selective forces that drove their evolution in past environments. Since the mid-1970s, paleontologist Stephen J. Gould and geneticist Richard Lewontin have been critical of adaptationism, especially as applied toward understanding human behavior and cognition. Perhaps the most prominent criticism they made was that adaptationist explanations were analogous to Rudyard Kipling's Just So Stories (outlandish explanations for questions such as how the elephant got its trunk). Since storytelling (through the generation of hypotheses and the making of inferences) is an inherent part of science, the criticism refers to the acceptance of stories without sufficient empirical evidence. In particular, Gould, Lewontin, and their colleagues argue that adaptationists often use inappropriate evidentiary standards for identifying adaptations and their functions, and that they often fail to consider alternative hypotheses to adaptation. Playing prominently in both of these criticisms are the concepts of constraint, spandrel, and exaptation. In this article we discuss the standards of evidence that could be used to identify adaptations and when and how they may be appropriately used. Moreover, building an empirical case that certain features of a trait are best explained by exaptation, spandrel, or constraint requires demonstrating that the trait's features cannot be better accounted for by adaptationist hypotheses. Thus, we argue that the testing of alternatives requires the consideration, testing, and systematic rejection of adaptationist hypotheses. Where possible, we illustrate our points with examples taken from human behavior and cognition.

Carbon limitation patterns in buried and open urban streams

EPA Science Inventory

Urban streams alternate between darkened buried segments dominated by heterotrophic processes and lighted open segments dominated by autotrophic processes. We hypothesized that labile carbon leaking from autotrophic cells would reduce heterotrophic carbon limitation in open chan...

Alternative hypotheses to explain why biodiversity-ecosystem functioning relationships are concave-up in some natural ecosystems but concave-down in manipulative experiments.

PubMed

Mora, Camilo; Danovaro, Roberto; Loreau, Michel

2014-06-25

Recent studies of the relationship between biodiversity and functioning in marine ecosystems have yielded non-saturating patterns that contrast sharply with the results of experimental studies, where ecosystem functioning rapidly saturates with increases in biodiversity. Here we provide a simple theoretical framework of three alternative hypotheses that, individually or combined, are likely to explain this contrast: i) the use of functional richness instead of species richness, ii) an increased production efficiency of species in producing biomass when more ecological interactions are present, and iii) the fact that communities are likely assembled in an ordered succession of species from low to high ecological efficiency. Our results provide theoretical support for concave-up biodiversity-ecosystem functioning relationships in natural ecosystems and confirm that the loss of species can have substantially larger effects on the functioning of natural ecosystems than anticipated from controlled manipulative experiments.

Alternative hypotheses to explain why biodiversity-ecosystem functioning relationships are concave-up in some natural ecosystems but concave-down in manipulative experiments

PubMed Central

Mora, Camilo; Danovaro, Roberto; Loreau, Michel

2014-01-01

Recent studies of the relationship between biodiversity and functioning in marine ecosystems have yielded non-saturating patterns that contrast sharply with the results of experimental studies, where ecosystem functioning rapidly saturates with increases in biodiversity. Here we provide a simple theoretical framework of three alternative hypotheses that, individually or combined, are likely to explain this contrast: i) the use of functional richness instead of species richness, ii) an increased production efficiency of species in producing biomass when more ecological interactions are present, and iii) the fact that communities are likely assembled in an ordered succession of species from low to high ecological efficiency. Our results provide theoretical support for concave-up biodiversity-ecosystem functioning relationships in natural ecosystems and confirm that the loss of species can have substantially larger effects on the functioning of natural ecosystems than anticipated from controlled manipulative experiments. PMID:24962477

An observational study of the effectiveness of alternative care providers in the management of obstructive sleep apnea.

PubMed

Pendharkar, Sachin R; Dechant, Anthony; Bischak, Diane P; Tsai, Willis H; Stevenson, Ann-Marie; Hanly, Patrick J

2016-04-01

Alternative care providers have been proposed as a substitute for physician-based management of obstructive sleep apnea. The purpose of this study was to describe the clinical course of patients with a new diagnosis of obstructive sleep apnea who were treated with continuous positive airway pressure and followed by alternative care providers at a tertiary care sleep clinic. It was hypothesized that care by alternative care providers would result in improvement of daytime sleepiness and satisfactory treatment adherence, and that a specific number of follow-up visits could be identified after which clinical outcomes no longer improved. The Epworth Sleepiness Scale score was measured for each patient at baseline and at each alternative care provider visit. Patients were discharged when they demonstrated a significant improvement in sleepiness and were adherent to therapy. The Epworth Sleepiness Scale score decreased by 3.9 points from baseline to discharge. Patients with three or more visits required more follow-up time to achieve the same clinical improvement as those with only two visits. Continuous positive airway pressure adherence was comparable to previous studies of physician-led care and improved with ongoing alternative care provider follow-up. The current results suggest that clinical care by alternative care providers leads to continued improvements in sleepiness in patients with obstructive sleep apnea who are treated with continuous positive airway pressure, and that a minority of patients require longer follow-up to achieve a satisfactory clinical response to therapy. © 2015 European Sleep Research Society.

Dissolution of hypotheses in biochemistry: three case studies.

PubMed

Fry, Michael

2016-12-01

The history of biochemistry and molecular biology is replete with examples of erroneous theories that persisted for considerable lengths of time before they were rejected. This paper examines patterns of dissolution of three such erroneous hypotheses: The idea that nucleic acids are tetrads of the four nucleobases ('the tetranucleotide hypothesis'); the notion that proteins are collinear with their encoding genes in all branches of life; and the hypothesis that proteins are synthesized by reverse action of proteolytic enzymes. Analysis of these cases indicates that amassed contradictory empirical findings did not prompt critical experimental testing of the prevailing theories nor did they elicit alternative hypotheses. Rather, the incorrect models collapsed when experiments that were not purposely designed to test their validity exposed new facts.

Why Do Sex Chromosomes Stop Recombining?

PubMed

Ponnikas, Suvi; Sigeman, Hanna; Abbott, Jessica K; Hansson, Bengt

2018-04-28

It is commonly assumed that sex chromosomes evolve recombination suppression because selection favours linkage between sex-determining and sexually antagonistic genes. However, although the role of sexual antagonism during sex chromosome evolution has attained strong support from theory, experimental and observational evidence is rare or equivocal. Here, we highlight alternative, often neglected, hypotheses for recombination suppression on sex chromosomes, which invoke meiotic drive, heterozygote advantage, and genetic drift, respectively. We contrast the hypotheses, the situations when they are likely to be of importance, and outline why it is surprisingly difficult to test them. Lastly, we discuss future research directions (including modelling, population genomics, comparative approaches, and experiments) to disentangle the different hypotheses of sex chromosome evolution. Copyright © 2018 Elsevier Ltd. All rights reserved.

Translating evidence based violence and drug use prevention to obesity prevention: development and construction of the pathways program.

PubMed

Sakuma, Kari-Lyn K; Riggs, Nathaniel R; Pentz, Mary Ann

2012-04-01

Effective school-based obesity prevention programs are needed to prevent and reduce the growing obesity risk among youth. Utilizing the evidence-rich areas of violence and substance use prevention, translation science may provide an efficient means for developing curricula across multiple health behaviors. This paper introduces Pathways to Health, a school-based obesity prevention program that was developed by translating from evidence-based violence and drug use prevention programs, Promoting Alternative THinking Strategies and the Midwestern Prevention Project STAR (STAR). We illustrate how a hypothesized underlying behavior change mechanism in two domains of risk behavior, violence and substance use, can be applied to obesity prevention. A 4-step translational process is provided and may be relevant for use in developing other curricula to address multiple health risk behaviors. Practical application and decision points are also provided.

Translating evidence based violence and drug use prevention to obesity prevention: development and construction of the Pathways program

PubMed Central

Sakuma, Kari-Lyn K.; Riggs, Nathaniel R.; Pentz, Mary Ann

2012-01-01

Effective school-based obesity prevention programs are needed to prevent and reduce the growing obesity risk among youth. Utilizing the evidence-rich areas of violence and substance use prevention, translation science may provide an efficient means for developing curricula across multiple health behaviors. This paper introduces Pathways to Health, a school-based obesity prevention program that was developed by translating from evidence-based violence and drug use prevention programs, Promoting Alternative THinking Strategies and the Midwestern Prevention Project STAR (STAR). We illustrate how a hypothesized underlying behavior change mechanism in two domains of risk behavior, violence and substance use, can be applied to obesity prevention. A 4-step translational process is provided and may be relevant for use in developing other curricula to address multiple health risk behaviors. Practical application and decision points are also provided. PMID:21987475

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

Eliseeva, Ekaterina A.; Spears, Michael; Chan, Wanyu R.

Background – This study investigated the associations of ventilation rates (VRs), estimated from indoor CO2 concentrations, in offices with the amount of respiratory infections, illness absences, and building-related health symptoms in occupants. Methods – Office buildings were recruited from three California climate zones. In one or more study spaces within each building, real-time logging sensors measured carbon dioxide, temperature, and relative humidity for one year. Ventilation rates were estimated using daily peak CO2 levels, and also using an alternative metric. Data on occupants and health outcomes were collected through web-based surveys every three months. Multivariate models were used to assessmore » relationships between metrics of ventilation rate or CO2 and occupant outcomes. For all outcomes, negative associations were hypothesized with VR metrics, and positive associations with CO2 metrics. Results – Difficulty recruiting buildings and low survey response limited sample size and study power. In 16 studied spaces within 9 office buildings, VRs were uniformly high over the year, from twice to over nine times the California office VR standard (7 L/s or 15 cfm per person). VR and CO2 metrics had no statistically significant relationships with occupant outcomes, except for a small significantly positive association of the alternative VR metric with respiratory illness-related absence, contrary to hypotheses. Conclusions– The very high time-averaged VRs in the California office buildings studied presumably resulted from “economizer cycles” bringing in large volumes of outdoor air; however, in almost all buildings even the estimated minimum VRs supplied (without the economizer) substantially exceeded the minimum required VR. These high VRs may explain the absence of hypothesized relationships with occupant outcomes. Among uniformly high VRs, little variation in contaminant concentration and occupant effects would be expected. These findings may provide initial evidence for an upper bound of the range of VRs within which increased VRs provide benefits in reducing illness absence.« less

The Sherlock Holmes method in clinical practice.

PubMed

Sopeña, B

2014-04-01

This article lists the integral elements of the Sherlock Holmes method, which is based on the intelligent collection of information through detailed observation, careful listening and thorough examination. The information thus obtained is analyzed to develop the main and alternative hypotheses, which are shaped during the deductive process until the key leading to the solution is revealed. The Holmes investigative method applied to clinical practice highlights the advisability of having physicians reason through and seek out the causes of the disease with the data obtained from acute observation, a detailed review of the medical history and careful physical examination. Copyright © 2013 Elsevier España, S.L. All rights reserved.

The distribution of P-values in medical research articles suggested selective reporting associated with statistical significance.

PubMed

Perneger, Thomas V; Combescure, Christophe

2017-07-01

Published P-values provide a window into the global enterprise of medical research. The aim of this study was to use the distribution of published P-values to estimate the relative frequencies of null and alternative hypotheses and to seek irregularities suggestive of publication bias. This cross-sectional study included P-values published in 120 medical research articles in 2016 (30 each from the BMJ, JAMA, Lancet, and New England Journal of Medicine). The observed distribution of P-values was compared with expected distributions under the null hypothesis (i.e., uniform between 0 and 1) and the alternative hypothesis (strictly decreasing from 0 to 1). P-values were categorized according to conventional levels of statistical significance and in one-percent intervals. Among 4,158 recorded P-values, 26.1% were highly significant (P < 0.001), 9.1% were moderately significant (P ≥ 0.001 to < 0.01), 11.7% were weakly significant (P ≥ 0.01 to < 0.05), and 53.2% were nonsignificant (P ≥ 0.05). We noted three irregularities: (1) high proportion of P-values <0.001, especially in observational studies, (2) excess of P-values equal to 1, and (3) about twice as many P-values less than 0.05 compared with those more than 0.05. The latter finding was seen in both randomized trials and observational studies, and in most types of analyses, excepting heterogeneity tests and interaction tests. Under plausible assumptions, we estimate that about half of the tested hypotheses were null and the other half were alternative. This analysis suggests that statistical tests published in medical journals are not a random sample of null and alternative hypotheses but that selective reporting is prevalent. In particular, significant results are about twice as likely to be reported as nonsignificant results. Copyright © 2017 Elsevier Inc. All rights reserved.

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

PubMed Central

Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R.

2015-01-01

Motivation: Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters. Results: In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: julio@iim.csic.es or saezrodriguez@ebi.ac.uk PMID:26002881

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

PubMed

Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R

2015-09-15

Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no information about the kinetic parameters. In this work, we combine a logic-based formalism, to describe all the possible regulatory structures for a given dynamic model of a pathway, with mixed-integer dynamic optimization (MIDO). This framework aims to simultaneously identify the regulatory structure (represented by binary parameters) and the real-valued parameters that are consistent with the available experimental data, resulting in a logic-based differential equation model. The alternative to this would be to perform real-valued parameter estimation for each possible model structure, which is not tractable for models of the size presented in this work. The performance of the method presented here is illustrated with several case studies: a synthetic pathway problem of signaling regulation, a two-component signal transduction pathway in bacterial homeostasis, and a signaling network in liver cancer cells. Supplementary data are available at Bioinformatics online. julio@iim.csic.es or saezrodriguez@ebi.ac.uk. © The Author 2015. Published by Oxford University Press.

Are evolutionary hypotheses for motion sickness "just-so" stories?

PubMed

Oman, Charles M

2012-01-01

Vertebrates have evolved rapidly conditionable nausea and vomiting reflexes mediated by gut and brainstem receptors, clearly as a defense against neurotoxin ingestion. In 1977 Treisman proposed that sensory orientation linkages to emetic centers evolved for the same reason, and that motion sickness was an accidental byproduct. It was an "adaptationist" explanation for motion sickness, since it assumed that evolution has shaped all phenotypic traits for survival advantage. Treisman's "poison" theory is plausible, and frequently cited as the accepted scientific explanation for motion sickness. However, alternative explanations have been proposed. The creation of hypotheses is an essential part of science - provided they are testable. This paper reviews the evidence for the Poison theory and several other adaptationist explanations. These hypotheses are certainly not "just-so stories", but supporting evidence is equivocal, and contradictory evidence exists Parsimony suggests an alternative "pluralistic" view: The vertebrate reticular formation maintains oxygenated blood flow to the brain, discriminates unexpected sensory stimuli- including postural disturbances, and detects and expels ingested neurotoxins. The three systems share neuroarchitectural elements but normally function independently. Brainstem sensory conflict neurons normally discriminate brief postural disturbances, but can be abnormally stimulated during prolonged passive transport (e.g. by boat, beginning about 150-200 generations ago). Sensory conflict signals cross couple into the neurotoxin expulsion and avoidance system, producing an arguably maladaptive emetic phenotype.

LIFESPAN: A tool for the computer-aided design of longitudinal studies

PubMed Central

Brandmaier, Andreas M.; von Oertzen, Timo; Ghisletta, Paolo; Hertzog, Christopher; Lindenberger, Ulman

2015-01-01

Researchers planning a longitudinal study typically search, more or less informally, a multivariate space of possible study designs that include dimensions such as the hypothesized true variance in change, indicator reliability, the number and spacing of measurement occasions, total study time, and sample size. The main search goal is to select a research design that best addresses the guiding questions and hypotheses of the planned study while heeding applicable external conditions and constraints, including time, money, feasibility, and ethical considerations. Because longitudinal study selection ultimately requires optimization under constraints, it is amenable to the general operating principles of optimization in computer-aided design. Based on power equivalence theory (MacCallum et al., 2010; von Oertzen, 2010), we propose a computational framework to promote more systematic searches within the study design space. Starting with an initial design, the proposed framework generates a set of alternative models with equal statistical power to detect hypothesized effects, and delineates trade-off relations among relevant parameters, such as total study time and the number of measurement occasions. We present LIFESPAN (Longitudinal Interactive Front End Study Planner), which implements this framework. LIFESPAN boosts the efficiency, breadth, and precision of the search for optimal longitudinal designs. Its initial version, which is freely available at http://www.brandmaier.de/lifespan, is geared toward the power to detect variance in change as specified in a linear latent growth curve model. PMID:25852596

Mindset switching increases the use of 'want-based' over 'should-based' behaviors

PubMed Central

Zhang, Nan-Nan; Xu, Dai-Xuan

2018-01-01

This study examines the consequences of mindset switching on behavioral choices in want/should conflicts. Building on the insights of the ego depletion literature, we propose that mindset switching depletes individuals’ self-control resources and therefore prompts the choice of want behavior, which provides immediate pleasure, over should behavior, which provides long-term utility. Four laboratory experiments with university students that stimulated individuals to switch mindsets were conducted to test our hypotheses. Experiment 1 demonstrated that switching between individualist and collectivist mindsets increased the subjects’ tendency to prefer popular magazines over scientific journals. Experiment 2 replicated the results by testing the relationship between an abstract/concrete mindset-switching task and want/should online behavioral choices. The mediating effect of ego depletion was also supported. Experiment 3 retested the main effect of language-switching on reading choices, and the mediating effect of ego-depletion. Experiment 3 also tested the moderating effect of the Need for Cognition, and eliminated the alternative explanation of cognitive fatigue. In Experiment 4, actual food choices were used as the direct measure of want/should behaviors to test the robustness of our findings. The results consistently supported our hypotheses that mindset switching has significant effects on behavioral choices in terms of overindulgence, such as increasing want behavior and thus foregoing should behavior. PMID:29709003

The Weak Spots in Contemporary Science (and How to Fix Them).

PubMed

Wicherts, Jelte M

2017-11-27

In this review, the author discusses several of the weak spots in contemporary science, including scientific misconduct, the problems of post hoc hypothesizing (HARKing), outcome switching, theoretical bloopers in formulating research questions and hypotheses, selective reading of the literature, selective citing of previous results, improper blinding and other design failures, p-hacking or researchers' tendency to analyze data in many different ways to find positive (typically significant) results, errors and biases in the reporting of results, and publication bias. The author presents some empirical results highlighting problems that lower the trustworthiness of reported results in scientific literatures, including that of animal welfare studies. Some of the underlying causes of these biases are discussed based on the notion that researchers are only human and hence are not immune to confirmation bias, hindsight bias, and minor ethical transgressions. The author discusses solutions in the form of enhanced transparency, sharing of data and materials, (post-publication) peer review, pre-registration, registered reports, improved training, reporting guidelines, replication, dealing with publication bias, alternative inferential techniques, power, and other statistical tools.

When passion makes the heart grow colder: the role of passion in alternative goal suppression.

PubMed

Bélanger, Jocelyn J; Lafrenière, Marc-André K; Vallerand, Robert J; Kruglanski, Arie W

2013-01-01

Quality of goal engagement and alternative goal suppression were investigated in this research. Integrating the dualistic model of passion (Vallerand et al., 2003) with goal-systems theory (Kruglanski et al., 2002), we hypothesized that obsessive passion--associated with recurrent goal-conflicts--would predict greater alternative goal suppression (i.e., goal-shielding) than would harmonious passion--characterized by effective synthesis of the passionate activity with other life domains. Results from 5 laboratory studies supported these hypotheses. In Study 1, participants' dispositional measures of harmonious and obsessive passion were correlated with an implicit measure of goal-shielding. Obsessive (but not harmonious) passion predicted the suppression of alternative goals and the progressive inhibition of unfamiliar goals. In Study 2, we extended these findings by demonstrating the interrelation between quality of goal engagement and goal-commitment such that goal-shielding effects were enhanced, but only for goals in conflict with other life domains (vs. well-integrated goals). In Study 3, the causal influence of passion on goal-shielding was supported via an experimental manipulation of passion. In Study 4, we replicated and extended Studies 1 and 3 by experimentally demonstrating that obsessive (but not harmonious) passion is a mindset conducive to the development of inhibitory links with alternative goals. Study 5 explored the psychological costs associated with repeated unconscious goal suppression by examining its effects on the depletion of self-regulatory resources. Collectively, the present results suggest that the qualitative distinction between obsessive and harmonious passion has implications for the goal-shielding effect and for subsequent self-regulatory behavior.

Spatial spread of the West Africa Ebola epidemic.

PubMed

Kramer, Andrew M; Pulliam, J Tomlin; Alexander, Laura W; Park, Andrew W; Rohani, Pejman; Drake, John M

2016-08-01

Controlling Ebola outbreaks and planning an effective response to future emerging diseases are enhanced by understanding the role of geography in transmission. Here we show how epidemic expansion may be predicted by evaluating the relative probability of alternative epidemic paths. We compared multiple candidate models to characterize the spatial network over which the 2013-2015 West Africa epidemic of Ebola virus spread and estimate the effects of geographical covariates on transmission during peak spread. The best model was a generalized gravity model where the probability of transmission between locations depended on distance, population density and international border closures between Guinea, Liberia and Sierra Leone and neighbouring countries. This model out-performed alternative models based on diffusive spread, the force of infection, mobility estimated from cell phone records and other hypothesized patterns of spread. These findings highlight the importance of integrated geography to epidemic expansion and may contribute to identifying both the most vulnerable unaffected areas and locations of maximum intervention value.

Spatial spread of the West Africa Ebola epidemic

PubMed Central

Pulliam, J. Tomlin; Alexander, Laura W.; Rohani, Pejman; Drake, John M.

2016-01-01

Controlling Ebola outbreaks and planning an effective response to future emerging diseases are enhanced by understanding the role of geography in transmission. Here we show how epidemic expansion may be predicted by evaluating the relative probability of alternative epidemic paths. We compared multiple candidate models to characterize the spatial network over which the 2013–2015 West Africa epidemic of Ebola virus spread and estimate the effects of geographical covariates on transmission during peak spread. The best model was a generalized gravity model where the probability of transmission between locations depended on distance, population density and international border closures between Guinea, Liberia and Sierra Leone and neighbouring countries. This model out-performed alternative models based on diffusive spread, the force of infection, mobility estimated from cell phone records and other hypothesized patterns of spread. These findings highlight the importance of integrated geography to epidemic expansion and may contribute to identifying both the most vulnerable unaffected areas and locations of maximum intervention value. PMID:27853607

No sodium in the vapour plumes of Enceladus.

PubMed

Schneider, Nicholas M; Burger, Matthew H; Schaller, Emily L; Brown, Michael E; Johnson, Robert E; Kargel, Jeffrey S; Dougherty, Michele K; Achilleos, Nicholas A

2009-06-25

The discovery of water vapour and ice particles erupting from Saturn's moon Enceladus fuelled speculation that an internal ocean was the source. Alternatively, the source might be ice warmed, melted or crushed by tectonic motions. Sodium chloride (that is, salt) is expected to be present in a long-lived ocean in contact with a rocky core. Here we report a ground-based spectroscopic search for atomic sodium near Enceladus that places an upper limit on the mixing ratio in the vapour plumes orders of magnitude below the expected ocean salinity. The low sodium content of escaping vapour, together with the small fraction of salt-bearing particles, argues against a situation in which a near-surface geyser is fuelled by a salty ocean through cracks in the crust. The lack of observable sodium in the vapour is consistent with a wide variety of alternative eruption sources, including a deep ocean, a freshwater reservoir, or ice. The existing data may be insufficient to distinguish between these hypotheses.

Lexically-based learning and early grammatical development.

PubMed

Lieven, E V; Pine, J M; Baldwin, G

1997-02-01

Pine & Lieven (1993) suggest that a lexically-based positional analysis can account for the structure of a considerable proportion of children's early multiword corpora. The present study tests this claim on a second, larger sample of eleven children aged between 1;0 and 3;0 from a different social background, and extends the analysis to later in development. Results indicate that the positional analysis can account for a mean of 60% of all the children's multiword utterances and that the great majority of all other utterances are defined as frozen by the analysis. Alternative explanations of the data based on hypothesizing underlying syntactic or semantic relations are investigated through analyses of pronoun case marking and of verbs with prototypical agent-patient roles. Neither supports the view that the children's utterances are being produced on the basis of general underlying rules and categories. The implications of widespread distributional learning in early language development are discussed.

Creativity and inductive reasoning: the relationship between divergent thinking and performance on Wasons 246 task.

PubMed

Vartanian, Oshin; Martindale, Colin; Kwiatkowski, Jonna

2003-05-01

This study was an investigation of the relationship between potential creativityas measured by fluency scores on the Alternate Uses Testand performance on Wasons 246 task. As hypothesized, participants who were successful in discovering the rule had significantly higher fluency scores. Successful participants also generated higher frequencies of confirmatory and disconfirmatory hypotheses, but a multiple regression analysis using the stepwise method revealed that the frequency of generating disconfirmatory hypotheses and fluency scores were the only two significant factors in task outcome. The results also supported earlier studies where disconfirmation was shown to play a more important role in the later stages of hypothesis testing. This was especially true of successful participants, who employed a higher frequency of disconfirmatory hypotheses after receiving feedback on the first announcement. These results imply that successful participants benefited from the provision of feedback on the first announcement by switching to a more successful strategy in the hypothesis-testing sequence.

Adaptive inference for distinguishing credible from incredible patterns in nature

USGS Publications Warehouse

Holling, Crawford S.; Allen, Craig R.

2002-01-01

Strong inference is a powerful and rapid tool that can be used to identify and explain patterns in molecular biology, cell biology, and physiology. It is effective where causes are single and separable and where discrimination between pairwise alternative hypotheses can be determined experimentally by a simple yes or no answer. But causes in ecological systems are multiple and overlapping and are not entirely separable. Frequently, competing hypotheses cannot be distinguished by a single unambiguous test, but only by a suite of tests of different kinds, that produce a body of evidence to support one line of argument and not others. We call this process "adaptive inference". Instead of pitting each member of a pair of hypotheses against each other, adaptive inference relies on the exuberant invention of multiple, competing hypotheses, after which carefully structured comparative data are used to explore the logical consequences of each. Herein we present an example that demonstrates the attributes of adaptive inference that have developed out of a 30-year study of the resilience of ecosystems.

FORUM: Dynamics and Causation of Environmental Equity, Locally Unwanted Land Uses, and Neighborhood Changes

PubMed

Liu

1997-09-01

/ Why are some environmental risks distributed disproportionately in the neighborhoods of the minorities and the poor? A hypothesis was proposed in a recent study that market dynamics contributed to the current environmental inequity. That is, locally unwanted land uses (LULUs) make the host communities home to more poor people and people of color. This hypothesis was allegedly supported by a Houston case study, whereby its author analyzed the postsiting changes of the socioeconomic characteristics of the neighborhoods surrounding solid waste facilities. I argue that such an analysis of postsiting changes alone is insufficient to test the causation hypothesis. Instead, I propose a conceptual framework for analysis of environmental equity dynamics and causation. I suggest that the presiting neighborhood dynamics and the characteristics of control neighborhoods be analyzed as the first test for the causation hypothesis. Furthermore, I present theories of neighborhood change and then examine alternative hypotheses that these theories offer for explaining neighborhood changes and for the roles of LULUs in neighborhood changes. These alternative hypotheses should be examined when analyzing the relationship between LULUs and neighborhood changes in a metropolitan area. Using this framework of analysis, I revisited the Houston case. First, I found no evidence that provided support for the hypothesis that the presence of LULUs made the neighborhoods home to more blacks and poor people, contrary to the conclusion made by the previous study. Second, I examined alternative hypotheses for explaining neighborhood changes-invasion-succession, other push forces, and neighborhood life-cycle; the former two might offer better explanation.KEY WORDS: Environmental equity and justice; Locally unwanted lane uses; Siting; Market dynamics; Invasion-succession; Neighborhood changes

Comparing models of Red Knot population dynamics

USGS Publications Warehouse

McGowan, Conor P.

2015-01-01

Predictive population modeling contributes to our basic scientific understanding of population dynamics, but can also inform management decisions by evaluating alternative actions in virtual environments. Quantitative models mathematically reflect scientific hypotheses about how a system functions. In Delaware Bay, mid-Atlantic Coast, USA, to more effectively manage horseshoe crab (Limulus polyphemus) harvests and protect Red Knot (Calidris canutus rufa) populations, models are used to compare harvest actions and predict the impacts on crab and knot populations. Management has been chiefly driven by the core hypothesis that horseshoe crab egg abundance governs the survival and reproduction of migrating Red Knots that stopover in the Bay during spring migration. However, recently, hypotheses proposing that knot dynamics are governed by cyclical lemming dynamics garnered some support in data analyses. In this paper, I present alternative models of Red Knot population dynamics to reflect alternative hypotheses. Using 2 models with different lemming population cycle lengths and 2 models with different horseshoe crab effects, I project the knot population into the future under environmental stochasticity and parametric uncertainty with each model. I then compare each model's predictions to 10 yr of population monitoring from Delaware Bay. Using Bayes' theorem and model weight updating, models can accrue weight or support for one or another hypothesis of population dynamics. With 4 models of Red Knot population dynamics and only 10 yr of data, no hypothesis clearly predicted population count data better than another. The collapsed lemming cycle model performed best, accruing ~35% of the model weight, followed closely by the horseshoe crab egg abundance model, which accrued ~30% of the weight. The models that predicted no decline or stable populations (i.e. the 4-yr lemming cycle model and the weak horseshoe crab effect model) were the most weakly supported.

Diagnostic Accuracy and Feasibility of Serological Tests on Filter Paper Samples for Outbreak Detection of T.b. gambiense Human African Trypanosomiasis

PubMed Central

Hasker, Epco; Lutumba, Pascal; Mumba, Dieudonné; Lejon, Veerle; Büscher, Phillipe; Kande, Victor; Muyembe, Jean Jacques; Menten, Joris; Robays, Jo; Boelaert, Marleen

2010-01-01

Control of human African trypanosomiasis (HAT) in the Democratic Republic of Congo is based on mass population screening by mobile teams; a costly and labor-intensive approach. We hypothesized that blood samples collected on filter paper by village health workers and processed in a central laboratory might be a cost-effective alternative. We estimated sensitivity and specificity of micro-card agglutination test for trypanosomiasis (micro-CATT) and enzyme-linked immunosorbent assay (ELISA)/T.b. gambiense on filter paper samples compared with parasitology-based case classification and used the results in a Monte Carlo simulation of a lot quality assurance sampling (LQAS) approach. Micro-CATT and ELISA/T.b. gambiense showed acceptable sensitivity (92.7% [95% CI 87.4–98.0%] and 82.2% [95% CI 75.3–90.4%]) and very high specificity (99.4% [95% CI 99.0–99.9%] and 99.8% [95% CI 99.5–100%]), respectively. Conditional on high sample size per lot (≥ 60%), both tests could reliably distinguish a 2% from a zero prevalence at village level. Alternatively, these tests could be used to identify individual HAT suspects for subsequent confirmation. PMID:20682885

Developing risk hypotheses and selecting species for assessing non-target impacts of GM trees with novel traits: the case of altered-lignin pine trees.

PubMed

Malone, Louise A; Todd, Jacqui H; Burgess, Elisabeth P J; Walter, Christian; Wagner, Armin; Barratt, Barbara I P

2010-01-01

A procedure is presented for developing environmental risk hypotheses associated with the deployment of forest trees genetically modified to have altered wood properties and for selecting non-target species to test these hypotheses. Altered-lignin Pinus radiata trees intended for use in New Zealand are used as a hypothetical case study to illustrate our approach. Firstly, environmental management goals (such as wood production, flood control or preservation of biodiversity) were identified and linked to the forest attributes they require. Necessary conditions for each attribute were listed and appropriate assessment endpoints for them developed. For example, biological control of pests may be one condition necessary for a forest to have healthy trees, and the diversity and abundance of natural enemy species in the forest could be an appropriate assessment endpoint for measuring this condition. A conceptual model describing the relationships between an altered-lignin GM pine tree and potentially affected invertebrates and micro-organisms in a plantation forest was used to develop a set of risk hypotheses describing how the GM trees might affect each assessment endpoint. Because purified lignin does not represent the properties it imparts to wood, maximum hazard dose tests with non-target organisms, as are used to inform toxin risk assessment, cannot be conducted. Alternative experiments, based on current knowledge of the responses of organisms to lignin, must be designed. A screening method was adapted and applied to a database of invertebrate species known to inhabit New Zealand pine forests to identify and prioritize non-target invertebrate species that could be used as experimental subjects for examining these hypotheses. The screening model and its application are presented, along with a set of recommendations for pre-release tests with GM pines and potentially affected invertebrates and micro-organisms. © ISBR, EDP Sciences, 2011.

Origin of the moon - The collision hypothesis

NASA Technical Reports Server (NTRS)

Stevenson, D. J.

1987-01-01

Theoretical models of lunar origin involving one or more collisions between the earth and other large sun-orbiting bodies are examined in a critical review. Ten basic propositions of the collision hypothesis (CH) are listed; observational data on mass and angular momentum, bulk chemistry, volatile depletion, trace elements, primordial high temperatures, and orbital evolution are summarized; and the basic tenets of alternative models (fission, capture, and coformation) are reviewed. Consideration is given to the thermodynamics of large impacts, rheological and dynamical problems, numerical simulations based on the CH, disk evolution models, and the chemical implications of the CH. It is concluded that the sound arguments and evidence supporting the CH are not (yet) sufficient to rule out other hypotheses.

Unravelling the nocturnal appearance of bogue Boops boops shoals in the anthropogenically modified shallow littoral.

PubMed

Mavraki, N; Georgiadis, M; Koutsikopoulos, C; Tzanatos, E

2016-05-01

In the present study the role of the nocturnal migration of bogue Boops boops shoals to anthropogenically modified shallow littoral locations was examined, evaluating four alternative hypotheses: (1) feeding, (2) reproduction, (3) attraction of B. boops to artificial light and (4) concealment in the darkness related to predation avoidance. All hypotheses apart from predation avoidance were rejected, as B. boops tended to concentrate in shaded locations of wider illuminated areas, a finding not only important concerning fish behaviour, but also with significant management implications. © 2016 The Fisheries Society of the British Isles.

Spatial Mismatch: A Third Generation Survey.

ERIC Educational Resources Information Center

Eagan, J. Vincent

1999-01-01

The spatial mismatch argument hypothesizes that racial discrimination in the housing market, together with the suburbanization of low skilled jobs, contributes significantly to the high unemployment and/or low wages of inner city minority workers. Surveys recent spatial mismatch literature and discusses policy alternatives, focusing on areas…

Parental Behaviors and Beliefs, Child Temperament, and Attachment Disorganization

ERIC Educational Resources Information Center

Wang, Feihong; Cox, Martha J.; Mills-Koonce, Roger; Snyder, Patricia

2015-01-01

This research examined alternative mechanisms in the etiology of attachment disorganization. The authors hypothesized that negative intrusive parenting would significantly predict children's attachment disorganization at age 12 months within a diverse community sample. Of more substantial interest, the authors tested moderational mechanisms in the…

Developmental pathways to depressive symptoms in adolescence: A multi-wave prospective study of negative emotionality, stressors, and anxiety

PubMed Central

Barrocas, Andrea L.; Hankin, Benjamin L.

2014-01-01

This study examined two potential developmental pathways through which the temperament risk factor of negative emotionality (NE) leads to prospective increases in depressive symptoms through the mediating role of stressors and anxious symptoms in a sample of early to middle adolescents (N=350, 6th–10th graders). The primary hypothesized model was that baseline NE leads to increased stressors, which results in increases in anxious arousal, which culminates with elevated depressive symptoms. An alternate model hypothesized that baseline NE leads to increased anxious arousal, which results in increases in stressors, and this culminates in elevated depressive symptoms. Youth completed self-report measures of NE, stressors, anxious arousal, and depressive symptoms at four time-points. Path analysis supported the primary model and showed that the mediating influence of stressors and anxious arousal explained 78% of the association between NE and prospective elevations in depressive symptoms. The alternate model was not supported. Neither gender nor age were moderators. PMID:21249517

The Effects of Computerized Information Systems on Juvenile Courts

ERIC Educational Resources Information Center

Albrecht, Gary L.

1976-01-01

Organizational theorists alternatively hypothesized that computerized information systems (CIS) will produce no necessary changes, centralization, or decentralization in juvenile courts. This hypothesis is supported by the results of a four year study on the phenomenon. Suggestions are offered for improving the juvenile judicial system through…

Skin exposure promotes a Th2 - dependent sensitization to peanut allergens

USDA-ARS?s Scientific Manuscript database

Sensitization to foods often occurs in infancy without known prior oral exposure, which suggests that alternative routes of exposure contribute to food allergy. We hypothesized that peanut activates innate immune pathways in the skin that promote sensitization. We tested this hypothesis by topical...

Going to the 'Dogs' to Test Hypotheses.

ERIC Educational Resources Information Center

Kramm, Kenneth R.

1982-01-01

Describes an alternative method for using live animals in the classroom. A toy dog, the "Trail Tracker Hound Dog" (manufactured by CPG Products Corporation, Cincinnati, Ohio), is used to encourage development of such skills as observation, hypothesis testing, and collection and analysis of scientific data. (Author/JN)

Testing Alternative Hypotheses about Animal Behavior.

ERIC Educational Resources Information Center

Baker, William P.; Lang, Michael; Lawson, Anton E.

Research indicates that the effectiveness of instruction in the elementary classroom is enhanced when it incorporates materials that actively engage students in the generation of scientific explanations. To this end, this document describes an exercise that allows Kindergarten students to explore the basic principles of animal behavior in an…

The Development of Cooperative Relationships: An Alternative to Mandated Equality

ERIC Educational Resources Information Center

Thompson, Rexford L.

1978-01-01

It was hypothesized that as cooperative relationships increase among retarded individuals, and between them and nonretarded persons, the effects of noncooperative relationships--passivity and withdrawal--will correspondingly decrease and be replaced by an enlargement of socio-emotional development among the clients involved. (Author/SBH)

Selection of species and sampling areas: The importance of inference

Treesearch

Paul Stephen Corn

2009-01-01

Inductive inference, the process of drawing general conclusions from specific observations, is fundamental to the scientific method. Platt (1964) termed conclusions obtained through rigorous application of the scientific method as "strong inference" and noted the following basic steps: generating alternative hypotheses; devising experiments, the...

Explicit tests of palaeodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia).

PubMed

Bossu, Christen M; Beaulieu, Jeremy M; Ceas, Patrick A; Near, Thomas J

2013-11-01

The alteration in palaeodrainage river connections has shaped patterns of speciation, genetic diversity and the geographical distribution of the species-rich freshwater fauna of North America. The integration of ancestral range reconstruction methods and divergence time estimates provides an opportunity to infer palaeodrainage connectivity and test alternative palaeodrainage hypotheses. Members of the Orangethroat Darter clade, Ceasia, are endemic to southeastern North America and occur north and south of the Pleistocene glacial front, a distributional pattern that makes this clade of closely related species an ideal system to investigate the number and location of glacial refugia and compare alternative hypotheses regarding the proposed evolution of the Teays-Mahomet palaeodrainage. This study utilized time-calibrated mitochondrial and nuclear gene phylogenies and present-day geographical distributions to investigate hypothesized Teays-Mahomet River connections through time using a dispersal-extinction-cladogenesis (DEC) framework. Results of DEC ancestral area reconstructions indicate that the Teays-Mahomet River was a key dispersal route between disjunct highland regions connecting the Mississippi River tributaries to the Old-Ohio Drainage minimally at two separate occasions during the Pleistocene. There was a dynamic interplay between palaeodrainage connections through time and postglacial range expansion from three glacial refugia that shaped the current genetic structure and geographical distributions of the species that comprise Ceasia. © 2013 John Wiley & Sons Ltd.

Environmental risk factors for cancers of the brain and nervous system: the use of ecological data to generate hypotheses.

PubMed

de Vocht, Frank; Hannam, Kimberly; Buchan, Iain

2013-05-01

There is a public health need to balance timely generation of hypotheses with cautious causal inference. For rare cancers this is particularly challenging because standard epidemiological study designs may not be able to elucidate causal factors in an early period of newly emerging risks. Alternative methodologies need to be considered for generating and shaping hypotheses prior to definitive investigation. To evaluate whether open-access databases can be used to explore links between potential risk factors and cancers at an ecological level, using the case study of brain and nervous system cancers as an example. National age-adjusted cancer incidence rates were obtained from the GLOBOCAN 2008 resource and combined with data from the United Nations Development Report and the World Bank list of development indicators. Data were analysed using multivariate regression models. Cancer rates, potential confounders and environmental risk factors were available for 165 of 208 countries. 2008 national incidences of brain and nervous system cancers were associated with continent, gross national income in 2008 and Human Development Index Score. The only exogenous risk factor consistently associated with higher incidence was the penetration rate of mobile/cellular telecommunications subscriptions, although other factors were highlighted. According to these ecological results the latency period is at least 11-12 years, but probably more than 20 years. Missing data on cancer incidence and for other potential risk factors prohibit more detailed investigation of exposure-response associations and/or explore other hypotheses. Readily available ecological data may be underused, particularly for the study of risk factors for rare diseases and those with long latencies. The results of ecological analyses in general should not be overinterpreted in causal inference, but equally they should not be ignored where alternative signals of aetiology are lacking.

Reach and effectiveness of DVD and in-person diabetes self-management education.

PubMed

Glasgow, Russell E; Edwards, Linda L; Whitesides, Holly; Carroll, Nikki; Sanders, Tristan J; McCray, Barbara L

2009-12-01

To evaluate the reach and effectiveness of a diabetes self-management DVD compared to classroom-based instruction. A hybrid preference/randomized design was used with participants assigned to Choice v. Randomized and DVD v. Class conditions. One hundred and eighty-nine adults with type 2 diabetes participated. Key outcomes included self-management behaviours, process measures including DVD implementation and hypothesized mediators and clinical risk factors. In the Choice condition, four times as many participants chose the mailed DVD as selected Class-based instruction (38.8 v. 9.4%, p<0.001). At the 6-month follow-up, the DVD produced results generally not significantly different than classroom-based instruction, but a combined Class plus DVD condition did not improve outcomes beyond those produced by the classes alone. The DVD appears to have merit as an efficient and appealing alternative to brief classroom-based diabetes education, and the hybrid design is recommended to provide estimates of programme reach.

On the Origin of Pantepui montane biotas: A Perspective Based on the Phylogeny of Aulacorhynchus toucanets

PubMed Central

Bonaccorso, Elisa; Guayasamin, Juan M.

2013-01-01

To understand the origin of Pantepui montane biotas, we studied the biogeography of toucanets in the genus Aulacorhynchus. These birds are ideal for analyzing historical relationships among Neotropical montane regions, given their geographic distribution from Mexico south to Bolivia, including northern Venezuela (Cordillera de la Costa), and the Pantepui. Analyses were based on molecular phylogenies using mitochondrial and nuclear DNA sequences. Topology tests were applied to compare alternative hypotheses that may explain the current distribution of Aulacorhynchus toucanets, in the context of previous hypotheses of the origin of Pantepui montane biotas. Biogeographic reconstructions in RASP and Lagrange were used to estimate the ancestral area of the genus, and an analysis in BEAST was used to estimate a time framework for its diversification. A sister relationship between the Pantepui and Andes+Cordillera de la Costa was significantly more likely than topologies indicating other hypothesis for the origin of Pantepui populations. The Andes was inferred as the ancestral area for Aulacorhynchus, and the group has diversified since the late Miocene. The biogeographic patterns found herein, in which the Andes are the source for biotas of other regions, are consistent with those found for flowerpiercers and tanagers, and do not support the hypothesis of the geologically old Pantepui as a source of Neotropical montain diversity. Based on the high potential for cryptic speciation and isolation of Pantepui populations, we consider that phylogenetic studies of additional taxa are important from a conservation perspective. PMID:23840663

On the Origin of Pantepui montane biotas: A Perspective Based on the Phylogeny of Aulacorhynchus toucanets.

PubMed

Bonaccorso, Elisa; Guayasamin, Juan M

2013-01-01

To understand the origin of Pantepui montane biotas, we studied the biogeography of toucanets in the genus Aulacorhynchus. These birds are ideal for analyzing historical relationships among Neotropical montane regions, given their geographic distribution from Mexico south to Bolivia, including northern Venezuela (Cordillera de la Costa), and the Pantepui. Analyses were based on molecular phylogenies using mitochondrial and nuclear DNA sequences. Topology tests were applied to compare alternative hypotheses that may explain the current distribution of Aulacorhynchus toucanets, in the context of previous hypotheses of the origin of Pantepui montane biotas. Biogeographic reconstructions in RASP and Lagrange were used to estimate the ancestral area of the genus, and an analysis in BEAST was used to estimate a time framework for its diversification. A sister relationship between the Pantepui and Andes+Cordillera de la Costa was significantly more likely than topologies indicating other hypothesis for the origin of Pantepui populations. The Andes was inferred as the ancestral area for Aulacorhynchus, and the group has diversified since the late Miocene. The biogeographic patterns found herein, in which the Andes are the source for biotas of other regions, are consistent with those found for flowerpiercers and tanagers, and do not support the hypothesis of the geologically old Pantepui as a source of Neotropical montain diversity. Based on the high potential for cryptic speciation and isolation of Pantepui populations, we consider that phylogenetic studies of additional taxa are important from a conservation perspective.

Evaluation of hypothesized adverse outcome pathway linking thyroid peroxidase inhibition to fish early life stage toxicity

EPA Science Inventory

There is an interest in developing alternatives to the fish early-life stage (FELS) test (OECD test guideline 210), for predicting adverse outcomes (e.g., impacts on growth and survival) using less resource-intensive methods. Development and characterization of adverse outcome pa...

Initial investigation of a hypothesized link between thyroid peroxidase inhibition and fish early-life stage toxicity

EPA Science Inventory

There is an interest in developing alternatives to the fish early-life stage (FELS) test (OECD test guideline 210), for predicting adverse outcomes (e.g., impacts on growth and survival) using less resource-intensive methods. Development and characterization of adverse outcome pa...

Computational Modeling to Evaluate Alternative Hypotheses for the Linkage of Aromatase Inhibition to Vitellogenin Levels in Fathead Minnows

EPA Science Inventory

Aromatase converts testosterone to estradiol (E2). In fish, E2 concentrations control hepatic synthesis of the glycolipoprotein vitellogenin (VTG), an egg yolk precursor protein essential to oocyte development and larval survival. Fathead minnows were exposed to the aromatase in...

Planning, Conducting, and Documenting Data Analysis for Program Improvement

ERIC Educational Resources Information Center

Winer, Abby; Taylor, Cornelia; Derrington, Taletha; Lucas, Anne

2015-01-01

This 2015 document was developed to help technical assistance (TA) providers and state staff define and limit the scope of data analysis for program improvement efforts, including the State Systemic Improvement Plan (SSIP); develop a plan for data analysis; document alternative hypotheses and additional analyses as they are generated; and…

Reduced oxygen utilization in septic shock: disorder or adaptation?

PubMed

Steiner, Alexandre A

2015-01-01

A fall in oxygen utilization during septic or endotoxic shock is thought to reflect circulatory hypoxia or mitochondrial dysfunction, but these pathology-oriented hypotheses do not explain all clinical observations. Here we discuss an alternative hypothesis of how oxygen utilization could fall as the result of a physiological thermometabolic adaptation.

Social Diversity, Institutions and Trust: A Cross-National Analysis

ERIC Educational Resources Information Center

Tsai, Ming-Chang; Laczko, Leslie; Bjornskov, Christian

2011-01-01

This cross-national investigation examines hypotheses derived from two major alternative perspectives on the determinants of trust in contemporary societies. Is a society's level of generalized trust a function of its ethnic composition, or of its type of governance and political system? The argument that social diversity (ethnic, linguistic, and…

Effects of Gum Chewing on Appetite and Digestion

ClinicalTrials.gov

2013-05-28

The Null Hypothesis is That Food Rheology Will Have no Effect on These Indices.; The Alternate Hypothesis is That Increased Mechanical Stimulation Will Result in Stronger Satiation/Satiety and Reduced Energy Intake.; Further, it is Hypothesized That the Effects of Mastication Will be Less Evident in Obese Compared to Lean Individuals.

Reduced Interference from Memory Testing: A Postretrieval Monitoring Account

ERIC Educational Resources Information Center

Pierce, Benton H.; Gallo, David A.; McCain, Jason L.

2017-01-01

Initial learning can interfere with subsequent learning (proactive interference [PI]), but recent work indicates initial testing can reduce PI. Here, we tested 2 alternative hypotheses of this effect: Does testing reduce PI by constraining retrieval to the target list, or by facilitating a postretrieval monitoring process? Participants first…

A Decision Support System for Energy Policy Analysis.

DTIC Science & Technology

1980-07-01

new realities or hypothesized realities to the modeling system. Lack of a PDL would make the system inflexible and accessible only to a patient ... expert . Certainly, given the present ratio of costs of personnel to costs of computers, the alternative of presenting data in its raw form is acceptable

Impact of Scaffolding and Question Structure on the Gender Gap

ERIC Educational Resources Information Center

Dawkins, Hillary; Hedgeland, Holly; Jordan, Sally

2017-01-01

We address previous hypotheses about possible factors influencing the gender gap in attainment in physics. Specifically, previous studies claim that scaffolding may preferentially benefit female students, and we present some alternative conclusions surrounding this hypothesis. By taking both student attainment level and the degree of question…

Young (late Amazonian), near-surface, ground ice features near the equator, Athabasca Valles, Mars

USGS Publications Warehouse

Burr, D.M.; Soare, R.J.; Wan, Bun Tseung J.-M.; Emery, J.P.

2005-01-01

A suite of four feature types in a ???20 km2 area near 10?? N, 204?? W in Athabasca Valles is interpreted to have resulted from near-surface ground ice. These features include mounds, conical forms with rimmed summit depressions, flatter irregularly-shaped forms with raised rims, and polygonal terrain. Based on morphology, size, and analogy to terrestrial ground ice forms, these Athabascan features are interpreted as pingos, collapsing pingos, pingo scars, and thermal contraction polygons, respectively. Thermal Infrared Mapping Spectrometer (THEMIS) data and geological features in the area are consistent with a sedimentary substrate underlying these features. These observations lead us to favor a ground ice interpretation, although we do not rule out volcanic and especially glaciofluvial hypotheses. The hypothesized ground ice that formed the mounds and rimmed features may have been emplaced via the deposition of saturated sediment during flooding; an alternative scenario invokes magmatically cycled groundwater. The ground ice implicit in the hypothesized thermal contraction polygons may have derived either from this flooding/ground water, or from atmospheric water vapor. The lack of obvious flood modification of the mounds and rimmed features indicates that they formed after the most recent flood inundated the area. Analogy with terrestrial pingos suggests that ground ice may be still extant within the positive relief mounds. As the water that flooded down Athabasca Valles emerged via a volcanotectonic fissure from a deep aquifer, any extant pingo ice may contain evidence of a deep subsurface biosphere. ?? 2005 Elsevier Inc. All rights reserved.

Tracing the footsteps of Sherlock Holmes: cognitive representations of hypothesis testing.

PubMed

Van Wallendael, L R; Hastie, R

1990-05-01

A well-documented phenomenon in opinion-revision literature is subjects' failure to revise probability estimates for an exhaustive set of mutually exclusive hypotheses in a complementary manner. However, prior research has not addressed the question of whether such behavior simply represents a misunderstanding of mathematical rules, or whether it is a consequence of a cognitive representation of hypotheses that is at odds with the Bayesian notion of a set relationship. Two alternatives to the Bayesian representation, a belief system (Shafer, 1976) and a system of independent hypotheses, were proposed, and three experiments were conducted to examine cognitive representations of hypothesis sets in the testing of multiple competing hypotheses. Subjects were given brief murder mysteries to solve and allowed to request various types of information about the suspects; after having received each new piece of information, subjects rated each suspect's probability of being the murderer. Presence and timing of suspect eliminations were varied in the first two experiments; the final experiment involved the varying of percentages of clues that referred to more than one suspect (for example, all of the female suspects). The noncomplementarity of opinion revisions remained a strong phenomenon in all conditions. Information-search data refuted the idea that subjects represented hypotheses as a Bayesian set; further study of the independent hypotheses theory and Shaferian belief functions as descriptive models is encouraged.

Time is up: increasing shadow price of time in primary-care office visits.

PubMed

Tai-Seale, Ming; McGuire, Thomas

2012-04-01

A physician's own time is a scarce resource in primary care, and the physician must constantly evaluate the gain from spending more time with the current patient against moving to address the health-care needs of the next. We formulate and test two alternative hypotheses. The first hypothesis is based on the premise that with time so scarce, physicians equalize the marginal value of time across patients. The second, alternative hypothesis states that physicians allocate the same time to each patient, regardless of how much the patient benefits from the time at the margin. For our empirical work, we examine the presence of a sharply increasing subjective shadow price of time around the 'target' time using video recordings of 385 visits by elderly patients to their primary care physician. We structure the data at the 'topic' level and find evidence consistent with the alternative hypothesis. Specifically, time elapsed within a visit is a very strong determinant of the current topic being the 'last topic'. This finding implies the physician's shadow price of time is rising during the course of a visit. We consider whether dislodging a target-time mentality from physicians (and patients) might contribute to more productive primary care practice. Copyright © 2011 John Wiley & Sons, Ltd.

Who Resembles Whom? Mimetic and Coincidental Look-Alikes among Tropical Reef Fishes

PubMed Central

Robertson, D. Ross

2013-01-01

Studies of mimicry among tropical reef-fishes usually give little or no consideration to alternative explanations for behavioral associations between unrelated, look-alike species that benefit the supposed mimic. I propose and assess such an alternative explanation. With mimicry the mimic resembles its model, evolved to do so in response to selection by the mimicry target, and gains evolved benefits from that resemblance. In the alternative, the social-trap hypothesis, a coincidental resemblance of the model to the “mimic” inadvertently attracts the latter to it, and reinforcement of this social trapping by learned benefits leads to the “mimic” regularly associating with the model. I examine three well known cases of supposed aggressive mimicry among reef-fishes in relation to nine predictions from these hypotheses, and assess which hypothesis offers a better explanation for each. One case, involving precise and complex morphological and behavioral resemblance, is strongly consistent with mimicry, one is inconclusive, and one is more consistent with a social-trap based on coincidental, imprecise resemblance. Few cases of supposed interspecific mimicry among tropical reef fishes have been examined in depth, and many such associations may involve social traps arising from generalized, coincidental resemblance. Mimicry may be much less common among these fishes than is generally thought. PMID:23372795

Is the fish embryo toxicity test (FET) with the zebrafish (Danio rerio) a potential alternative for the fish acute toxicity test?

PubMed

Lammer, E; Carr, G J; Wendler, K; Rawlings, J M; Belanger, S E; Braunbeck, Th

2009-03-01

The fish acute toxicity test is a mandatory component in the base set of data requirements for ecotoxicity testing. The fish acute toxicity test is not compatible with most current animal welfare legislation because mortality is the primary endpoint and it is often hypothesized that fish suffer distress and perhaps pain. Animal alternative considerations have also been incorporated into new European REACH regulations through strong advocacy for the reduction of testing with live animals. One of the most promising alternative approaches to classical acute fish toxicity testing with live fish is the fish embryo toxicity (FET) test. The FET has been a mandatory component in routine whole effluent testing in Germany since 2005 and has already been standardized at the international level. In order to analyze the applicability of the FET also in chemical testing, a comparative re-evaluation of both fish and fish embryo toxicity data was carried out for a total of 143 substances, and statistical approaches were developed to evaluate the correlation between fish and fish embryo toxicity data. Results confirm that fish embryo tests are neither better nor worse than acute fish toxicity tests and provide strong scientific support for the FET as a surrogate for the acute fish toxicity test.

Intelligent Data Visualization for Cross-Checking Spacecraft System Diagnosis

NASA Technical Reports Server (NTRS)

Ong, James C.; Remolina, Emilio; Breeden, David; Stroozas, Brett A.; Mohammed, John L.

2012-01-01

Any reasoning system is fallible, so crew members and flight controllers must be able to cross-check automated diagnoses of spacecraft or habitat problems by considering alternate diagnoses and analyzing related evidence. Cross-checking improves diagnostic accuracy because people can apply information processing heuristics, pattern recognition techniques, and reasoning methods that the automated diagnostic system may not possess. Over time, cross-checking also enables crew members to become comfortable with how the diagnostic reasoning system performs, so the system can earn the crew s trust. We developed intelligent data visualization software that helps users cross-check automated diagnoses of system faults more effectively. The user interface displays scrollable arrays of timelines and time-series graphs, which are tightly integrated with an interactive, color-coded system schematic to show important spatial-temporal data patterns. Signal processing and rule-based diagnostic reasoning automatically identify alternate hypotheses and data patterns that support or rebut the original and alternate diagnoses. A color-coded matrix display summarizes the supporting or rebutting evidence for each diagnosis, and a drill-down capability enables crew members to quickly view graphs and timelines of the underlying data. This system demonstrates that modest amounts of diagnostic reasoning, combined with interactive, information-dense data visualizations, can accelerate system diagnosis and cross-checking.

Chaos Versus Noisy Periodicity: Alternative Hypotheses for Childhood Epidemics

NASA Astrophysics Data System (ADS)

Olsen, L. F.; Schaffer, W. M.

1990-08-01

Whereas case rates for some childhood diseases (chickenpox) often vary according to an almost regular annual cycle, the incidence of more efficiently transmitted infections such as measles is more variable. Three hypotheses have been proposed to account for such fluctuations. (i) Irregular dynamics result from random shocks to systems with stable equilibria. (ii) The intrinsic dynamics correspond to biennial cycles that are subject to stochastic forcing. (iii) Aperiodic fluctuations are intrinsic to the epidemiology. Comparison of real world data and epidemiological models suggests that measles epidemics are inherently chaotic. Conversely, the extent to which chickenpox outbreaks approximate a yearly cycle depends inversely on the population size.

Environmental Stability of Plasmonic Biosensors Based on Natural versus Artificial Antibody.

PubMed

Luan, Jingyi; Xu, Ting; Cashin, John; Morrissey, Jeremiah J; Kharasch, Evan D; Singamaneni, Srikanth

2018-06-13

Plasmonic biosensors based on the refractive index sensitivity of localized surface plasmon resonance (LSPR) are considered to be highly promising for on-chip and point-of-care biodiagnostics. However, most of the current plasmonic biosensors employ natural antibodies as biorecognition elements, which can easily lose their biorecognition ability upon exposure to environmental stressors (e.g., temperature and humidity). Plasmonic biosensors relying on molecular imprints as recognition elements (artificial antibodies) are hypothesized to be an attractive alternative for applications in resource-limited settings due to their excellent thermal, chemical, and environmental stability. In this work, we provide a comprehensive comparison of the stability of plasmonic biosensors based on natural and artificial antibodies. Although the natural antibody-based plasmonic biosensors exhibit superior sensitivity, their stability (temporal, thermal, and chemical) was found to be vastly inferior to those based on artificial antibodies. Our results convincingly demonstrate that these novel classes of artificial antibody-based plasmonic biosensors are highly attractive for point-of-care and resource-limited conditions where tight control over transport, storage, and handling conditions is not possible.

The biasing effect of clinical history on physical examination diagnostic accuracy.

PubMed

Sibbald, Matthew; Cavalcanti, Rodrigo B

2011-08-01

Literature on diagnostic test interpretation has shown that access to clinical history can both enhance diagnostic accuracy and increase diagnostic error. Knowledge of clinical history has also been shown to enhance the more complex cognitive task of physical examination diagnosis, possibly by enabling early hypothesis generation. However, it is unclear whether clinicians adhere to these early hypotheses in the face of unexpected physical findings, thus resulting in diagnostic error. A sample of 180 internal medicine residents received a short clinical history and conducted a cardiac physical examination on a high-fidelity simulator. Resident Doctors (Residents) were randomised to three groups based on the physical findings in the simulator. The concordant group received physical examination findings consistent with the diagnosis that was most probable based on the clinical history. Discordant groups received findings associated with plausible alternative diagnoses which either lacked expected findings (indistinct discordant) or contained unexpected findings (distinct discordant). Physical examination diagnostic accuracy and physical examination findings were analysed. Physical examination diagnostic accuracy varied significantly among groups (75 ± 44%, 2 ± 13% and 31 ± 47% in the concordant, indistinct discordant and distinct discordant groups, respectively (F(2,177)  = 53, p < 0.0001). Of the 115 Residents who were diagnostically unsuccessful, 33% adhered to their original incorrect hypotheses. Residents verbalised an average of 12 findings (interquartile range: 10-14); 58 ± 17% were correct and the percentage of correct findings was similar in all three groups (p = 0.44). Residents showed substantially decreased diagnostic accuracy when faced with discordant physical findings. The majority of trainees given discordant physical findings rejected their initial hypotheses, but were still diagnostically unsuccessful. These results suggest that overcoming the bias induced by a misleading clinical history may involve two independent steps: rejection of the incorrect initial hypothesis, and selection of the correct diagnosis. Educational strategies focused solely on prompting clinicians to re-examine their hypotheses may be insufficient to reduce diagnostic error. © Blackwell Publishing Ltd 2011.

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

Fraley, John J.; Marotz, Brian L.; DosSantos, Joseph M.

In this document we present fisheries losses, mitigation alternatives, and recommendations to protect, mitigate, and enhance resident fish and aquatic habitat affected by the construction and operation of Hungry Horse Dam. This plan addresses six separate program measures in the 1987 Columbia Basin Fish and Wildlife Program. We designed the plan to be closely coordinated in terms of dam operations, funding, and activities with the Kerr Mitigation Plan presently before the Federal Energy Regulatory Commission. This document represents a mitigation plan for consideration by the Northwest Power Planning Council process; it is not an implementation plan. Flathead Lake is onemore » of the cleanest lakes of its size in the world. The exceptional water quality and unique native fisheries make the Flathead Lake/River system extremely valuable to the economy and quality of life in the basin. The recreational fishery in Flathead Lake has an estimated value of nearly eight million dollars annually. This mitigation process represents our best opportunity to reduce the impacts of hydropower in this valuable aquatic system and increase angling opportunity. We based loss estimates and mitigation alternatives on an extensive data base, agency reports, nationally and internationally peer-reviewed scientific articles, and an innovative biological model for Hungry Horse Reservoir and the Flathead River. We conducted an extensive, 14-month scoping and consultation process with agency representatives, representatives of citizen groups, and the general public. This consultation process helped identify issues, areas of agreement, areas of conflict, and advantages and disadvantages of mitigation alternatives. The results of the scoping and consultation process helped shape our mitigation plan. Our recommended plan is based firmly on principles of adaptive management and recognition of biological uncertainty. After we receive direction from the NPPC, we will add more detailed hypotheses and other features necessary for a long-term implementation plan.« less

Alternative Lipid Emulsions in the Critically Ill: A Systematic Review of the Evidence

PubMed Central

Manzanares, William; Dhaliwal, Rupinder; Jurewitsch, Brian; Stapleton, Renee D.; Jeejeebhoy, Khursheed N.; Heyland, Daren K.

2015-01-01

Introduction Parenteral lipid emulsions (LEs) are commonly rich in long-chain triglycerides (LCT) derived from soybean oil (SO). SO containing emulsions may promote systemic inflammation and therefore may adversely affect clinical outcomes. We hypothesized that alternative oil-based LEs (SO-sparing strategies) may improve clinical outcomes in critically ill adult patients compared to SO emulsion only products. The purpose of this systematic review was to evaluate the effect of parenteral SO-sparing strategies on clinical outcomes in intensive care unit (ICU) patients. Methods We searched computerized databases from 1980 to 2013. We included randomized controlled trials (RCTs) conducted in critically ill adult patients that evaluated SO-sparing strategies versus SO-based LEs in the context of parenteral nutrition (PN). Results A total of 12 RCTs met inclusion criteria. When the results of these RCTs that were statistically aggregated, SO-sparing strategies were associated with clinically important reductions in mortality (risk ratio RR= 0.83, 95% confidence intervals CI 0.62, 1.11, P = 0.20), in duration of ventilation (weighted mean difference, WMD −2.57, 95% CI −5.51, 0.37, P= 0.09), and in ICU length of stay (WMD −2.31, 95% CI −5.28, 0.66, P= 0.13) but none of these differences were statistically significant. SO-sparing strategies had no effect on infectious complications (RR=1.13, 95% CI 0.87, 1.46, P=0.35). Conclusion Alternative oil-based LEs may be associated with clinically important reductions in mortality, duration of ventilation, and ICU LOS but lack of statistical precision precludes any clinical recommendations at this time. Further research is warranted to confirm these potential positive treatment effects. PMID:23812404

Alternative lipid emulsions in the critically ill: a systematic review of the evidence.

PubMed

Manzanares, William; Dhaliwal, Rupinder; Jurewitsch, Brian; Stapleton, Renee D; Jeejeebhoy, Khursheed N; Heyland, Daren K

2013-10-01

Parenteral lipid emulsions (LEs) are commonly rich in long-chain triglycerides derived from soybean oil (SO). SO-containing emulsions may promote systemic inflammation and therefore may adversely affect clinical outcomes. We hypothesized that alternative oil-based LEs (SO-sparing strategies) may improve clinical outcomes in critically ill adult patients compared to products containing SO emulsion only. The purpose of this systematic review was to evaluate the effect of parenteral SO-sparing strategies on clinical outcomes in intensive care unit (ICU) patients. We searched computerized databases from 1980 to 2013. We included randomized controlled trials (RCTs) conducted in critically ill adult patients that evaluated SO-sparing strategies versus SO-based LEs in the context of parenteral nutrition. A total of 12 RCTs met the inclusion criteria. When the results of these RCTs were statistically aggregated, SO-sparing strategies were associated with clinically important reductions in mortality (risk ratio, RR 0.83; 95 % confidence intervals, CI 0.62, 1.11; P = 0.20), in duration of ventilation (weighted mean difference, WMD -2.57; 95 % CI -5.51, 0.37; P = 0.09), and in ICU length of stay (LOS) (WMD -2.31; 95 % CI -5.28, 0.66; P = 0.13) but none of these differences were statistically significant. SO-sparing strategies had no effect on infectious complications (RR 1.13; 95 % CI 0.87, 1.46; P = 0.35). Alternative oil-based LEs may be associated with clinically important reductions in mortality, duration of ventilation, and ICU LOS but lack of statistical precision precludes any clinical recommendations at this time. Further research is warranted to confirm these potential positive treatment effects.

IYPT problems teach high school students about teamwork and the scientific method

NASA Astrophysics Data System (ADS)

Kochanski, K.; Klishin, A.

2015-12-01

Laboratory work is often STEM students' primary exposure to key creative and communicative skills in the sciences, including experimental design, trouble shooting, team work, and oral presentations. The International Young Physicists' Tournament (IYPT) teaches these skills by inviting high school students to investigate simple unsolved systems instead of reproducing familiar results. Students work in teams to form hypotheses, gather data, and present their results orally in a tournament format. The IYPT has published 17 questions yearly since 1988, and its archives are an efficient source of experimental problems for outreach programs and have also been used for first-year undergraduate project classes (Planisic, 2009). We present insights and outcomes from two schools in which we introduced a new extracurricular program based on the IYPT model. Twenty-four students worked in small teams for three hours per day for six weeks. Surprisingly, most teams chose problems in unfamiliar subject areas such as fluid dynamics, and tailored their approaches to take advantage of individual skills including soldering, photography, and theoretical analysis. As the program progressed, students developed an increasingly intuitive understanding of the scientific method. They began to discuss the repeatability of their experiments without prompting, and were increasingly willing to describe alternative hypotheses.

Unemployment and ill health: understanding the relationship.

PubMed Central

Bartley, M

1994-01-01

OBJECTIVE--To review research relevant to understanding the psychological, social, and biological pathways by which unemployment may affect health risk; to consider the importance of four specific mechanisms; and to indicate some directions for future research. CRITERIA FOR INCLUSION AND EXCLUSION OF PUBLISHED STUDIES--Studies were chosen to illustrate the development of four major hypotheses regarding the relationship between unemployment and ill health, as well as the present state of knowledge. The review therefore includes some much-cited "classics" drawn from a long time span. Where recent reviews already exist relevant to individual mechanisms, these are referred to. Recent (since 1987) reports were sought by searching the BIDS data base. Particular effort was made to locate studies which enabled alternative hypotheses to be evaluated, and to point out where existing evidence is inconsistent or incomplete, indicating the need for further research. CONCLUSIONS--To understand the relationship between unemployment and ill health and mortality, four mechanisms need to be considered: the role of relative poverty; social isolation and loss of self esteem; health related behaviour (including that associated with membership of certain types of "subculture"); and the effect that a spell of unemployment has on subsequent employment patterns. PMID:7964329

Voc Degradation in TF-VLS Grown InP Solar Cells

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

Sun, Yubo; Sun, Xingshu; Johnston, Steve

2016-11-21

Here we consider two hypotheses to explain the open-circuit voltage (VOC) degradation observed in thin-film vapor-liquid-solid (TF-VLS) grown p-type InP photovoltaic cells: bandgap narrowing and local shunting. First, a bandgap (Eg) narrowing effect is hypothesized, based on the surface inhomogeneity of VLS InP captured by the photoluminescence (PL) image. The PL data was used to estimate a spatially-resolved active VOC across surface of the InP sample. Combining this data with the effective Jsc allowed an assessment of the I-V characteristics of individual unit cells. Next, an H-SPICE diode compact model was utilized to reproduce the I-V characteristics of the wholemore » sample. We find a good fit to the I-V performance of TF-VLS grown InP solar cell. Second, a local shunting effect was also considered as an alternative explanation of the VOC degradation effect. Again, PL image data was used, and small local shunt resistance was added in arbitrary elementary unit cells to represent certain dark spots seen in the PL image and dictate the VOC degradation occurred in the sample.« less

Resampling-Based Empirical Bayes Multiple Testing Procedures for Controlling Generalized Tail Probability and Expected Value Error Rates: Focus on the False Discovery Rate and Simulation Study

PubMed Central

Dudoit, Sandrine; Gilbert, Houston N.; van der Laan, Mark J.

2014-01-01

Summary This article proposes resampling-based empirical Bayes multiple testing procedures for controlling a broad class of Type I error rates, defined as generalized tail probability (gTP) error rates, gTP(q, g) = Pr(g(Vn, Sn) > q), and generalized expected value (gEV) error rates, gEV(g) = E[g(Vn, Sn)], for arbitrary functions g(Vn, Sn) of the numbers of false positives Vn and true positives Sn. Of particular interest are error rates based on the proportion g(Vn, Sn) = Vn/(Vn + Sn) of Type I errors among the rejected hypotheses, such as the false discovery rate (FDR), FDR = E[Vn/(Vn + Sn)]. The proposed procedures offer several advantages over existing methods. They provide Type I error control for general data generating distributions, with arbitrary dependence structures among variables. Gains in power are achieved by deriving rejection regions based on guessed sets of true null hypotheses and null test statistics randomly sampled from joint distributions that account for the dependence structure of the data. The Type I error and power properties of an FDR-controlling version of the resampling-based empirical Bayes approach are investigated and compared to those of widely-used FDR-controlling linear step-up procedures in a simulation study. The Type I error and power trade-off achieved by the empirical Bayes procedures under a variety of testing scenarios allows this approach to be competitive with or outperform the Storey and Tibshirani (2003) linear step-up procedure, as an alternative to the classical Benjamini and Hochberg (1995) procedure. PMID:18932138

Assessment of Damage to Nucleic Acids and Repair Machinery in Salmonella typhimurium Exposed to Chlorine

PubMed Central

Phe, M. H.; Hajj Chehade, M.; Guilloteau, H.; Merlin, C.; Block, J. C.

2009-01-01

Water disinfection is usually evaluated using mandatory methods based on cell culturability. However, such methods do not consider the potential of cells to recover, which should also be kept as low as possible. In this paper, we hypothesized that a successful disinfection is achieved only when the applied chlorine leads to both intracellular nucleic acid damage and strong alterations of the DNA repair machinery. Monitoring the SOS system responsiveness with a umuC’-‘lacZ reporter fusion, we found that the expression of this important cellular machinery was altered after the beginning of membrane permeabilization but prior to the total decline of both the cell culturability and the nucleic acid integrity as revealed by Sybr-II staining. Rapid measurement of such nucleic acid alterations by fluorochrome-based staining could be used as an alternative method for assessing the effectiveness of disinfection with chlorine. PMID:19936107

Anticipation - the underlying science of sport. Report on research in progress

NASA Astrophysics Data System (ADS)

Nadin, Mihai

2015-05-01

Professional sport practitioners intuitively acknowledge anticipation. Sports researchers sometimes discuss it. Still, there is little data-based evidence to characterize the role anticipation plays in human performance. Even less documented is the distinction between reaction and anticipation. This text presents the real-time quantification environment developed as an AnticipationScope™. Based on a very large data harvest from this experimental set-up, hypotheses regarding the role of anticipation in sport are advanced. The conclusion is that while preparation and reaction play an important role in sports performance, in the final analysis anticipation distinguishes the professional from other sport practitioners. Work in progress is presented with the aim of engaging the community of researchers in the design of alternative methods for quantifying anticipation and for processing the data. Generalization from sport to human performance is one of the intended outcomes of this research.

Logic as Marr's Computational Level: Four Case Studies.

PubMed

Baggio, Giosuè; van Lambalgen, Michiel; Hagoort, Peter

2015-04-01

We sketch four applications of Marr's levels-of-analysis methodology to the relations between logic and experimental data in the cognitive neuroscience of language and reasoning. The first part of the paper illustrates the explanatory power of computational level theories based on logic. We show that a Bayesian treatment of the suppression task in reasoning with conditionals is ruled out by EEG data, supporting instead an analysis based on defeasible logic. Further, we describe how results from an EEG study on temporal prepositions can be reanalyzed using formal semantics, addressing a potential confound. The second part of the article demonstrates the predictive power of logical theories drawing on EEG data on processing progressive constructions and on behavioral data on conditional reasoning in people with autism. Logical theories can constrain processing hypotheses all the way down to neurophysiology, and conversely neuroscience data can guide the selection of alternative computational level models of cognition. Copyright © 2014 Cognitive Science Society, Inc.

The picture superiority effect: support for the distinctiveness model.

PubMed

Mintzer, M Z; Snodgrass, J G

1999-01-01

The form change paradigm was used to explore the basis for the picture superiority effect. Recognition memory for studied pictures and words was tested in their study form or the alternate form. Form change cost was defined as the difference between recognition performance for same and different form items. Based on the results of Experiment 1 and previous studies, it was difficult to determine the relative cost for studied pictures and words due to a reversal of the mirror effect. We hypothesized that the reversed mirror effect results from subjects' basing their recognition decisions on their assumptions about the study form. Experiments 2 and 3 confirmed this hypothesis and generated a method for evaluating the relative cost for pictures and words despite the reversed mirror effect. More cost was observed for pictures than words, supporting the distinctiveness model of the picture superiority effect.

Handwriting individualization using distance and rarity

NASA Astrophysics Data System (ADS)

Tang, Yi; Srihari, Sargur; Srinivasan, Harish

2012-01-01

Forensic individualization is the task of associating observed evidence with a specific source. The likelihood ratio (LR) is a quantitative measure that expresses the degree of uncertainty in individualization, where the numerator represents the likelihood that the evidence corresponds to the known and the denominator the likelihood that it does not correspond to the known. Since the number of parameters needed to compute the LR is exponential with the number of feature measurements, a commonly used simplification is the use of likelihoods based on distance (or similarity) given the two alternative hypotheses. This paper proposes an intermediate method which decomposes the LR as the product of two factors, one based on distance and the other on rarity. It was evaluated using a data set of handwriting samples, by determining whether two writing samples were written by the same/different writer(s). The accuracy of the distance and rarity method, as measured by error rates, is significantly better than the distance method.

Evoked fear and effects of appeals on attitudes to performing breast self-examination: an information-processing perspective.

PubMed

Ruiter, R A; Kok, G; Verplanken, B; Brug, J

2001-06-01

The effect of fear arousal on attitude toward participating in early detection activities [i.e. breast self-examination (BSE)] was studied from an information-processing perspective. It was hypothesized that fear arousal motivates respondents to more argument-based processing of fear-relevant persuasive information. Respondents first read information about breast cancer in which fear was manipulated. After measuring fear arousal, respondents read a persuasive message about performing BSE. Analyses with reported fear, but not manipulated fear, found support for the hypothesis. Respondents who reported mild fear of breast cancer based their attitude toward BSE more on the arguments provided than respondents who reported low fear of breast cancer. This finding suggests that the use of fear arousal may be an efficient tool in health education practice. However, alternative interpretations are provided, in addition to the suggestion to be careful with using fear arousal in health education messages.

Bovid mortality profiles in paleoecological context falsify hypotheses of endurance running-hunting and passive scavenging by early Pleistocene hominins

NASA Astrophysics Data System (ADS)

Bunn, Henry T.; Pickering, Travis Rayne

2010-11-01

The world's first archaeological traces from 2.6 million years ago (Ma) at Gona, in Ethiopia, include sharp-edged cutting tools and cut-marked animal bones, which indicate consumption of skeletal muscle by early hominin butchers. From that point, evidence of hominin meat-eating becomes increasingly more common throughout the Pleistocene archaeological record. Thus, the substantive debate about hominin meat-eating now centers on mode(s) of carcass resource acquisition. Two prominent hypotheses suggest, alternatively, (1) that early Homo hunted ungulate prey by running them to physiological failure and then dispatching them, or (2) that early Homo was relegated to passively scavenging carcass residues abandoned by carnivore predators. Various paleontologically testable predictions can be formulated for both hypotheses. Here we test four predictions concerning age-frequency distributions for bovids that contributed carcass remains to the 1.8 Ma. old FLK 22 Zinjanthropus (FLK Zinj, Olduvai Gorge, Tanzania) fauna, which zooarchaeological and taphonomic data indicate was formed predominantly by early Homo. In all but one case, the bovid mortality data from FLK Zinj violate test predictions of the endurance running-hunting and passive scavenging hypotheses. When combined with other taphonomic data, these results falsify both hypotheses, and lead to the hypothesis that early Homo operated successfully as an ambush predator.

Use it or lose it: reproductive implications of ecological specialization in a haematophagous ectoparasite.

PubMed

Arbiv, A; Khokhlova, I S; Ovadia, O; Novoplansky, A; Krasnov, B R

2012-06-01

Using experimentally induced disruptive selection, we tested two hypotheses regarding the evolution of specialization in parasites. The 'trade-off' hypothesis suggests that adaptation to a specific host may come at the expense of a reduced performance when exploiting another host. The alternative 'relaxed selection' hypothesis suggests that the ability to exploit a given host would deteriorate when becoming obsolete. Three replicate populations of a flea Xenopsylla ramesis were maintained on each of two rodent hosts, Meriones crassus and Dipodillus dasyurus, for nine generations. Fleas maintained on a specific host species for a few generations substantially decreased their reproductive performance when transferred to an alternative host species, whereas they generally did not increase their performance on their maintenance host. The results support the 'relaxed selection' hypothesis of the evolution of ecological specialization in haematophagous ectoparasites, while suggesting that trade-offs are unlikely drivers of specialization. Further work is needed to study the extent by which the observed specializations are based on epigenetic or genetic modifications. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Therapeutic Effects of Human Amniotic Fluid-Derived Stem Cells on Renal Interstitial Fibrosis in a Murine Model of Unilateral Ureteral Obstruction

PubMed Central

Yin, Zhongcheng; Zhou, Xudong; Li, Xiaoju; Xiao, Aiguo

2013-01-01

Interstitial fibrosis is regarded as the main pathway for the progression of chronic kidney disease (CKD) and is often associated with severe renal dysfunction. Stem cell-based therapies may provide alternative approaches for the treatment of CKD. Human amniotic fluid-derived stem cells (hAFSCs) are a novel stem cell population, which exhibit both embryonic and mesenchymal stem cell characteristics. Herein, the present study investigated whether the transplantation of hAFSCs into renal tissues could improve renal interstitial fibrosis in a murine model of unilateral ureteral obstruction (UUO). We showed that hAFSCs provided a protective effect and alleviated interstitial fibrosis as reflected by an increase in microvascular density; additionally, hAFSCs treatment beneficially modulated protein levels of vascular endothelial growth factor (VEGF), hypoxia inducible factor-1α (HIF-1α) and transforming growth factor-β1 (TGF-β1). Therefore, we hypothesize that hAFSCs could represent an alternative, readily available source of stem cells that can be applied for the treatment of renal interstitial fibrosis. PMID:23724119

Community Detection for Correlation Matrices

NASA Astrophysics Data System (ADS)

MacMahon, Mel; Garlaschelli, Diego

2015-04-01

A challenging problem in the study of complex systems is that of resolving, without prior information, the emergent, mesoscopic organization determined by groups of units whose dynamical activity is more strongly correlated internally than with the rest of the system. The existing techniques to filter correlations are not explicitly oriented towards identifying such modules and can suffer from an unavoidable information loss. A promising alternative is that of employing community detection techniques developed in network theory. Unfortunately, this approach has focused predominantly on replacing network data with correlation matrices, a procedure that we show to be intrinsically biased because of its inconsistency with the null hypotheses underlying the existing algorithms. Here, we introduce, via a consistent redefinition of null models based on random matrix theory, the appropriate correlation-based counterparts of the most popular community detection techniques. Our methods can filter out both unit-specific noise and system-wide dependencies, and the resulting communities are internally correlated and mutually anticorrelated. We also implement multiresolution and multifrequency approaches revealing hierarchically nested subcommunities with "hard" cores and "soft" peripheries. We apply our techniques to several financial time series and identify mesoscopic groups of stocks which are irreducible to a standard, sectorial taxonomy; detect "soft stocks" that alternate between communities; and discuss implications for portfolio optimization and risk management.

Status change during adulthood: life-history by-product or kin selection based on reproductive value?

PubMed Central

Combes, S. L.; Altmann, J.

2001-01-01

When dominance status predicts fitness, most adaptive models of dominance relationships among cercopithecine primate females predict lifetime maintenance of status. These models and alternative ones positing rank decline as a non-adaptive by-product have remained largely untested, however, because lifetime status of older adults has been virtually unknown for natural populations. In a 25-year study of adult female savannah baboons (Papio cynocephalus), in each of three social groups, rank losses were common among the 66 females that lived past median adult age. These losses were not accounted for by loss in relative rank from group growth or by loss in absolute rank from reversals in rank between members of different maternal families or between sisters. Rather, females that had mature daughters experienced loss of dominance status to these offspring, a characteristic of all but the top-ranking matriline of each group. Among proposed hypotheses for rank reversals between adults, that of kin selection based on relative reproductive value is most clearly supported by these data. In contrast, observed patterns of rank loss are not consistent with alternative models that postulate that changes during adult lifespan are a product of accumulated risk, physical decline during ageing, or coalitionary support among females within or between matrilines. PMID:11429136

Evolutionary Diversification of New Caledonian Araucaria

PubMed Central

Kranitz, Mai Lan; Biffin, Edward; Clark, Alexandra; Hollingsworth, Michelle L.; Ruhsam, Markus; Gardner, Martin F.; Thomas, Philip; Mill, Robert R.; Ennos, Richard A.; Gaudeul, Myriam; Lowe, Andrew J.; Hollingsworth, Peter M.

2014-01-01

New Caledonia is a global biodiversity hotspot. Hypotheses for its biotic richness suggest either that the island is a ‘museum’ for an old Gondwana biota or alternatively it has developed following relatively recent long distance dispersal and in situ radiation. The conifer genus Araucaria (Araucariaceae) comprises 19 species globally with 13 endemic to this island. With a typically Gondwanan distribution, Araucaria is particularly well suited to testing alternative biogeographic hypotheses concerning the origins of New Caledonian biota. We derived phylogenetic estimates using 11 plastid and rDNA ITS2 sequence data for a complete sampling of Araucaria (including multiple accessions of each of the 13 New Caledonian Araucaria species). In addition, we developed a dataset comprising 4 plastid regions for a wider taxon sample to facilitate fossil based molecular dating. Following statistical analyses to identify a credible and internally consistent set of fossil constraints, divergence times estimated using a Bayesian relaxed clock approach were contrasted with geological scenarios to explore the biogeographic history of Araucaria. The phylogenetic data resolve relationships within Araucariaceae and among the main lineages in Araucaria, but provide limited resolution within the monophyletic New Caledonian species group. Divergence time estimates suggest a Late Cretaceous-Cenozoic radiation of extant Araucaria and a Neogene radiation of the New Caledonian lineage. A molecular timescale for the evolution of Araucariaceae supports a relatively recent radiation, and suggests that earlier (pre-Cenozoic) fossil types assigned to Araucaria may have affinities elsewhere in Araucariaceae. While additional data will be required to adequately resolve relationships among the New Caledonian species, their recent origin is consistent with overwater dispersal following Eocene emersion of New Caledonia but is too old to support a single dispersal from Australia to Norfolk Island for the radiation of the Pacific Araucaria sect. Eutacta clade. PMID:25340350

Differences in the Weighting and Choice of Evidence for Plausible versus Implausible Causes

ERIC Educational Resources Information Center

Goedert, Kelly M.; Ellefson, Michelle R.; Rehder, Bob

2014-01-01

Individuals have difficulty changing their causal beliefs in light of contradictory evidence. We hypothesized that this difficulty arises because people facing implausible causes give greater consideration to causal alternatives, which, because of their use of a positive test strategy, leads to differential weighting of contingency evidence.…

Effect of protein supplementation on forage utilization by cattle in annual grass-dominated rangelands in the Channel Scablands of Eastern Washington

USDA-ARS?s Scientific Manuscript database

Medusahead (Taeniatherum caput-medusae [L.] Nevski) has become a major component replacing vegetation on the Channeled Scablands of eastern Washington. Livestock typically avoid grazing medusahead and forage alternatives are becoming limited in the region. We hypothesized that protein supplementat...

The effect of resource history on the functioning of soil microbial communities is maintained across time

Treesearch

A. Keiser; M. Strickland; N. Fierer; M. Bradford

2011-01-01

Historical resource conditions appear to influence microbial community function. With time, historical influences might diminish as populations respond to the contemporary environment. Alternatively, they may persist given factors such as contrasting genetic potentials for adaptation to a new environment. Using experimental microcosms, we test competing hypotheses that...

Peer Sexual Harassment: Finding Voice, Changing Culture

ERIC Educational Resources Information Center

Martin, Jennifer L.

2005-01-01

This intervention study examines the problem of sexual harassment in an alternative high school for at-risk students. It was hypothesized that creating a forum where girls felt safe to share their experiences would increase their awareness of sexual harassment and its effects, eventually contributing to a decrease in incidents of sexual harassment…

Microbial infection affects egg viability and incubation behavior in a tropical passerine.

Treesearch

Mark I. Cook; Steven R. Beissinger; Gary A. Toranzos; Roberto A. Arendt Rodriguez

2004-01-01

Many avian species initiate incubation before clutch completion, which causes eggs to hatch asynchronously. This influences brood competitive dynamics and often results in nestling mortality. The prevailing hypotheses contend that parents incubate early because asynchronous hatching provides fitness benefits to parents or surviving offspring. An alternative idea is...

Developmental Dissociation in the Neural Responses to Simple Multiplication and Subtraction Problems

ERIC Educational Resources Information Center

Prado, Jérôme; Mutreja, Rachna; Booth, James R.

2014-01-01

Mastering single-digit arithmetic during school years is commonly thought to depend upon an increasing reliance on verbally memorized facts. An alternative model, however, posits that fluency in single-digit arithmetic might also be achieved via the increasing use of efficient calculation procedures. To test between these hypotheses, we used a…

How Do Transformational Leaders Transform Organizations? A Study of the Relationship between Leadership and Entrepreneurship

ERIC Educational Resources Information Center

Eyal, Ori; Kark, Ronit

2004-01-01

The aim of this study is to discover the relationship between different leadership styles and alternative entrepreneurial strategies in the not-for-profit public school system. We develop a conceptual framework for understanding various strategies of corporate entrepreneurship. Accordingly, we hypothesize that transformational leadership can…

Hyperactivity in Boys with Attention-Deficit/Hyperactivity Disorder (ADHD): A Ubiquitous Core Symptom or Manifestation of Working Memory Deficits?

ERIC Educational Resources Information Center

Rapport, Mark D.; Bolden, Jennifer; Kofler, Michael J.; Sarver, Dustin E.; Raiker, Joseph S.; Alderson, R. Matt

2009-01-01

Hyperactivity is currently considered a core and ubiquitous feature of attention-deficit/hyperactivity disorder (ADHD); however, an alternative model challenges this premise and hypothesizes a functional relationship between working memory (WM) and activity level. The current study investigated whether children's activity level is functionally…

Determining the Exchangeability of Concept Map and Problem-Solving Essay Scores

ERIC Educational Resources Information Center

Hollenbeck, Keith; Twyman, Todd; Tindal, Gerald

2006-01-01

This study investigated the score exchangeability of concept maps with problem-solving essays. Of interest was whether sixth-grade students' concept maps predicted their scores on essay responses that used concept map content. Concept maps were hypothesized to be alternatives to performance assessments for content-area domain knowledge in science.…

The Individual Consistency of Acquiescence and Extreme Response Style in Self-Report Questionnaires

ERIC Educational Resources Information Center

Weijters, Bert; Geuens, Maggie; Schillewaert, Niels

2010-01-01

The severity of bias in respondents' self-reports due to acquiescence response style (ARS) and extreme response style (ERS) depends strongly on how consistent these response styles are over the course of a questionnaire. In the literature, different alternative hypotheses on response style (in)consistency circulate. Therefore, nine alternative…

An Eye-Movement Analysis of the Refutation Effect in Reading Science Text

ERIC Educational Resources Information Center

Ariasi, N.; Hyönä, J.; Kaakinen, J. K.; Mason, L.

2017-01-01

In this study, we used eye-tracking methodology for deeper understanding of the refutation text effect on online text comprehension. A refutation text acknowledges the reader's alternative conceptions about a phenomenon, refutes them and presents the correct conceptions. We tested two hypotheses about its facilitation effect: the coherence…

Multilevel and Single-Level Models for Measured and Latent Variables When Data Are Clustered

ERIC Educational Resources Information Center

Stapleton, Laura M.; McNeish, Daniel M.; Yang, Ji Seung

2016-01-01

Multilevel models are often used to evaluate hypotheses about relations among constructs when data are nested within clusters (Raudenbush & Bryk, 2002), although alternative approaches are available when analyzing nested data (Binder & Roberts, 2003; Sterba, 2009). The overarching goal of this article is to suggest when it is appropriate…

Hydrologic responses to climate change: considering geographic context and alternative hypotheses

Treesearch

J.A. Jones

2011-01-01

One of the most significant consequences of climate warming is the likely change in streamflow as a result of warming air temperatures. Hydrologists have responded to the challenge of understanding these effects. Many recent studies quantify historical trends in streamflow and usually attribute these trends to climate warming, via altered evapotranspiration and...

Remission of Maternal Depression: Relations to Family Functioning and Youth Internalizing and Externalizing Symptoms

ERIC Educational Resources Information Center

Foster, Cynthia Ewell; Webster, Melissa C.; Weissman, Myrna M.; Pilowsky, Daniel J.; Wickramaratne, Priya J.; Talati, Ardesheer; Rush, A. John; Hughes, Carroll W.; Garber, Judy; Malloy, Erin; Cerda, Gabrielle; Kornstein, Susan G.; Alpert, Jonathan E.; Wisniewski, Stephen R.; Trivedi, Madhukar H.; Fava, Maurizio; King, Cheryl A.

2008-01-01

Family functioning and parenting were hypothesized to mediate the relation between remission of maternal depression and children's psychosocial adjustment. Participants were 114 mother-child dyads participating in the Sequenced Treatment Alternatives to Relieve Depression Child 3-month follow-up. All mothers had been diagnosed with major…

An Aptitude-Strategy Interaction in Linear Syllogistic Reading. Technical Report No. 15.

ERIC Educational Resources Information Center

Sternberg, Robert J.; Weil, Evelyn M.

An aptitude-strategy interaction in linear syllogistic reasoning was tested on 144 undergraduate and graduate students of both sexes. It was hypothesized that the efficiency of each of four alternative strategies--control, visual, algorithmic, and mixed--would depend upon the subjects' pattern of verbal and spatial abilities. Two tests of verbal…

Development, Discouragement, or Diversion? New Evidence on the Effects of College Remediation Policy

ERIC Educational Resources Information Center

Scott-Clayton, Judith; Rodriguez, Olga

2015-01-01

Half of all college students will enroll in remedial coursework but evidence of its effectiveness is mixed. Using a regression-discontinuity design with data from a large urban community college system, we make three contributions. First, we articulate three alternative hypotheses regarding the potential impacts of remediation. Second, in addition…

The Focusing of Responsibility: An Alternative Hypothesis in Help-Demanding Situations.

ERIC Educational Resources Information Center

Misavage, Robert; Richardson, James T.

The "diffusion of responsibility" hypothesis as an explanation of helping behavior (or lack of same) is qualified by suggesting that the hypothesis applies only in non-interacting situations. It is hypothesized that interacting groups who are aware of a help-demanding situation actually focus the responsibility and, therefore, take action as a…

Engagement and disengagement in mutual-help addiction recovery housing: a test of affective events theory.

PubMed

Beasley, Christopher R; Jason, Leonard A

2015-06-01

This study tested an affective events theory (AET) model in the Oxford House network of recovery homes. Residents' congruence with their home (P-E fit) was hypothesized to directly influence behavior that supported the house and other residents-citizenship behavior. We further hypothesized P-E fit would be related to member intentions to leave, with attitudes toward the home mediating that relationship. To assess this, we administered a cross-sectional national survey to 296 residents of 83 randomly selected Oxford Houses. Although the AET model demonstrated good fit with the data, an alternative model fit better. This alternative model suggested an additional indirect relationship between P-E fit and citizenship mediated by attitudes. Results suggested affective experiences such as feeling like one fits with a community may influence engagement and disengagement. There appears to be a direct influence of fit on citizenship behavior and an indirect influence of fit through recovery home attitudes on both citizenship and intentions to leave the home. We conclude affective experiences could be important for community engagement and disengagement but AET may need to integrate cognitive dissonance theory.

Toward brain-actuated car applications: Self-paced control with a motor imagery-based brain-computer interface.

PubMed

Yu, Yang; Zhou, Zongtan; Yin, Erwei; Jiang, Jun; Tang, Jingsheng; Liu, Yadong; Hu, Dewen

2016-10-01

This study presented a paradigm for controlling a car using an asynchronous electroencephalogram (EEG)-based brain-computer interface (BCI) and presented the experimental results of a simulation performed in an experimental environment outside the laboratory. This paradigm uses two distinct MI tasks, imaginary left- and right-hand movements, to generate a multi-task car control strategy consisting of starting the engine, moving forward, turning left, turning right, moving backward, and stopping the engine. Five healthy subjects participated in the online car control experiment, and all successfully controlled the car by following a previously outlined route. Subject S1 exhibited the most satisfactory BCI-based performance, which was comparable to the manual control-based performance. We hypothesize that the proposed self-paced car control paradigm based on EEG signals could potentially be used in car control applications, and we provide a complementary or alternative way for individuals with locked-in disorders to achieve more mobility in the future, as well as providing a supplementary car-driving strategy to assist healthy people in driving a car. Copyright © 2016 Elsevier Ltd. All rights reserved.

Properties of hypothesis testing techniques and (Bayesian) model selection for exploration-based and theory-based (order-restricted) hypotheses.

PubMed

Kuiper, Rebecca M; Nederhoff, Tim; Klugkist, Irene

2015-05-01

In this paper, the performance of six types of techniques for comparisons of means is examined. These six emerge from the distinction between the method employed (hypothesis testing, model selection using information criteria, or Bayesian model selection) and the set of hypotheses that is investigated (a classical, exploration-based set of hypotheses containing equality constraints on the means, or a theory-based limited set of hypotheses with equality and/or order restrictions). A simulation study is conducted to examine the performance of these techniques. We demonstrate that, if one has specific, a priori specified hypotheses, confirmation (i.e., investigating theory-based hypotheses) has advantages over exploration (i.e., examining all possible equality-constrained hypotheses). Furthermore, examining reasonable order-restricted hypotheses has more power to detect the true effect/non-null hypothesis than evaluating only equality restrictions. Additionally, when investigating more than one theory-based hypothesis, model selection is preferred over hypothesis testing. Because of the first two results, we further examine the techniques that are able to evaluate order restrictions in a confirmatory fashion by examining their performance when the homogeneity of variance assumption is violated. Results show that the techniques are robust to heterogeneity when the sample sizes are equal. When the sample sizes are unequal, the performance is affected by heterogeneity. The size and direction of the deviations from the baseline, where there is no heterogeneity, depend on the effect size (of the means) and on the trend in the group variances with respect to the ordering of the group sizes. Importantly, the deviations are less pronounced when the group variances and sizes exhibit the same trend (e.g., are both increasing with group number). © 2014 The British Psychological Society.

The deep metaphysics of quantum gravity: The seventeenth century legacy and an alternative ontology beyond substantivalism and relationism

NASA Astrophysics Data System (ADS)

Slowik, Edward

2013-11-01

This essay presents an alternative to contemporary substantivalist and relationist interpretations of quantum gravity hypotheses by means of an historical comparison with the ontology of space in the seventeenth century. Utilizing differences in the spatial geometry between the foundational theory and the theory derived from the foundational, in conjunction with nominalism and platonism, it will be argued that there are crucial similarities between seventeenth century and contemporary theories of space, and that these similarities reveal a host of underlying conceptual issues that the substantival/relational dichotomy fails to distinguish.

Detecting the contagion effect in mass killings; a constructive example of the statistical advantages of unbinned likelihood methods.

PubMed

Towers, Sherry; Mubayi, Anuj; Castillo-Chavez, Carlos

2018-01-01

When attempting to statistically distinguish between a null and an alternative hypothesis, many researchers in the life and social sciences turn to binned statistical analysis methods, or methods that are simply based on the moments of a distribution (such as the mean, and variance). These methods have the advantage of simplicity of implementation, and simplicity of explanation. However, when null and alternative hypotheses manifest themselves in subtle differences in patterns in the data, binned analysis methods may be insensitive to these differences, and researchers may erroneously fail to reject the null hypothesis when in fact more sensitive statistical analysis methods might produce a different result when the null hypothesis is actually false. Here, with a focus on two recent conflicting studies of contagion in mass killings as instructive examples, we discuss how the use of unbinned likelihood methods makes optimal use of the information in the data; a fact that has been long known in statistical theory, but perhaps is not as widely appreciated amongst general researchers in the life and social sciences. In 2015, Towers et al published a paper that quantified the long-suspected contagion effect in mass killings. However, in 2017, Lankford & Tomek subsequently published a paper, based upon the same data, that claimed to contradict the results of the earlier study. The former used unbinned likelihood methods, and the latter used binned methods, and comparison of distribution moments. Using these analyses, we also discuss how visualization of the data can aid in determination of the most appropriate statistical analysis methods to distinguish between a null and alternate hypothesis. We also discuss the importance of assessment of the robustness of analysis results to methodological assumptions made (for example, arbitrary choices of number of bins and bin widths when using binned methods); an issue that is widely overlooked in the literature, but is critical to analysis reproducibility and robustness. When an analysis cannot distinguish between a null and alternate hypothesis, care must be taken to ensure that the analysis methodology itself maximizes the use of information in the data that can distinguish between the two hypotheses. The use of binned methods by Lankford & Tomek (2017), that examined how many mass killings fell within a 14 day window from a previous mass killing, substantially reduced the sensitivity of their analysis to contagion effects. The unbinned likelihood methods used by Towers et al (2015) did not suffer from this problem. While a binned analysis might be favorable for simplicity and clarity of presentation, unbinned likelihood methods are preferable when effects might be somewhat subtle.

Detecting the contagion effect in mass killings; a constructive example of the statistical advantages of unbinned likelihood methods

PubMed Central

Mubayi, Anuj; Castillo-Chavez, Carlos

2018-01-01

Background When attempting to statistically distinguish between a null and an alternative hypothesis, many researchers in the life and social sciences turn to binned statistical analysis methods, or methods that are simply based on the moments of a distribution (such as the mean, and variance). These methods have the advantage of simplicity of implementation, and simplicity of explanation. However, when null and alternative hypotheses manifest themselves in subtle differences in patterns in the data, binned analysis methods may be insensitive to these differences, and researchers may erroneously fail to reject the null hypothesis when in fact more sensitive statistical analysis methods might produce a different result when the null hypothesis is actually false. Here, with a focus on two recent conflicting studies of contagion in mass killings as instructive examples, we discuss how the use of unbinned likelihood methods makes optimal use of the information in the data; a fact that has been long known in statistical theory, but perhaps is not as widely appreciated amongst general researchers in the life and social sciences. Methods In 2015, Towers et al published a paper that quantified the long-suspected contagion effect in mass killings. However, in 2017, Lankford & Tomek subsequently published a paper, based upon the same data, that claimed to contradict the results of the earlier study. The former used unbinned likelihood methods, and the latter used binned methods, and comparison of distribution moments. Using these analyses, we also discuss how visualization of the data can aid in determination of the most appropriate statistical analysis methods to distinguish between a null and alternate hypothesis. We also discuss the importance of assessment of the robustness of analysis results to methodological assumptions made (for example, arbitrary choices of number of bins and bin widths when using binned methods); an issue that is widely overlooked in the literature, but is critical to analysis reproducibility and robustness. Conclusions When an analysis cannot distinguish between a null and alternate hypothesis, care must be taken to ensure that the analysis methodology itself maximizes the use of information in the data that can distinguish between the two hypotheses. The use of binned methods by Lankford & Tomek (2017), that examined how many mass killings fell within a 14 day window from a previous mass killing, substantially reduced the sensitivity of their analysis to contagion effects. The unbinned likelihood methods used by Towers et al (2015) did not suffer from this problem. While a binned analysis might be favorable for simplicity and clarity of presentation, unbinned likelihood methods are preferable when effects might be somewhat subtle. PMID:29742115

Dimensionality and summary measures of the SF-36 v1.6: comparison of scale- and item-based approach across ECRHS II adults population.

PubMed

Grassi, Mario; Nucera, Andrea

2010-01-01

The objective of this study was twofold: 1) to confirm the hypothetical eight scales and two-component summaries of the questionnaire Short Form 36 Health Survey (SF-36), and 2) to evaluate the performance of two alternative measures to the original physical component summary (PCS) and mental component summary (MCS). We performed principal component analysis (PCA) based on 35 items, after optimal scaling via multiple correspondence analysis (MCA), and subsequently on eight scales, after standard summative scoring. Item-based summary measures were planned. Data from the European Community Respiratory Health Survey II follow-up of 8854 subjects from 25 centers were analyzed to cross-validate the original and the novel PCS and MCS. Overall, the scale- and item-based comparison indicated that the SF-36 scales and summaries meet the supposed dimensionality. However, vitality, social functioning, and general health items did not fit data optimally. The novel measures, derived a posteriori by unit-rule from an oblique (correlated) MCA/PCA solution, are simple item sums or weighted scale sums where the weights are the raw scale ranges. These item-based scores yielded consistent scale-summary results for outliers profiles, with an expected known-group differences validity. We were able to confirm the hypothesized dimensionality of eight scales and two summaries of the SF-36. The alternative scoring reaches at least the same required standards of the original scoring. In addition, it can reduce the item-scale inconsistencies without loss of predictive validity.

A comparison of regression methods for model selection in individual-based landscape genetic analysis.

PubMed

Shirk, Andrew J; Landguth, Erin L; Cushman, Samuel A

2018-01-01

Anthropogenic migration barriers fragment many populations and limit the ability of species to respond to climate-induced biome shifts. Conservation actions designed to conserve habitat connectivity and mitigate barriers are needed to unite fragmented populations into larger, more viable metapopulations, and to allow species to track their climate envelope over time. Landscape genetic analysis provides an empirical means to infer landscape factors influencing gene flow and thereby inform such conservation actions. However, there are currently many methods available for model selection in landscape genetics, and considerable uncertainty as to which provide the greatest accuracy in identifying the true landscape model influencing gene flow among competing alternative hypotheses. In this study, we used population genetic simulations to evaluate the performance of seven regression-based model selection methods on a broad array of landscapes that varied by the number and type of variables contributing to resistance, the magnitude and cohesion of resistance, as well as the functional relationship between variables and resistance. We also assessed the effect of transformations designed to linearize the relationship between genetic and landscape distances. We found that linear mixed effects models had the highest accuracy in every way we evaluated model performance; however, other methods also performed well in many circumstances, particularly when landscape resistance was high and the correlation among competing hypotheses was limited. Our results provide guidance for which regression-based model selection methods provide the most accurate inferences in landscape genetic analysis and thereby best inform connectivity conservation actions. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Total antioxidant content of alternatives to refined sugar.

PubMed

Phillips, Katherine M; Carlsen, Monica H; Blomhoff, Rune

2009-01-01

Oxidative damage is implicated in the etiology of cancer, cardiovascular disease, and other degenerative disorders. Recent nutritional research has focused on the antioxidant potential of foods, while current dietary recommendations are to increase the intake of antioxidant-rich foods rather than supplement specific nutrients. Many alternatives to refined sugar are available, including raw cane sugar, plant saps/syrups (eg, maple syrup, agave nectar), molasses, honey, and fruit sugars (eg, date sugar). Unrefined sweeteners were hypothesized to contain higher levels of antioxidants, similar to the contrast between whole and refined grain products. To compare the total antioxidant content of natural sweeteners as alternatives to refined sugar. The ferric-reducing ability of plasma (FRAP) assay was used to estimate total antioxidant capacity. Major brands of 12 types of sweeteners as well as refined white sugar and corn syrup were sampled from retail outlets in the United States. Substantial differences in total antioxidant content of different sweeteners were found. Refined sugar, corn syrup, and agave nectar contained minimal antioxidant activity (<0.01 mmol FRAP/100 g); raw cane sugar had a higher FRAP (0.1 mmol/100 g). Dark and blackstrap molasses had the highest FRAP (4.6 to 4.9 mmol/100 g), while maple syrup, brown sugar, and honey showed intermediate antioxidant capacity (0.2 to 0.7 mmol FRAP/100 g). Based on an average intake of 130 g/day refined sugars and the antioxidant activity measured in typical diets, substituting alternative sweeteners could increase antioxidant intake an average of 2.6 mmol/day, similar to the amount found in a serving of berries or nuts. Many readily available alternatives to refined sugar offer the potential benefit of antioxidant activity.

A power comparison of generalized additive models and the spatial scan statistic in a case-control setting.

PubMed

Young, Robin L; Weinberg, Janice; Vieira, Verónica; Ozonoff, Al; Webster, Thomas F

2010-07-19

A common, important problem in spatial epidemiology is measuring and identifying variation in disease risk across a study region. In application of statistical methods, the problem has two parts. First, spatial variation in risk must be detected across the study region and, second, areas of increased or decreased risk must be correctly identified. The location of such areas may give clues to environmental sources of exposure and disease etiology. One statistical method applicable in spatial epidemiologic settings is a generalized additive model (GAM) which can be applied with a bivariate LOESS smoother to account for geographic location as a possible predictor of disease status. A natural hypothesis when applying this method is whether residential location of subjects is associated with the outcome, i.e. is the smoothing term necessary? Permutation tests are a reasonable hypothesis testing method and provide adequate power under a simple alternative hypothesis. These tests have yet to be compared to other spatial statistics. This research uses simulated point data generated under three alternative hypotheses to evaluate the properties of the permutation methods and compare them to the popular spatial scan statistic in a case-control setting. Case 1 was a single circular cluster centered in a circular study region. The spatial scan statistic had the highest power though the GAM method estimates did not fall far behind. Case 2 was a single point source located at the center of a circular cluster and Case 3 was a line source at the center of the horizontal axis of a square study region. Each had linearly decreasing logodds with distance from the point. The GAM methods outperformed the scan statistic in Cases 2 and 3. Comparing sensitivity, measured as the proportion of the exposure source correctly identified as high or low risk, the GAM methods outperformed the scan statistic in all three Cases. The GAM permutation testing methods provide a regression-based alternative to the spatial scan statistic. Across all hypotheses examined in this research, the GAM methods had competing or greater power estimates and sensitivities exceeding that of the spatial scan statistic.

A power comparison of generalized additive models and the spatial scan statistic in a case-control setting

PubMed Central

2010-01-01

Background A common, important problem in spatial epidemiology is measuring and identifying variation in disease risk across a study region. In application of statistical methods, the problem has two parts. First, spatial variation in risk must be detected across the study region and, second, areas of increased or decreased risk must be correctly identified. The location of such areas may give clues to environmental sources of exposure and disease etiology. One statistical method applicable in spatial epidemiologic settings is a generalized additive model (GAM) which can be applied with a bivariate LOESS smoother to account for geographic location as a possible predictor of disease status. A natural hypothesis when applying this method is whether residential location of subjects is associated with the outcome, i.e. is the smoothing term necessary? Permutation tests are a reasonable hypothesis testing method and provide adequate power under a simple alternative hypothesis. These tests have yet to be compared to other spatial statistics. Results This research uses simulated point data generated under three alternative hypotheses to evaluate the properties of the permutation methods and compare them to the popular spatial scan statistic in a case-control setting. Case 1 was a single circular cluster centered in a circular study region. The spatial scan statistic had the highest power though the GAM method estimates did not fall far behind. Case 2 was a single point source located at the center of a circular cluster and Case 3 was a line source at the center of the horizontal axis of a square study region. Each had linearly decreasing logodds with distance from the point. The GAM methods outperformed the scan statistic in Cases 2 and 3. Comparing sensitivity, measured as the proportion of the exposure source correctly identified as high or low risk, the GAM methods outperformed the scan statistic in all three Cases. Conclusions The GAM permutation testing methods provide a regression-based alternative to the spatial scan statistic. Across all hypotheses examined in this research, the GAM methods had competing or greater power estimates and sensitivities exceeding that of the spatial scan statistic. PMID:20642827

Individual-Based Ant-Plant Networks: Diurnal-Nocturnal Structure and Species-Area Relationship

PubMed Central

Dáttilo, Wesley; Fagundes, Roberth; Gurka, Carlos A. Q.; Silva, Mara S. A.; Vieira, Marisa C. L.; Izzo, Thiago J.; Díaz-Castelazo, Cecília; Del-Claro, Kleber; Rico-Gray, Victor

2014-01-01

Despite the importance and increasing knowledge of ecological networks, sampling effort and intrapopulation variation has been widely overlooked. Using continuous daily sampling of ants visiting three plant species in the Brazilian Neotropical savanna, we evaluated for the first time the topological structure over 24 h and species-area relationships (based on the number of extrafloral nectaries available) in individual-based ant-plant networks. We observed that diurnal and nocturnal ant-plant networks exhibited the same pattern of interactions: a nested and non-modular pattern and an average level of network specialization. Despite the high similarity in the ants’ composition between the two collection periods, ant species found in the central core of highly interacting species totally changed between diurnal and nocturnal sampling for all plant species. In other words, this “night-turnover” suggests that the ecological dynamics of these ant-plant interactions can be temporally partitioned (day and night) at a small spatial scale. Thus, it is possible that in some cases processes shaping mutualistic networks formed by protective ants and plants may be underestimated by diurnal sampling alone. Moreover, we did not observe any effect of the number of extrafloral nectaries on ant richness and their foraging on such plants in any of the studied ant-plant networks. We hypothesize that competitively superior ants could monopolize individual plants and allow the coexistence of only a few other ant species, however, other alternative hypotheses are also discussed. Thus, sampling period and species-area relationship produces basic information that increases our confidence in how individual-based ant-plant networks are structured, and the need to consider nocturnal records in ant-plant network sampling design so as to decrease inappropriate inferences. PMID:24918750

Model Selection in Historical Research Using Approximate Bayesian Computation

PubMed Central

Rubio-Campillo, Xavier

2016-01-01

Formal Models and History Computational models are increasingly being used to study historical dynamics. This new trend, which could be named Model-Based History, makes use of recently published datasets and innovative quantitative methods to improve our understanding of past societies based on their written sources. The extensive use of formal models allows historians to re-evaluate hypotheses formulated decades ago and still subject to debate due to the lack of an adequate quantitative framework. The initiative has the potential to transform the discipline if it solves the challenges posed by the study of historical dynamics. These difficulties are based on the complexities of modelling social interaction, and the methodological issues raised by the evaluation of formal models against data with low sample size, high variance and strong fragmentation. Case Study This work examines an alternate approach to this evaluation based on a Bayesian-inspired model selection method. The validity of the classical Lanchester’s laws of combat is examined against a dataset comprising over a thousand battles spanning 300 years. Four variations of the basic equations are discussed, including the three most common formulations (linear, squared, and logarithmic) and a new variant introducing fatigue. Approximate Bayesian Computation is then used to infer both parameter values and model selection via Bayes Factors. Impact Results indicate decisive evidence favouring the new fatigue model. The interpretation of both parameter estimations and model selection provides new insights into the factors guiding the evolution of warfare. At a methodological level, the case study shows how model selection methods can be used to guide historical research through the comparison between existing hypotheses and empirical evidence. PMID:26730953

Recognition Memory for Hue: Prototypical Bias and the Role of Labeling

ERIC Educational Resources Information Center

Kelly, Laura Jane; Heit, Evan

2017-01-01

How does the concurrent use of language affect perception and memory for exemplars? Labels cue more general category information than a specific exemplar. Applying labels can affect the resulting memory for an exemplar. Here 3 alternative hypotheses are proposed for the role of labeling an exemplar at encoding: (a) labels distort memory toward the…

A Study in West German Stabilization Policy, 1956-1974. German Studies Notes. First Draft.

ERIC Educational Resources Information Center

Neumann, Manfred J. M.

The dominant driving force of past movements in West German output and prices is investigated and a review of government policy undertaken to stabilize these movements is presented. Three alternative impulse hypotheses are tested: the monetary, the fiscal, and the foreign impulse hypothesis. The major results of the tests are that: (1) monetary…

Equality and Illusion: Gender and Tenure in Art History Careers

ERIC Educational Resources Information Center

Rudd, Elizabeth; Morrison, Emory; Sadrozinski, Renate; Nerad, Maresi; Cerny, Joseph

2008-01-01

Using a national survey of 508 art history Ph.D.s including data on graduate school performance and careers 10-15 years post-Ph.D., this study investigates gender, family, and academic tenure in art history, the humanities field with the highest proportion of women. Alternative hypotheses derived from three perspectives--termed here "clockwork,"…

Brief Report: Eye Movements during Visual Search Tasks Indicate Enhanced Stimulus Discriminability in Subjects with PDD

ERIC Educational Resources Information Center

Kemner, Chantal; van Ewijk, Lizet; van Engeland, Herman; Hooge, Ignace

2008-01-01

Subjects with PDD excel on certain visuo-spatial tasks, amongst which visual search tasks, and this has been attributed to enhanced perceptual discrimination. However, an alternative explanation is that subjects with PDD show a different, more effective search strategy. The present study aimed to test both hypotheses, by measuring eye movements…

The Biasing Effects of Unmodeled ARMA Time Series Processes on Latent Growth Curve Model Estimates

ERIC Educational Resources Information Center

Sivo, Stephen; Fan, Xitao; Witta, Lea

2005-01-01

The purpose of this study was to evaluate the robustness of estimated growth curve models when there is stationary autocorrelation among manifest variable errors. The results suggest that when, in practice, growth curve models are fitted to longitudinal data, alternative rival hypotheses to consider would include growth models that also specify…

Bilateral Saccadic Eye Movements and Tactile Stimulation, but Not Auditory Stimulation, Enhance Memory Retrieval

ERIC Educational Resources Information Center

Nieuwenhuis, Sander; Elzinga, Bernet M.; Ras, Priscilla H.; Berends, Floris; Duijs, Peter; Samara, Zoe; Slagter, Heleen A.

2013-01-01

Recent research has shown superior memory retrieval when participants make a series of horizontal saccadic eye movements between the memory encoding phase and the retrieval phase compared to participants who do not move their eyes or move their eyes vertically. It has been hypothesized that the rapidly alternating activation of the two hemispheres…

Assessment Outcome Is Weakly Correlated with Lecture Attendance: Influence of Learning Style and Use of Alternative Materials

ERIC Educational Resources Information Center

Horton, Dane M.; Wiederman, Steven D.; Saint, David A.

2012-01-01

The relation between lecture attendance and learning is surprisingly weak, and the role of learning styles in this is poorly understood. We hypothesized that 1) academic performance is related to lecture attendance and 2) learning style influences lecture attendance and, consequently, affects performance. We also speculated that the availability…

The Potential for Improving Science Education Through Transdisciplinary Integration with Art Education.

ERIC Educational Resources Information Center

Lutz, John E.

The purpose of this study was to analyze data collected from participants in the Pennsylvania Governor's School for the Arts (PGSA) in terms of their relevance to science education. Its objective was to investigate relationships between variables common to the arts and sciences as a means for hypothesizing alternative approaches for growth in…

Similarity Attracts: An Analysis of Recruitment Decisions in Academia

ERIC Educational Resources Information Center

Roebken, Heinke

2010-01-01

The finding and the recruiting of scientists have been a long-standing issue in higher education. Due to the dearth of reliable evidence on scholarly potential at an early stage of a scientist's career, the hiring department often has to look for alternative assessment criteria. Drawing on the similarity-attraction theory, it is hypothesized that…

Impact of Self-Correction on Extrovert and Introvert Students in EFL Writing Progress

ERIC Educational Resources Information Center

Hajimohammadi, Reza; Makundan, Jayakaran

2011-01-01

To investigate the impact of self-correction method as an alternative to the traditional teacher-correction method, on the one side, and to evaluate the impact of personality traits of Extroversion/Introversion, on the other side, on the writing progress of the pre-intermediate learners three null-hypotheses were proposed. In spite of students…

Robust Evaluation Matrix: Towards a More Principled Offline Exploration of Instructional Policies

ERIC Educational Resources Information Center

Doroudi, Shayan; Aleven, Vincent; Brunskill, Emma

2017-01-01

The gold standard for identifying more effective pedagogical approaches is to perform an experiment. Unfortunately, frequently a hypothesized alternate way of teaching does not yield an improved effect. Given the expense and logistics of each experiment, and the enormous space of potential ways to improve teaching, it would be highly preferable if…

Influence of Labeling on Ratings of Infants: A Prematurity Prejudice.

ERIC Educational Resources Information Center

Miller, Michael D.; Ottinger, Donald R.

Two full term and two preterm infants were videotaped while being administered six items from the Brazelton Scale. Infants were assigned alternately the labels "preterm" and "fullterm" and shown to a group of 256 undergraduate students. It was hypothesized that: (1) subjects who view infants labeled as preterm would rate them lower on objective…

Formant Centralization Ratio: A Proposal for a New Acoustic Measure of Dysarthric Speech

ERIC Educational Resources Information Center

Sapir, Shimon; Ramig, Lorraine O.; Spielman, Jennifer L.; Fox, Cynthia

2010-01-01

Purpose: The vowel space area (VSA) has been used as an acoustic metric of dysarthric speech, but with varying degrees of success. In this study, the authors aimed to test an alternative metric to the VSA--the "formant centralization ratio" (FCR), which is hypothesized to more effectively differentiate dysarthric from healthy speech and register…

ADHD and Working Memory: The Impact of Central Executive Deficits and Exceeding Storage/Rehearsal Capacity on Observed Inattentive Behavior

ERIC Educational Resources Information Center

Kofler, Michael J.; Rapport, Mark D.; Bolden, Jennifer; Sarver, Dustin E.; Raiker, Joseph S.

2010-01-01

Inattentive behavior is considered a core and pervasive feature of ADHD; however, an alternative model challenges this premise and hypothesizes a functional relationship between working memory deficits and inattentive behavior. The current study investigated whether inattentive behavior in children with ADHD is functionally related to the…

Effects of climatic gradients on genetic differentiation of Caragana on the Ordos Plateau, China

Treesearch

Jiuyan Yang; Samuel A. Cushman; Jie Yang; Mingbo Yang; Tiejun Bao

2013-01-01

The genus Caragana (Fabr.) in the Ordos Plateau of Inner Mongolia, China, provides a strong opportunity to investigate patterns of genetic differentiation along steep climatic gradients, and to identify the environmental factors most likely to be responsible for driving the radiation. This study used a factorial, multi-model approach to evaluate alternative hypotheses...

The effects of B0, B20 and B100 soy biodiesel exhaust on aconitine-induced cardiac arrhythmia in spontaneously hypertensive rats

EPA Science Inventory

CONTEXT: Diesel exhaust (DE) has been shown to increase the risk of cardiac arrhythmias. Although biodiesel has been proposed as a "safer" alternative to diesel, it is still uncertain whether it actually poses less threat.OBJECTIVE: We hypothesized that exposure to pure or 20% so...

Serial Learning in Rats: A Test of Three Hypotheses

ERIC Educational Resources Information Center

Capaldi, E. J.; Miller, Ronald Mellado

2004-01-01

Findings obtained by providing rats with a single fixed series of events, A-B-C-..., often are equally compatible with three alternative serial learning interpretations: that the signal for items is (A) their position in the series (position view), (B) the prior item of the series (chaining view), and (C) one, two, or more prior items of the…

A multiple hypotheses uncertainty analysis in hydrological modelling: about model structure, landscape parameterization, and numerical integration

NASA Astrophysics Data System (ADS)

Pilz, Tobias; Francke, Till; Bronstert, Axel

2016-04-01

Until today a large number of competing computer models has been developed to understand hydrological processes and to simulate and predict streamflow dynamics of rivers. This is primarily the result of a lack of a unified theory in catchment hydrology due to insufficient process understanding and uncertainties related to model development and application. Therefore, the goal of this study is to analyze the uncertainty structure of a process-based hydrological catchment model employing a multiple hypotheses approach. The study focuses on three major problems that have received only little attention in previous investigations. First, to estimate the impact of model structural uncertainty by employing several alternative representations for each simulated process. Second, explore the influence of landscape discretization and parameterization from multiple datasets and user decisions. Third, employ several numerical solvers for the integration of the governing ordinary differential equations to study the effect on simulation results. The generated ensemble of model hypotheses is then analyzed and the three sources of uncertainty compared against each other. To ensure consistency and comparability all model structures and numerical solvers are implemented within a single simulation environment. First results suggest that the selection of a sophisticated numerical solver for the differential equations positively affects simulation outcomes. However, already some simple and easy to implement explicit methods perform surprisingly well and need less computational efforts than more advanced but time consuming implicit techniques. There is general evidence that ambiguous and subjective user decisions form a major source of uncertainty and can greatly influence model development and application at all stages.

Neural Mechanisms of Credit Assignment in a Multicue Environment

PubMed Central

Kolling, Nils; Brown, Joshua W.; Rushworth, Matthew

2016-01-01

In complex environments, many potential cues can guide a decision or be assigned responsibility for the outcome of the decision. We know little, however, about how humans and animals select relevant information sources that should guide behavior. We show that subjects solve this relevance selection and credit assignment problem by selecting one cue and its association with a particular outcome as the main focus of a hypothesis. To do this, we examined learning while using a task design that allowed us to estimate the focus of each subject's hypotheses on a trial-by-trial basis. When a prediction is confirmed by the outcome, then credit for the outcome is assigned to that cue rather than an alternative. Activity in medial frontal cortex is associated with the assignment of credit to the cue that is the main focus of the hypothesis. However, when the outcome disconfirms a prediction, the focus shifts between cues, and the credit for the outcome is assigned to an alternative cue. This process of reselection for credit assignment to an alternative cue is associated with lateral orbitofrontal cortex. SIGNIFICANCE STATEMENT Learners should infer which features of environments are predictive of significant events, such as rewards. This “credit assignment” problem is particularly challenging when any of several cues might be predictive. We show that human subjects solve the credit assignment problem by implicitly “hypothesizing” which cue is relevant for predicting subsequent outcomes, and then credit is assigned according to this hypothesis. This process is associated with a distinctive pattern of activity in a part of medial frontal cortex. By contrast, when unexpected outcomes occur, hypotheses are redirected toward alternative cues, and this process is associated with activity in lateral orbitofrontal cortex. PMID:26818500

How the dual process model of human cognition can inform efforts to de‐implement ineffective and harmful clinical practices: A preliminary model of unlearning and substitution

PubMed Central

Rose, Adam J.; Hartmann, Christine W.; van Bodegom‐Vos, Leti; Graham, Ian D.; Wood, Suzanne J.; Majerczyk, Barbara R.; Good, Chester B.; Pogach, Leonard M.; Ball, Sherry L.; Au, David H.; Aron, David C.

2018-01-01

Abstract Rationale and objectives One way to understand medical overuse at the clinician level is in terms of clinical decision‐making processes that are normally adaptive but become maladaptive. In psychology, dual process models of cognition propose 2 decision‐making processes. Reflective cognition is a conscious process of evaluating options based on some combination of utility, risk, capabilities, and/or social influences. Automatic cognition is a largely unconscious process occurring in response to environmental or emotive cues based on previously learned, ingrained heuristics. De‐implementation strategies directed at clinicians may be conceptualized as corresponding to cognition: (1) a process of unlearning based on reflective cognition and (2) a process of substitution based on automatic cognition. Results We define unlearning as a process in which clinicians consciously change their knowledge, beliefs, and intentions about an ineffective practice and alter their behaviour accordingly. Unlearning has been described as “the questioning of established knowledge, habits, beliefs and assumptions as a prerequisite to identifying inappropriate or obsolete knowledge underpinning and/or embedded in existing practices and routines.” We hypothesize that as an unintended consequence of unlearning strategies clinicians may experience “reactance,” ie, feel their professional prerogative is being violated and, consequently, increase their commitment to the ineffective practice. We define substitution as replacing the ineffective practice with one or more alternatives. A substitute is a specific alternative action or decision that either precludes the ineffective practice or makes it less likely to occur. Both approaches may work independently, eg, a substitute could displace an ineffective practice without changing clinicians' knowledge, and unlearning could occur even if no alternative exists. For some clinical practice, unlearning and substitution strategies may be most effectively used together. Conclusions By taking into account the dual process model of cognition, we may be able to design de‐implementation strategies matched to clinicians' decision‐making processes and avoid unintended consequence. PMID:29314508

Protocol Design Challenges in the Detection of Awareness in Aware Subjects Using EEG Signals.

PubMed

Henriques, J; Gabriel, D; Grigoryeva, L; Haffen, E; Moulin, T; Aubry, R; Pazart, L; Ortega, J-P

2016-10-01

Recent studies have evidenced serious difficulties in detecting covert awareness with electroencephalography-based techniques both in unresponsive patients and in healthy control subjects. This work reproduces the protocol design in two recent mental imagery studies with a larger group comprising 20 healthy volunteers. The main goal is assessing if modifications in the signal extraction techniques, training-testing/cross-validation routines, and hypotheses evoked in the statistical analysis, can provide solutions to the serious difficulties documented in the literature. The lack of robustness in the results advises for further search of alternative protocols more suitable for machine learning classification and of better performing signal treatment techniques. Specific recommendations are made using the findings in this work. © EEG and Clinical Neuroscience Society (ECNS) 2014.

Linguistic Phylogenies Support Back-Migration from Beringia to Asia

PubMed Central

Sicoli, Mark A.; Holton, Gary

2014-01-01

Recent arguments connecting Na-Dene languages of North America with Yeniseian languages of Siberia have been used to assert proof for the origin of Native Americans in central or western Asia. We apply phylogenetic methods to test support for this hypothesis against an alternative hypothesis that Yeniseian represents a back-migration to Asia from a Beringian ancestral population. We coded a linguistic dataset of typological features and used neighbor-joining network algorithms and Bayesian model comparison based on Bayes factors to test the fit between the data and the linguistic phylogenies modeling two dispersal hypotheses. Our results support that a Dene-Yeniseian connection more likely represents radiation out of Beringia with back-migration into central Asia than a migration from central or western Asia to North America. PMID:24621925

Delinquency and Peer Acceptance in Adolescence: A Within-Person Test of Moffitt’s Hypotheses

PubMed Central

Rulison, Kelly L; Kreager, Derek A.; Osgood, D. Wayne

2015-01-01

We tested two hypotheses derived from Moffitt’s (1993) taxonomic theory of antisocial behavior, both of which are central to her explanation for the rise in delinquency during adolescence. Specifically, we tested whether persistently delinquent individuals become more accepted by their peers during adolescence and whether individuals who abstain from delinquent behavior become less accepted. Participants were 4,359 adolescents from 14 communities in the PROSPER study, which assessed friendship networks and delinquency from 6th (M = 11.8 years) to 9th (M = 15.3 years) grade. We operationalized peer acceptance as: number of nominations received (indegree centrality), attractiveness as a friend (adjusted indegree centrality), and network bridging potential (betweenness centrality) and tested the hypotheses using multilevel modeling. Contrary to Moffitt’s hypothesis, persistently delinquent youth did not become more accepted between early and middle adolescence, and although abstainers were less accepted in early adolescence, they became more accepted over time. Results were similar for boys and girls; when differences occurred, they provided no support for Moffitt’s hypotheses for boys and were opposite of her hypotheses for girls. Sensitivity analyses using alternative strategies and additional data to identify persistently delinquent adolescents produced similar results. We explore the implications of these results for Moffitt’s assertions that social mimicry of persistently antisocial adolescents leads to increases in delinquency and that social isolation leads to abstention. PMID:25243328

Integrating modeling, monitoring, and management to reduce critical uncertainties in water resource decision making.

PubMed

Peterson, James T; Freeman, Mary C

2016-12-01

Stream ecosystems provide multiple, valued services to society, including water supply, waste assimilation, recreation, and habitat for diverse and productive biological communities. Managers striving to sustain these services in the face of changing climate, land uses, and water demands need tools to assess the potential effectiveness of alternative management actions, and often, the resulting tradeoffs between competing objectives. Integrating predictive modeling with monitoring data in an adaptive management framework provides a process by which managers can reduce model uncertainties and thus improve the scientific bases for subsequent decisions. We demonstrate an integration of monitoring data with a dynamic, metapopulation model developed to assess effects of streamflow alteration on fish occupancy in a southeastern US stream system. Although not extensive (collected over three years at nine sites), the monitoring data allowed us to assess and update support for alternative population dynamic models using model probabilities and Bayes rule. We then use the updated model weights to estimate the effects of water withdrawal on stream fish communities and demonstrate how feedback in the form of monitoring data can be used to improve water resource decision making. We conclude that investment in more strategic monitoring, guided by a priori model predictions under alternative hypotheses and an adaptive sampling design, could substantially improve the information available to guide decision-making and management for ecosystem services from lotic systems. Published by Elsevier Ltd.

Implementation of a framework for multi-species, multi-objective adaptive management in Delaware Bay

USGS Publications Warehouse

McGowan, Conor P.; Smith, David R.; Nichols, James D.; Lyons, James E.; Sweka, John A.; Kalasz, Kevin; Niles, Lawrence J.; Wong, Richard; Brust, Jeffrey; Davis, Michelle C.; Spear, Braddock

2015-01-01

Decision analytic approaches have been widely recommended as well suited to solving disputed and ecologically complex natural resource management problems with multiple objectives and high uncertainty. However, the difference between theory and practice is substantial, as there are very few actual resource management programs that represent formal applications of decision analysis. We applied the process of structured decision making to Atlantic horseshoe crab harvest decisions in the Delaware Bay region to develop a multispecies adaptive management (AM) plan, which is currently being implemented. Horseshoe crab harvest has been a controversial management issue since the late 1990s. A largely unregulated horseshoe crab harvest caused a decline in crab spawning abundance. That decline coincided with a major decline in migratory shorebird populations that consume horseshoe crab eggs on the sandy beaches of Delaware Bay during spring migration. Our approach incorporated multiple stakeholders, including fishery and shorebird conservation advocates, to account for diverse management objectives and varied opinions on ecosystem function. Through consensus building, we devised an objective statement and quantitative objective function to evaluate alternative crab harvest policies. We developed a set of competing ecological models accounting for the leading hypotheses on the interaction between shorebirds and horseshoe crabs. The models were initially weighted based on stakeholder confidence in these hypotheses, but weights will be adjusted based on monitoring and Bayesian model weight updating. These models were used together to predict the effects of management actions on the crab and shorebird populations. Finally, we used a dynamic optimization routine to identify the state dependent optimal harvest policy for horseshoe crabs, given the possible actions, the stated objectives and our competing hypotheses about system function. The AM plan was reviewed, accepted and implemented by the Atlantic States Marine Fisheries Commission in 2012 and 2013. While disagreements among stakeholders persist, structured decision making enabled unprecedented progress towards a transparent and consensus driven management plan for crabs and shorebirds in Delaware Bay.

The evolution of the genetic code: Impasses and challenges.

PubMed

Kun, Ádám; Radványi, Ádám

2018-02-01

The origin of the genetic code and translation is a "notoriously difficult problem". In this survey we present a list of questions that a full theory of the genetic code needs to answer. We assess the leading hypotheses according to these criteria. The stereochemical, the coding coenzyme handle, the coevolution, the four-column theory, the error minimization and the frozen accident hypotheses are discussed. The integration of these hypotheses can account for the origin of the genetic code. But experiments are badly needed. Thus we suggest a host of experiments that could (in)validate some of the models. We focus especially on the coding coenzyme handle hypothesis (CCH). The CCH suggests that amino acids attached to RNA handles enhanced catalytic activities of ribozymes. Alternatively, amino acids without handles or with a handle consisting of a single adenine, like in contemporary coenzymes could have been employed. All three scenarios can be tested in in vitro compartmentalized systems. Copyright © 2017 Elsevier B.V. All rights reserved.

Examining a model of life satisfaction among unemployed adults.

PubMed

Duffy, Ryan D; Bott, Elizabeth M; Allan, Blake A; Torrey, Carrie L

2013-01-01

The present study examined a model of life satisfaction among a diverse sample of 184 adults who had been unemployed for an average of 10.60 months. Using the Lent (2004) model of life satisfaction as a framework, a model was tested with 5 hypothesized predictor variables: optimism, job search self-efficacy, job search support, job search behaviors, and work volition. After adding a path in the model from optimism to work volition, the hypothesized model was found to be a good fit for the data and a better fit than a more parsimonious, alternative model. In the hypothesized model, optimism, work volition, job search self-efficacy, and job search support were each found to significantly relate to life satisfaction, accounting for 35% of the variance. Additionally, using 50,000 bootstrapped samples, optimism was found to have a significant indirect effect on life satisfaction as mediated by job search self-efficacy, job search support, and work volition. Implications for research and practice are discussed. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Family support and acceptance, gay male identity formation, and psychological adjustment: a path model.

PubMed

Elizur, Y; Ziv, M

2001-01-01

While heterosexist family undermining has been demonstrated to be a developmental risk factor in the life of persons with same-gender orientation, the issue of protective family factors is both controversial and relatively neglected. In this study of Israeli gay males (N = 114), we focused on the interrelations of family support, family acceptance and family knowledge of gay orientation, and gay male identity formation, and their effects on mental health and self-esteem. A path model was proposed based on the hypotheses that family support, family acceptance, family knowledge, and gay identity formation have an impact on psychological adjustment, and that family support has an effect on gay identity formation that is mediated by family acceptance. The assessment of gay identity formation was based on an established stage model that was streamlined for cross-cultural practice by defining three basic processes of same-gender identity formation: self-definition, self-acceptance, and disclosure (Elizur & Mintzer, 2001). The testing of our conceptual path model demonstrated an excellent fit with the data. An alternative model that hypothesized effects of gay male identity on family acceptance and family knowledge did not fit the data. Interpreting these results, we propose that the main effect of family support/acceptance on gay identity is related to the process of disclosure, and that both general family support and family acceptance of same-gender orientation play a significant role in the psychological adjustment of gay men.

Parasite infracommunities of a specialized marine fish species in a compound community dominated by generalist parasites.

PubMed

Lanfranchi, A L; Rossin, M A; Timi, J T

2009-12-01

The structure and composition of parasite communities of Mullus argentinae were analysed under two alternative hypotheses in a sample of 75 specimens caught off Mar del Plata, Argentina (38 degrees 27'S, 57 degrees 90'W). The first, based on the dominance of trophically transmitted larval parasites of low host-specificity among fish species in the region, predicts that infracommunities will be random subsets of regionally available species. The second, based on previous studies on other mullids, predicts that infracommunities will be dominated by adult digeneans. The parasite fauna of goatfishes was mainly composed of endoparasites, with metacercariae of Prosorhynchus australis accounting for most individual parasites and greatly affecting infracommunity descriptors. Its importance was reinforced by the low number of trophically transmitted larval parasites. Both hypotheses were refuted; parasite communities were not dominated either by trophically transmitted larval parasites of low host-specificity or by adult digeneans. Prosorhynchus australis was the only species displaying any degree of phylogenetic specificity. Therefore, the influence of phylogenetic factors seems to exceed that of ecological ones in determining the observed structure of infracommunities. However, it is precisely host ecology that allows P. australis to become the determinant of infracommunity structure by constraining the acquisition of other parasites. Studies aiming to determine the relative importance of evolutionary and ecological processes as structuring forces of parasite communities should take into account not only the identity and specificity of their component parasites, but also their availability in the compound community.

New Cosmic Scales as a Cornerstone for the Evolutionary Processes, Energetic Resources and Activity Phenomena of the Non-Stable Universe

NASA Astrophysics Data System (ADS)

Avetissian, A. K.

2017-07-01

New cosmic scales, completely different from the Plank's scales, have been disclosed in the frame of so called “Non-Inflationary Cosmology” (NIC), created by the author during last decade. The proposed new ideas shed light on some hidden inaccuracies within the essence of Planck's scales in Modern Cosmology, so the new scales have been nominated as “NAIRI (New Alternative Ideas Regenerating Irregularities) Cosmic Scales” (NCS). The NCS is believed to be realistic due to qualitative and quantitative correspondences with observational and experimental data. The basic concept about NCS has been created based on two hypotheses about cosmological time-evolution of Planck's constant and multi-photon processes. Together with the hypothesis about domination of Bose-statistics in the early Universe and the possibility of large-scale Bose-condensate, these predictions have been converted into phenomena, based on which the bases of alternative theory of cosmology have been investigated. The predicted by the author “Cosmic Small (Local) Bang” (CSB) phenomenon has been investigated in the model of galaxy, and as a consequence of CSB the possibility of Super-Strong Shock Wave (SSW) has been postulated. Thus, based on phenomena CSB and SSW, NIC guarantees the non-accretion mechanism of generation of galaxies and super-massive black holes in their core, as well as creation of supernovas and massive stars (super-massive stars exceeding also 100M⊙). The possibility of gravitational radiation (GR) by the central black hole of the galaxy, even by the disk (or whole galaxy!) has been investigated.

Fossil moonseeds from the Paleogene of West Gondwana (Patagonia, Argentina).

PubMed

Jud, Nathan A; Iglesias, Ari; Wilf, Peter; Gandolfo, Maria A

2018-06-08

The fossil record is critical for testing biogeographic hypotheses. Menispermaceae (moonseeds) are a widespread family with a rich fossil record and alternative hypotheses related to their origin and diversification. The family is well-represented in Cenozoic deposits of the northern hemisphere, but the record in the southern hemisphere is sparse. Filling in the southern record of moonseeds will improve our ability to evaluate alternative biogeographic hypotheses. Fossils were collected from the Salamanca (early Paleocene, Danian) and the Huitrera (early Eocene, Ypresian) formations in Chubut Province, Argentina. We photographed them using light microscopy, epifluorescence, and scanning electron microscopy and compared the fossils with similar extant and fossil Menispermaceae using herbarium specimens and published literature. We describe fossil leaves and endocarps attributed to Menispermaceae from Argentinean Patagonia. The leaves are identified to the family, and the endocarps are further identified to the tribe Cissampelideae. The Salamancan endocarp is assigned to the extant genus Stephania. These fossils significantly expand the known range of Menispermaceae in South America, and they include the oldest (ca. 64 Ma) unequivocal evidence of the family worldwide. Our findings highlight the importance of West Gondwana in the evolution of Menispermaceae during the Paleogene. Currently, the fossil record does not discern between a Laurasian or Gondwanan origin; however, it does demonstrate that Menispermaceae grew well outside the tropics by the early Paleocene. The endocarps' affinity with Cissampelideae suggests that diversification of the family was well underway by the earliest Paleocene. © 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.

Archaeological data provide alternative hypotheses on Pacific herring (Clupea pallasii) distribution, abundance, and variability

PubMed Central

McKechnie, Iain; Lepofsky, Dana; Moss, Madonna L.; Butler, Virginia L.; Orchard, Trevor J.; Coupland, Gary; Foster, Fredrick; Caldwell, Megan; Lertzman, Ken

2014-01-01

Pacific herring (Clupea pallasii), a foundation of coastal social-ecological systems, is in decline throughout much of its range. We assembled data on fish bones from 171 archaeological sites from Alaska, British Columbia, and Washington to provide proxy measures of past herring distribution and abundance. The dataset represents 435,777 fish bones, dating throughout the Holocene, but primarily to the last 2,500 y. Herring is the single-most ubiquitous fish taxon (99% ubiquity) and among the two most abundant taxa in 80% of individual assemblages. Herring bones are archaeologically abundant in all regions, but are superabundant in the northern Salish Sea and southwestern Vancouver Island areas. Analyses of temporal variability in 50 well-sampled sites reveals that herring exhibits consistently high abundance (>20% of fish bones) and consistently low variance (<10%) within the majority of sites (88% and 96%, respectively). We pose three alternative hypotheses to account for the disjunction between modern and archaeological herring populations. We reject the first hypothesis that the archaeological data overestimate past abundance and underestimate past variability. We are unable to distinguish between the second two hypotheses, which both assert that the archaeological data reflect a higher mean abundance of herring in the past, but differ in whether variability was similar to or less than that observed recently. In either case, sufficient herring was consistently available to meet the needs of harvesters, even if variability is damped in the archaeological record. These results provide baseline information prior to herring depletion and can inform modern management. PMID:24550468

Assessing Different Causes of Crown-of-Thorns Starfish Outbreaks and Appropriate Responses for Management on the Great Barrier Reef

PubMed Central

Babcock, Russell C.; Dambacher, Jeffrey M.; Morello, Elisabetta B.; Plagányi, Éva E.; Hayes, Keith R.; Sweatman, Hugh P. A.; Pratchett, Morgan S.

2016-01-01

The crown-of-thorns starfish Acanthaster planci (COTS) has contributed greatly to declines in coral cover on Australia’s Great Barrier Reef, and remains one of the major acute disturbances on Indo-Pacific coral reefs. Despite uncertainty about the underlying causes of outbreaks and the management responses that might address them, few studies have critically and directly compared competing hypotheses. This study uses qualitative modelling to compare hypotheses relating to outbreak initiation, explicitly considering the potential role of positive feedbacks, elevated nutrients, and removal of starfish predators by fishing. When nutrients and fishing are considered in isolation, the models indicate that a range of alternative hypotheses are capable of explaining outbreak initiation with similar levels of certainty. The models also suggest that outbreaks may be caused by multiple factors operating simultaneously, rather than by single proximal causes. As the complexity and realism of the models increased, the certainty of outcomes decreased, but key areas that require further research to improve the structure of the models were identified. Nutrient additions were likely to result in outbreaks only when COTS larvae alone benefitted from nutrients. Similarly, the effects of fishing on the decline of corals depended on the complexity of interactions among several categories of fishes. Our work suggests that management approaches which seek to be robust to model structure uncertainty should allow for multiple potential causes of outbreaks. Monitoring programs can provide tests of alternative potential causes of outbreaks if they specifically monitor all key taxa at reefs that are exposed to appropriate combinations of potential causal factors. PMID:28036360

An alternating treatment comparison of oral and total communications training programs with echolalic autistic children.

PubMed Central

Barrera, R D; Sulzer-Azaroff, B

1983-01-01

An alternating treatment comparison was conducted of the relative effectiveness of oral and total communication training models for teaching expressive labeling skills to three echolalic autistic children. The results of this comparison demonstrated that total communication proved to be the most successful approach with each of the subjects. In addition, the replication of these findings both within and across subjects suggest that total communication may be, in general, the most effective of these two training models for teaching basic vocal language skills to echolalic children. A number of hypotheses are presented that may provide a basis for the demonstrated effect. PMID:6654770

The intercrater plains of Mercury and the Moon: Their nature, origin and role in terrestrial planet evolution. Alternative thermal histories. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Leake, M. A.

1982-01-01

Interpretations supporting a differentiated, once active Mercury are listed. Alternative scenarios of the planet's thermal history involve: different distributions of accreted materials, including uranium and thorium-rich materials; variations of early melting; and different modes of plains and scarp formation. Arguments are advanced which strongly favor plains formation by volcanism, lack of a primordial surface, and possible identification of remnant tensional features. Studies of remotely sensed data which strongly suggest a modestly homogeneous surface of silicates imply core separation. Reasons for accepting or rejecting various hypotheses for thermal histories of the planet are mentioned.

Suggestions for presenting the results of data analyses

USGS Publications Warehouse

Anderson, David R.; Link, William A.; Johnson, Douglas H.; Burnham, Kenneth P.

2001-01-01

We give suggestions for the presentation of research results from frequentist, information-theoretic, and Bayesian analysis paradigms, followed by several general suggestions. The information-theoretic and Bayesian methods offer alternative approaches to data analysis and inference compared to traditionally used methods. Guidance is lacking on the presentation of results under these alternative procedures and on nontesting aspects of classical frequentists methods of statistical analysis. Null hypothesis testing has come under intense criticism. We recommend less reporting of the results of statistical tests of null hypotheses in cases where the null is surely false anyway, or where the null hypothesis is of little interest to science or management.

What is freedom--and does wealth cause it?

PubMed

Iyer, Ravi; Motyl, Matt; Graham, Jesse

2013-10-01

The target article's climato-economic theory will benefit by allowing for bidirectional effects and the heterogeneity of types of freedom, in order to more fully capture the coevolution of societal wealth and freedom. We also suggest alternative methods of testing climato-economic theory, such as longitudinal analyses of these countries' histories and micro-level experiments of each of the theory's hypotheses.

Why replication is important in landscape genetics: American black bear in the Rocky Mountains

Treesearch

R. A. Short Bull; Samuel Cushman; R. Mace; T. Chilton; K. C. Kendall; E. L. Landguth; Michael Schwartz; Kevin McKelvey; Fred W. Allendorf; G. Luikart

2011-01-01

We investigated how landscape features influence gene flow of black bears by testing the relative support for 36 alternative landscape resistance hypotheses, including isolation by distance (IBD) in each of 12 study areas in the north central U.S. Rocky Mountains. The study areas all contained the same basic elements, but differed in extent of forest fragmentation,...

Net Flux of Amino Acids Across the Portal-drained Viscera and Liver of the Ewe During Abomasal Infusion of Protein and Glucose

USDA-ARS?s Scientific Manuscript database

Decreasing the fraction of amino acids metabolized by the mucosal cells may increase the fraction of AA being released into the blood. A potential mechanism to reduce AA catabolism by mucosal cells is to provide an alternative source of energy. We hypothesized that increasing glucose flow to the s...

[Power metabolism from neurons and a glia to the whole brain: norm, pathology and correction].

PubMed

Zil'berter, Iu I; Zil'berter, T M

2012-01-01

The review outlines current state of the thepretical, methodological and applies aspects of brain's energy homeostasis. Authors suggest reconsidering the exclusive role of glucose as an energy substrate (ES) at both neuronal and systemic levels discussing recent research data on qualitative composition of ES pool in the brain. The role of ES alternative to glucose, e.g., lactate and ketone bodies, is examined. The hypotheses of intracellular and astrocyte-neuron lactate shuttles are discussed along with the hypotheses of astrocyte-neuron shuttle of ketone bodies, the selfish brain theory and suppositions on homeostatic versus non-homeostatic ES supply chains. In conclusion, authors argue that exogenous native ES may be used for prevention and treatment of neurodegenerative diseases.

Tumor immunology.

PubMed

Mocellin, Simone; Lise, Mario; Nitti, Donato

2007-01-01

Advances in tumor immunology are supporting the clinical implementation of several immunological approaches to cancer in the clinical setting. However, the alternate success of current immunotherapeutic regimens underscores the fact that the molecular mechanisms underlying immune-mediated tumor rejection are still poorly understood. Given the complexity of the immune system network and the multidimensionality of tumor/host interactions, the comprehension of tumor immunology might greatly benefit from high-throughput microarray analysis, which can portrait the molecular kinetics of immune response on a genome-wide scale, thus accelerating the discovery pace and ultimately catalyzing the development of new hypotheses in cell biology. Although in its infancy, the implementation of microarray technology in tumor immunology studies has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to an effective immune response against cancer. Although the general principles of microarray-based gene profiling have rapidly spread in the scientific community, the need for mastering this technique to produce meaningful data and correctly interpret the enormous output of information generated by this technology is critical and represents a tremendous challenge for investigators, as outlined in the first section of this book. In the present Chapter, we report on some of the most significant results obtained with the application of DNA microarray in this oncology field.

Plant ecosystem responses to rising atmospheric CO2: applying a "two-timing" approach to assess alternative hypotheses for mechanisms of nutrient limitation

NASA Astrophysics Data System (ADS)

Medlyn, B.; Jiang, M.; Zaehle, S.

2017-12-01

There is now ample experimental evidence that the response of terrestrial vegetation to rising atmospheric CO2 concentration is modified by soil nutrient availability. How to represent nutrient cycling processes is thus a key consideration for vegetation models. We have previously used model intercomparison to demonstrate that models incorporating different assumptions predict very different responses at Free-Air CO2 Enrichment experiments. Careful examination of model outputs has provided some insight into the reasons for the different model outcomes, but it is difficult to attribute outcomes to specific assumptions. Here we investigate the impact of individual assumptions in a generic plant carbon-nutrient cycling model. The G'DAY (Generic Decomposition And Yield) model is modified to incorporate alternative hypotheses for nutrient cycling. We analyse the impact of these assumptions in the model using a simple analytical approach known as "two-timing". This analysis identifies the quasi-equilibrium behaviour of the model at the time scales of the component pools. The analysis provides a useful mathematical framework for probing model behaviour and identifying the most critical assumptions for experimental study.

Male-Male Clasping May Be Part of an Alternative Reproductive Tactic in Xenopus laevis

PubMed Central

Rhodes, Heather J.; Stevenson, Rachel J.; Ego, Courtney L.

2014-01-01

Male Xenopus laevis frogs have been observed to clasp other males in a sustained, amplectant position, the purpose of which is unknown. We examined three possible hypotheses for this counter-intuitive behavior: 1) clasping males fail to discriminate the sex of the frogs they clasp; 2) male-male clasping is an aggressive or dominant behavior; or 3) that males clasp other males to gain proximity to breeding events and possibly engage in sperm competition. Our data, gathered through a series of behavioral experiments in the laboratory, refute the first two hypotheses. We found that males did not clasp indiscriminately, but showed a sex preference, with most males preferentially clasping a female, but a proportion preferentially clasping another male. Males that clasped another male when there was no female present were less likely to “win” reproductive access in a male-male-female triad, indicating that they did not establish dominance through clasping. However, those males did gain proximity to oviposition by continued male-male clasping in the presence of the female. Thus, our findings are consistent with, but cannot confirm, the third hypothesis of male-male clasping as an alternative reproductive tactic. PMID:24849114

In search of greener pastures: Using satellite images to predict the effects of environmental change on zebra migration

NASA Astrophysics Data System (ADS)

Bartlam-Brooks, Hattie L. A.; Beck, Pieter S. A.; Bohrer, Gil; Harris, Stephen

2013-12-01

ungulate migrations occurred in most grassland and boreal woodland ecosystems, but many have been lost due to increasing habitat loss and fragmentation. With the rate of environmental change increasing, identifying and prioritizing migration routes for conservation has taken on a new urgency. Understanding the cues that drive long-distance animal movements is critical to predicting the fate of migrations under different environmental change scenarios and how large migratory herbivores will respond to increasing resource heterogeneity and anthropogenic influences. We used an individual-based modeling approach to investigate the influence of environmental conditions, monitored using satellite data, on departure date and movement speed of migrating zebras in Botswana. Daily zebra movements between dry and rainy season ranges were annotated with coincident observations of precipitation from the Tropical Rainfall Measuring Mission data set and Moderate Resolution Imaging Spectroradiometer-derived normalized difference vegetation index (NDVI). An array of increasingly complex movement models representing alternative hypotheses regarding the environmental cues and controls for movement was parameterized and tested. The best and most justified model predicted daily zebra movement as two linear functions of precipitation rate and NDVI and included a modeled departure date as a function of cumulative precipitation. The model was highly successful at replicating both the timing and pace of seven actual migrations observed using GPS telemetry (R2 = 0.914). It shows how zebras rapidly adjust their movement to changing environmental conditions during migration and are able to reverse migration to avoid adverse conditions or exploit renewed resource availability, a nomadic behavior which should lend them a degree of resilience to climate and environmental change. Our results demonstrate how competing individual-based migration models, informed by freely available satellite data, can be used to evaluate the weight of evidence for multiple hypotheses regarding the use of environmental cues in animal movement. This modeling framework can be applied to quantify how animals adapt the timing and pace of their movements to prevailing environmental conditions and to forecast migrations in near real time or under alternative environmental scenarios.

Identifying novel drug indications through automated reasoning.

PubMed

Tari, Luis; Vo, Nguyen; Liang, Shanshan; Patel, Jagruti; Baral, Chitta; Cai, James

2012-01-01

With the large amount of pharmacological and biological knowledge available in literature, finding novel drug indications for existing drugs using in silico approaches has become increasingly feasible. Typical literature-based approaches generate new hypotheses in the form of protein-protein interactions networks by means of linking concepts based on their cooccurrences within abstracts. However, this kind of approaches tends to generate too many hypotheses, and identifying new drug indications from large networks can be a time-consuming process. In this work, we developed a method that acquires the necessary facts from literature and knowledge bases, and identifies new drug indications through automated reasoning. This is achieved by encoding the molecular effects caused by drug-target interactions and links to various diseases and drug mechanism as domain knowledge in AnsProlog, a declarative language that is useful for automated reasoning, including reasoning with incomplete information. Unlike other literature-based approaches, our approach is more fine-grained, especially in identifying indirect relationships for drug indications. To evaluate the capability of our approach in inferring novel drug indications, we applied our method to 943 drugs from DrugBank and asked if any of these drugs have potential anti-cancer activities based on information on their targets and molecular interaction types alone. A total of 507 drugs were found to have the potential to be used for cancer treatments. Among the potential anti-cancer drugs, 67 out of 81 drugs (a recall of 82.7%) are indeed known cancer drugs. In addition, 144 out of 289 drugs (a recall of 49.8%) are non-cancer drugs that are currently tested in clinical trials for cancer treatments. These results suggest that our method is able to infer drug indications (original or alternative) based on their molecular targets and interactions alone and has the potential to discover novel drug indications for existing drugs.

Supervised Learning Based Hypothesis Generation from Biomedical Literature.

PubMed

Sang, Shengtian; Yang, Zhihao; Li, Zongyao; Lin, Hongfei

2015-01-01

Nowadays, the amount of biomedical literatures is growing at an explosive speed, and there is much useful knowledge undiscovered in this literature. Researchers can form biomedical hypotheses through mining these works. In this paper, we propose a supervised learning based approach to generate hypotheses from biomedical literature. This approach splits the traditional processing of hypothesis generation with classic ABC model into AB model and BC model which are constructed with supervised learning method. Compared with the concept cooccurrence and grammar engineering-based approaches like SemRep, machine learning based models usually can achieve better performance in information extraction (IE) from texts. Then through combining the two models, the approach reconstructs the ABC model and generates biomedical hypotheses from literature. The experimental results on the three classic Swanson hypotheses show that our approach outperforms SemRep system.

Disclosure of Complementary and Alternative Medicine to Conventional Medical Providers: Variation by Race/Ethnicity and Type of CAM

PubMed Central

Chao, Maria T.; Wade, Christine; Kronenberg, Fredi

2009-01-01

Background Complementary and alternative medicine (CAM) is often used alongside conventional medical care, yet fewer than half of patients disclose CAM use to medical doctors. CAM disclosure is particularly low among racial/ethnic minorities, but reasons for differences, such as type of CAM used or quality of conventional healthcare, have not been explored. Objective We tested the hypotheses that disclosure of CAM use to medical doctors is higher for provider-based CAM and among non-Hispanic whites, and that access to and quality of conventional medical care account for racial/ethnic differences in CAM disclosure. Methods Bivariate and multiple variable analyses of the 2002 National Health Interview Survey and 2001 Health Care Quality Survey were performed. Results Disclosure of CAM use to medical providers was higher for provider-based than self-care CAM. Disclosure of any CAM was associated with access to and quality of conventional care and higher among non-Latino whites relative to minorities. Having a regular doctor and quality patient–provider relationship mitigated racial/ethnic differences in CAM disclosure. Conclusion Insufficient disclosure of CAM use to conventional providers, particularly for self-care practices and among minority populations, represents a serious challenge in medical encounter communications. Efforts to improve disclosure of CAM use should be aimed at improving consistency of care and patient–physician communication across racial/ethnic groups. PMID:19024232

An omnibus test for the global null hypothesis.

PubMed

Futschik, Andreas; Taus, Thomas; Zehetmayer, Sonja

2018-01-01

Global hypothesis tests are a useful tool in the context of clinical trials, genetic studies, or meta-analyses, when researchers are not interested in testing individual hypotheses, but in testing whether none of the hypotheses is false. There are several possibilities how to test the global null hypothesis when the individual null hypotheses are independent. If it is assumed that many of the individual null hypotheses are false, combination tests have been recommended to maximize power. If, however, it is assumed that only one or a few null hypotheses are false, global tests based on individual test statistics are more powerful (e.g. Bonferroni or Simes test). However, usually there is no a priori knowledge on the number of false individual null hypotheses. We therefore propose an omnibus test based on cumulative sums of the transformed p-values. We show that this test yields an impressive overall performance. The proposed method is implemented in an R-package called omnibus.

Null but not void: considerations for hypothesis testing.

PubMed

Shaw, Pamela A; Proschan, Michael A

2013-01-30

Standard statistical theory teaches us that once the null and alternative hypotheses have been defined for a parameter, the choice of the statistical test is clear. Standard theory does not teach us how to choose the null or alternative hypothesis appropriate to the scientific question of interest. Neither does it tell us that in some cases, depending on which alternatives are realistic, we may want to define our null hypothesis differently. Problems in statistical practice are frequently not as pristinely summarized as the classic theory in our textbooks. In this article, we present examples in statistical hypothesis testing in which seemingly simple choices are in fact rich with nuance that, when given full consideration, make the choice of the right hypothesis test much less straightforward. Published 2012. This article is a US Government work and is in the public domain in the USA.

Disentangling dynamic networks: Separated and joint expressions of functional connectivity patterns in time.

PubMed

Leonardi, Nora; Shirer, William R; Greicius, Michael D; Van De Ville, Dimitri

2014-12-01

Resting-state functional connectivity (FC) is highly variable across the duration of a scan. Groups of coevolving connections, or reproducible patterns of dynamic FC (dFC), have been revealed in fluctuating FC by applying unsupervised learning techniques. Based on results from k-means clustering and sliding-window correlations, it has recently been hypothesized that dFC may cycle through several discrete FC states. Alternatively, it has been proposed to represent dFC as a linear combination of multiple FC patterns using principal component analysis. As it is unclear whether sparse or nonsparse combinations of FC patterns are most appropriate, and as this affects their interpretation and use as markers of cognitive processing, the goal of our study was to evaluate the impact of sparsity by performing an empirical evaluation of simulated, task-based, and resting-state dFC. To this aim, we applied matrix factorizations subject to variable constraints in the temporal domain and studied both the reproducibility of ensuing representations of dFC and the expression of FC patterns over time. During subject-driven tasks, dFC was well described by alternating FC states in accordance with the nature of the data. The estimated FC patterns showed a rich structure with combinations of known functional networks enabling accurate identification of three different tasks. During rest, dFC was better described by multiple FC patterns that overlap. The executive control networks, which are critical for working memory, appeared grouped alternately with externally or internally oriented networks. These results suggest that combinations of FC patterns can provide a meaningful way to disentangle resting-state dFC. © 2014 The Authors. Human Brain Mapping published by Wiley Periodicals, Inc.

Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation

PubMed Central

Pargett, Michael; Rundell, Ann E.; Buzzard, Gregery T.; Umulis, David M.

2014-01-01

Discovery in developmental biology is often driven by intuition that relies on the integration of multiple types of data such as fluorescent images, phenotypes, and the outcomes of biochemical assays. Mathematical modeling helps elucidate the biological mechanisms at play as the networks become increasingly large and complex. However, the available data is frequently under-utilized due to incompatibility with quantitative model tuning techniques. This is the case for stem cell regulation mechanisms explored in the Drosophila germarium through fluorescent immunohistochemistry. To enable better integration of biological data with modeling in this and similar situations, we have developed a general parameter estimation process to quantitatively optimize models with qualitative data. The process employs a modified version of the Optimal Scaling method from social and behavioral sciences, and multi-objective optimization to evaluate the trade-off between fitting different datasets (e.g. wild type vs. mutant). Using only published imaging data in the germarium, we first evaluated support for a published intracellular regulatory network by considering alternative connections of the same regulatory players. Simply screening networks against wild type data identified hundreds of feasible alternatives. Of these, five parsimonious variants were found and compared by multi-objective analysis including mutant data and dynamic constraints. With these data, the current model is supported over the alternatives, but support for a biochemically observed feedback element is weak (i.e. these data do not measure the feedback effect well). When also comparing new hypothetical models, the available data do not discriminate. To begin addressing the limitations in data, we performed a model-based experiment design and provide recommendations for experiments to refine model parameters and discriminate increasingly complex hypotheses. PMID:24626201

Low Temperature Plasma Kills SCaBER Cancer Cells

NASA Astrophysics Data System (ADS)

Barekzi, Nazir; van Way, Lucas; Laroussi, Mounir

2013-09-01

Squamous cell carcinoma of the bladder is a rare type of bladder cancer that forms as a result of chronic irritation of the epithelial lining of the bladder. The cell line used in this study is SCaBER (ATCC® HTB-3™) derived from squamous cell carcinoma of the human urinary bladder. Current treatments of bladder cancer include surgery, radiation and chemotherapy. However, the cost of these treatments, the potential toxicity of the chemotherapeutic agents and the systemic side-effects warrant an alternative to current cancer treatment. This paper represents preliminary studies to determine the effects of biologically tolerant plasma (BTP) on a cell line of human bladder cancer cells. Previous work by our group using the plasma pencil revealed the efficacy of BTP on leukemia cells suspended in solution. Based on these earlier findings we hypothesized that the plasma exposure would elicit a similar programmed cell death in the SCaBER cells. Trypan blue exclusion and MTT assays revealed the cell killing after exposure to BTP. Our study indicates that low temperature plasma generated by ionizing helium gas and the reactive species may be a suitable and safe alternative for cancer therapy.

Statistical evidence for common ancestry: Application to primates.

PubMed

Baum, David A; Ané, Cécile; Larget, Bret; Solís-Lemus, Claudia; Ho, Lam Si Tung; Boone, Peggy; Drummond, Chloe P; Bontrager, Martin; Hunter, Steven J; Saucier, William

2016-06-01

Since Darwin, biologists have come to recognize that the theory of descent from common ancestry (CA) is very well supported by diverse lines of evidence. However, while the qualitative evidence is overwhelming, we also need formal methods for quantifying the evidential support for CA over the alternative hypothesis of separate ancestry (SA). In this article, we explore a diversity of statistical methods using data from the primates. We focus on two alternatives to CA, species SA (the separate origin of each named species) and family SA (the separate origin of each family). We implemented statistical tests based on morphological, molecular, and biogeographic data and developed two new methods: one that tests for phylogenetic autocorrelation while correcting for variation due to confounding ecological traits and a method for examining whether fossil taxa have fewer derived differences than living taxa. We overwhelmingly rejected both species and family SA with infinitesimal P values. We compare these results with those from two companion papers, which also found tremendously strong support for the CA of all primates, and discuss future directions and general philosophical issues that pertain to statistical testing of historical hypotheses such as CA. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Alternative splicing regulation in tumor necrosis factor-mediated inflammation.

PubMed

López-Urrutia, Eduardo; Campos-Parra, Alma; Herrera, Luis Alonso; Pérez-Plasencia, Carlos

2017-11-01

It is generally accepted that alternative splicing has an effect on disease when it leads to conspicuous changes in relevant proteins, but that the combinatorial effect of several small modifications can have marked outcomes as well. Inflammation is a complex process involving numerous signaling pathways, among which the tumor necrosis factor (TNF) pathway is one of the most studied. Signaling pathways are commonly represented as intricate cascades of molecular interactions that eventually lead to the activation of one or several genes. Alternative splicing is a common means of controlling protein expression in time and space; therefore, it can modulate the outcome of signaling pathways through small changes in their elements. Notably, the overall process is tightly regulated, which is easily overlooked when analyzing the pathway as a whole. The present review summarizes recent studies of the alternative splicing of key players of the TNF pathway leading to inflammation, and hypothesizes on the cumulative results of those modifications and the impact on cancer development.

Alternative splicing regulation in tumor necrosis factor-mediated inflammation

PubMed Central

López-Urrutia, Eduardo; Campos-Parra, Alma; Herrera, Luis Alonso; Pérez-Plasencia, Carlos

2017-01-01

It is generally accepted that alternative splicing has an effect on disease when it leads to conspicuous changes in relevant proteins, but that the combinatorial effect of several small modifications can have marked outcomes as well. Inflammation is a complex process involving numerous signaling pathways, among which the tumor necrosis factor (TNF) pathway is one of the most studied. Signaling pathways are commonly represented as intricate cascades of molecular interactions that eventually lead to the activation of one or several genes. Alternative splicing is a common means of controlling protein expression in time and space; therefore, it can modulate the outcome of signaling pathways through small changes in their elements. Notably, the overall process is tightly regulated, which is easily overlooked when analyzing the pathway as a whole. The present review summarizes recent studies of the alternative splicing of key players of the TNF pathway leading to inflammation, and hypothesizes on the cumulative results of those modifications and the impact on cancer development. PMID:29113151

The subthalamic nucleus during decision-making with multiple alternatives.

PubMed

Keuken, Max C; Van Maanen, Leendert; Bogacz, Rafal; Schäfer, Andreas; Neumann, Jane; Turner, Robert; Forstmann, Birte U

2015-10-01

Several prominent neurocomputational models predict that an increase of choice alternatives is modulated by increased activity in the subthalamic nucleus (STN). In turn, increased STN activity allows prolonged accumulation of information. At the same time, areas in the medial frontal cortex such as the anterior cingulate cortex (ACC) and the pre-SMA are hypothesized to influence the information processing in the STN. This study set out to test concrete predictions of STN activity in multiple-alternative decision-making using a multimodal combination of 7 Tesla structural and functional Magnetic Resonance Imaging, and ancestral graph (AG) modeling. The results are in line with the predictions in that increased STN activity was found with an increasing amount of choice alternatives. In addition, our study shows that activity in the ACC is correlated with activity in the STN without directly modulating it. This result sheds new light on the information processing streams between medial frontal cortex and the basal ganglia. © 2015 Wiley Periodicals, Inc.

Repositioning the substrate activity screening (SAS) approach as a fragment-based method for identification of weak binders.

PubMed

Gladysz, Rafaela; Cleenewerck, Matthias; Joossens, Jurgen; Lambeir, Anne-Marie; Augustyns, Koen; Van der Veken, Pieter

2014-10-13

Fragment-based drug discovery (FBDD) has evolved into an established approach for "hit" identification. Typically, most applications of FBDD depend on specialised cost- and time-intensive biophysical techniques. The substrate activity screening (SAS) approach has been proposed as a relatively cheap and straightforward alternative for identification of fragments for enzyme inhibitors. We have investigated SAS for the discovery of inhibitors of oncology target urokinase (uPA). Although our results support the key hypotheses of SAS, we also encountered a number of unreported limitations. In response, we propose an efficient modified methodology: "MSAS" (modified substrate activity screening). MSAS circumvents the limitations of SAS and broadens its scope by providing additional fragments and more coherent SAR data. As well as presenting and validating MSAS, this study expands existing SAR knowledge for the S1 pocket of uPA and reports new reversible and irreversible uPA inhibitor scaffolds. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Testing the Developmental Origins of Health and Disease Hypothesis for Psychopathology Using Family-Based Quasi-Experimental Designs

PubMed Central

D’Onofrio, Brian M.; Class, Quetzal A.; Lahey, Benjamin B.; Larsson, Henrik

2014-01-01

The Developmental Origin of Health and Disease (DOHaD) hypothesis is a broad theoretical framework that emphasizes how early risk factors have a causal influence on psychopathology. Researchers have raised concerns about the causal interpretation of statistical associations between early risk factors and later psychopathology because most existing studies have been unable to rule out the possibility of environmental and genetic confounding. In this paper we illustrate how family-based quasi-experimental designs can test the DOHaD hypothesis by ruling out alternative hypotheses. We review the logic underlying sibling-comparison, co-twin control, offspring of siblings/twins, adoption, and in vitro fertilization designs. We then present results from studies using these designs focused on broad indices of fetal development (low birth weight and gestational age) and a particular teratogen, smoking during pregnancy. The results provide mixed support for the DOHaD hypothesis for psychopathology, illustrating the critical need to use design features that rule out unmeasured confounding. PMID:25364377

Laser vibrometer measurements and middle ear prostheses

NASA Astrophysics Data System (ADS)

Flock, Stephen T.; Dornhoffer, John; Ferguson, Scott

1997-05-01

One of us has developed an improved partial ossicular replacement prosthesis that is easier to implant and, based on pilot clinical measurements, results in better high-frequency hearing as compared to patients receiving one of the alternative prostheses. It is hypothesized that the primary reason for this is because of the relatively light weight (about 25 mg) and low compliance of the prosthesis, which could conceivably result in better high frequency vibrational characteristics. The purpose of our initial work was to develop an instrument suitable for objectively testing the vibrational characteristics of prostheses. We have developed a laser based device suitable for measuring the vibrational characteristics of the oval window or other structures of the middle ear. We have tested this device using a piezoelectric transducer excited at audio frequencies, as well as on the oval window in human temporal bones harvested from cadavers. The results illustrate that it is possible to non-invasively monitor the vibrational characteristics of anatomic structures with a very inexpensive photonic device.

Manipulating the Alpha Level Cannot Cure Significance Testing.

PubMed

Trafimow, David; Amrhein, Valentin; Areshenkoff, Corson N; Barrera-Causil, Carlos J; Beh, Eric J; Bilgiç, Yusuf K; Bono, Roser; Bradley, Michael T; Briggs, William M; Cepeda-Freyre, Héctor A; Chaigneau, Sergio E; Ciocca, Daniel R; Correa, Juan C; Cousineau, Denis; de Boer, Michiel R; Dhar, Subhra S; Dolgov, Igor; Gómez-Benito, Juana; Grendar, Marian; Grice, James W; Guerrero-Gimenez, Martin E; Gutiérrez, Andrés; Huedo-Medina, Tania B; Jaffe, Klaus; Janyan, Armina; Karimnezhad, Ali; Korner-Nievergelt, Fränzi; Kosugi, Koji; Lachmair, Martin; Ledesma, Rubén D; Limongi, Roberto; Liuzza, Marco T; Lombardo, Rosaria; Marks, Michael J; Meinlschmidt, Gunther; Nalborczyk, Ladislas; Nguyen, Hung T; Ospina, Raydonal; Perezgonzalez, Jose D; Pfister, Roland; Rahona, Juan J; Rodríguez-Medina, David A; Romão, Xavier; Ruiz-Fernández, Susana; Suarez, Isabel; Tegethoff, Marion; Tejo, Mauricio; van de Schoot, Rens; Vankov, Ivan I; Velasco-Forero, Santiago; Wang, Tonghui; Yamada, Yuki; Zoppino, Felipe C M; Marmolejo-Ramos, Fernando

2018-01-01

We argue that making accept/reject decisions on scientific hypotheses, including a recent call for changing the canonical alpha level from p = 0.05 to p = 0.005, is deleterious for the finding of new discoveries and the progress of science. Given that blanket and variable alpha levels both are problematic, it is sensible to dispense with significance testing altogether. There are alternatives that address study design and sample size much more directly than significance testing does; but none of the statistical tools should be taken as the new magic method giving clear-cut mechanical answers. Inference should not be based on single studies at all, but on cumulative evidence from multiple independent studies. When evaluating the strength of the evidence, we should consider, for example, auxiliary assumptions, the strength of the experimental design, and implications for applications. To boil all this down to a binary decision based on a p -value threshold of 0.05, 0.01, 0.005, or anything else, is not acceptable.

Positive youth development programs for adolescents with greater psychosocial needs: evaluation based on program implementers.

PubMed

Shek, Daniel T L; Ng, Catalina S M; Law, Moon Y M

2017-02-01

As program implementers' views are seldom included in program evaluation and there are few related studies in different Chinese communities, this study examined the perceptions of the program implementers who implemented the Tier 2 Program of the P.A.T.H.S. Program in Hong Kong. The Tier 2 Program was designed to promote the development of adolescents with greater psychosocial needs. In the community-based P.A.T.H.S. Project, 400 program implementers completed a subjective outcome evaluation form (Form D) for program implementers. Consistent with the previous findings, program implementers generally held positive views towards the program, implementers, and program effectiveness and their views towards these three domains did not differ across grades. In line with the hypotheses, perceived program quality and perceived implementer quality predicted program effectiveness. The present findings provided an alternative perspective showing that the Tier 2 Program was well received by the program implementers and they regarded the program to be beneficial to the program participants.

Manipulating the Alpha Level Cannot Cure Significance Testing

PubMed Central

Trafimow, David; Amrhein, Valentin; Areshenkoff, Corson N.; Barrera-Causil, Carlos J.; Beh, Eric J.; Bilgiç, Yusuf K.; Bono, Roser; Bradley, Michael T.; Briggs, William M.; Cepeda-Freyre, Héctor A.; Chaigneau, Sergio E.; Ciocca, Daniel R.; Correa, Juan C.; Cousineau, Denis; de Boer, Michiel R.; Dhar, Subhra S.; Dolgov, Igor; Gómez-Benito, Juana; Grendar, Marian; Grice, James W.; Guerrero-Gimenez, Martin E.; Gutiérrez, Andrés; Huedo-Medina, Tania B.; Jaffe, Klaus; Janyan, Armina; Karimnezhad, Ali; Korner-Nievergelt, Fränzi; Kosugi, Koji; Lachmair, Martin; Ledesma, Rubén D.; Limongi, Roberto; Liuzza, Marco T.; Lombardo, Rosaria; Marks, Michael J.; Meinlschmidt, Gunther; Nalborczyk, Ladislas; Nguyen, Hung T.; Ospina, Raydonal; Perezgonzalez, Jose D.; Pfister, Roland; Rahona, Juan J.; Rodríguez-Medina, David A.; Romão, Xavier; Ruiz-Fernández, Susana; Suarez, Isabel; Tegethoff, Marion; Tejo, Mauricio; van de Schoot, Rens; Vankov, Ivan I.; Velasco-Forero, Santiago; Wang, Tonghui; Yamada, Yuki; Zoppino, Felipe C. M.; Marmolejo-Ramos, Fernando

2018-01-01

We argue that making accept/reject decisions on scientific hypotheses, including a recent call for changing the canonical alpha level from p = 0.05 to p = 0.005, is deleterious for the finding of new discoveries and the progress of science. Given that blanket and variable alpha levels both are problematic, it is sensible to dispense with significance testing altogether. There are alternatives that address study design and sample size much more directly than significance testing does; but none of the statistical tools should be taken as the new magic method giving clear-cut mechanical answers. Inference should not be based on single studies at all, but on cumulative evidence from multiple independent studies. When evaluating the strength of the evidence, we should consider, for example, auxiliary assumptions, the strength of the experimental design, and implications for applications. To boil all this down to a binary decision based on a p-value threshold of 0.05, 0.01, 0.005, or anything else, is not acceptable. PMID:29867666

Considerations of Elder Sibling Closeness in Predicting Younger Sibling Substance Use: Social Learning versus Social Bonding Explanations

PubMed Central

Samek, Diana R.; Rueter, Martha A.

2011-01-01

Adolescent siblings are often similar in a variety of adjustment outcomes, yet little is known about the processes that explain sibling influences during adolescence. Two alternative explanations were tested, attachment (based in social bonding theory) and anaclitic identification (based in social learning theory). Hypotheses were tested using a sample of 613 adolescent sibling pairs (206 non-adopted, 407 adopted; elder sibling Mage = 16.1, younger sibling Mage = 13.8) across three sibling contexts (gender composition, age difference, and genetic similarity). Attachment explanations were supported such that the greater the perceived sibling emotional and behavioral closeness, the lower the likelihood of substance use; however, there were considerable moderating effects of sibling gender composition. Anaclitic identification explanations were not supported; closeness and elder sibling substance use did not interact to predict younger sibling substance use. Overall, this research adds to a body of work demonstrating important sibling influences on adolescent substance use. PMID:21988080

Boundaries on Range-Range Constrained Admissible Regions for Optical Space Surveillance

NASA Astrophysics Data System (ADS)

Gaebler, J. A.; Axelrad, P.; Schumacher, P. W., Jr.

We propose a new type of admissible-region analysis for track initiation in multi-satellite problems when apparent angles measured at known stations are the only observable. The goal is to create an efficient and parallelizable algorithm for computing initial candidate orbits for a large number of new targets. It takes at least three angles-only observations to establish an orbit by traditional means. Thus one is faced with a problem that requires N-choose-3 sets of calculations to test every possible combination of the N observations. An alternative approach is to reduce the number of combinations by making hypotheses of the range to a target along the observed line-of-sight. If realistic bounds on the range are imposed, consistent with a given partition of the space of orbital elements, a pair of range possibilities can be evaluated via Lambert’s method to find candidate orbits for that that partition, which then requires Nchoose- 2 times M-choose-2 combinations, where M is the average number of range hypotheses per observation. The contribution of this work is a set of constraints that establish bounds on the range-range hypothesis region for a given element-space partition, thereby minimizing M. Two effective constraints were identified, which together, constrain the hypothesis region in range-range space to nearly that of the true admissible region based on an orbital partition. The first constraint is based on the geometry of the vacant orbital focus. The second constraint is based on time-of-flight and Lagrange’s form of Kepler’s equation. A complete and efficient parallelization of the problem is possible on this approach because the element partitions can be arbitrary and can be handled independently of each other.

Impact of competitor species composition on predicting diameter growth and survival rates of Douglas-fir trees in southwestern Oregon

USGS Publications Warehouse

Bravo, Felipe; Hann, D.W.; Maguire, Douglas A.

2001-01-01

Mixed conifer and hardwood stands in southwestern Oregon were studied to explore the hypothesis that competition effects on individual-tree growth and survival will differ according to the species comprising the competition measure. Likewise, it was hypothesized that competition measures should extrapolate best if crown-based surrogates are given preference over diameter-based (basal area based) surrogates. Diameter growth and probability of survival were modeled for individual Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) trees growing in pure stands. Alternative models expressing one-sided and two-sided competition as a function of either basal area or crown structure were then applied to other plots in which Douglas-fir was mixed with other conifers and (or) hardwood species. Crown-based variables outperformed basal area based variables as surrogates for one-sided competition in both diameter growth and survival probability, regardless of species composition. In contrast, two-sided competition was best represented by total basal area of competing trees. Surrogates reflecting differences in crown morphology among species relate more closely to the mechanics of competition for light and, hence, facilitate extrapolation to species combinations for which no observations are available.

[Aquatic Ecological Index based on freshwater (ICE(RN-MAE)) for the Rio Negro watershed, Colombia].

PubMed

Forero, Laura Cristina; Longo, Magnolia; John Jairo, Ramirez; Guillermo, Chalar

2014-04-01

Aquatic Ecological Index based on freshwater (ICE(RN-MAE)) for the Rio Negro watershed, Colombia. Available indices to assess the ecological status of rivers in Colombia are mostly based on subjective hypotheses about macroinvertebrate tolerance to pollution, which have important limitations. Here we present the application of a method to establish an index of ecological quality for lotic systems in Colombia. The index, based on macroinvertebrate abundance and physicochemical variables, was developed as an alternative to the BMWP-Col index. The method consists on determining an environmental gradient from correlations between physicochemical variables and abundance. The scores obtained in each sampling point are used in a standardized correlation for a model of weighted averages (WA). In the WA model abundances are also weighted to estimate the optimum and tolerance values of each taxon; using this information we estimated the index of ecological quality based also on macroinvertebrate (ICE(RN-MAE)) abundance in each sampling site. Subsequently, we classified all sites using the index and concentrations of total phosphorus (TP) in a cluster analysis. Using TP and ICE(RN-MAE), mean, maximum, minimum and standard deviation, we defined threshold values corresponding to three categories of ecological status: good, fair and critical.

Emotional nonacceptance within the context of traumatic event exposure: The explanatory role of anxiety sensitivity for traumatic stress symptoms and disability among Latinos in a primary care setting.

PubMed

Viana, Andres G; Paulus, Daniel J; Bakhshaie, Jafar; Garza, Monica; Valdivieso, Jeanette; Ochoa-Perez, Melissa; Lemaire, Chad; Cardoso, Jodi Berger; Zvolensky, Michael J

Research has found that Latinos (versus non-Latino Whites) evince higher rates of posttraumatic stress symptoms (PTS) and posttraumatic stress disorder (PTSD), yet little attention has been given to intra-individual, emotion-related processes to explicate the higher incidence of these symptoms among Latinos. Participants included 183 trauma-exposed adult Latinos (88.5% female; Mage=37.7, SD=10.7 and 93.4% reported Spanish as their first language) who attended a community-based primary healthcare clinic in Houston. It was hypothesized that anxiety sensitivity would explain the relation between emotional nonacceptance and traumatic stress symptoms, namely re-experiencing, avoidance, and arousal difficulties as well as overall disability. Additionally, it was expected that the observed effects would be evident above and beyond the variance accounted for by number of traumas reported, gender, age, marital status, educational status, years living in the U.S., and negative affectivity. Consistent with our hypotheses, difficulties accepting negative emotions were associated with increased trauma-related re-experiencing, avoidance, and arousal difficulties. Additionally, anxiety sensitivity was an underlying mechanism in the association between emotional nonacceptance and all but one facet of traumatic stress symptoms (i.e., re-experiencing symptoms) and disability. Alternative models yielded no significant effects, providing greater confidence in the direction of the hypothesized effects. Findings are discussed in the context of their significance for informing the development of specialized intervention strategies that target anxiety sensitivity for Latinos in primary care with elevated risk for PTS and PTSD by their heightened levels of emotional nonacceptance. Copyright © 2016 Elsevier Inc. All rights reserved.

A novel approach to PTSD modeling in rats reveals alternating patterns of limbic activity in different types of stress reaction.

PubMed

Ritov, G; Boltyansky, B; Richter-Levin, G

2016-05-01

Human reactions to trauma exposure are extremely diverse, with some individuals exhibiting only time-limited distress and others qualifying for posttraumatic stress disorder diagnosis (PTSD). Furthermore, whereas most PTSD patients mainly display fear-based symptoms, a minority of patients display a co-morbid anhedonic phenotype. We employed an individual profiling approach to model these intriguing facets of the psychiatric condition in underwater-trauma exposed rats. Based on long-term assessments of anxiety-like and anhedonic behaviors, our analysis uncovered three separate phenotypes of stress response; an anxious, fear-based (38%), a co-morbid, fear-anhedonic (15%), and an exposed-unaffected group (47%). Immunohistochemical assessments for cellular activation (c-Fos) and activation of inhibition (c-Fos+GAD67) revealed a differential involvement of limbic regions and distinct co-activity patterns for each of these phenotypes, validating the behavioral categorization. In accordance with recent neurocognitive hypotheses for posttraumatic depression, we show that enhanced pretrauma anxiety predicts the progression of posttraumatic anhedonia only in the fear-anhedonic phenotype.

Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME

PubMed Central

Berthold, Michael R.; Hedrick, Michael P.; Gilson, Michael K.

2015-01-01

Today’s large, public databases of protein–small molecule interaction data are creating important new opportunities for data mining and integration. At the same time, new graphical user interface-based workflow tools offer facile alternatives to custom scripting for informatics and data analysis. Here, we illustrate how the large protein-ligand database BindingDB may be incorporated into KNIME workflows as a step toward the integration of pharmacological data with broader biomolecular analyses. Thus, we describe a collection of KNIME workflows that access BindingDB data via RESTful webservices and, for more intensive queries, via a local distillation of the full BindingDB dataset. We focus in particular on the KNIME implementation of knowledge-based tools to generate informed hypotheses regarding protein targets of bioactive compounds, based on notions of chemical similarity. A number of variants of this basic approach are tested for seven existing drugs with relatively ill-defined therapeutic targets, leading to replication of some previously confirmed results and discovery of new, high-quality hits. Implications for future development are discussed. Database URL: www.bindingdb.org PMID:26384374

Academic satisfaction among Latino/a and White men and women engineering students.

PubMed

Flores, Lisa Y; Navarro, Rachel L; Lee, Hang Shim; Addae, Dorothy A; Gonzalez, Rebecca; Luna, Laura L; Jacquez, Ricardo; Cooper, Sonya; Mitchell, Martha

2014-01-01

The current study tests a model of academic satisfaction in engineering based on Lent, Brown, and Hackett's (1994, 2000) social cognitive career theory among a sample of 527 engineering majors attending a Hispanic serving institution. The findings indicated that (a) an alternative bidirectional model fit the data for the full sample; (b) all of the hypothesized relations were significant for the full sample, except the path from engineering interests to goals; (c) social cognitive career theory predictors accounted for a significant amount of variance in engineering goals (26.6%) and academic satisfaction (45.1%); and (d) the model parameters did not vary across men and women or across Latino/a and White engineering undergraduate students. Implications for research and practice are discussed in relation to persistence in engineering among women and Latinos/as. (c) 2014 APA, all rights reserved.

What affects public acceptance of recycled and desalinated water?

PubMed Central

Dolnicar, Sara; Hurlimann, Anna; Grün, Bettina

2011-01-01

This paper identifies factors that are associated with higher levels of public acceptance for recycled and desalinated water. For the first time, a wide range of hypothesized factors, both of socio-demographic and psychographic nature, are included simultaneously. The key results, based on a survey study of about 3000 respondents are that: (1) drivers of the stated likelihood of using desalinated water differ somewhat from drivers of the stated likelihood of using recycled water; (2) positive perceptions of, and knowledge about, the respective water source are key drivers for the stated likelihood of usage; and (3) awareness of water scarcity, as well as prior experience with using water from alternative sources, increases the stated likelihood of use. Practical recommendations for public policy makers, such as key messages to be communicated to the public, are derived. PMID:20950834

Glycosylation status of vitamin D binding protein in cancer patients

PubMed Central

Rehder, Douglas S; Nelson, Randall W; Borges, Chad R

2009-01-01

On the basis of the results of activity studies, previous reports have suggested that vitamin D binding protein (DBP) is significantly or even completely deglycosylated in cancer patients, eliminating the molecular precursor of the immunologically important Gc macrophage activating factor (GcMAF), a glycosidase-derived product of DBP. The purpose of this investigation was to directly determine the relative degree of O-linked trisaccharide glycosylation of serum-derived DBP in human breast, colorectal, pancreatic, and prostate cancer patients. Results obtained by electrospray ionization-based mass spectrometric immunoassay showed that there was no significant depletion of DBP trisaccharide glycosylation in the 56 cancer patients examined relative to healthy controls. These results suggest that alternative hypotheses regarding the molecular and/or structural origins of GcMAF must be considered to explain the relative inability of cancer patient serum to activate macrophages. PMID:19642159

Glycosylation status of vitamin D binding protein in cancer patients.

PubMed

Rehder, Douglas S; Nelson, Randall W; Borges, Chad R

2009-10-01

On the basis of the results of activity studies, previous reports have suggested that vitamin D binding protein (DBP) is significantly or even completely deglycosylated in cancer patients, eliminating the molecular precursor of the immunologically important Gc macrophage activating factor (GcMAF), a glycosidase-derived product of DBP. The purpose of this investigation was to directly determine the relative degree of O-linked trisaccharide glycosylation of serum-derived DBP in human breast, colorectal, pancreatic, and prostate cancer patients. Results obtained by electrospray ionization-based mass spectrometric immunoassay showed that there was no significant depletion of DBP trisaccharide glycosylation in the 56 cancer patients examined relative to healthy controls. These results suggest that alternative hypotheses regarding the molecular and/or structural origins of GcMAF must be considered to explain the relative inability of cancer patient serum to activate macrophages.

Antibacterial activity of graphene layers

NASA Astrophysics Data System (ADS)

Dybowska-Sarapuk, Ł.; Kotela, A.; Krzemiński, J.; Janczak, D.; Wróblewska, M.; Marchel, H.; Łegorz, P.; Jakubowska, M.

2016-09-01

The bacterial biofilm is a direct cause of complications in management of various medical conditions. There is an ongoing search for a feasible method to prevent its growth, as an alternative to antibiotics, which are ineffective. The aim of the study was to prepare and evaluate a detailed algorithm for production of graphene coatings, using economically efficient methods of printed electronics (such as ink-jet printing or spray coating), and assess their antibacterial properties. Based on the preliminary results of our work we suggest that graphene coating may inhibit the formation of microbial biofilms. Further research is needed to verify antibacterial properties of graphene coatings and its future applications in prevention of biofilm-related infections, e.g. by coating surgical instruments, catheters or tracheostomy tubes. In addition, we propose a series of hypotheses to be evaluated in further work.

Learning about Bones at a Science Museum: Examining the Alternate Hypotheses of Ceiling Effect and Prior Knowledge

ERIC Educational Resources Information Center

Judson, Eugene

2012-01-01

Groups of children at a science museum were pre- and post-assessed with a type of concept map, known as personal meaning maps, to determine what new understandings, if any, they were gaining from participation in a series of structured hands-on activities about bones and the process of bones healing. Close examination was made regarding whether…

Translational Control in Bone Marrow Failure

DTIC Science & Technology

2015-05-01

HCLS1 associated protein X-1 (HAX1), cause hereditary forms of neutropenia . Previously, competing hypotheses have posited that mutant forms of...derived induced pluripotent stem cell (iPSC) model of ELANE-associated neutropenia . During the second year of this project, in order to facilitate...pathology. 3 2. KEY WORDS neutropenia bone marrow failure neutrophil elastase ELANE HAX1 alternate translation induced pluripotent stem cells (iPSC

Quantified Choice of Root-Mean-Square Errors of Approximation for Evaluation and Power Analysis of Small Differences between Structural Equation Models

ERIC Educational Resources Information Center

Li, Libo; Bentler, Peter M.

2011-01-01

MacCallum, Browne, and Cai (2006) proposed a new framework for evaluation and power analysis of small differences between nested structural equation models (SEMs). In their framework, the null and alternative hypotheses for testing a small difference in fit and its related power analyses were defined by some chosen root-mean-square error of…

Pure visual imagery as a potential approach to achieve three classes of control for implementation of BCI in non-motor disorders

NASA Astrophysics Data System (ADS)

Sousa, Teresa; Amaral, Carlos; Andrade, João; Pires, Gabriel; Nunes, Urbano J.; Castelo-Branco, Miguel

2017-08-01

Objective. The achievement of multiple instances of control with the same type of mental strategy represents a way to improve flexibility of brain-computer interface (BCI) systems. Here we test the hypothesis that pure visual motion imagery of an external actuator can be used as a tool to achieve three classes of electroencephalographic (EEG) based control, which might be useful in attention disorders. Approach. We hypothesize that different numbers of imagined motion alternations lead to distinctive signals, as predicted by distinct motion patterns. Accordingly, a distinct number of alternating sensory/perceptual signals would lead to distinct neural responses as previously demonstrated using functional magnetic resonance imaging (fMRI). We anticipate that differential modulations should also be observed in the EEG domain. EEG recordings were obtained from twelve participants using three imagery tasks: imagery of a static dot, imagery of a dot with two opposing motions in the vertical axis (two motion directions) and imagery of a dot with four opposing motions in vertical or horizontal axes (four directions). The data were analysed offline. Main results. An increase of alpha-band power was found in frontal and central channels as a result of visual motion imagery tasks when compared with static dot imagery, in contrast with the expected posterior alpha decreases found during simple visual stimulation. The successful classification and discrimination between the three imagery tasks confirmed that three different classes of control based on visual motion imagery can be achieved. The classification approach was based on a support vector machine (SVM) and on the alpha-band relative spectral power of a small group of six frontal and central channels. Patterns of alpha activity, as captured by single-trial SVM closely reflected imagery properties, in particular the number of imagined motion alternations. Significance. We found a new mental task based on visual motion imagery with potential for the implementation of multiclass (3) BCIs. Our results are consistent with the notion that frontal alpha synchronization is related with high internal processing demands, changing with the number of alternation levels during imagery. Together, these findings suggest the feasibility of pure visual motion imagery tasks as a strategy to achieve multiclass control systems with potential for BCI and in particular, neurofeedback applications in non-motor (attentional) disorders.

LIMSI @ 2014 Clinical Decision Support Track

DTIC Science & Technology

2014-11-01

MeSH and BoW runs) was based on the automatic generation of disease hypotheses for which we used data from OrphaNet [4] and the Disease Symptom Knowledge...with the MeSH terms of the top 5 disease hypotheses generated for the case reports. Compared to the other participants we achieved low scores...clinical question types. Query expansion (for both MeSH and BoW runs) was based on the automatic generation of disease hypotheses for which we used data

Editorial: Bayesian benefits for child psychology and psychiatry researchers.

PubMed

Oldehinkel, Albertine J

2016-09-01

For many scientists, performing statistical tests has become an almost automated routine. However, p-values are frequently used and interpreted incorrectly; and even when used appropriately, p-values tend to provide answers that do not match researchers' questions and hypotheses well. Bayesian statistics present an elegant and often more suitable alternative. The Bayesian approach has rarely been applied in child psychology and psychiatry research so far, but the development of user-friendly software packages and tutorials has placed it well within reach now. Because Bayesian analyses require a more refined definition of hypothesized probabilities of possible outcomes than the classical approach, going Bayesian may offer the additional benefit of sparkling the development and refinement of theoretical models in our field. © 2016 Association for Child and Adolescent Mental Health.

The effect of alternative work arrangements on women's well-being: a demand-control model.

PubMed

Kelloway, E K; Gottlieb, B H

1998-01-01

The growth of women's participation in the labor force and evidence of the conflict they experience between job and family demands have spurred many employers to introduce alternative work arrangements such as flextime, job sharing, and telecommuting. Drawing on data gained from a sample of women (N = 998) in two large Canadian organizations, this study evaluates two mediational models of the impact of alternative work arrangements on women's stress and family role competence. Specifically, it tests and finds support for the hypotheses that (a) work arrangements involving scheduling flexibility (telecommuting and flextime) promote these aspects of women's well-being by increasing their perceived control over their time, and (b) arrangements involving reduced hours of employment (part-time employment and job sharing) promote well-being by reducing perceived job overload. Discussion of these findings centers on their implications for employed women, their employers, and future research.

Linking river management to species conservation using dynamic landscape scale models

USGS Publications Warehouse

Freeman, Mary C.; Buell, Gary R.; Hay, Lauren E.; Hughes, W. Brian; Jacobson, Robert B.; Jones, John W.; Jones, S.A.; LaFontaine, Jacob H.; Odom, Kenneth R.; Peterson, James T.; Riley, Jeffrey W.; Schindler, J. Stephen; Shea, C.; Weaver, J.D.

2013-01-01

Efforts to conserve stream and river biota could benefit from tools that allow managers to evaluate landscape-scale changes in species distributions in response to water management decisions. We present a framework and methods for integrating hydrology, geographic context and metapopulation processes to simulate effects of changes in streamflow on fish occupancy dynamics across a landscape of interconnected stream segments. We illustrate this approach using a 482 km2 catchment in the southeastern US supporting 50 or more stream fish species. A spatially distributed, deterministic and physically based hydrologic model is used to simulate daily streamflow for sub-basins composing the catchment. We use geographic data to characterize stream segments with respect to channel size, confinement, position and connectedness within the stream network. Simulated streamflow dynamics are then applied to model fish metapopulation dynamics in stream segments, using hypothesized effects of streamflow magnitude and variability on population processes, conditioned by channel characteristics. The resulting time series simulate spatially explicit, annual changes in species occurrences or assemblage metrics (e.g. species richness) across the catchment as outcomes of management scenarios. Sensitivity analyses using alternative, plausible links between streamflow components and metapopulation processes, or allowing for alternative modes of fish dispersal, demonstrate large effects of ecological uncertainty on model outcomes and highlight needed research and monitoring. Nonetheless, with uncertainties explicitly acknowledged, dynamic, landscape-scale simulations may prove useful for quantitatively comparing river management alternatives with respect to species conservation.

Paths of Effects from Preschool to Adult Well-Being: A Confirmatory Analysis of the Child-Parent Center Program

PubMed Central

Reynolds, Arthur J.; Ou, Suh-Ruu

2013-01-01

We investigated the contribution of five hypotheses to the estimated effects of preschool in the Child-Parent Centers on occupational prestige, felony arrest, and depressive symptoms in adulthood in the Chicago Longitudinal Study. An alternative-intervention, quasi-experimental design included over 1,400 low-income participants (93% of whom were black) who attended preschool for 1–2 years or the usual early educational intervention and were traced to age 24. LISREL analysis of five hypotheses (cognitive advantage, family support, school support, motivational advantage, and social adjustment) indicated that while each individually accounted for part of the estimated direct effect of preschool on adult well-being, the best-fitting model across outcomes included indicators of all five hypotheses. The full model completely accounted for the direct effect of preschool on occupational prestige and official felony arrest, and 79% on depression symptoms. Key mediators included cognitive skills at school entry, school quality in the elementary grades, juvenile arrest, and school completion. The identified processes may help establish, strengthen, and sustain effects in other programs and settings. PMID:21410923

T. rex, the Crater of Doom, and the Nature of Scientific Discovery

NASA Astrophysics Data System (ADS)

Lawson, Antone

Working from the 1970s to the early 1990s, Walter Alvarez and his research team sought the cause of the mass extinction that claimed the dinosaurs 65 million years ago. The present paper discusses that research in terms of eight puzzling observations, eight episodes of hypothetico-predictive reasoning, enumerative induction, and Jung's interrogative theory of scientific discovery. The Alvarez case history paints scientific discovery as a process in which causal questions are raised and answered through the creative use of analogical reasoning followed by an equally creative process of hypothesis testing in which predicted and observed results are compared. According to this account, puzzling observations, causal hypotheses, and imagined tests drive investigations and the search for evidence. Two implications follow. The first concerns the education of new scientists and science education researchers and the need to more clearly differentiate hypotheses from predictions in the research process. The second concerns standard science classroom instruction that should more frequently engage students in open inquiries that raise causal questions and encourage the generation of alternative causal hypotheses, which can then be explicitly tested in a hypothetico-predictive fashion.

Interrelationships of Heterozygosity, Growth Rate and Heterozygote Deficiencies in the Coot Clam, Mulinia Lateralis

PubMed Central

Gaffney, P. M.; Scott, T. M.; Koehn, R. K.; Diehl, W. J.

1990-01-01

Allozyme surveys of marine invertebrates commonly report heterozygote deficiencies, a correlation between multiple locus heterozygosity and size, or both. Hypotheses advanced to account for these phenomena include inbreeding, null alleles, selection, spatial or temporal Wahlund effects, aneuploidy and molecular imprinting. Previous studies have been unable to clearly distinguish among these alternative hypotheses. This report analyzes a large data set (1906 individuals, 15 allozyme loci) from a single field collection of the coot clam Mulinia lateralis and demonstrates (1) significant heterozygote deficiencies at 13 of 15 loci, (2) a correlation between the magnitude of heterozygote deficiency at a locus and the effect of heterozygosity at that locus on shell length, and (3) a distribution of multilocus heterozygosity which deviates from that predicted by observed single-locus heterozygosities. A critical examination of the abovementioned hypotheses as sources of these findings rules out inbreeding, null alleles, aneuploidy, population mixing and imprinting as sole causes. The pooling of larval subpopulations subjected to varying degrees of selection, aneuploidy or imprinting could account for the patterns observed in this study. PMID:2311919

Diagnosis by integrating model-based reasoning with knowledge-based reasoning

NASA Technical Reports Server (NTRS)

Bylander, Tom

1988-01-01

Our research investigates how observations can be categorized by integrating a qualitative physical model with experiential knowledge. Our domain is diagnosis of pathologic gait in humans, in which the observations are the gait motions, muscle activity during gait, and physical exam data, and the diagnostic hypotheses are the potential muscle weaknesses, muscle mistimings, and joint restrictions. Patients with underlying neurological disorders typically have several malfunctions. Among the problems that need to be faced are: the ambiguity of the observations, the ambiguity of the qualitative physical model, correspondence of the observations and hypotheses to the qualitative physical model, the inherent uncertainty of experiential knowledge, and the combinatorics involved in forming composite hypotheses. Our system divides the work so that the knowledge-based reasoning suggests which hypotheses appear more likely than others, the qualitative physical model is used to determine which hypotheses explain which observations, and another process combines these functionalities to construct a composite hypothesis based on explanatory power and plausibility. We speculate that the reasoning architecture of our system is generally applicable to complex domains in which a less-than-perfect physical model and less-than-perfect experiential knowledge need to be combined to perform diagnosis.

The critically endangered forest owlet Heteroglaux blewitti is nested within the currently recognized Athene clade: A century-old debate addressed.

PubMed

Koparde, Pankaj; Mehta, Prachi; Reddy, Sushma; Ramakrishnan, Uma; Mukherjee, Shomita; Robin, V V

2018-01-01

Range-restricted species generally have specific niche requirements and may often have unique evolutionary histories. Unfortunately, many of these species severely lack basic research, resulting in poor conservation strategies. The phylogenetic relationship of the Critically Endangered Forest Owlet Heteroglaux blewitti has been the subject of a century-old debate. The current classifications based on non-phylogenetic comparisons of morphology place the small owls of Asia into three genera, namely, Athene, Glaucidium, and Heteroglaux. Based on morphological and anatomical data, H. blewitti has been alternatively hypothesized to belong within Athene, Glaucidium, or its own monotypic genus Heteroglaux. To test these competing hypotheses, we sequenced six loci (~4300 bp data) and performed phylogenetic analyses of owlets. Mitochondrial and nuclear trees were not congruent in their placement of H. blewitti. However, both mitochondrial and nuclear combined datasets showed strong statistical support with high maximum likelihood bootstrap (>/ = 90) and Bayesian posterior probability values (>/ = 0.98) for H. blewitti being nested in the currently recognized Athene group, but not sister to Indian A. brama. The divergence of H. blewitti from its sister taxa was between 4.3 and 5.7 Ma coinciding with a period of drastic climatic changes in the Indian subcontinent. This study presented the first genetic analysis of H. blewitti, a Critically Endangered species, and addressed the long debate on the relationships of the Athene-Heteroglaux-Glaucidium complex. We recommend further studies with more data and complete taxon sampling to understand the biogeography of Indian Athene species.

Is exposure to formaldehyde in air causally associated with leukemia?—A hypothesis-based weight-of-evidence analysis

PubMed Central

Rhomberg, Lorenz R; Bailey, Lisa A; Goodman, Julie E; Hamade, Ali K; Mayfield, David

2011-01-01

Recent scientific debate has focused on the potential for inhaled formaldehyde to cause lymphohematopoietic cancers, particularly leukemias, in humans. The concern stems from certain epidemiology studies reporting an association, although particulars of endpoints and dosimetry are inconsistent across studies and several other studies show no such effects. Animal studies generally report neither hematotoxicity nor leukemia associated with formaldehyde inhalation, and hematotoxicity studies in humans are inconsistent. Formaldehyde's reactivity has been thought to preclude systemic exposure following inhalation, and its apparent inability to reach and affect the target tissues attacked by known leukemogens has, heretofore, led to skepticism regarding its potential to cause human lymphohematopoietic cancers. Recently, however, potential modes of action for formaldehyde leukemogenesis have been hypothesized, and it has been suggested that formaldehyde be identified as a known human leukemogen. In this article, we apply our hypothesis-based weight-of-evidence (HBWoE) approach to evaluate the large body of evidence regarding formaldehyde and leukemogenesis, attending to how human, animal, and mode-of-action results inform one another. We trace the logic of inference within and across all studies, and articulate how one could account for the suite of available observations under the various proposed hypotheses. Upon comparison of alternative proposals regarding what causal processes may have led to the array of observations as we see them, we conclude that the case fora causal association is weak and strains biological plausibility. Instead, apparent association between formaldehyde inhalation and leukemia in some human studies is better interpreted as due to chance or confounding. PMID:21635189

Two hypothetical nystagmus procedures: augmented tenotomy and reattachment and augmented tendon suture (Sans tenotomy).

PubMed

Dell'Osso, Louis F; Tomsak, Robert L; Thurtell, Matthew J

2009-01-01

To review the hypothetical mechanism and therapeutic benefits of the four-muscle tenotomy and reattachment (T&R) procedure using knowledge accrued over the 10 years since its proposal; to describe an augmented tendon suture (ATS) technique to improve the procedure based on one of the originally suggested alternative methods (mechanical); and to hypothesize a new ATS procedure to achieve the same therapeutic benefits without extraocular muscle tenotomy or reattachment to the globe. Standard surgical methods were used. The T&R procedure damps and improves infantile nystagmus syndrome (INS) waveforms, improves eXtended Nystagmus Acuity Function (NAFX) values, broadens the NAFX peak versus gaze angle, and damps slow eye movements but not saccades. The T&R procedure also damps acquired pendular and downbeat nystagmus, decreasing the patients' oscillopsia, and lowers the target acquisition time in INS. The T&R procedure directly affects only the enthesis of the tendon; there is idiosyncratic variation in the distribution of afferent fibers in the tendons. The ATS technique consists of placing several additional sutures in the tendon proximal to the tenotomy. Based on the hypothetical proprioceptive mechanism for the beneficial effects of the T&R procedure, the authors hypothesize that the ATS technique will maximize the therapeutic benefits and that an ATS procedure, using only tendon sutures without tenotomy, will duplicate the therapeutic effects of T&R. Eliminating the tenotomy component results in a simpler procedure more suitable for single-session, multi-muscle surgery that may be required for improving the waveforms of multiplanar nystagmus and less prone to cause complications. Copyright 2009, SLACK Incorporated.

The critically endangered forest owlet Heteroglaux blewitti is nested within the currently recognized Athene clade: A century-old debate addressed

PubMed Central

Mehta, Prachi; Reddy, Sushma; Ramakrishnan, Uma

2018-01-01

Range-restricted species generally have specific niche requirements and may often have unique evolutionary histories. Unfortunately, many of these species severely lack basic research, resulting in poor conservation strategies. The phylogenetic relationship of the Critically Endangered Forest Owlet Heteroglaux blewitti has been the subject of a century-old debate. The current classifications based on non-phylogenetic comparisons of morphology place the small owls of Asia into three genera, namely, Athene, Glaucidium, and Heteroglaux. Based on morphological and anatomical data, H. blewitti has been alternatively hypothesized to belong within Athene, Glaucidium, or its own monotypic genus Heteroglaux. To test these competing hypotheses, we sequenced six loci (~4300 bp data) and performed phylogenetic analyses of owlets. Mitochondrial and nuclear trees were not congruent in their placement of H. blewitti. However, both mitochondrial and nuclear combined datasets showed strong statistical support with high maximum likelihood bootstrap (>/ = 90) and Bayesian posterior probability values (>/ = 0.98) for H. blewitti being nested in the currently recognized Athene group, but not sister to Indian A. brama. The divergence of H. blewitti from its sister taxa was between 4.3 and 5.7 Ma coinciding with a period of drastic climatic changes in the Indian subcontinent. This study presented the first genetic analysis of H. blewitti, a Critically Endangered species, and addressed the long debate on the relationships of the Athene-Heteroglaux-Glaucidium complex. We recommend further studies with more data and complete taxon sampling to understand the biogeography of Indian Athene species. PMID:29401484

The Paradox of Abstraction: Precision Versus Concreteness.

PubMed

Iliev, Rumen; Axelrod, Robert

2017-06-01

We introduce a novel measure of abstractness based on the amount of information of a concept computed from its position in a semantic taxonomy. We refer to this measure as precision. We propose two alternative ways to measure precision, one based on the path length from a concept to the root of the taxonomic tree, and another one based on the number of direct and indirect descendants. Since more information implies greater processing load, we hypothesize that nouns higher in precision will have a processing disadvantage in a lexical decision task. We contrast precision to concreteness, a common measure of abstractness based on the proportion of sensory-based information associated with a concept. Since concreteness facilitates cognitive processing, we predict that while both concreteness and precision are measures of abstractness, they will have opposite effects on performance. In two studies we found empirical support for our hypothesis. Precision and concreteness had opposite effects on latency and accuracy in a lexical decision task, and these opposite effects were observable while controlling for word length, word frequency, affective content and semantic diversity. Our results support the view that concepts organization includes amodal semantic structures which are independent of sensory information. They also suggest that we should distinguish between sensory-based and amount-of-information-based abstractness.

Using electroretinograms and multi-model inference to identify spectral classes of photoreceptors and relative opsin expression levels

PubMed Central

2017-01-01

Understanding how individual photoreceptor cells factor in the spectral sensitivity of a visual system is essential to explain how they contribute to the visual ecology of the animal in question. Existing methods that model the absorption of visual pigments use templates which correspond closely to data from thin cross-sections of photoreceptor cells. However, few modeling approaches use a single framework to incorporate physical parameters of real photoreceptors, which can be fused, and can form vertical tiers. Akaike’s information criterion (AICc) was used here to select absorptance models of multiple classes of photoreceptor cells that maximize information, given visual system spectral sensitivity data obtained using extracellular electroretinograms and structural parameters obtained by histological methods. This framework was first used to select among alternative hypotheses of photoreceptor number. It identified spectral classes from a range of dark-adapted visual systems which have between one and four spectral photoreceptor classes. These were the velvet worm, Principapillatus hitoyensis, the branchiopod water flea, Daphnia magna, normal humans, and humans with enhanced S-cone syndrome, a condition in which S-cone frequency is increased due to mutations in a transcription factor that controls photoreceptor expression. Data from the Asian swallowtail, Papilio xuthus, which has at least five main spectral photoreceptor classes in its compound eyes, were included to illustrate potential effects of model over-simplification on multi-model inference. The multi-model framework was then used with parameters of spectral photoreceptor classes and the structural photoreceptor array kept constant. The goal was to map relative opsin expression to visual pigment concentration. It identified relative opsin expression differences for two populations of the bluefin killifish, Lucania goodei. The modeling approach presented here will be useful in selecting the most likely alternative hypotheses of opsin-based spectral photoreceptor classes, using relative opsin expression and extracellular electroretinography. PMID:28740757

Using electroretinograms and multi-model inference to identify spectral classes of photoreceptors and relative opsin expression levels.

PubMed

Lessios, Nicolas

2017-01-01

Understanding how individual photoreceptor cells factor in the spectral sensitivity of a visual system is essential to explain how they contribute to the visual ecology of the animal in question. Existing methods that model the absorption of visual pigments use templates which correspond closely to data from thin cross-sections of photoreceptor cells. However, few modeling approaches use a single framework to incorporate physical parameters of real photoreceptors, which can be fused, and can form vertical tiers. Akaike's information criterion (AIC c ) was used here to select absorptance models of multiple classes of photoreceptor cells that maximize information, given visual system spectral sensitivity data obtained using extracellular electroretinograms and structural parameters obtained by histological methods. This framework was first used to select among alternative hypotheses of photoreceptor number. It identified spectral classes from a range of dark-adapted visual systems which have between one and four spectral photoreceptor classes. These were the velvet worm, Principapillatus hitoyensis , the branchiopod water flea, Daphnia magna , normal humans, and humans with enhanced S-cone syndrome, a condition in which S-cone frequency is increased due to mutations in a transcription factor that controls photoreceptor expression. Data from the Asian swallowtail, Papilio xuthus , which has at least five main spectral photoreceptor classes in its compound eyes, were included to illustrate potential effects of model over-simplification on multi-model inference. The multi-model framework was then used with parameters of spectral photoreceptor classes and the structural photoreceptor array kept constant. The goal was to map relative opsin expression to visual pigment concentration. It identified relative opsin expression differences for two populations of the bluefin killifish, Lucania goodei . The modeling approach presented here will be useful in selecting the most likely alternative hypotheses of opsin-based spectral photoreceptor classes, using relative opsin expression and extracellular electroretinography.

The Effect of Military Enlistment on Earnings and Education

DTIC Science & Technology

2011-01-01

to compensate individuals for their sacrifice and service (a “compensating wage differential ”). We do not directly test these alternative hypotheses...earnings effects are attributable to a compensating wage differential . For Category I and II enlistees, it seems likely that this differential explains...the need for the military to pay a compensating wage differential to attract young men and women to endure the hardships of military service. Some of

Enhancing Post-Traumatic Pain Relief with Alternative Perineural Drugs

DTIC Science & Technology

2013-11-01

producing long- duration, sensory-specific nerve block with minimal toxicity . We assessed the efficacy of the adjuvants clonidine (C), buprenorphine...influence on either LA- or M- induced nerve block. Further analysis of M effects indicated that peripheral nerve block and toxicity were due to a...hoping to identify a means to produce a nerve block in the absence of toxicity . We also hypothesized that potassium channel openers might directly

Role of selection versus historical isolation in racial differentiation of ponderosa pine in southern Oregon: an investigation of alternative hypotheses.

Treesearch

Frank C. Sorensen; Nancy L. Mandel; Jan E. Aagaard

2001-01-01

Continuous populations identified as Pacific and North Plateau races of ponderosa pine (Pinus ponderosa P. Laws. ex C. Laws.) are parapatric along the crest of the Cascade Range in southern Oregon. A 3-year common-garden study of bud phenology and seedling vigor was performed to estimate the nature and magnitude of differentiation between races, to...

An impact hypothesis for Venus argon anomalies

NASA Astrophysics Data System (ADS)

Kaula, W. M.; Newman, W. I.

1997-03-01

The Ar-36+38 argon-excess anomally of Venus has been hypothesized to have its origin in the impact of an outer solar system body of about 100-km diameter. A critical evaluation is made of this hypothesis and its competitors; it is judged that its status must for the time being remain one of 'Sherlock Holmes' type, in that something so improbable must be accepted when all alternatives are eliminated.

Molecular Phylogenies indicate a Paleo-Tibetan Origin of Himalayan Lazy Toads (Scutiger).

PubMed

Hofmann, Sylvia; Stöck, Matthias; Zheng, Yuchi; Ficetola, Francesco G; Li, Jia-Tang; Scheidt, Ulrich; Schmidt, Joachim

2017-06-12

The Himalaya presents an outstanding geologically active orogen and biodiversity hotspot. However, our understanding of the historical biogeography of its fauna is far from comprehensive. Many taxa are commonly assumed to have originated from China-Indochina and dispersed westward along the Himalayan chain. Alternatively, the "Tibetan-origin hypothesis" suggests primary diversification of lineages in Paleo-Tibet, and secondary diversification along the slopes of the later uplifted Greater Himalaya. We test these hypotheses in high-mountain megophryid anurans (Scutiger). Extensive sampling from High Asia, and analyses of mitochondrial (2839 bp) and nuclear DNA (2208 bp), using Bayesian and Maximum likelihood phylogenetics, suggest that the Himalayan species form a distinct clade, possibly older than those from the eastern Himalaya-Tibet orogen. While immigration from China-Indochina cannot be excluded, our data may indicate that Himalayan Scutiger originated to the north of the Himalaya by colonization from Paleo-Tibet and then date back to the Oligocene. High intraspecific diversity of Scutiger implies limited migration across mountains and drainages along the Himalaya. While our study strengthens support for a "Tibetan-origin hypothesis", current sampling (10/22 species; 1 revalidated: S. occidentalis) remains insufficient to draw final conclusions on Scutiger but urges comparative phylogeographers to test alternative, geologically supported hypotheses for a true future understanding of Himalayan biogeography.

Specific impairments of rule induction in different frontal lobe subgroups.

PubMed

Reverberi, Carlo; Lavaroni, Antonio; Gigli, Gian Luigi; Skrap, Miran; Shallice, Tim

2005-01-01

The neural correlates of inductive reasoning are still poorly understood. In order to explore them, we administered a revised version of the Brixton test, a rule attainment task, to a group of 40 patients with a focal frontal brain lesion of mixed aetiology and to 43 control subjects. To interpret an impairment on the test as suggesting an inductive reasoning deficit a number of alternative hypotheses need first to be considered, namely whether the Brixton impairment could be explained by: (i) a working memory deficit; (ii) a monitoring deficit; (iii) a difficulty in applying an already induced rule; (iv) greater impulsivity. The patients with left lateral (LL) frontal lesions were significantly impaired on the Brixton test; more importantly they were the only group in which none of the alternative hypotheses we explored proved able to explain the flawed performance. In sharp contrast, right lateral lesion patients did not make significantly more errors on the Brixton test than controls, but they produced three times more capture errors (a sign of impaired monitoring processes). The results were interpreted as suggesting functional dissociations between inductive reasoning, monitoring and working memory and a localisation of key processes for induction in left lateral frontal cortex and in right lateral cortex for monitoring and checking.

The sub-inhibitory theory for antibiotic growth promoters.

PubMed

Broom, Leon J

2017-09-01

Antibiotics have played a critical role in the prevention, control, and treatment of bacterial diseases in humans and animals, and as growth promoters (AGPs) when used at sub-therapeutic concentrations in animal production. Numerous hypotheses have been proposed for the effectiveness of AGPs, which have largely centered on the beneficial modulation of the intestinal microbiota. However, these hypotheses have been doubted by some researchers, as AGPs are fed at concentrations that would typically be below minimum inhibitory concentrations (sub-MIC) for the antibiotic used. More recently, pro-inflammatory immune responses have been associated with poor growth performance, and this, along with reported direct, anti-inflammatory effects of some antibiotics, have led to suggestions that reducing the nutrient cost of (intestinal) inflammation may explain the growth promoting or permitting effect of AGPs. However, doubts about antibacterial effects of AGPs, and the search for alternative explanations, overlook the sub-MIC effects of antibiotics. This paper summarizes some of the reported sub-MIC effects of antibiotics and considers these in the context of helping to explain the mode of action of AGPs and effects seen in studies in vivo. This leads to suggestions for the features that alternatives to AGPs could exhibit to achieve similar performance efficacy as AGPs. © 2017 Poultry Science Association Inc.

Impact of retreatment with an artemisinin-based combination on malaria incidence and its potential selection of resistant strains: study protocol for a randomized controlled clinical trial

PubMed Central

2013-01-01

Background Artemisinin-based combination therapy is currently recommended by the World Health Organization as first-line treatment of uncomplicated malaria. Recommendations were adapted in 2010 regarding rescue treatment in case of treatment failure. Instead of quinine monotherapy, it should be combined with an antibiotic with antimalarial properties; alternatively, another artemisinin-based combination therapy may be used. However, for informing these policy changes, no clear evidence is yet available. The need to provide the policy makers with hard data on the appropriate rescue therapy is obvious. We hypothesize that the efficacy of the same artemisinin-based combination therapy used as rescue treatment is as efficacious as quinine + clindamycin or an alternative artemisinin-based combination therapy, without the risk of selecting drug resistant strains. Design We embed a randomized, open label, three-arm clinical trial in a longitudinal cohort design following up children with uncomplicated malaria until they are malaria parasite free for 4 weeks. The study is conducted in both the Democratic Republic of Congo and Uganda and performed in three steps. In the first step, the pre-randomized controlled trial (RCT) phase, children aged 12 to 59 months with uncomplicated malaria are treated with the recommended first-line drug and constitute a cohort that is passively followed up for 42 days. If the patients experience an uncomplicated malaria episode between days 14 and 42 of follow-up, they are randomized either to quinine + clindamycin, or an alternative artemisinin-based combination therapy, or the same first-line artemisinin-based combination therapy to be followed up for 28 additional days. If between days 14 and 28 the patients experience a recurrent parasitemia, they are retreated with the recommended first-line regimen and actively followed up for another 28 additional days (step three; post-RCT phase). The same methodology is followed for each subsequent failure. In any case, all patients without an infection at day 28 are classified as treatment successes and reach a study endpoint. The RCT phase allows the comparison of the safety and efficacy of three rescue treatments. The prolonged follow-up of all children until they are 28 days parasite-free allows us to assess epidemiological-, host- and parasite-related predictors for repeated malaria infection. Trial registration NCT01374581 and PACTR201203000351114 PMID:24059911

Using the Landlab toolkit to evaluate and compare alternative geomorphic and hydrologic model formulations

NASA Astrophysics Data System (ADS)

Tucker, G. E.; Adams, J. M.; Doty, S. G.; Gasparini, N. M.; Hill, M. C.; Hobley, D. E. J.; Hutton, E.; Istanbulluoglu, E.; Nudurupati, S. S.

2016-12-01

Developing a better understanding of catchment hydrology and geomorphology ideally involves quantitative hypothesis testing. Often one seeks to identify the simplest mathematical and/or computational model that accounts for the essential dynamics in the system of interest. Development of alternative hypotheses involves testing and comparing alternative formulations, but the process of comparison and evaluation is made challenging by the rigid nature of many computational models, which are often built around a single assumed set of equations. Here we review a software framework for two-dimensional computational modeling that facilitates the creation, testing, and comparison of surface-dynamics models. Landlab is essentially a Python-language software library. Its gridding module allows for easy generation of a structured (raster, hex) or unstructured (Voronoi-Delaunay) mesh, with the capability to attach data arrays to particular types of element. Landlab includes functions that implement common numerical operations, such as gradient calculation and summation of fluxes within grid cells. Landlab also includes a collection of process components, which are encapsulated pieces of software that implement a numerical calculation of a particular process. Examples include downslope flow routing over topography, shallow-water hydrodynamics, stream erosion, and sediment transport on hillslopes. Individual components share a common grid and data arrays, and they can be coupled through the use of a simple Python script. We illustrate Landlab's capabilities with a case study of Holocene landscape development in the northeastern US, in which we seek to identify a collection of model components that can account for the formation of a series of incised canyons that have that developed since the Laurentide ice sheet last retreated. We compare sets of model ingredients related to (1) catchment hydrologic response, (2) hillslope evolution, and (3) stream channel and gully incision. The case-study example demonstrates the value of exploring multiple working hypotheses, in the form of multiple alternative model components.

Corticomuscular transmission of tremor signals by propriospinal neurons in Parkinson's disease.

PubMed

Hao, Manzhao; He, Xin; Xiao, Qin; Alstermark, Bror; Lan, Ning

2013-01-01

Cortical oscillatory signals of single and double tremor frequencies act together to cause tremor in the peripheral limbs of patients with Parkinson's disease (PD). But the corticospinal pathway that transmits the tremor signals has not been clarified, and how alternating bursts of antagonistic muscle activations are generated from the cortical oscillatory signals is not well understood. This paper investigates the plausible role of propriospinal neurons (PN) in C3-C4 in transmitting the cortical oscillatory signals to peripheral muscles. Kinematics data and surface electromyogram (EMG) of tremor in forearm were collected from PD patients. A PN network model was constructed based on known neurophysiological connections of PN. The cortical efferent signal of double tremor frequencies were integrated at the PN network, whose outputs drove the muscles of a virtual arm (VA) model to simulate tremor behaviors. The cortical efferent signal of single tremor frequency actuated muscle spindles. By comparing tremor data of PD patients and the results of model simulation, we examined two hypotheses regarding the corticospinal transmission of oscillatory signals in Parkinsonian tremor. Hypothesis I stated that the oscillatory cortical signals were transmitted via the mono-synaptic corticospinal pathways bypassing the PN network. The alternative hypothesis II stated that they were transmitted by way of PN multi-synaptic corticospinal pathway. Simulations indicated that without the PN network, the alternating burst patterns of antagonistic muscle EMGs could not be reliably generated, rejecting the first hypothesis. However, with the PN network, the alternating burst patterns of antagonist EMGs were naturally reproduced under all conditions of cortical oscillations. The results suggest that cortical commands of single and double tremor frequencies are further processed at PN to compute the alternating burst patterns in flexor and extensor muscles, and the neuromuscular dynamics demonstrated a frequency dependent damping on tremor, which may prevent tremor above 8 Hz to occur.

Corticomuscular Transmission of Tremor Signals by Propriospinal Neurons in Parkinson's Disease

PubMed Central

Hao, Manzhao; He, Xin; Xiao, Qin; Alstermark, Bror; Lan, Ning

2013-01-01

Cortical oscillatory signals of single and double tremor frequencies act together to cause tremor in the peripheral limbs of patients with Parkinson's disease (PD). But the corticospinal pathway that transmits the tremor signals has not been clarified, and how alternating bursts of antagonistic muscle activations are generated from the cortical oscillatory signals is not well understood. This paper investigates the plausible role of propriospinal neurons (PN) in C3–C4 in transmitting the cortical oscillatory signals to peripheral muscles. Kinematics data and surface electromyogram (EMG) of tremor in forearm were collected from PD patients. A PN network model was constructed based on known neurophysiological connections of PN. The cortical efferent signal of double tremor frequencies were integrated at the PN network, whose outputs drove the muscles of a virtual arm (VA) model to simulate tremor behaviors. The cortical efferent signal of single tremor frequency actuated muscle spindles. By comparing tremor data of PD patients and the results of model simulation, we examined two hypotheses regarding the corticospinal transmission of oscillatory signals in Parkinsonian tremor. Hypothesis I stated that the oscillatory cortical signals were transmitted via the mono-synaptic corticospinal pathways bypassing the PN network. The alternative hypothesis II stated that they were transmitted by way of PN multi-synaptic corticospinal pathway. Simulations indicated that without the PN network, the alternating burst patterns of antagonistic muscle EMGs could not be reliably generated, rejecting the first hypothesis. However, with the PN network, the alternating burst patterns of antagonist EMGs were naturally reproduced under all conditions of cortical oscillations. The results suggest that cortical commands of single and double tremor frequencies are further processed at PN to compute the alternating burst patterns in flexor and extensor muscles, and the neuromuscular dynamics demonstrated a frequency dependent damping on tremor, which may prevent tremor above 8 Hz to occur. PMID:24278189

Health need and the use of alternative medicine among adults who do not use conventional medicine

PubMed Central

2010-01-01

Background We hypothesize that a substantial portion of individuals who forgo conventional care in a given year turn to some form of alternative medicine. This study also examines whether individuals who use only alternative medicine will differ substantially in health and sociodemographic status from individuals using neither alternative medicine nor conventional care in a given year. To identify those factors that predict alternative medicine use in those not using conventional care, we employed the socio-behavioral model of healthcare utilization. Methods The current study is a cross-sectional regression analysis using data from the 2002 National Health Interview Survey. Data were collected in-person from 31,044 adults throughout the 50 states and the District of Columbia. Results 19.3% of adults (38.3 million) did not use conventional care in a 12 month period, although 39.5% of these individuals (14.7 million) reported having one or more problems with their health. Of those not using conventional care, 24.8% (9.5 million) used alternative medicine. Users of alternative medicine had more health needs and were more likely to delay conventional care because of both cost and non-cost factors compared to those not using alternative medicine. While individual predisposing factors (gender, education) were positively associated with alternative medicine use, enabling factors (poverty status, insurance coverage) were not. Conclusions We found that a quarter of individuals who forgo conventional care in a given year turn towards alternative medicine. Our study suggests that the potential determinants of using only alternative medicine are multifactorial. Future research is needed to examine the decision process behind an individual's choice to use alternative medicine but not conventional medicine and the clinical outcomes of this choice. PMID:20670418

Functions of perch relocations in a communal night roost of wintering bald eagles

USGS Publications Warehouse

Yackel Adams, A.A.; Skagen, S.K.; Knight, R.L.

2000-01-01

We investigated the functions of perch relocations within a communal night roost of wintering bald eagles (Haliaeetus leucocephalus) along the Nooksack River, Washington, during two winters. We tested seven predictions of two nonexclusive hypotheses: (1) bald eagles relocate within roosts to assess foraging success of conspecifics and (2) bald eagles relocate to obtain thermoregulatory benefits from an improved microclimate. Additionally, we gathered descriptive information to allow refinement of further alternative hypotheses. We rejected the hypothesis that relocations are a means of assessing foraging success. Contrary to our expectations, immature eagles did not relocate to be closer to adults, and relocations were less frequent when food was less abundant. Our data support the hypothesis that eagles relocate within night roosts to obtain a favorable microclimate during winters when they are subjected to cold stress and food stress. In both winters, relocations were more frequent in the evening than in the morning. In both winters, most evening relocations were to the center of the roost rather than to its edge, and the frequency of relocation to the center was greater when temperatures were low. The microclimate hypothesis, however, explains only a limited number of relocations. Based on our findings, it is likely that relocation has multiple functions, including establishing and (or) maintaining foraging associations, establishing and (or) maintaining social-dominance hierarchies when food is less abundant, and nonsocial activities.

What is the function of hippocampal theta rhythm?--Linking behavioral data to phasic properties of field potential and unit recording data.

PubMed

Hasselmo, Michael E

2005-01-01

The extensive physiological data on hippocampal theta rhythm provide an opportunity to evaluate hypotheses about the role of theta rhythm for hippocampal network function. Computational models based on these hypotheses help to link behavioral data with physiological measurements of different variables during theta rhythm. This paper reviews work on network models in which theta rhythm contributes to the following functions: (1) separating the dynamics of encoding and retrieval, (2) enhancing the context-dependent retrieval of sequences, (3) buffering of novel information in entorhinal cortex (EC) for episodic encoding, and (4) timing interactions between prefrontal cortex and hippocampus for memory-guided action selection. Modeling shows how these functional mechanisms are related to physiological data from the hippocampal formation, including (1) the phase relationships of synaptic currents during theta rhythm measured by current source density analysis of electroencephalographic data from region CA1 and dentate gyrus, (2) the timing of action potentials, including the theta phase precession of single place cells during running on a linear track, the context-dependent changes in theta phase precession across trials on each day, and the context-dependent firing properties of hippocampal neurons in spatial alternation (e.g., "splitter cells"), (3) the cholinergic regulation of sustained activity in entorhinal cortical neurons, and (4) the phasic timing of prefrontal cortical neurons relative to hippocampal theta rhythm. Copyright 2005 Wiley-Liss, Inc.

Validation of Alternative In Vitro Methods to Animal Testing: Concepts, Challenges, Processes and Tools.

PubMed

Griesinger, Claudius; Desprez, Bertrand; Coecke, Sandra; Casey, Warren; Zuang, Valérie

This chapter explores the concepts, processes, tools and challenges relating to the validation of alternative methods for toxicity and safety testing. In general terms, validation is the process of assessing the appropriateness and usefulness of a tool for its intended purpose. Validation is routinely used in various contexts in science, technology, the manufacturing and services sectors. It serves to assess the fitness-for-purpose of devices, systems, software up to entire methodologies. In the area of toxicity testing, validation plays an indispensable role: "alternative approaches" are increasingly replacing animal models as predictive tools and it needs to be demonstrated that these novel methods are fit for purpose. Alternative approaches include in vitro test methods, non-testing approaches such as predictive computer models up to entire testing and assessment strategies composed of method suites, data sources and decision-aiding tools. Data generated with alternative approaches are ultimately used for decision-making on public health and the protection of the environment. It is therefore essential that the underlying methods and methodologies are thoroughly characterised, assessed and transparently documented through validation studies involving impartial actors. Importantly, validation serves as a filter to ensure that only test methods able to produce data that help to address legislative requirements (e.g. EU's REACH legislation) are accepted as official testing tools and, owing to the globalisation of markets, recognised on international level (e.g. through inclusion in OECD test guidelines). Since validation creates a credible and transparent evidence base on test methods, it provides a quality stamp, supporting companies developing and marketing alternative methods and creating considerable business opportunities. Validation of alternative methods is conducted through scientific studies assessing two key hypotheses, reliability and relevance of the test method for a given purpose. Relevance encapsulates the scientific basis of the test method, its capacity to predict adverse effects in the "target system" (i.e. human health or the environment) as well as its applicability for the intended purpose. In this chapter we focus on the validation of non-animal in vitro alternative testing methods and review the concepts, challenges, processes and tools fundamental to the validation of in vitro methods intended for hazard testing of chemicals. We explore major challenges and peculiarities of validation in this area. Based on the notion that validation per se is a scientific endeavour that needs to adhere to key scientific principles, namely objectivity and appropriate choice of methodology, we examine basic aspects of study design and management, and provide illustrations of statistical approaches to describe predictive performance of validated test methods as well as their reliability.

Conformationally constrained peptides target the allosteric kinase dimer interface and inhibit EGFR activation.

PubMed

Fulton, Melody D; Hanold, Laura E; Ruan, Zheng; Patel, Sneha; Beedle, Aaron M; Kannan, Natarajan; Kennedy, Eileen J

2018-03-15

Although EGFR is a highly sought-after drug target, inhibitor resistance remains a challenge. As an alternative strategy for kinase inhibition, we sought to explore whether allosteric activation mechanisms could effectively be disrupted. The kinase domain of EGFR forms an atypical asymmetric dimer via head-to-tail interactions and serves as a requisite for kinase activation. The kinase dimer interface is primarily formed by the H-helix derived from one kinase monomer and the small lobe of the second monomer. We hypothesized that a peptide designed to resemble the binding surface of the H-helix may serve as an effective disruptor of EGFR dimerization and activation. A library of constrained peptides was designed to mimic the H-helix of the kinase domain and interface side chains were optimized using molecular modeling. Peptides were constrained using peptide "stapling" to structurally reinforce an alpha-helical conformation. Peptide stapling was demonstrated to notably enhance cell permeation of an H-helix derived peptide termed EHBI2. Using cell-based assays, EHBI2 was further shown to significantly reduce EGFR activity as measured by EGFR phosphorylation and phosphorylation of the downstream signaling substrate Akt. To our knowledge, this is the first H-helix-based compound targeting the asymmetric interface of the kinase domain that can successfully inhibit EGFR activation and signaling. This study presents a novel, alternative targeting site for allosteric inhibition of EGFR. Copyright © 2017 Elsevier Ltd. All rights reserved.

How to take arms against central apneas in heart failure.

PubMed

Borrelli, Chiara; Aimo, Alberto; Mirizzi, Gianluca; Passino, Claudio; Vergaro, Giuseppe; Emdin, Michele; Giannoni, Alberto

2017-10-01

Introduction Despite being a risk mediator in several observational studies, central apneas are currently orphan of treatment in heart failure. After the neutral effects on survival of two randomized controlled trials (RCTs) based on the use of positive airway pressure (the CANPAP and SERVE-HF trials), two alternative hypotheses have been formulated: 1) Periodic breathing/Cheyne-Stokes respiration (PB/CSR) in HF is protective. Indeed, the Naughton's hypothesis assumes that hyperventilation leads to increased cardiac output, lung volume, oxygen storage and reduced muscle sympathetic nerve activity, while central apnea to respiratory muscle rest and hypoxia-induced erythropoiesis. 2) The use of positive airway pressure is just a wrong treatment for PB/CSR. If this is the case, the search for novel potential alternative treatment approaches is mandatory in HF. Areas covered This review will focus on the crucial issue of whether PB/CSR should be treated or not in HF, first by outlining the ideal design of pathophysiological studies to test the Naughton's hypothesis and second by summarizing the treatment strategies so far proposed for PB/CSR in HF and identifying the most promising options to be tested in future RCTs. Expert commentary It is likely that PB/CSR may be compensatory in some cases, but after a certain threshold (to be defined) it becomes maladaptive with negative prognostic meaning in HF. The development of a pathophysiologically based treatment targeting feedback resetting and neurohormonal activation underlying PB/CSR is likely to be the best option to obtain survival benefits in HF.

How the dual process model of human cognition can inform efforts to de-implement ineffective and harmful clinical practices: A preliminary model of unlearning and substitution.

PubMed

Helfrich, Christian D; Rose, Adam J; Hartmann, Christine W; van Bodegom-Vos, Leti; Graham, Ian D; Wood, Suzanne J; Majerczyk, Barbara R; Good, Chester B; Pogach, Leonard M; Ball, Sherry L; Au, David H; Aron, David C

2018-02-01

One way to understand medical overuse at the clinician level is in terms of clinical decision-making processes that are normally adaptive but become maladaptive. In psychology, dual process models of cognition propose 2 decision-making processes. Reflective cognition is a conscious process of evaluating options based on some combination of utility, risk, capabilities, and/or social influences. Automatic cognition is a largely unconscious process occurring in response to environmental or emotive cues based on previously learned, ingrained heuristics. De-implementation strategies directed at clinicians may be conceptualized as corresponding to cognition: (1) a process of unlearning based on reflective cognition and (2) a process of substitution based on automatic cognition. We define unlearning as a process in which clinicians consciously change their knowledge, beliefs, and intentions about an ineffective practice and alter their behaviour accordingly. Unlearning has been described as "the questioning of established knowledge, habits, beliefs and assumptions as a prerequisite to identifying inappropriate or obsolete knowledge underpinning and/or embedded in existing practices and routines." We hypothesize that as an unintended consequence of unlearning strategies clinicians may experience "reactance," ie, feel their professional prerogative is being violated and, consequently, increase their commitment to the ineffective practice. We define substitution as replacing the ineffective practice with one or more alternatives. A substitute is a specific alternative action or decision that either precludes the ineffective practice or makes it less likely to occur. Both approaches may work independently, eg, a substitute could displace an ineffective practice without changing clinicians' knowledge, and unlearning could occur even if no alternative exists. For some clinical practice, unlearning and substitution strategies may be most effectively used together. By taking into account the dual process model of cognition, we may be able to design de-implementation strategies matched to clinicians' decision-making processes and avoid unintended consequence. © 2018 The Authors. Journal of Evaluation in Clinical Practice published by John Wiley & Sons, Ltd.

Chronic Artificial Blue-Enriched White Light Is an Effective Countermeasure to Delayed Circadian Phase and Neurobehavioral Decrements

PubMed Central

Najjar, Raymond P.; Wolf, Luzian; Taillard, Jacques; Schlangen, Luc J. M.; Salam, Alex

2014-01-01

Studies in Polar Base stations, where personnel have no access to sunlight during winter, have reported circadian misalignment, free-running of the sleep-wake rhythm, and sleep problems. Here we tested light as a countermeasure to circadian misalignment in personnel of the Concordia Polar Base station during the polar winter. We hypothesized that entrainment of the circadian pacemaker to a 24-h light-dark schedule would not occur in all crew members (n = 10) exposed to 100–300 lux of standard fluorescent white (SW) light during the daytime, and that chronic non-time restricted daytime exposure to melanopsin-optimized blue-enriched white (BE) light would establish an a stable circadian phase, in participants, together with increased cognitive performance and mood levels. The lighting schedule consisted of an alternation between SW lighting (2 weeks), followed by a BE lighting (2 weeks) for a total of 9 weeks. Rest-activity cycles assessed by actigraphy showed a stable rest-activity pattern under both SW and BE light. No difference was found between light conditions on the intra-daily stability, variability and amplitude of activity, as assessed by non-parametric circadian analysis. As hypothesized, a significant delay of about 30 minutes in the onset of melatonin secretion occurred with SW, but not with BE light. BE light significantly enhanced well being and alertness compared to SW light. We propose that the superior efficacy of blue-enriched white light versus standard white light involves melanopsin-based mechanisms in the activation of the non-visual functions studied, and that their responses do not dampen with time (over 9-weeks). This work could lead to practical applications of light exposure in working environment where background light intensity is chronically low to moderate (polar base stations, power plants, space missions, etc.), and may help design lighting strategies to maintain health, productivity, and personnel safety. PMID:25072880

Testing hypotheses for differences between linear regression lines

Treesearch

Stanley J. Zarnoch

2009-01-01

Five hypotheses are identified for testing differences between simple linear regression lines. The distinctions between these hypotheses are based on a priori assumptions and illustrated with full and reduced models. The contrast approach is presented as an easy and complete method for testing for overall differences between the regressions and for making pairwise...

Robust Stereo Visual Odometry Using Improved RANSAC-Based Methods for Mobile Robot Localization

PubMed Central

Liu, Yanqing; Gu, Yuzhang; Li, Jiamao; Zhang, Xiaolin

2017-01-01

In this paper, we present a novel approach for stereo visual odometry with robust motion estimation that is faster and more accurate than standard RANSAC (Random Sample Consensus). Our method makes improvements in RANSAC in three aspects: first, the hypotheses are preferentially generated by sampling the input feature points on the order of ages and similarities of the features; second, the evaluation of hypotheses is performed based on the SPRT (Sequential Probability Ratio Test) that makes bad hypotheses discarded very fast without verifying all the data points; third, we aggregate the three best hypotheses to get the final estimation instead of only selecting the best hypothesis. The first two aspects improve the speed of RANSAC by generating good hypotheses and discarding bad hypotheses in advance, respectively. The last aspect improves the accuracy of motion estimation. Our method was evaluated in the KITTI (Karlsruhe Institute of Technology and Toyota Technological Institute) and the New Tsukuba dataset. Experimental results show that the proposed method achieves better results for both speed and accuracy than RANSAC. PMID:29027935

The Somatic Genomic Landscape of Glioblastoma

PubMed Central

Brennan, Cameron W.; Verhaak, Roel G.W.; McKenna, Aaron; Campos, Benito; Noushmehr, Houtan; Salama, Sofie R.; Zheng, Siyuan; Chakravarty, Debyani; Sanborn, J. Zachary; Berman, Samuel H.; Beroukhim, Rameen; Bernard, Brady; Wu, Chang-Jiun; Genovese, Giannicola; Shmulevich, Ilya; Barnholtz-Sloan, Jill; Zou, Lihua; Vegesna, Rahulsimham; Shukla, Sachet A.; Ciriello, Giovanni; Yung, WK; Zhang, Wei; Sougnez, Carrie; Mikkelsen, Tom; Aldape, Kenneth; Bigner, Darell D.; Van Meir, Erwin G.; Prados, Michael; Sloan, Andrew; Black, Keith L.; Eschbacher, Jennifer; Finocchiaro, Gaetano; Friedman, William; Andrews, David W.; Guha, Abhijit; Iacocca, Mary; O’Neill, Brian P.; Foltz, Greg; Myers, Jerome; Weisenberger, Daniel J.; Penny, Robert; Kucherlapati, Raju; Perou, Charles M.; Hayes, D. Neil; Gibbs, Richard; Marra, Marco; Mills, Gordon B.; Lander, Eric; Spellman, Paul; Wilson, Richard; Sander, Chris; Weinstein, John; Meyerson, Matthew; Gabriel, Stacey; Laird, Peter W.; Haussler, David; Getz, Gad; Chin, Lynda

2013-01-01

We describe the landscape of somatic genomic alterations based on multi-dimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer. PMID:24120142

Multiple hypotheses testing of fish incidence patterns in an urbanized ecosystem

USGS Publications Warehouse

Chizinski, C.J.; Higgins, C.L.; Shavlik, C.E.; Pope, K.L.

2006-01-01

Ecological and evolutionary theories have focused traditionally on natural processes with little attempt to incorporate anthropogenic influences despite the fact that humans are such an integral part of virtually all ecosystems. A series of alternate models that incorporated anthropogenic factors and traditional ecological mechanisms of invasion to account for fish incidence patterns in urban lakes was tested. The models were based on fish biology, human intervention, and habitat characteristics. However, the only models to account for empirical patterns were those that included fish invasiveness, which incorporated species-specific information about overall tolerance and fecundity. This suggests that species-specific characteristics are more important in general distributional patterns than human-mediated dispersal. Better information of illegal stocking activities is needed to improve human-mediated models, and more insight into basic life history of ubiquitous species is needed to truly understand underlying mechanisms of biotic homogenization. ?? Springer 2005.

Observed Emotional and Behavioral Indicators of Motivation Predict School Readiness in Head Start Graduates

PubMed Central

Berhenke, Amanda; Miller, Alison L.; Brown, Eleanor; Seifer, Ronald; Dickstein, Susan

2011-01-01

Emotions and behaviors observed during challenging tasks are hypothesized to be valuable indicators of young children's motivation, the assessment of which may be particularly important for children at risk for school failure. The current study demonstrated reliability and concurrent validity of a new observational assessment of motivation in young children. Head Start graduates completed challenging puzzle and trivia tasks during their kindergarten year. Children's emotion expression and task engagement were assessed based on their observed facial and verbal expressions and behavioral cues. Hierarchical regression analyses revealed that observed persistence and shame predicted teacher ratings of children's academic achievement, whereas interest, anxiety, pride, shame, and persistence predicted children's social skills and learning-related behaviors. Children's emotional and behavioral responses to challenge thus appeared to be important indicators of school success. Observation of such responses may be a useful and valid alternative to self-report measures of motivation at this age. PMID:21949599

Lay theories of gender identity disorder.

PubMed

Furnham, Adrian; Sen, Radhika

2013-01-01

This study examined lay theories regarding gender identity disorder (GID). Pilot interviews were completed with participants (n = 10) regarding their views on possible causes and treatments of GID. Participants (mainly young British people and students; n = 124) then completed a questionnaire that was based on the interviews and a review of the salient literature on lay theories. As hypothesized, participants believed most in biomedical causes and treatments of GID. Factor analysis (with varimax rotation) identified 4 factors in relation to causes of GID: upbringing and personal factors, pregnancy and brain abnormalities, environmental factors, and biomedical causes. Five factors that were identified in relation to the cure/treatment of GID were psychological assistance and personal factors, extreme medical and behavioral changes, alternative therapies, external factors, and medical treatments. The results indicated that participants neither agreed nor strongly disagreed about causes and cures regarding GID, but that these beliefs were logically related. Limitations, particularly of sampling, were considered.

The somatic genomic landscape of glioblastoma.

PubMed

Brennan, Cameron W; Verhaak, Roel G W; McKenna, Aaron; Campos, Benito; Noushmehr, Houtan; Salama, Sofie R; Zheng, Siyuan; Chakravarty, Debyani; Sanborn, J Zachary; Berman, Samuel H; Beroukhim, Rameen; Bernard, Brady; Wu, Chang-Jiun; Genovese, Giannicola; Shmulevich, Ilya; Barnholtz-Sloan, Jill; Zou, Lihua; Vegesna, Rahulsimham; Shukla, Sachet A; Ciriello, Giovanni; Yung, W K; Zhang, Wei; Sougnez, Carrie; Mikkelsen, Tom; Aldape, Kenneth; Bigner, Darell D; Van Meir, Erwin G; Prados, Michael; Sloan, Andrew; Black, Keith L; Eschbacher, Jennifer; Finocchiaro, Gaetano; Friedman, William; Andrews, David W; Guha, Abhijit; Iacocca, Mary; O'Neill, Brian P; Foltz, Greg; Myers, Jerome; Weisenberger, Daniel J; Penny, Robert; Kucherlapati, Raju; Perou, Charles M; Hayes, D Neil; Gibbs, Richard; Marra, Marco; Mills, Gordon B; Lander, Eric; Spellman, Paul; Wilson, Richard; Sander, Chris; Weinstein, John; Meyerson, Matthew; Gabriel, Stacey; Laird, Peter W; Haussler, David; Getz, Gad; Chin, Lynda

2013-10-10

We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer. Copyright © 2013 Elsevier Inc. All rights reserved.

Entraining IDyOT: Timing in the Information Dynamics of Thinking

PubMed Central

Forth, Jamie; Agres, Kat; Purver, Matthew; Wiggins, Geraint A.

2016-01-01

We present a novel hypothetical account of entrainment in music and language, in context of the Information Dynamics of Thinking model, IDyOT. The extended model affords an alternative view of entrainment, and its companion term, pulse, from earlier accounts. The model is based on hierarchical, statistical prediction, modeling expectations of both what an event will be and when it will happen. As such, it constitutes a kind of predictive coding, with a particular novel hypothetical implementation. Here, we focus on the model's mechanism for predicting when a perceptual event will happen, given an existing sequence of past events, which may be musical or linguistic. We propose a range of tests to validate or falsify the model, at various different levels of abstraction, and argue that computational modeling in general, and this model in particular, can offer a means of providing limited but useful evidence for evolutionary hypotheses. PMID:27803682

Modern Antarctic acorn worms form tubes.

PubMed

Halanych, Kenneth M; Cannon, Johanna T; Mahon, Andrew R; Swalla, Billie J; Smith, Craig R

2013-01-01

Acorn worms, or enteropneusts, are vermiform hemichordates that occupy an important position in deuterostome phylogeny. Allied to pterobranch hemichordates, small colonial tube dwellers, modern enteropneusts were thought to be tubeless. However, understanding of hemichordate diversity is poor, as evidenced by absence of reports from some oceanic regions and recent descriptions of large epibenthic deep-water enteropneusts, Torquaratoridae. Here we show, based on expeditions to Antarctica, that some acorn worms produce conspicuous tubes that persist for days. Interestingly, recent fossil descriptions show a Middle Cambrian acorn worm lived in tubes, leading to speculation that these fossils may have been pterobranch forbearers. Our discovery provides the alternative interpretation that these fossils are similar to modern-day torquaratorids and that some behaviours have been conserved for over 500 million years. Moreover, the frequency of Antarctic enteropneusts observed attests to our limited knowledge of Antarctic marine ecosystems, and strengthens hypotheses relating more northern deep-sea fauna to Antarctic shelf fauna.

Physician-patient argumentation and communication, comparing Toulmin's model, pragma-dialectics, and American sociolinguistics.

PubMed

Rivera, Francisco Javier Uribe; Artmann, Elizabeth

2015-12-01

This article discusses the application of theories of argumentation and communication to the field of medicine. Based on a literature review, the authors compare Toulmin's model, pragma-dialectics, and the work of Todd and Fisher, derived from American sociolinguistics. These approaches were selected because they belong to the pragmatic field of language. The main results were: pragma-dialectics characterizes medical reasoning more comprehensively, highlighting specific elements of the three disciplines of argumentation: dialectics, rhetoric, and logic; Toulmin's model helps substantiate the declaration of diagnostic and therapeutic hypotheses, and as part of an interpretive medicine, approximates the pragma-dialectical approach by including dialectical elements in the process of formulating arguments; Fisher and Todd's approach allows characterizing, from a pragmatic analysis of speech acts, the degree of symmetry/asymmetry in the doctor-patient relationship, while arguing the possibility of negotiating treatment alternatives.

Lay Theories of Gender Identity Disorder

PubMed Central

Sen, Radhika

2013-01-01

This study examined lay theories regarding gender identity disorder (GID). Pilot interviews were completed with participants (n = 10) regarding their views on possible causes and treatments of GID. Participants (mainly young British people and students; n = 124) then completed a questionnaire that was based on the interviews and a review of the salient literature on lay theories. As hypothesized, participants believed most in biomedical causes and treatments of GID. Factor analysis (with varimax rotation) identified 4 factors in relation to causes of GID: upbringing and personal factors, pregnancy and brain abnormalities, environmental factors, and biomedical causes. Five factors that were identified in relation to the cure/treatment of GID were psychological assistance and personal factors, extreme medical and behavioral changes, alternative therapies, external factors, and medical treatments. The results indicated that participants neither agreed nor strongly disagreed about causes and cures regarding GID, but that these beliefs were logically related. Limitations, particularly of sampling, were considered. PMID:24059967

Observed Emotional and Behavioral Indicators of Motivation Predict School Readiness in Head Start Graduates.

PubMed

Berhenke, Amanda; Miller, Alison L; Brown, Eleanor; Seifer, Ronald; Dickstein, Susan

2011-01-01

Emotions and behaviors observed during challenging tasks are hypothesized to be valuable indicators of young children's motivation, the assessment of which may be particularly important for children at risk for school failure. The current study demonstrated reliability and concurrent validity of a new observational assessment of motivation in young children. Head Start graduates completed challenging puzzle and trivia tasks during their kindergarten year. Children's emotion expression and task engagement were assessed based on their observed facial and verbal expressions and behavioral cues. Hierarchical regression analyses revealed that observed persistence and shame predicted teacher ratings of children's academic achievement, whereas interest, anxiety, pride, shame, and persistence predicted children's social skills and learning-related behaviors. Children's emotional and behavioral responses to challenge thus appeared to be important indicators of school success. Observation of such responses may be a useful and valid alternative to self-report measures of motivation at this age.

Sequential Probability Ratio Test for Spacecraft Collision Avoidance Maneuver Decisions

NASA Technical Reports Server (NTRS)

Carpenter, J. Russell; Markley, F. Landis

2013-01-01

A document discusses sequential probability ratio tests that explicitly allow decision-makers to incorporate false alarm and missed detection risks, and are potentially less sensitive to modeling errors than a procedure that relies solely on a probability of collision threshold. Recent work on constrained Kalman filtering has suggested an approach to formulating such a test for collision avoidance maneuver decisions: a filter bank with two norm-inequality-constrained epoch-state extended Kalman filters. One filter models the null hypotheses that the miss distance is inside the combined hard body radius at the predicted time of closest approach, and one filter models the alternative hypothesis. The epoch-state filter developed for this method explicitly accounts for any process noise present in the system. The method appears to work well using a realistic example based on an upcoming, highly elliptical orbit formation flying mission.

Alternative Splicing of STAT3 Is Affected by RNA Editing.

PubMed

Goldberg, Lior; Abutbul-Amitai, Mor; Paret, Gideon; Nevo-Caspi, Yael

2017-05-01

A-to-I RNA editing, carried out by adenosine deaminase acting on RNA (ADAR) enzymes, is an epigenetic phenomenon of posttranscriptional modifications on pre-mRNA. RNA editing in intronic sequences may influence alternative splicing of flanking exons. We have previously shown that conditions that induce editing result in elevated expression of signal transducer and activator of transcription 3 (STAT3), preferentially the alternatively-spliced STAT3β isoform. Mechanisms regulating alternative splicing of STAT3 have not been elucidated. STAT3 undergoes A-to-I RNA editing in an intron residing in proximity to the alternatively spliced exon. We hypothesized that RNA editing plays a role in regulating alternative splicing toward STAT3β. In this study we extend our observation connecting RNA editing to the preferential induction of STAT3β expression. We study the involvement of ADAR1 in STAT3 editing and reveal the connection between editing and alternative splicing of STAT3. Deferoaxamine treatment caused the induction in STAT3 RNA editing and STAT3β expression. Silencing ADAR1 caused a decrease in STAT3 editing and expression with a preferential decrease in STAT3β. Cells transfected with a mutated minigene showed preferential splicing toward the STAT3β transcript. Editing in the STAT3 intron is performed by ADAR1 and affects STAT3 alternative splicing. These results suggest that RNA editing is one of the molecular mechanisms regulating the expression of STAT3β.

Manual praxis in stone tool manufacture: implications for language evolution.

PubMed

Ruck, Lana

2014-12-01

Alternative functions of the left-hemisphere dominant Broca's region have induced hypotheses regarding the evolutionary parallels between manual praxis and language in humans. Many recent studies on Broca's area reveal several assumptions about the cognitive mechanisms that underlie both functions, including: (1) an accurate, finely controlled body schema, (2) increasing syntactical abilities, particularly for goal-oriented actions, and (3) bilaterality and fronto-parietal connectivity. Although these characteristics are supported by experimental paradigms, many researchers have failed to acknowledge a major line of evidence for the evolutionary development of these traits: stone tools. The neuroscience of stone tool manufacture is a viable proxy for understanding evolutionary aspects of manual praxis and language, and may provide key information for evaluating competing hypotheses on the co-evolution of these cognitive domains in our species. Copyright © 2014 Elsevier Inc. All rights reserved.

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data.

PubMed

Palero, Ferran; Lopes, Joao; Abelló, Pere; Macpherson, Enrique; Pascual, Marta; Beaumont, Mark A

2009-11-09

Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods. Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data.

Science Awareness and Science Literacy through the Basic Physics Course: Physics with a bit of Metaphysics?

NASA Astrophysics Data System (ADS)

Rusli, Aloysius

2016-08-01

Until the 1980s, it is well known and practiced in Indonesian Basic Physics courses, to present physics by its effective technicalities: The ideally elastic spring, the pulley and moving blocks, the thermodynamics of ideal engine models, theoretical electrostatics and electrodynamics with model capacitors and inductors, wave behavior and its various superpositions, and hopefully closed with a modern physics description. A different approach was then also experimented with, using the Hobson and Moore texts, stressing the alternative aim of fostering awareness, not just mastery, of science and the scientific method. This is hypothesized to be more in line with the changed attitude of the so-called Millenials cohort who are less attentive if not interested, and are more used to multi-tasking which suits their shorter span of attention. The upside is increased awareness of science and the scientific method. The downside is that they are getting less experience of the scientific method which intensely bases itself on critical observation, analytic thinking to set up conclusions or hypotheses, and checking consistency of the hypotheses with measured data. Another aspect is recognition that the human person encompasses both the reasoning capacity and the mental- spiritual-cultural capacity. This is considered essential, as the world grows even smaller due to increased communication capacity, causing strong interactions, nonlinear effects, and showing that value systems become more challenging and challenged due to physics / science and its cosmology, which is successfully based on the scientific method. So students should be made aware of the common basis of these two capacities: the assumptions, the reasoning capacity and the consistency assumption. This shows that the limits of science are their set of basic quantifiable assumptions, and the limits of the mental-spiritual-cultural aspects of life are their set of basic metaphysical (non-quantifiable) assumptions. The bridging between these two human aspects of life, can lead to a “why” of science, and a “meaning” of life. A progress report on these efforts is presented, essentially being of the results indicated by an extended format of the usual weekly reporting used previously in Basic Physics lectures.

The Relationship Between Oil and Gas Industry Investment in Alternative Energy and Corporate Social Responsibility

NASA Astrophysics Data System (ADS)

Konyushikhin, Maxim

The U.S. Energy Information Administration forecasted energy consumption in the United States to increase approximately 19% between 2006 and 2030, or about 0.7% annually. The research problem addressed in this study was that the oil and gas industry's interest in alternative energy is contrary to its current business objectives and profit goals. The purpose of the quantitative study was to explore the relationship between oil and gas industry investments in alternative energy and corporate social responsibilities. Research questions addressed the relationship between alternative energy investment and corporate social responsibility, the role of oil and gas companies in alternative energy investment, and why these companies chose to invest in alternative energy sources. Systems theory was the conceptual framework, and data were collected from a sample of 25 companies drawn from the 28,000 companies in the oil and gas industry from 2004 to 2009. Multiple regression and correlation analysis were used to answer the research questions and test hypotheses using corporate financial data and company profiles related to alternative energy investment and corporate social responsibility in terms of oil and gas industry financial support of programs that serve the greater social good. Results indicated significant relationships between alternative energy investment and corporate social responsibility. With an increasing global population with energy requirements in excess of what is available using traditional means, the industry should increase investment in alternative sources. The research results may promote positive social change by increasing public awareness regarding the degree to which oil and gas companies invest in developing alternative energy sources, which might, in turn, inspire public pressure on companies in the oil and gas industry to pursue use of alternative energy.

Comment on “The reduction of friction in long-runout landslides as an emergent phenomenon” by Brandon C. Johnson et al.

USGS Publications Warehouse

Iverson, Richard M.

2016-01-01

Results from a highly idealized, 2-D computational model indicate that dynamic normal-stress rarefactions might cause friction reduction in long-runout landslides, but the physical relevance of the idealized dynamics has not been confirmed by experimental tests. More importantly, the model results provide no evidence that refutes alternative hypotheses about friction reduction mechanisms. One alternative hypothesis, which is strongly supported by field evidence, experimental data, and the predictions of a well-constrained computational model, involves development of high pore fluid pressures in deforming landslide material or overridden bed material. However, no scientific basis exists for concluding that a universal mechanism is responsible for friction reduction in all long-runout landslides.

Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops

PubMed Central

Saqib, Hafiz Sohaib Ahmed; You, Minsheng

2017-01-01

Conservation biological control emphasizes natural and other non-crop vegetation as a source of natural enemies to focal crops. There is an unmet need for better methods to identify the types of vegetation that are optimal to support specific natural enemies that may colonize the crops. Here we explore the commonality of the spider assemblage—considering abundance and diversity (H)—in brassica crops with that of adjacent non-crop and non-brassica crop vegetation. We employ spatial-based multivariate ordination approaches, hierarchical clustering and spatial eigenvector analysis. The small-scale mixed cropping and high disturbance frequency of southern Chinese vegetation farming offered a setting to test the role of alternate vegetation for spider conservation. Our findings indicate that spider families differ markedly in occurrence with respect to vegetation type. Grassy field margins, non-crop vegetation, taro and sweetpotato harbour spider morphospecies and functional groups that are also present in brassica crops. In contrast, pumpkin and litchi contain spiders not found in brassicas, and so may have little benefit for conservation biological control services for brassicas. Our findings also illustrate the utility of advanced statistical approaches for identifying spatial relationships between natural enemies and the land uses most likely to offer alternative habitats for conservation biological control efforts that generates testable hypotheses for future studies. PMID:29085741

A sup-score test for the cure fraction in mixture models for long-term survivors.

PubMed

Hsu, Wei-Wen; Todem, David; Kim, KyungMann

2016-12-01

The evaluation of cure fractions in oncology research under the well known cure rate model has attracted considerable attention in the literature, but most of the existing testing procedures have relied on restrictive assumptions. A common assumption has been to restrict the cure fraction to a constant under alternatives to homogeneity, thereby neglecting any information from covariates. This article extends the literature by developing a score-based statistic that incorporates covariate information to detect cure fractions, with the existing testing procedure serving as a special case. A complication of this extension, however, is that the implied hypotheses are not typical and standard regularity conditions to conduct the test may not even hold. Using empirical processes arguments, we construct a sup-score test statistic for cure fractions and establish its limiting null distribution as a functional of mixtures of chi-square processes. In practice, we suggest a simple resampling procedure to approximate this limiting distribution. Our simulation results show that the proposed test can greatly improve efficiency over tests that neglect the heterogeneity of the cure fraction under the alternative. The practical utility of the methodology is illustrated using ovarian cancer survival data with long-term follow-up from the surveillance, epidemiology, and end results registry. © 2016, The International Biometric Society.

Physical concepts in the development of constitutive equations

NASA Technical Reports Server (NTRS)

Cassenti, B. N.

1985-01-01

Proposed viscoplastic material models include in their formulation observed material response but do not generally incorporate principles from thermodynamics, statistical mechanics, and quantum mechanics. Numerous hypotheses were made for material response based on first principles. Many of these hypotheses were tested experimentally. The proposed viscoplastic theories and the experimental basis of these hypotheses must be checked against the hypotheses. The physics of thermodynamics, statistical mechanics and quantum mechanics, and the effects of defects, are reviewed for their application to the development of constitutive laws.

Organizational Learning and Innovation Performance: A Review of the Literature and the Development of a Conceptual Framework and Research Hypotheses

ERIC Educational Resources Information Center

Wang, Yu-Lin; Ellinger, Andrea D.

2008-01-01

The purpose of this paper is to develop a conceptual framework and research hypotheses based upon a thorough review of the conceptual and limited published empirical research in the organizational learning and innovation performance literatures. Hypotheses indicate the relationships between organizational learning, its antecedent, perception of…

Black/White Differences in Adolescent Drug Use: A Test of Six Hypotheses

ERIC Educational Resources Information Center

Rote, Sunshine M.; Taylor, John

2014-01-01

Six specific hypotheses have been developed to account for why Caucasians have higher rates of drug use compared to African-Americans. This article utilizes data from a South Florida-based community study of 893 young adults (1998-2002) to test these hypotheses. Specifically, Caucasians (1) initiate drug use at younger ages than African-Americans…

Social networks and smoking: exploring the effects of peer influence and smoker popularity through simulations.

PubMed

Schaefer, David R; Adams, Jimi; Haas, Steven A

2013-10-01

Adolescent smoking and friendship networks are related in many ways that can amplify smoking prevalence. Understanding and developing interventions within such a complex system requires new analytic approaches. We draw on recent advances in dynamic network modeling to develop a technique that explores the implications of various intervention strategies targeted toward micro-level processes. Our approach begins by estimating a stochastic actor-based model using data from one school in the National Longitudinal Study of Adolescent Health. The model provides estimates of several factors predicting friendship ties and smoking behavior. We then use estimated model parameters to simulate the coevolution of friendship and smoking behavior under potential intervention scenarios. Namely, we manipulate the strength of peer influence on smoking and the popularity of smokers relative to nonsmokers. We measure how these manipulations affect smoking prevalence, smoking initiation, and smoking cessation. Results indicate that both peer influence and smoking-based popularity affect smoking behavior and that their joint effects are nonlinear. This study demonstrates how a simulation-based approach can be used to explore alternative scenarios that may be achievable through intervention efforts and offers new hypotheses about the association between friendship and smoking.

Social Networks and Smoking: Exploring the Effects of Influence and Smoker Popularity through Simulations

PubMed Central

Schaefer, David R.; adams, jimi; Haas, Steven A.

2015-01-01

Adolescent smoking and friendship networks are related in many ways that can amplify smoking prevalence. Understanding and developing interventions within such a complex system requires new analytic approaches. We draw upon recent advances in dynamic network modeling to develop a technique that explores the implications of various intervention strategies targeted toward micro-level processes. Our approach begins by estimating a stochastic actor-based model using data from one school in the National Longitudinal Study of Adolescent Health. The model provides estimates of several factors predicting friendship ties and smoking behavior. We then use estimated model parameters to simulate the co-evolution of friendship and smoking behavior under potential intervention scenarios. Namely, we manipulate the strength of peer influence on smoking and the popularity of smokers relative to nonsmokers. We measure how these manipulations affect smoking prevalence, smoking initiation, and smoking cessation. Results indicate that both peer influence and smoking-based popularity affect smoking behavior, and that their joint effects are nonlinear. This study demonstrates how a simulation-based approach can be used to explore alternative scenarios that may be achievable through intervention efforts and offers new hypotheses about the association between friendship and smoking. PMID:24084397

Emergence of a coherent and cohesive swarm based on mutual anticipation

PubMed Central

Murakami, Hisashi; Niizato, Takayuki; Gunji, Yukio-Pegio

2017-01-01

Collective behavior emerging out of self-organization is one of the most striking properties of an animal group. Typically, it is hypothesized that each individual in an animal group tends to align its direction of motion with those of its neighbors. Most previous models for collective behavior assume an explicit alignment rule, by which an agent matches its velocity with that of neighbors in a certain neighborhood, to reproduce a collective order pattern by simple interactions. Recent empirical studies, however, suggest that there is no evidence for explicit matching of velocity, and that collective polarization arises from interactions other than those that follow the explicit alignment rule. We here propose a new lattice-based computational model that does not incorporate the explicit alignment rule but is based instead on mutual anticipation and asynchronous updating. Moreover, we show that this model can realize densely collective motion with high polarity. Furthermore, we focus on the behavior of a pair of individuals, and find that the turning response is drastically changed depending on the distance between two individuals rather than the relative heading, and is consistent with the empirical observations. Therefore, the present results suggest that our approach provides an alternative model for collective behavior. PMID:28406173

Drug Target Protein-Protein Interaction Networks: A Systematic Perspective

PubMed Central

2017-01-01

The identification and validation of drug targets are crucial in biomedical research and many studies have been conducted on analyzing drug target features for getting a better understanding on principles of their mechanisms. But most of them are based on either strong biological hypotheses or the chemical and physical properties of those targets separately. In this paper, we investigated three main ways to understand the functional biomolecules based on the topological features of drug targets. There are no significant differences between targets and common proteins in the protein-protein interactions network, indicating the drug targets are neither hub proteins which are dominant nor the bridge proteins. According to some special topological structures of the drug targets, there are significant differences between known targets and other proteins. Furthermore, the drug targets mainly belong to three typical communities based on their modularity. These topological features are helpful to understand how the drug targets work in the PPI network. Particularly, it is an alternative way to predict potential targets or extract nontargets to test a new drug target efficiently and economically. By this way, a drug target's homologue set containing 102 potential target proteins is predicted in the paper. PMID:28691014

A learning progression based teaching module on the causes of seasons

NASA Astrophysics Data System (ADS)

Galano, S.

2016-03-01

In this paper, we report about designing and validating a teaching learning module based on a learning progression and focused on the causes of seasons. An initial learning progression about the Celestial Motion big idea -causes of seasons, lunar and solar eclipse and Moon phases- was developed and validated. Existing curricula, research studies on alternative conceptions about these phenomena, and students' answers to an open questionnaire were the starting point to develop initial learning progressions; then, a two-tier multiple-choice questionnaire was designed to validate and improve it. The questionnaire was submitted to about 300 secondary-school students whose answers were used to revise the hypothesized learning progressions. This improved version of the learning progression was used to design a module focused on the causes of seasons in which students were engaged in quantitative measurements with a photovoltaic panel to explain changes of the Sun rays' flow on the Earth's surface over the year. The efficacy of our module in improving students' understanding of the phenomenon of the seasons was tested using our questionnaire as pre- and post-test.

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

PubMed Central

Huang, Ruili; Xia, Menghang; Sakamuru, Srilatha; Zhao, Jinghua; Shahane, Sampada A.; Attene-Ramos, Matias; Zhao, Tongan; Austin, Christopher P.; Simeonov, Anton

2016-01-01

Target-specific, mechanism-oriented in vitro assays post a promising alternative to traditional animal toxicology studies. Here we report the first comprehensive analysis of the Tox21 effort, a large-scale in vitro toxicity screening of chemicals. We test ∼10,000 chemicals in triplicates at 15 concentrations against a panel of nuclear receptor and stress response pathway assays, producing more than 50 million data points. Compound clustering by structure similarity and activity profile similarity across the assays reveals structure–activity relationships that are useful for the generation of mechanistic hypotheses. We apply structural information and activity data to build predictive models for 72 in vivo toxicity end points using a cluster-based approach. Models based on in vitro assay data perform better in predicting human toxicity end points than animal toxicity, while a combination of structural and activity data results in better models than using structure or activity data alone. Our results suggest that in vitro activity profiles can be applied as signatures of compound mechanism of toxicity and used in prioritization for more in-depth toxicological testing. PMID:26811972

Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

PubMed

Ruhlman, Tracey A; Zhang, Jin; Blazier, John C; Sabir, Jamal S M; Jansen, Robert K

2017-04-01

There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats. © 2017 Botanical Society of America.

Predicted effect of landscape position on wildlife habitat value of Conservation Reserve Enhancement Program wetlands in a tile-drained agricultural region

USGS Publications Warehouse

Otis, David L.; Crumpton, William R.; Green, David; Loan-Wilsey, Anna; Cooper, Tom; Johnson, Rex R.

2013-01-01

Justification for investment in restored or constructed wetland projects are often based on presumed net increases in ecosystem services. However, quantitative assessment of performance metrics is often difficult and restricted to a single objective. More comprehensive performance assessments could help inform decision-makers about trade-offs in services provided by alternative restoration program design attributes. The primary goal of the Iowa Conservation Reserve Enhancement Program is to establish wetlands that efficiently remove nitrates from tile-drained agricultural landscapes. A secondary objective is provision of wildlife habitat. We used existing wildlife habitat models to compare relative net change in potential wildlife habitat value for four alternative landscape positions of wetlands within the watershed. Predicted species richness and habitat value for birds, mammals, amphibians, and reptiles generally increased as the wetland position moved lower in the watershed. However, predicted average net increase between pre- and post-project value was dependent on taxonomic group. The increased average wetland area and changes in surrounding upland habitat composition among landscape positions were responsible for these differences. Net change in predicted densities of several grassland bird species at the four landscape positions was variable and species-dependent. Predicted waterfowl breeding activity was greater for lower drainage position wetlands. Although our models are simplistic and provide only a predictive index of potential habitat value, we believe such assessment exercises can provide a tool for coarse-level comparisons of alternative proposed project attributes and a basis for constructing informed hypotheses in auxiliary empirical field studies.

Recursive Fury: Conspiracist Ideation in the Blogosphere in Response to Research on Conspiracist Ideation

PubMed Central

Lewandowsky, Stephan; Cook, John; Oberauer, Klaus; Marriott, Michael

2013-01-01

Conspiracist ideation has been repeatedly implicated in the rejection of scientific propositions, although empirical evidence to date has been sparse. A recent study involving visitors to climate blogs found that conspiracist ideation was associated with the rejection of climate science and the rejection of other scientific propositions such as the link between lung cancer and smoking, and between HIV and AIDS (Lewandowsky et al., in press; LOG12 from here on). This article analyses the response of the climate blogosphere to the publication of LOG12. We identify and trace the hypotheses that emerged in response to LOG12 and that questioned the validity of the paper’s conclusions. Using established criteria to identify conspiracist ideation, we show that many of the hypotheses exhibited conspiratorial content and counterfactual thinking. For example, whereas hypotheses were initially narrowly focused on LOG12, some ultimately grew in scope to include actors beyond the authors of LOG12, such as university executives, a media organization, and the Australian government. The overall pattern of the blogosphere’s response to LOG12 illustrates the possible role of conspiracist ideation in the rejection of science, although alternative scholarly interpretations may be advanced in the future. PMID:23508808

Effects of Age on Auditory and Cognitive Processing: Implications for Hearing Aid Fitting and Audiologic Rehabilitation

PubMed Central

Pichora-Fuller, M. Kathleen; Singh, Gurjit

2006-01-01

Recent advances in research and clinical practice concerning aging and auditory communication have been driven by questions about age-related differences in peripheral hearing, central auditory processing, and cognitive processing. A “site-of-lesion” view based on anatomic levels inspired research to test competing hypotheses about the contributions of changes at these three levels of the nervous system. A “processing” view based on psychologic functions inspired research to test alternative hypotheses about how lower-level sensory processes and higher-level cognitive processes interact. In the present paper, we suggest that these two views can begin to be unified following the example set by the cognitive neuroscience of aging. The early pioneers of audiology anticipated such a unified view, but today, advances in science and technology make it both possible and necessary. Specifically, we argue that a synthesis of new knowledge concerning the functional neuroscience of auditory cognition is necessary to inform the design and fitting of digital signal processing in “intelligent” hearing devices, as well as to inform best practices for resituating hearing aid fitting in a broader context of audiologic rehabilitation. Long-standing approaches to rehabilitative audiology should be revitalized to emphasize the important role that training and therapy play in promoting compensatory brain reorganization as older adults acclimatize to new technologies. The purpose of the present paper is to provide an integrated framework for understanding how auditory and cognitive processing interact when older adults listen, comprehend, and communicate in realistic situations, to review relevant models and findings, and to suggest how new knowledge about age-related changes in audition and cognition may influence future developments in hearing aid fitting and audiologic rehabilitation. PMID:16528429

[Autism and vaccinations: the end?].

PubMed

Artigas-Pallarés, J

2010-03-03

Of the different theories explaining the aetiology of autism, one that has achieved widespread popularity among the general public is the involvement of the MMR vaccine as the causation of autism. The connection between vaccines and autism rests upon two theories. On the one hand, the anti-measles fraction of the vaccine is attributed with the development of an enteropathy due to malabsorption, which would facilitate the absorption of toxic neuropeptides and the effects of this process on the brain would favour the appearance of autism. The other theory involves thimerosal (a combination of ethylmercury and thiosalicylate), which is used as a preservative in some vaccines, including the MMR. The data in favour of these hypotheses have led to a great amount of social alarm, especially in certain areas that are more inclined to accept 'alternative' therapies and hypotheses. This article analyses the data on which the involvement of the MMR vaccine in autism is based. It also underlines the weakness of the anti-vaccine arguments, as well as the forceful, convincing response, based on experimental and epidemiological work, that has been generated following the notable social unrest. Running parallel to the scientific debate, there has also been a legal discussion, which has arisen as a consequence of the more than 5,000 lawsuits filed in the United States, and in which the claims for financial compensation together amount to two thousand million dollars. On 12th February 2009, following a court hearing in which the specific case of a girl called Michelle Cedillo was taken as an example, the court ruled that the overall weight of the evidence was overwhelmingly opposed to the theories put forward by the plaintiffs.

HyQue: evaluating hypotheses using Semantic Web technologies.

PubMed

Callahan, Alison; Dumontier, Michel; Shah, Nigam H

2011-05-17

Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks. We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in Saccharomyces cerevisiae to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF. HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in S. cerevisiae. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and vice versa. HyQue hypotheses and data are available at http://semanticscience.org/projects/hyque.

Temporal and spatial stress-field reorientation in the footwall of two low-angle normal faults (lanf's): Implications for fault weakening and earthquake stress drops

NASA Astrophysics Data System (ADS)

Luther, A. L.; Axen, G. J.; Selverstone, J.

2011-12-01

Paleostress analyses from the footwall of the West Salton and Whipple detachment faults (WSD and WD, respectively), 2 lanfs, indicate both spatial and temporal stress field changes. Lanf's slip at a higher angle to S1 than predicted by Anderson. Hypotheses allowing slip on misoriented faults include a local stress field rotation in the fault zone, low friction materials, high pore-fluid pressure, and/or dynamic effects. The WSD, is part of the dextral-transtensional southern San Andreas fault system, slipped ~10 km from ~8 to 1 Ma, and the footwall exposures reflect only brittle deformation. The WD slipped at least ~40 km from ~25 to ~16 Ma, and has a mylonitic footwall overprinted by brittle deformation. Both lanf's were folded during extension. 80% of inversions that fit extension have a steeply-plunging S1, consistent with lanf slip at a high angle to S1. These require some weakening mechanism and the absence of known weak materials along these faults suggest pore-fluid pressure or dynamic effects are relevant. Most spatial S1 changes that occur are across minidetachments, which are faults sub-parallel to main faults that have similar damage zones that we interpret formed early in WD history, at the frictional-viscous transition [Selverstone et al. this session]. Their footwalls record a more moderately-plunging S1 than their hanging walls. Thus, we infer that older, deeper stress fields were rotated, consistent with a gradual rotation with depth. Alternating stress fields apparently affected many single outcrops and arise from mutually cross-cutting fracture sets that cannot be fit by a single stress field. In places where the alternation is between extensional and shortening fields, the shortening directions are subhorizontal, ~perpendicular to fold-axes and consistent with dextral-oblique slip in the case of the WSD. Commonly, S1 and S3 swap positions. In other places, two extensional stress fields differ, with S1 changing from a steep to a moderate angle to the lanf. We hypothesize that alternating stress fields result from earthquake stress drops large enough to allow at least 2 principal stresses to switch orientations. Either the differential stresses are small and similar to hypothesized stress drops or stress drops are larger than suggested by seismic data.

Merging Hydrologic, Geochemical, and Geophysical Approaches to Understand the Regolith Architecture of a Deeply Weathered Piedmont Critical Zone

NASA Astrophysics Data System (ADS)

Cosans, C.; Moore, J.; Harman, C. J.

2017-12-01

Located in the deeply weathered Piedmont in Maryland, Pond Branch has a rich legacy of hydrological and geochemical research dating back to the first geochemical mass balance study published in 1970. More recently, geophysical investigations including seismic and electrical resistivity tomography have characterized the subsurface at Pond Branch and contributed to new hypotheses about critical zone evolution. Heterogeneity in electrical resistivity in the shallow subsurface may suggest disparate flow paths for recharge, with some regions with low hydraulic conductivity generating perched flow, while other hillslope sections recharge to the much deeper regolith boundary. These shallow and deep flow paths are hypothesized to be somewhat hydrologically and chemically connected, with the spatially and temporally discontinuous connections resulting in different hydraulic responses to recharge and different concentrations of weathering solutes. To test this hypothesis, we combined modeling and field approaches. We modeled weathering solutes along the hypothesized flow paths using PFLOTRAN. We measured hydrologic gradients in the hillslopes and riparian zone using piezometer water levels. We collected geochemical data including major ions and silica. Weathering solute concentrations were measured directly in the precipitation, hillslope springs, and the riparian zone for comparison to modeled concentration values. End member mixing methods were used to determine contributions of precipitation, hillslopes, and riparian zone to the stream. Combining geophysical, geochemical, and hydrological methods may offer insights into the source of stream water and controls on chemical weathering. Previous hypotheses that Piedmont critical zone architecture results from a balance of erosion, soil, and weathering front advance rates cannot account for the inverted regolith structure observed through seismic investigations at Pond Branch. Recent alternative hypotheses including weathering along tectonically-induced fractures and weathering front advance have been proposed, but additional data are needed to test them. Developing a thorough, nuanced understanding of the geochemical and hydrological behavior of Pond Branch may help test and refine hypotheses for Piedmont critical zone evolution.

On the use of three hydrological models as hypotheses to investigate the behaviour of a small Mediterranean catchment

NASA Astrophysics Data System (ADS)

Ruiz Pérez, Guiomar; Latron, Jérôme; Llorens, Pilar; Gallart, Francesc; Francés, Félix

2017-04-01

Selecting an adequate hydrological model is the first step to carry out a rainfall-runoff modelling exercise. A hydrological model is a hypothesis of catchment functioning, encompassing a description of dominant hydrological processes and predicting how these processes interact to produce the catchment's response to external forcing. Current research lines emphasize the importance of multiple working hypotheses for hydrological modelling instead of only using a single model. In line with this philosophy, here different hypotheses were considered and analysed to simulate the nonlinear response of a small Mediterranean catchment and to progress in the analysis of its hydrological behaviour. In particular, three hydrological models were considered representing different potential hypotheses: two lumped models called LU3 and LU4, and one distributed model called TETIS. To determine how well each specific model performed and to assess whether a model was more adequate than another, we raised three complementary tests: one based on the analysis of residual errors series, another based on a sensitivity analysis and the last one based on using multiple evaluation criteria associated to the concept of Pareto frontier. This modelling approach, based on multiple working hypotheses, helped to improve our perceptual model of the catchment behaviour and, furthermore, could be used as a guidance to improve the performance of other environmental models.

Male Partners' Investment and Alternatives as Correlates of Women's Coerced First Sexual Intercourse in Chinese Dating Relationships: A Social Exchange Perspective.

PubMed

He, Shanshan; Tsang, Sandra

2016-10-01

Social exchange theory has great potential to help our understanding of dating partners' sexual interaction. Yet, to our knowledge, there is still no empirical study applying this theory to explain sexual coercion in the context of intimate relationships. This study examined the relationship between male partners' social exchange variables (investment and alternatives) and women's coerced first sexual intercourse in dating relationships, within both gender samples (not dyadic data). A total of 927 valid questionnaires were collected by purposive snowball sampling in five main cities in China of college students who were currently in a romantic relationship. Results showed that in the male sample, male partners' investment significantly and positively correlated with emotional manipulation coercive tactics, and their alternatives significantly and positively predicted defection threats as coercive tactics. In the female sample, there were no such observations. The research hypotheses of this study have been partially supported, and its implications and limitations are discussed.

Statistical Power of Alternative Structural Models for Comparative Effectiveness Research: Advantages of Modeling Unreliability.

PubMed

Coman, Emil N; Iordache, Eugen; Dierker, Lisa; Fifield, Judith; Schensul, Jean J; Suggs, Suzanne; Barbour, Russell

2014-05-01

The advantages of modeling the unreliability of outcomes when evaluating the comparative effectiveness of health interventions is illustrated. Adding an action-research intervention component to a regular summer job program for youth was expected to help in preventing risk behaviors. A series of simple two-group alternative structural equation models are compared to test the effect of the intervention on one key attitudinal outcome in terms of model fit and statistical power with Monte Carlo simulations. Some models presuming parameters equal across the intervention and comparison groups were underpowered to detect the intervention effect, yet modeling the unreliability of the outcome measure increased their statistical power and helped in the detection of the hypothesized effect. Comparative Effectiveness Research (CER) could benefit from flexible multi-group alternative structural models organized in decision trees, and modeling unreliability of measures can be of tremendous help for both the fit of statistical models to the data and their statistical power.

Alternative Splicing of Four Trafficking Genes Regulates Myofiber Structure and Skeletal Muscle Physiology.

PubMed

Giudice, Jimena; Loehr, James A; Rodney, George G; Cooper, Thomas A

2016-11-15

During development, transcriptional and post-transcriptional networks are coordinately regulated to drive organ maturation. Alternative splicing contributes by producing temporal-specific protein isoforms. We previously found that genes undergoing splicing transitions during mouse postnatal heart development are enriched for vesicular trafficking and membrane dynamics functions. Here, we show that adult trafficking isoforms are also expressed in adult skeletal muscle and hypothesize that striated muscle utilizes alternative splicing to generate specific isoforms required for function of adult tissue. We deliver morpholinos into flexor digitorum brevis muscles in adult mice to redirect splicing of four trafficking genes to the fetal isoforms. The splicing switch results in multiple structural and functional defects, including transverse tubule (T-tubule) disruption and dihydropyridine receptor alpha (DHPR) and Ryr1 mislocalization, impairing excitation-contraction coupling, calcium handling, and force generation. The results demonstrate a previously unrecognized role for trafficking functions in adult muscle tissue homeostasis and a specific requirement for the adult splice variants. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Attention moderates the fearlessness of psychopathic offenders

PubMed Central

Newman, Joseph P.; Curtin, John J.; Bertsch, Jeremy D.; Baskin-Sommers, Arielle R.

2009-01-01

Background Psychopathic behavior is generally attributed to a fundamental, amygdala-mediated deficit in fearlessness that undermines social conformity. An alternative view is that psychopathy involves an attention-related deficit that undermines the processing of peripheral information including fear stimuli. Methods We evaluated these alternative hypotheses by measuring fear-potentiated startle (FPS) in a group of 125 prisoners under experimental conditions that (a) focused attention directly on fear-relevant information or (b) established an alternative attentional focus. Psychopathy was assessed using Hare’s (1) Psychopathy Checklist-Revised (PCL-R). Results Psychopathic individuals displayed normal FPS under threat-focused conditions but manifested a significant deficit in FPS under alternative-focus conditions. Moreover, these findings were essentially unchanged when analyses employed the interpersonal-affective factor of the PCL-R instead of PCL-R total scores. Conclusions The results provide unprecedented evidence that higher-order cognitive processes moderate the fear deficits of psychopathic individuals. These findings suggest that psychopaths’ diminished reactivity to fear stimuli, and emotion-related cues more generally, reflect idiosyncrasies in attention that limit their processing of peripheral information. Although psychopathic individuals are commonly described as cold-blooded predators who are unmotivated to change, the attentional dysfunction identified in this study supports an alternative interpretation of their chronic disinhibition and insensitive interpersonal style. PMID:19793581

Pectus excavatum: history, hypotheses and treatment options

PubMed Central

Brochhausen, Christoph; Turial, Salmai; Müller, Felix K.P.; Schmitt, Volker H.; Coerdt, Wiltrud; Wihlm, Jean-Marie; Schier, Felix; Kirkpatrick, C. James

2012-01-01

Pectus excavatum and pectus carinatum represent the most frequent chest wall deformations. However, the pathogenesis is still poorly understood and research results remain inconsistent. To focus on the recent state of knowledge, we summarize and critically discuss the pathological concepts based on the history of these entities, beginning with the first description in the sixteenth century. Based on the early clinical descriptions, we review and discuss the different pathogenetic hypotheses. To open new perspectives for the potential pathomechanisms, the embryonic and foetal development of the ribs and the sternum is highlighted following the understanding that the origin of these deformities is given by the disruption in the maturation of the parasternal region. In the second, different therapeutical techniques are highlighted and based on the pathogenetic hypotheses and the embryological knowledge potential new biomaterial-based perspectives with interesting insights for tissue engineering-based treatment options are presented. PMID:22394989

Impact of scaffolding and question structure on the gender gap

NASA Astrophysics Data System (ADS)

Dawkins, Hillary; Hedgeland, Holly; Jordan, Sally

2017-12-01

We address previous hypotheses about possible factors influencing the gender gap in attainment in physics. Specifically, previous studies claim that scaffolding may preferentially benefit female students, and we present some alternative conclusions surrounding this hypothesis. By taking both student attainment level and the degree of question scaffolding into account, we identify questions that exhibit real bias in favor of male students. We find that both multidimensional context and use of diagrams are common elements of such questions.

The clinical and molecular genetic features of idiopathic infantile periodic alternating nystagmus

PubMed Central

Thomas, Mervyn G.; Crosier, Moira; Lindsay, Susan; Kumar, Anil; Thomas, Shery; Araki, Masasuke; Talbot, Chris J.; McLean, Rebecca J.; Surendran, Mylvaganam; Taylor, Katie; Leroy, Bart P.; Moore, Anthony T.; Hunter, David G.; Hertle, Richard W.; Tarpey, Patrick; Langmann, Andrea; Lindner, Susanne; Brandner, Martina

2011-01-01

Periodic alternating nystagmus consists of involuntary oscillations of the eyes with cyclical changes of nystagmus direction. It can occur during infancy (e.g. idiopathic infantile periodic alternating nystagmus) or later in life. Acquired forms are often associated with cerebellar dysfunction arising due to instability of the optokinetic-vestibular systems. Idiopathic infantile periodic alternating nystagmus can be familial or occur in isolation; however, very little is known about the clinical characteristics, genetic aetiology and neural substrates involved. Five loci (NYS1-5) have been identified for idiopathic infantile nystagmus; three are autosomal (NYS2, NYS3 and NYS4) and two are X-chromosomal (NYS1 and NYS5). We previously identified the FRMD7 gene on chromosome Xq26 (NYS1 locus); mutations of FRMD7 are causative of idiopathic infantile nystagmus influencing neuronal outgrowth and development. It is unclear whether the periodic alternating nystagmus phenotype is linked to NYS1, NYS5 (Xp11.4-p11.3) or a separate locus. From a cohort of 31 X-linked families and 14 singletons (70 patients) with idiopathic infantile nystagmus we identified 10 families and one singleton (21 patients) with periodic alternating nystagmus of which we describe clinical phenotype, genetic aetiology and neural substrates involved. Periodic alternating nystagmus was not detected clinically but only on eye movement recordings. The cycle duration varied from 90 to 280 s. Optokinetic reflex was not detectable horizontally. Mutations of the FRMD7 gene were found in all 10 families and the singleton (including three novel mutations). Periodic alternating nystagmus was predominantly associated with missense mutations within the FERM domain. There was significant sibship clustering of the phenotype although in some families not all affected members had periodic alternating nystagmus. In situ hybridization studies during mid-late human embryonic stages in normal tissue showed restricted FRMD7 expression in neuronal tissue with strong hybridization signals within the afferent arms of the vestibulo-ocular reflex consisting of the otic vesicle, cranial nerve VIII and vestibular ganglia. Similarly within the afferent arm of the optokinetic reflex we showed expression in the developing neural retina and ventricular zone of the optic stalk. Strong FRMD7 expression was seen in rhombomeres 1 to 4, which give rise to the cerebellum and the common integrator site for both these reflexes (vestibular nuclei). Based on the expression and phenotypic data, we hypothesize that periodic alternating nystagmus arises from instability of the optokinetic-vestibular systems. This study shows for the first time that mutations in FRMD7 can cause idiopathic infantile periodic alternating nystagmus and may affect neuronal circuits that have been implicated in acquired forms. PMID:21303855

Physiologic, Behavioral, and Histologic Responses to Various Euthanasia Methods in C57BL/6NTac Male Mice.

PubMed

Boivin, Gregory P; Bottomley, Michael A; Schiml, Patricia A; Goss, Lori; Grobe, Nadja

2017-01-01

Rodent euthanasia using exposure to increasing concentrations of CO2 has come under scrutiny due to concerns of potential pain during the euthanasia process. Alternatives to CO2, such as isoflurane and barbiturates, have been proposed as more humane methods of euthanasia. In this study, we examined 3 commonly used euthanasia methods in mice: intraperitoneal injection of pentobarbital-phenytoin solution, CO2 inhalation, and isoflurane anesthesia followed by CO2 inhalation. We hypothesized that pentobarbital-phenytoin euthanasia would cause fewer alterations in cardiovascular response, result in less behavioral evidence of pain or stress, and produce lower elevations in ACTH than would the isoflurane and CO2 methods, which we hypothesized would not differ in regard to these parameters. ACTH data suggested that pentobarbital-phenytoin euthanasia may be less stressful to mice than are isoflurane and CO2 euthanasia. Cardiovascular, behavioral, and activity data did not consistently or significantly support isoflurane or pentobarbital-phenytoin euthanasia as less stressful methods than CO2. Euthanasia with CO2 was the fastest method of the 3 techniques. Therefore, we conclude that using CO2 with or without isoflurane is an acceptable euthanasia method. Pathologic alterations in the lungs were most severe with CO2 euthanasia, and alternative euthanasia techniques likely are better suited for studies that rely on analysis of the lungs.

Resource availability controls fungal diversity across a plant diversity gradient

USGS Publications Warehouse

Waldrop, M.P.; Zak, D.R.; Blackwood, C.B.; Curtis, C.D.; Tilman, D.

2006-01-01

Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales. ?? 2006 Blackwell Publishing Ltd/CNRS.

Physiologic, Behavioral, and Histologic Responses to Various Euthanasia Methods in C57BL/6NTac Male Mice

PubMed Central

Boivin, Gregory P; Bottomley, Michael A; Schiml, Patricia A; Goss, Lori; Grobe, Nadja

2017-01-01

Rodent euthanasia using exposure to increasing concentrations of CO2 has come under scrutiny due to concerns of potential pain during the euthanasia process. Alternatives to CO2, such as isoflurane and barbiturates, have been proposed as more humane methods of euthanasia. In this study, we examined 3 commonly used euthanasia methods in mice: intraperitoneal injection of pentobarbital–phenytoin solution, CO2 inhalation, and isoflurane anesthesia followed by CO2 inhalation. We hypothesized that pentobarbital–phenytoin euthanasia would cause fewer alterations in cardiovascular response, result in less behavioral evidence of pain or stress, and produce lower elevations in ACTH than would the isoflurane and CO2 methods, which we hypothesized would not differ in regard to these parameters. ACTH data suggested that pentobarbital–phenytoin euthanasia may be less stressful to mice than are isoflurane and CO2 euthanasia. Cardiovascular, behavioral, and activity data did not consistently or significantly support isoflurane or pentobarbital–phenytoin euthanasia as less stressful methods than CO2. Euthanasia with CO2 was the fastest method of the 3 techniques. Therefore, we conclude that using CO2 with or without isoflurane is an acceptable euthanasia method. Pathologic alterations in the lungs were most severe with CO2 euthanasia, and alternative euthanasia techniques likely are better suited for studies that rely on analysis of the lungs. PMID:28905718

Unpacking commitment and exploration: preliminary validation of an integrative model of late adolescent identity formation.

PubMed

Luyckx, Koen; Goossens, Luc; Soenens, Bart; Beyers, Wim

2006-06-01

A model of identity formation comprising four structural dimensions (Commitment Making, Identification with Commitment, Exploration in Depth, and Exploration in Breadth) was developed through confirmatory factor analysis. In a sample of 565 emerging adults, this model provided a better fit than did alternative two- and three-dimensional models, thereby validating the unpacking of both exploration and commitment. Regression analyses indicated that Commitment Making was significantly related to family context in accordance with hypotheses. Identification with Commitment and both exploration dimensions were significantly related to adjustment and family context, again in accordance with hypotheses. Identification with Commitment was positively related to positive adjustment indicators and negatively to depressive symptoms, whereas Exploration in Breadth was positively related to depressive symptoms and substance use. Exploration in Depth, on the other hand, was positively related to academic adjustment and negatively to substance use. Implications and suggestions for future research are discussed.

Melanosomes or Microbes: Testing an Alternative Hypothesis for the Origin of Microbodies in Fossil Feathers

NASA Astrophysics Data System (ADS)

Moyer, Alison E.; Zheng, Wenxia; Johnson, Elizabeth A.; Lamanna, Matthew C.; Li, Da-Qing; Lacovara, Kenneth J.; Schweitzer, Mary H.

2014-03-01

Microbodies associated with fossil feathers, originally attributed to microbial biofilm, have been reinterpreted as melanosomes: pigment-containing, eukaryotic organelles. This interpretation generated hypotheses regarding coloration in non-avian and avian dinosaurs. Because melanosomes and microbes overlap in size, distribution and morphology, we re-evaluate both hypotheses. We compare melanosomes within feathers of extant chickens with patterns induced by microbial overgrowth on the same feathers, using scanning (SEM), field emission (FESEM) and transmission (TEM) electron microscopy. Melanosomes are always internal, embedded in a morphologically distinct keratinous matrix. Conversely, microbes grow across the surface of feathers in continuous layers, more consistent with published images from fossil feathers. We compare our results to both published literature and new data from a fossil feather ascribed to Gansus yumenensis (ANSP 23403). `Mouldic impressions' were observed in association with both the feather and sediment grains, supporting a microbial origin. We propose criteria for distinguishing between these two microbodies.

Psychological underpinnings of intrafamilial computer-mediated communication: a preliminary exploration of CMC uptake with parents and siblings.

PubMed

Goby, Valerie Priscilla

2011-06-01

This preliminary study investigates the uptake of computer-mediated communication (CMC) with parents and siblings, an area on which no research appears to have been conducted. Given the lack of relevant literature, grounded theory methodology was used and online focus group discussions were conducted in an attempt to generate suitable hypotheses for further empirical studies. Codification of the discussion data revealed various categories of meaning, namely: a perceived inappropriateness of CMC with members of family of origin; issues relating to the family generational gap; the nature of the offline sibling/parent relationship; the non-viability of online affordances such as planned self-disclosure, deception, identity construction; and disinhibition in interactions with family-of-origin members. These themes could be molded into hypotheses to assess the psychosocial limitations of CMC and to determine if it can indeed become a ubiquitous alternative to traditional communication modes as some scholars have claimed.

Social cognition and externalizing psychopathology: an investigation of the mediating role of language.

PubMed

Zadeh, Zohreh Yaghoub; Im-Bolter, Nancie; Cohen, Nancy J

2007-04-01

The present study integrates findings from three lines of research on the association of social cognition and externalizing psychopathology, language and externalizing psychopathology, and social cognition and language functioning using Structural Equation Modeling (SEM). To date these associations have been examined in pairs. A sample of 354 clinic-referred children (aged 7 to 14 years) recruited from a children's mental health centre were tested on measures of language, social cognition, working memory, and child psychopathology. We compared a hypothesized model presenting language functioning as a mediator of the association between social cognition and externalizing psychopathology to a model presenting the independent contribution of language and social cognition to externalizing psychopathology. As hypothesized, we found that the mediation model fits the data better than the alternative model. Our findings have implications for developing and modifying intervention techniques for children with dual language and externalizing psychopathology.

From what might have been to what must have been: counterfactual thinking creates meaning.

PubMed

Kray, Laura J; George, Linda G; Liljenquist, Katie A; Galinsky, Adam D; Tetlock, Philip E; Roese, Neal J

2010-01-01

Four experiments explored whether 2 uniquely human characteristics-counterfactual thinking (imagining alternatives to the past) and the fundamental drive to create meaning in life-are causally related. Rather than implying a random quality to life, the authors hypothesized and found that counterfactual thinking heightens the meaningfulness of key life experiences. Reflecting on alternative pathways to pivotal turning points even produced greater meaning than directly reflecting on the meaning of the event itself. Fate perceptions ("it was meant to be") and benefit-finding (recognition of positive consequences) were identified as independent causal links between counterfactual thinking and the construction of meaning. Through counterfactual reflection, the upsides to reality are identified, a belief in fate emerges, and ultimately more meaning is derived from important life events.

Evaluation of seven hypotheses for metamemory performance in rhesus monkeys

PubMed Central

Basile, Benjamin M.; Schroeder, Gabriel R.; Brown, Emily Kathryn; Templer, Victoria L.; Hampton, Robert R.

2014-01-01

Knowing the extent to which nonhumans and humans share mechanisms for metacognition will advance our understanding of cognitive evolution and will improve selection of model systems for biomedical research. Some nonhuman species avoid difficult cognitive tests, seek information when ignorant, or otherwise behave in ways consistent with metacognition. There is agreement that some nonhuman animals “succeed” in these metacognitive tasks, but little consensus about the cognitive mechanisms underlying performance. In one paradigm, rhesus monkeys visually searched for hidden food when ignorant of the location of the food, but acted immediately when knowledgeable. This result has been interpreted as evidence that monkeys introspectively monitored their memory to adaptively control information seeking. However, convincing alternative hypotheses have been advanced that might also account for the adaptive pattern of visual searching. We evaluated seven hypotheses using a computerized task in which monkeys chose either to take memory tests immediately or to see the answer again before proceeding to the test. We found no evidence to support the hypotheses of behavioral cue association, rote response learning, expectancy violation, response competition, generalized search strategy, or postural mediation. In contrast, we repeatedly found evidence to support the memory monitoring hypothesis. Monkeys chose to see the answer when memory was poor, either from natural variation or experimental manipulation. We found limited evidence that monkeys also monitored the fluency of memory access. Overall, the evidence indicates that rhesus monkeys can use memory strength as a discriminative cue for information seeking, consistent with introspective monitoring of explicit memory. PMID:25365530

On resilience studies of system detection and recovery techniques against stealthy insider attacks

NASA Astrophysics Data System (ADS)

Wei, Sixiao; Zhang, Hanlin; Chen, Genshe; Shen, Dan; Yu, Wei; Pham, Khanh D.; Blasch, Erik P.; Cruz, Jose B.

2016-05-01

With the explosive growth of network technologies, insider attacks have become a major concern to business operations that largely rely on computer networks. To better detect insider attacks that marginally manipulate network traffic over time, and to recover the system from attacks, in this paper we implement a temporal-based detection scheme using the sequential hypothesis testing technique. Two hypothetical states are considered: the null hypothesis that the collected information is from benign historical traffic and the alternative hypothesis that the network is under attack. The objective of such a detection scheme is to recognize the change within the shortest time by comparing the two defined hypotheses. In addition, once the attack is detected, a server migration-based system recovery scheme can be triggered to recover the system to the state prior to the attack. To understand mitigation of insider attacks, a multi-functional web display of the detection analysis was developed for real-time analytic. Experiments using real-world traffic traces evaluate the effectiveness of Detection System and Recovery (DeSyAR) scheme. The evaluation data validates the detection scheme based on sequential hypothesis testing and the server migration-based system recovery scheme can perform well in effectively detecting insider attacks and recovering the system under attack.

The Alternative Omen Effect: Illusory negative correlation between the outcomes of choice options.

PubMed

Marciano-Romm, Déborah; Romm, Assaf; Bourgeois-Gironde, Sacha; Deouell, Leon Y

2016-01-01

In situations of choice between uncertain options, one might get feedback on both the outcome of the chosen option and the outcome of the unchosen option ("the alternative"). Extensive research has shown that when both outcomes are eventually revealed, the alternative's outcome influences the way people evaluate their own outcome. In a series of experiments, we examined whether the outcome of the alternative plays an additional role in the decision-making process by creating expectations regarding the outcome of the chosen option. Specifically, we hypothesized that people see a good (bad) alternative's outcome as a bad (good) sign regarding their own outcome when the two outcomes are in fact uncorrelated, a phenomenon we call the "Alternative Omen Effect" (ALOE). Subjects had to repeatedly choose between two boxes, the outcomes of which were then sequentially revealed. In Experiments 1 and 2 the alternative's outcome was presented first, and we assessed the individual's prediction of their own outcome. In Experiment 3, subjects had to predict the alternative's outcome after seeing their own. We find that even though the two outcomes were in fact uncorrelated, people tended to see a good (bad) alternative outcome as a bad (good) sign regarding their own outcome. Importantly, this illusory negative correlation affected subsequent behavior and led to irrational choices. Furthermore, the order of presentation was critical: when the outcome of the chosen option was presented first, the effect disappeared, suggesting that this illusory negative correlation is influenced by self-relevance. We discuss the possible sources of this illusory correlation as well as its implications for research on counterfactual thinking. Copyright © 2015 Elsevier B.V. All rights reserved.

Coalescent Simulation and Paleodistribution Modeling for Tabebuia rosealba Do Not Support South American Dry Forest Refugia Hypothesis

PubMed Central

de Melo, Warita Alves; Lima-Ribeiro, Matheus S.; Terribile, Levi Carina

2016-01-01

Studies based on contemporary plant occurrences and pollen fossil records have proposed that the current disjunct distribution of seasonally dry tropical forests (SDTFs) across South America is the result of fragmentation of a formerly widespread and continuously distributed dry forest during the arid climatic conditions associated with the Last Glacial Maximum (LGM), which is known as the modern-day dry forest refugia hypothesis. We studied the demographic history of Tabebuia rosealba (Bignoniaceae) to understand the disjunct geographic distribution of South American SDTFs based on statistical phylogeography and ecological niche modeling (ENM). We specifically tested the dry forest refugia hypothesis; i.e., if the multiple and isolated patches of SDTFs are current climatic relicts of a widespread and continuously distributed dry forest during the LGM. We sampled 235 individuals across 18 populations in Central Brazil and analyzed the polymorphisms at chloroplast (trnS-trnG, psbA-trnH and ycf6-trnC intergenic spacers) and nuclear (ITS nrDNA) genomes. We performed coalescence simulations of alternative hypotheses under demographic expectations from two a priori biogeographic hypotheses (1. the Pleistocene Arc hypothesis and, 2. a range shift to Amazon Basin) and other two demographic expectances predicted by ENMs (3. expansion throughout the Neotropical South America, including Amazon Basin, and 4. retraction during the LGM). Phylogenetic analyses based on median-joining network showed haplotype sharing among populations with evidence of incomplete lineage sorting. Coalescent analyses showed smaller effective population sizes for T. roseoalba during the LGM compared to the present-day. Simulations and ENM also showed that its current spatial pattern of genetic diversity is most likely due to a scenario of range retraction during the LGM instead of the fragmentation from a once extensive and largely contiguous SDTF across South America, not supporting the South American dry forest refugia hypothesis. PMID:27458982

Obstetrics at Decisive Crossroads Regarding Pattern-Recognition of Fetal Heart Rate Decelerations: Scientific Principles and Lessons From Memetics.

PubMed

Sholapurkar, Shashikant L

2018-04-01

The survival of cardiotocography (CTG) as a tool for intrapartum fetal monitoring seems threatened somewhat unjustifiably and unwittingly despite the absence of better alternatives. Fetal heart rate (FHR) decelerations are center-stage (most important) in the interpretation of CTG with maximum impact on three-tier classification. The pattern-discrimination of FHR decelerations is inexorably linked to their nomenclature. Unscientific or flawed nomenclature of decelerations can explain the dysfunctional CTG interpretation leading to errors in detection of acidemic fetuses. There are three contrasting concepts about categorization of FHR decelerations: 1) all rapid decelerations (the vast majority) should be grouped as "variable" because they are predominantly due to cord-compression, 2) all decelerations are due to chemoreflex from fetal hypoxemia hence their timing is not important, and 3) FHR decelerations should be categorized into "early/late/variable" based primarily on their time relationship to contractions. These theoretical concepts are like memes (ideas/beliefs). Lessons from "memetics" are that the most popular, attractive or established beliefs may not necessarily be true, scientific, beneficial or even without harm. Decelerations coincident with contractions with trough corresponding to the peak of contractions cannot be explained by cord-compression or increasing hypoxia (from compromised uteroplacental perfusion, cord-compression or even cerebral hypoperfusion/anoxia purportedly conceivable from head-compression). Decelerations due to hypoxemia would be associated with delayed recovery of decelerations (lag phase). It is a scientific imperative to cast away disproven/falsified theories. Practices based on unscientific theories lead to patient harm. Clinicians should urgently adopt the categorization of FHR decelerations based primarily of the time relationship to contractions as originally proposed by Hon and Caldeyro-Barcia. This analytical review shows it to be underpinned by most robust physiological and scientific hypotheses unlike the other categorizations associated with untruthful hypotheses, irreconcilable fallacies and contradictions. Without truthful framework and meaningful pattern-recognition of FHR decelerations, the CTG will not fulfil its true potential.

Obstetrics at Decisive Crossroads Regarding Pattern-Recognition of Fetal Heart Rate Decelerations: Scientific Principles and Lessons From Memetics

PubMed Central

Sholapurkar, Shashikant L.

2018-01-01

The survival of cardiotocography (CTG) as a tool for intrapartum fetal monitoring seems threatened somewhat unjustifiably and unwittingly despite the absence of better alternatives. Fetal heart rate (FHR) decelerations are center-stage (most important) in the interpretation of CTG with maximum impact on three-tier classification. The pattern-discrimination of FHR decelerations is inexorably linked to their nomenclature. Unscientific or flawed nomenclature of decelerations can explain the dysfunctional CTG interpretation leading to errors in detection of acidemic fetuses. There are three contrasting concepts about categorization of FHR decelerations: 1) all rapid decelerations (the vast majority) should be grouped as “variable” because they are predominantly due to cord-compression, 2) all decelerations are due to chemoreflex from fetal hypoxemia hence their timing is not important, and 3) FHR decelerations should be categorized into “early/late/variable” based primarily on their time relationship to contractions. These theoretical concepts are like memes (ideas/beliefs). Lessons from “memetics” are that the most popular, attractive or established beliefs may not necessarily be true, scientific, beneficial or even without harm. Decelerations coincident with contractions with trough corresponding to the peak of contractions cannot be explained by cord-compression or increasing hypoxia (from compromised uteroplacental perfusion, cord-compression or even cerebral hypoperfusion/anoxia purportedly conceivable from head-compression). Decelerations due to hypoxemia would be associated with delayed recovery of decelerations (lag phase). It is a scientific imperative to cast away disproven/falsified theories. Practices based on unscientific theories lead to patient harm. Clinicians should urgently adopt the categorization of FHR decelerations based primarily of the time relationship to contractions as originally proposed by Hon and Caldeyro-Barcia. This analytical review shows it to be underpinned by most robust physiological and scientific hypotheses unlike the other categorizations associated with untruthful hypotheses, irreconcilable fallacies and contradictions. Without truthful framework and meaningful pattern-recognition of FHR decelerations, the CTG will not fulfil its true potential. PMID:29511418

Coalescent Simulation and Paleodistribution Modeling for Tabebuia rosealba Do Not Support South American Dry Forest Refugia Hypothesis.

PubMed

de Melo, Warita Alves; Lima-Ribeiro, Matheus S; Terribile, Levi Carina; Collevatti, Rosane G

2016-01-01

Studies based on contemporary plant occurrences and pollen fossil records have proposed that the current disjunct distribution of seasonally dry tropical forests (SDTFs) across South America is the result of fragmentation of a formerly widespread and continuously distributed dry forest during the arid climatic conditions associated with the Last Glacial Maximum (LGM), which is known as the modern-day dry forest refugia hypothesis. We studied the demographic history of Tabebuia rosealba (Bignoniaceae) to understand the disjunct geographic distribution of South American SDTFs based on statistical phylogeography and ecological niche modeling (ENM). We specifically tested the dry forest refugia hypothesis; i.e., if the multiple and isolated patches of SDTFs are current climatic relicts of a widespread and continuously distributed dry forest during the LGM. We sampled 235 individuals across 18 populations in Central Brazil and analyzed the polymorphisms at chloroplast (trnS-trnG, psbA-trnH and ycf6-trnC intergenic spacers) and nuclear (ITS nrDNA) genomes. We performed coalescence simulations of alternative hypotheses under demographic expectations from two a priori biogeographic hypotheses (1. the Pleistocene Arc hypothesis and, 2. a range shift to Amazon Basin) and other two demographic expectances predicted by ENMs (3. expansion throughout the Neotropical South America, including Amazon Basin, and 4. retraction during the LGM). Phylogenetic analyses based on median-joining network showed haplotype sharing among populations with evidence of incomplete lineage sorting. Coalescent analyses showed smaller effective population sizes for T. roseoalba during the LGM compared to the present-day. Simulations and ENM also showed that its current spatial pattern of genetic diversity is most likely due to a scenario of range retraction during the LGM instead of the fragmentation from a once extensive and largely contiguous SDTF across South America, not supporting the South American dry forest refugia hypothesis.

Comparative environmental and human health evaluations of thermolysis and solvolysis recycling technologies of carbon fiber reinforced polymer waste.

PubMed

Khalil, Y F

2018-06-01

This quantitative research aims to compare environmental and human health impacts associated with two recycling technologies of CFRP waste. The 'baseline' recycling technology is the conventional thermolysis process via pyrolysis and the 'alternative' recycling technology is an emerging chemical treatment via solvolysis using supercritical water (SCW) to digest the thermoset matrix. Two Gate-to-Gate recycling models are developed using GaBi LCA platform. The selected functional unit (FU) is 1 kg CFRP waste and the geographical boundary of this comparative LCIA is defined to be within the U.S. The results of this comparative assessment brought to light new insights about the environmental and human health impacts of CFRP waste recycling via solvolysis using SCW and, therefore, helped close a gap in the current state of knowledge about sustainability of SCW-based solvolysis as compared to pyrolysis. Two research questions are posed to identify whether solvolysis recycling offers more environmental and human health gains relative to the conventional pyrolysis recycling. These research questions lay the basis for formulating two null hypotheses (H 0,1 and H 0,2 ) and their associated research hypotheses (H 1,1 and H 1,2 ). LCIA results interpretation included 'base case' scenarios, 'sensitivity studies,' and 'scenarios analysis.' The results revealed that: (a) recycling via solvolysis using SCW exhibits no gains in environmental and human health impacts relative to those impacts associated with recycling via pyrolysis and (b) use of natural gas in lieu of electricity for pyrolyzer's heating reduces the environmental and human health impacts by 37% (lowest) and up to 95.7% (highest). It is recommended that on-going experimental efforts that focus only on identifying the best solvent for solvolysis-based recycling should also consider quantification of the energy intensity as well as environmental and human health impacts of the proposed solvents. Copyright © 2018 Elsevier Ltd. All rights reserved.

Remote detection of weak aftershocks of the DPRK underground explosions using waveform cross correlation

NASA Astrophysics Data System (ADS)

Le Bras, R.; Rozhkov, M.; Bobrov, D.; Kitov, I. O.; Sanina, I.

2017-12-01

Association of weak seismic signals generated by low-magnitude aftershocks of the DPRK underground tests into event hypotheses represent a challenge for routine automatic and interactive processing at the International Data Centre (IDC) of the Comprehensive Nuclear-Test-Ban Treaty Organization, due to the relatively low station density of the International Monitoring System (IMS) seismic network. Since 2011, as an alternative, the IDC has been testing various prototype techniques of signal detection and event creation based on waveform cross correlation. Using signals measured by seismic stations of the IMS from DPRK explosions as waveform templates, the IDC detected several small (estimated mb between 2.2 and 3.6) seismic events after two DPRK tests conducted on September 9, 2016 and September 3, 2017. The obtained detections were associated with reliable event hypothesis and then used to locate these events relative to the epicenters of the DPRK explosions. We observe high similarity of the detected signals with the corresponding waveform templates. The newly found signals also correlate well between themselves. In addition, the values of the signal-to-noise ratios (SNR) estimated using the traces of cross correlation coefficients, increase with template length (from 5 s to 150 s), providing strong evidence in favour of their spatial closeness, which allows interpreting them as explosion aftershocks. We estimated the relative magnitudes of all aftershocks using the ratio of RMS amplitudes of the master and slave signal in the cross correlation windows characterized by the highest SNR. Additional waveform data from regional non-IMS stations MDJ and SEHB provide independent validation of these aftershock hypotheses. Since waveform templates from any single master event may be sub-efficient at some stations, we have also developed a method of joint usage of the DPRK and the biggest aftershocks templates to build more robust event hypotheses.

About hypotheses and paradigms: exploring the Discreetness-Chance Paradigm.

PubMed

Kaellis, Eugene

2006-01-01

Hypotheses generally conform to paradigms which, over time, change, usually tardily, after they have become increasingly difficult to sustain under the impact of non-conforming evidence and alternative hypotheses, but more important, when they no longer are comfortably ensconced in the surrounding social-economic-political-cultural milieu. It is asserted that this milieu is the most important factor in shaping scientific theorizing. Some examples are cited: the rejection of the evidence that the world orbits around the sun (suspected by Pythagoras) in favor of centuries-long firm adherence to the Ptolemaic geocentric system; the early acceptance of Natural Selection in spite of its tautological essence and only conjectural supporting evidence, because it justified contemporaneous social-political ideologies as typified by, e.g., Spencer and Malthus. Economic, social, and cultural factors are cited as providing the ground, i.e., ideational substrate, for what is cited as the Discreetness-Chance Paradigm (DCP), that has increasingly dominated physics, biology, and medicine for over a century and which invokes small, discrete packets of energy/matter (quanta, genes, microorganisms, aberrant cells) functioning within an environment of statistical, not determined, causality. There is speculation on a possible paradigmatic shift from the DCP, which has fostered the proliferation, parallel with ("splitting") taxonomy, of alleged individual disease entities, their diagnoses, and, when available, their specific remedies, something particularly prominent in, e.g., psychiatry's Diagnostic and Statistical Manual, a codified compendium of alleged mental and behavioral disorders, but evident in any textbook of diagnosis and treatment of physical ailments. This presumed paradigm shift may be reflected in Western medicine, presently increasingly empirical and atomized, towards a growing acceptance of a more generalized, subject-oriented, approach to health and disease, a non-material-based system of energy flow dependent only on vitality, not anatomy; and a more cohesive, integrative patient-centered approach to therapy.

HyQue: evaluating hypotheses using Semantic Web technologies

PubMed Central

2011-01-01

Background Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks. Results We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in Saccharomyces cerevisiae to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF. Conclusions HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in S. cerevisiae. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and vice versa. HyQue hypotheses and data are available at http://semanticscience.org/projects/hyque. PMID:21624158

Exploring relation types for literature-based discovery.

PubMed

Preiss, Judita; Stevenson, Mark; Gaizauskas, Robert

2015-09-01

Literature-based discovery (LBD) aims to identify "hidden knowledge" in the medical literature by: (1) analyzing documents to identify pairs of explicitly related concepts (terms), then (2) hypothesizing novel relations between pairs of unrelated concepts that are implicitly related via a shared concept to which both are explicitly related. Many LBD approaches use simple techniques to identify semantically weak relations between concepts, for example, document co-occurrence. These generate huge numbers of hypotheses, difficult for humans to assess. More complex techniques rely on linguistic analysis, for example, shallow parsing, to identify semantically stronger relations. Such approaches generate fewer hypotheses, but may miss hidden knowledge. The authors investigate this trade-off in detail, comparing techniques for identifying related concepts to discover which are most suitable for LBD. A generic LBD system that can utilize a range of relation types was developed. Experiments were carried out comparing a number of techniques for identifying relations. Two approaches were used for evaluation: replication of existing discoveries and the "time slicing" approach.(1) RESULTS: Previous LBD discoveries could be replicated using relations based either on document co-occurrence or linguistic analysis. Using relations based on linguistic analysis generated many fewer hypotheses, but a significantly greater proportion of them were candidates for hidden knowledge. The use of linguistic analysis-based relations improves accuracy of LBD without overly damaging coverage. LBD systems often generate huge numbers of hypotheses, which are infeasible to manually review. Improving their accuracy has the potential to make these systems significantly more usable. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

The Effect of Domestication on Inhibitory Control: Wolves and Dogs Compared

PubMed Central

Marshall-Pescini, Sarah; Virányi, Zsófia; Range, Friederike

2015-01-01

Inhibitory control i.e. blocking an impulsive or prepotent response in favour of a more appropriate alternative, has been suggested to play an important role in cooperative behaviour. Interestingly, while dogs and wolves show a similar social organization, they differ in their intraspecific cooperation tendencies in that wolves rely more heavily on group coordination in regard to hunting and pup-rearing compared to dogs. Hence, based on the ‘canine cooperation’ hypothesis wolves should show better inhibitory control than dogs. On the other hand, through the domestication process, dogs may have been selected for cooperative tendencies towards humans and/or a less reactive temperament, which may in turn have affected their inhibitory control abilities. Hence, based on the latter hypothesis, we would expect dogs to show a higher performance in tasks requiring inhibitory control. To test the predictive value of these alternative hypotheses, in the current study two tasks; the ‘cylinder task’ and the ‘detour task’, which are designed to assess inhibitory control, were used to evaluate the performance of identically raised pack dogs and wolves. Results from the cylinder task showed a significantly poorer performance in wolves than identically-raised pack dogs (and showed that pack-dogs performed similarly to pet dogs with different training experiences), however contrary results emerged in the detour task, with wolves showing a shorter latency to success and less perseverative behaviour at the fence. Results are discussed in relation to previous studies using these paradigms and in terms of the validity of these two methods in assessing inhibitory control. PMID:25714840

The effect of domestication on inhibitory control: wolves and dogs compared.

PubMed

Marshall-Pescini, Sarah; Virányi, Zsófia; Range, Friederike

2015-01-01

Inhibitory control i.e. blocking an impulsive or prepotent response in favour of a more appropriate alternative, has been suggested to play an important role in cooperative behaviour. Interestingly, while dogs and wolves show a similar social organization, they differ in their intraspecific cooperation tendencies in that wolves rely more heavily on group coordination in regard to hunting and pup-rearing compared to dogs. Hence, based on the 'canine cooperation' hypothesis wolves should show better inhibitory control than dogs. On the other hand, through the domestication process, dogs may have been selected for cooperative tendencies towards humans and/or a less reactive temperament, which may in turn have affected their inhibitory control abilities. Hence, based on the latter hypothesis, we would expect dogs to show a higher performance in tasks requiring inhibitory control. To test the predictive value of these alternative hypotheses, in the current study two tasks; the 'cylinder task' and the 'detour task', which are designed to assess inhibitory control, were used to evaluate the performance of identically raised pack dogs and wolves. Results from the cylinder task showed a significantly poorer performance in wolves than identically-raised pack dogs (and showed that pack-dogs performed similarly to pet dogs with different training experiences), however contrary results emerged in the detour task, with wolves showing a shorter latency to success and less perseverative behaviour at the fence. Results are discussed in relation to previous studies using these paradigms and in terms of the validity of these two methods in assessing inhibitory control.

Patterns of threshold evolution in polyphenic insects under different developmental models.

PubMed

Tomkins, Joseph L; Moczek, Armin P

2009-02-01

Two hypotheses address the evolution of polyphenic traits in insects. Under the developmental reprogramming model, individuals exceeding a threshold follow a different developmental pathway from individuals below the threshold. This decoupling is thought to free selection to independently hone alternative morphologies, increasing phenotypic plasticity and morphological diversity. Under the alternative model, extreme positive allometry explains the existence of alternative phenotypes and divergent phenotypes are developmentally coupled by a continuous reaction norm, such that selection on either morph acts on both. We test the hypothesis that continuous reaction norm polyphenisms, evolve through changes in the allometric parameters of even the smallest males with minimal trait expression, whereas threshold polyphenisms evolve independent of the allometric parameters of individuals below the threshold. We compare two polyphenic species; the dung beetle Onthophagus taurus, whose allometry has been modeled both as a threshold polyphenism and a continuous reaction norm and the earwig Forficula auricularia, whose allometry is best modeled with a discontinuous threshold. We find that across populations of both species, variation in forceps or horn allometry in minor males are correlated to the population's threshold. These findings suggest that regardless of developmental mode, alternative morphs do not evolve independently of one another.

Muscle fiber type distribution in climbing Hawaiian gobioid fishes: ontogeny and correlations with locomotor performance.

PubMed

Cediel, Roberto A; Blob, Richard W; Schrank, Gordon D; Plourde, Robert C; Schoenfuss, Heiko L

2008-01-01

Three species of Hawaiian amphidromous gobioid fishes are remarkable in their ability to climb waterfalls up to several hundred meters tall. Juvenile Lentipes concolor and Awaous guamensis climb using rapid bursts of axial undulation, whereas juvenile Sicyopterus stimpsoni climb using much slower movements, alternately attaching oral and pelvic sucking disks to the substrate during prolonged bouts of several cycles. Based on these differing climbing styles, we hypothesized that propulsive musculature in juvenile L. concolor and A. guamensis would be dominated by white muscle fibers, whereas S. stimpsoni would exhibit a greater proportion of red muscle fibers than other climbing species. We further predicted that, because adults of these species shift from climbing to burst swimming as their main locomotor behavior, muscle from adult fish of all three species would be dominated by white fibers. To test these hypotheses, we used ATPase assays to evaluate muscle fiber type distribution in Hawaiian climbing gobies for three anatomical regions (midbody, anal, and tail). Axial musculature was dominated by white muscle fibers in juveniles of all three species, but juvenile S. stimpsoni had a significantly greater proportion of red fibers than the other two species. Fiber type proportions of adult fishes did not differ significantly from those of juveniles. Thus, muscle fiber type proportions in juveniles appear to help accommodate differences in locomotor demands among these species, indicating that they overcome the common challenge of waterfall climbing through both diverse behaviors and physiological specializations.

Interactions between chemical and climate stressors: A role for mechanistic toxicology in assessing climate change risks

USGS Publications Warehouse

Hooper, Michael J.; Ankley, Gerald T.; Cristol, Daniel A.; Maryoung, Lindley A.; Noyes, Pamela D.; Pinkerton, Kent E.

2013-01-01

Incorporation of global climate change (GCC) effects into assessments of chemical risk and injury requires integrated examinations of chemical and nonchemical stressors. Environmental variables altered by GCC (temperature, precipitation, salinity, pH) can influence the toxicokinetics of chemical absorption, distribution, metabolism, and excretion as well as toxicodynamic interactions between chemicals and target molecules. In addition, GCC challenges processes critical for coping with the external environment (water balance, thermoregulation, nutrition, and the immune, endocrine, and neurological systems), leaving organisms sensitive to even slight perturbations by chemicals when pushed to the limits of their physiological tolerance range. In simplest terms, GCC can make organisms more sensitive to chemical stressors, while alternatively, exposure to chemicals can make organisms more sensitive to GCC stressors. One challenge is to identify potential interactions between nonchemical and chemical stressors affecting key physiological processes in an organism. We employed adverse outcome pathways, constructs depicting linkages between mechanism-based molecular initiating events and impacts on individuals or populations, to assess how chemical- and climate-specific variables interact to lead to adverse outcomes. Case examples are presented for prospective scenarios, hypothesizing potential chemical–GCC interactions, and retrospective scenarios, proposing mechanisms for demonstrated chemical–climate interactions in natural populations. Understanding GCC interactions along adverse outcome pathways facilitates extrapolation between species or other levels of organization, development of hypotheses and focal areas for further research, and improved inputs for risk and resource injury assessments.

Improved probability of detection of ecological “surprises”

PubMed Central

Lindenmayer, D. B.; Likens, G. E.; Krebs, C. J.; Hobbs, R. J.

2010-01-01

Ecological “surprises” are defined as unexpected findings about the natural environment. They are critically important in ecology because they are catalysts for questioning and reformulating views of the natural world, help shape assessments of the veracity of a priori predictions about ecological trends and phenomena, and underpin questioning of effectiveness of resource management. Despite the importance of ecological surprises, major gaps in understanding remain about how studies might be done differently or done better to improve the ability to identify them. We outline the kinds of ecological surprises that have arisen from long-term research programs that we lead in markedly different ecosystems around the world. Based on these case studies, we identify important lessons to guide both existing studies and new investigations to detect ecological surprises more readily, better anticipate unusual ecological phenomena, and take proactive steps to plan for and alleviate “undesirable” ecological surprises. Some of these lessons include: (i) maintain existing, and instigate new, long-term studies; (ii) conduct a range of kinds of parallel and concurrent research in a given target area; (iii) better use past literature and conceptual models of the target ecosystem in posing good questions and developing hypotheses and alternative hypotheses; and (iv) increase the capacity for ecological research to take advantage of opportunities arising from major natural disturbances. We argue that the increased anticipatory capability resulting from these lessons is critical given that ecological surprises may become more prevalent because of climate change and multiple and interacting environmental stressors. PMID:21098660

INTERACTIONS BETWEEN CHEMICAL AND CLIMATE STRESSORS: A ROLE FOR MECHANISTIC TOXICOLOGY IN ASSESSING CLIMATE CHANGE RISKS

PubMed Central

Hooper, Michael J; Ankley, Gerald T; Cristol, Daniel A; Maryoung, Lindley A; Noyes, Pamela D; Pinkerton, Kent E

2013-01-01

Incorporation of global climate change (GCC) effects into assessments of chemical risk and injury requires integrated examinations of chemical and nonchemical stressors. Environmental variables altered by GCC (temperature, precipitation, salinity, pH) can influence the toxicokinetics of chemical absorption, distribution, metabolism, and excretion as well as toxicodynamic interactions between chemicals and target molecules. In addition, GCC challenges processes critical for coping with the external environment (water balance, thermoregulation, nutrition, and the immune, endocrine, and neurological systems), leaving organisms sensitive to even slight perturbations by chemicals when pushed to the limits of their physiological tolerance range. In simplest terms, GCC can make organisms more sensitive to chemical stressors, while alternatively, exposure to chemicals can make organisms more sensitive to GCC stressors. One challenge is to identify potential interactions between nonchemical and chemical stressors affecting key physiological processes in an organism. We employed adverse outcome pathways, constructs depicting linkages between mechanism-based molecular initiating events and impacts on individuals or populations, to assess how chemical- and climate-specific variables interact to lead to adverse outcomes. Case examples are presented for prospective scenarios, hypothesizing potential chemical–GCC interactions, and retrospective scenarios, proposing mechanisms for demonstrated chemical–climate interactions in natural populations. Understanding GCC interactions along adverse outcome pathways facilitates extrapolation between species or other levels of organization, development of hypotheses and focal areas for further research, and improved inputs for risk and resource injury assessments. Environ. Toxicol. Chem. 2013;32:32–48. © 2012 SETAC PMID:23136056

Virtual Lead Identification of Farnesyltransferase Inhibitors Based on Ligand and Structure-Based Pharmacophore Techniques

PubMed Central

Al-Balas, Qosay A.; Amawi, Haneen A.; Hassan, Mohammad A.; Qandil, Amjad M.; Almaaytah, Ammar M.; Mhaidat, Nizar M.

2013-01-01

Farnesyltransferase enzyme (FTase) is considered an essential enzyme in the Ras signaling pathway associated with cancer. Thus, designing inhibitors for this enzyme might lead to the discovery of compounds with effective anticancer activity. In an attempt to obtain effective FTase inhibitors, pharmacophore hypotheses were generated using structure-based and ligand-based approaches built in Discovery Studio v3.1. Knowing the presence of the zinc feature is essential for inhibitor’s binding to the active site of FTase enzyme; further customization was applied to include this feature in the generated pharmacophore hypotheses. These pharmacophore hypotheses were thoroughly validated using various procedures such as ROC analysis and ligand pharmacophore mapping. The validated pharmacophore hypotheses were used to screen 3D databases to identify possible hits. Those which were both high ranked and showed sufficient ability to bind the zinc feature in active site, were further refined by applying drug-like criteria such as Lipiniski’s “rule of five” and ADMET filters. Finally, the two candidate compounds (ZINC39323901 and ZINC01034774) were allowed to dock using CDOCKER and GOLD in the active site of FTase enzyme to optimize hit selection. PMID:24276257

Virtual lead identification of farnesyltransferase inhibitors based on ligand and structure-based pharmacophore techniques.

PubMed

Al-Balas, Qosay A; Amawi, Haneen A; Hassan, Mohammad A; Qandil, Amjad M; Almaaytah, Ammar M; Mhaidat, Nizar M

2013-05-27

Farnesyltransferase enzyme (FTase) is considered an essential enzyme in the Ras signaling pathway associated with cancer. Thus, designing inhibitors for this enzyme might lead to the discovery of compounds with effective anticancer activity. In an attempt to obtain effective FTase inhibitors, pharmacophore hypotheses were generated using structure-based and ligand-based approaches built in Discovery Studio v3.1. Knowing the presence of the zinc feature is essential for inhibitor's binding to the active site of FTase enzyme; further customization was applied to include this feature in the generated pharmacophore hypotheses. These pharmacophore hypotheses were thoroughly validated using various procedures such as ROC analysis and ligand pharmacophore mapping. The validated pharmacophore hypotheses were used to screen 3D databases to identify possible hits. Those which were both high ranked and showed sufficient ability to bind the zinc feature in active site, were further refined by applying drug-like criteria such as Lipiniski's "rule of five" and ADMET filters. Finally, the two candidate compounds (ZINC39323901 and ZINC01034774) were allowed to dock using CDOCKER and GOLD in the active site of FTase enzyme to optimize hit selection.

Combining Theory-Driven Evaluation and Causal Loop Diagramming for Opening the 'Black Box' of an Intervention in the Health Sector: A Case of Performance-Based Financing in Western Uganda.

PubMed

Renmans, Dimitri; Holvoet, Nathalie; Criel, Bart

2017-09-03

Increased attention on "complexity" in health systems evaluation has resulted in many different methodological responses. Theory-driven evaluations and systems thinking are two such responses that aim for better understanding of the mechanisms underlying given outcomes. Here, we studied the implementation of a performance-based financing intervention by the Belgian Technical Cooperation in Western Uganda to illustrate a methodological strategy of combining these two approaches. We utilized a systems dynamics tool called causal loop diagramming (CLD) to generate hypotheses feeding into a theory-driven evaluation. Semi-structured interviews were conducted with 30 health workers from two districts (Kasese and Kyenjojo) and with 16 key informants. After CLD, we identified three relevant hypotheses: "success to the successful", "growth and underinvestment", and "supervision conundrum". The first hypothesis leads to increasing improvements in performance, as better performance leads to more incentives, which in turn leads to better performance. The latter two hypotheses point to potential bottlenecks. Thus, the proposed methodological strategy was a useful tool for identifying hypotheses that can inform a theory-driven evaluation. The hypotheses are represented in a comprehensible way while highlighting the underlying assumptions, and are more easily falsifiable than hypotheses identified without using CLD.

Adaptive management: Chapter 1

USGS Publications Warehouse

Allen, Craig R.; Garmestani, Ahjond S.; Allen, Craig R.; Garmestani, Ahjond S.

2015-01-01

Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive management has explicit structure, including a careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. The process is iterative, and serves to reduce uncertainty, build knowledge and improve management over time in a goal-oriented and structured process.

Adaptive management

USGS Publications Warehouse

Allen, Craig R.; Garmestani, Ahjond S.

2015-01-01

Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive management has explicit structure, including a careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. The process is iterative, and serves to reduce uncertainty, build knowledge and improve management over time in a goal-oriented and structured process.

Study of an Alternative Career Path for Deck Officers in the Hellenic Navy

DTIC Science & Technology

2013-03-01

Motivated individuals stay with a task long enough to achieve their goal. (pp. 72-73) Perhaps, the most well-known theory of motivation is Abraham Maslow’s...hierarchy of needs.” Maslow hypothesized that, within every human being, there exists a hierarchy of five needs. These are shown in Figure 3...actualization. Maslow separated the five steps into higher and lower order needs. The big difference between higher and lower order needs is that higher

Contemporary immigration: theoretical perspectives on its determinants and modes of incorporation.

PubMed

Portes, A; Borocz, J

1989-01-01

This article reviews conventional theories about different aspects of labor migration: its origins, stability over time, and patterns of migrant settlement. For each of these aspects, the authors provide alternative explanatory hypotheses derived from the notions of increasing articulation of the international system and the social embeddedness of its various subprocesses, including labor flows. A typology of sources and outcomes of contemporary immigration is presented as a heuristic device to organize the diversity of such movements as described in the empirical literature.

APOL1 Oligomerization as the Key Mediator of Kidney Disease in African Americans

DTIC Science & Technology

2015-10-01

kidney disease that accounts for the high rate of kidney disease in African Americans. This work is based on the hypothesize that APOL1 kidney disease...microscopy- based approaches. 15. SUBJECT TERMS Kidney, ESRD, APOL1, African American 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER...is based on the hypothesize that APOL1 kidney disease in African Americans results from abnormal aggregation of the APOL1 risk variant protein in an

Modeling social transmission dynamics of unhealthy behaviors for evaluating prevention and treatment interventions on childhood obesity.

PubMed

Frerichs, Leah M; Araz, Ozgur M; Huang, Terry T-K

2013-01-01

Research evidence indicates that obesity has spread through social networks, but lever points for interventions based on overlapping networks are not well studied. The objective of our research was to construct and parameterize a system dynamics model of the social transmission of behaviors through adult and youth influence in order to explore hypotheses and identify plausible lever points for future childhood obesity intervention research. Our objectives were: (1) to assess the sensitivity of childhood overweight and obesity prevalence to peer and adult social transmission rates, and (2) to test the effect of combinations of prevention and treatment interventions on the prevalence of childhood overweight and obesity. To address the first objective, we conducted two-way sensitivity analyses of adult-to-child and child-to-child social transmission in relation to childhood overweight and obesity prevalence. For the second objective, alternative combinations of prevention and treatment interventions were tested by varying model parameters of social transmission and weight loss behavior rates. Our results indicated child overweight and obesity prevalence might be slightly more sensitive to the same relative change in the adult-to-child compared to the child-to-child social transmission rate. In our simulations, alternatives with treatment alone, compared to prevention alone, reduced the prevalence of childhood overweight and obesity more after 10 years (1.2-1.8% and 0.2-1.0% greater reduction when targeted at children and adults respectively). Also, as the impact of adult interventions on children was increased, the rank of six alternatives that included adults became better (i.e., resulting in lower 10 year childhood overweight and obesity prevalence) than alternatives that only involved children. The findings imply that social transmission dynamics should be considered when designing both prevention and treatment intervention approaches. Finally, targeting adults may be more efficient, and research should strengthen and expand adult-focused interventions that have a high residual impact on children.

Modeling Social Transmission Dynamics of Unhealthy Behaviors for Evaluating Prevention and Treatment Interventions on Childhood Obesity

PubMed Central

Frerichs, Leah M.; Araz, Ozgur M.; Huang, Terry T. – K.

2013-01-01

Research evidence indicates that obesity has spread through social networks, but lever points for interventions based on overlapping networks are not well studied. The objective of our research was to construct and parameterize a system dynamics model of the social transmission of behaviors through adult and youth influence in order to explore hypotheses and identify plausible lever points for future childhood obesity intervention research. Our objectives were: (1) to assess the sensitivity of childhood overweight and obesity prevalence to peer and adult social transmission rates, and (2) to test the effect of combinations of prevention and treatment interventions on the prevalence of childhood overweight and obesity. To address the first objective, we conducted two-way sensitivity analyses of adult-to-child and child-to-child social transmission in relation to childhood overweight and obesity prevalence. For the second objective, alternative combinations of prevention and treatment interventions were tested by varying model parameters of social transmission and weight loss behavior rates. Our results indicated child overweight and obesity prevalence might be slightly more sensitive to the same relative change in the adult-to-child compared to the child-to-child social transmission rate. In our simulations, alternatives with treatment alone, compared to prevention alone, reduced the prevalence of childhood overweight and obesity more after 10 years (1.2–1.8% and 0.2–1.0% greater reduction when targeted at children and adults respectively). Also, as the impact of adult interventions on children was increased, the rank of six alternatives that included adults became better (i.e., resulting in lower 10 year childhood overweight and obesity prevalence) than alternatives that only involved children. The findings imply that social transmission dynamics should be considered when designing both prevention and treatment intervention approaches. Finally, targeting adults may be more efficient, and research should strengthen and expand adult-focused interventions that have a high residual impact on children. PMID:24358234

Incorporating covariates into fisheries stock assessment models with application to Pacific herring.

PubMed

Deriso, Richard B; Maunder, Mark N; Pearson, Walter H

2008-07-01

We present a framework for evaluating the cause of fishery declines by integrating covariates into a fisheries stock assessment model. This allows the evaluation of fisheries' effects vs. natural and other human impacts. The analyses presented are based on integrating ecological science and statistics and form the basis for environmental decision-making advice. Hypothesis tests are described to rank hypotheses and determine the size of a multiple covariate model. We extend recent developments in integrated analysis and use novel methods to produce effect size estimates that are relevant to policy makers and include estimates of uncertainty. Results can be directly applied to evaluate trade-offs among alternative management decisions. The methods and results are also broadly applicable outside fisheries stock assessment. We show that multiple factors influence populations and that analysis of factors in isolation can be misleading. We illustrate the framework by applying it to Pacific herring of Prince William Sound, Alaska (USA). The Pacific herring stock that spawns in Prince William Sound is a stock that has collapsed, but there are several competing or alternative hypotheses to account for the initial collapse and subsequent lack of recovery. Factors failing the initial screening tests for statistical significance included indicators of the 1989 Exxon Valdez oil spill, coho salmon predation, sea lion predation, Pacific Decadal Oscillation, Northern Oscillation Index, and effects of containment in the herring egg-on-kelp pound fishery. The overall results indicate that the most statistically significant factors related to the lack of recovery of the herring stock involve competition or predation by juvenile hatchery pink salmon on herring juveniles. Secondary factors identified in the analysis were poor nutrition in the winter, ocean (Gulf of Alaska) temperature in the winter, the viral hemorrhagic septicemia virus, and the pathogen Ichthyophonus hoferi. The implication of this result to fisheries management in Prince William Sound is that it may well be difficult to simultaneously increase the production of pink salmon and maintain a viable Pacific herring fishery. The impact can be extended to other commercially important fisheries, and a whole ecosystem approach may be needed to evaluate the costs and benefits of salmon hatcheries.

Targeting autocrine HB-EGF signaling with specific ADAM12 inhibition using recombinant ADAM12 prodomain

NASA Astrophysics Data System (ADS)

Miller, Miles A.; Moss, Marcia L.; Powell, Gary; Petrovich, Robert; Edwards, Lori; Meyer, Aaron S.; Griffith, Linda G.; Lauffenburger, Douglas A.

2015-10-01

Dysregulation of ErbB-family signaling underlies numerous pathologies and has been therapeutically targeted through inhibiting ErbB-receptors themselves or their cognate ligands. For the latter, “decoy” antibodies have been developed to sequester ligands including heparin-binding epidermal growth factor (HB-EGF); however, demonstrating sufficient efficacy has been difficult. Here, we hypothesized that this strategy depends on properties such as ligand-receptor binding affinity, which varies widely across the known ErbB-family ligands. Guided by computational modeling, we found that high-affinity ligands such as HB-EGF are more difficult to target with decoy antibodies compared to low-affinity ligands such as amphiregulin (AREG). To address this issue, we developed an alternative method for inhibiting HB-EGF activity by targeting its cleavage from the cell surface. In a model of the invasive disease endometriosis, we identified A Disintegrin and Metalloproteinase 12 (ADAM12) as a protease implicated in HB-EGF shedding. We designed a specific inhibitor of ADAM12 based on its recombinant prodomain (PA12), which selectively inhibits ADAM12 but not ADAM10 or ADAM17. In endometriotic cells, PA12 significantly reduced HB-EGF shedding and resultant cellular migration. Overall, specific inhibition of ligand shedding represents a possible alternative to decoy antibodies, especially for ligands such as HB-EGF that exhibit high binding affinity and localized signaling.

A left cerebellar pathway mediates language in prematurely-born young adults

PubMed Central

Constable, R. Todd; Vohr, Betty R.; Scheinost, Dustin; Benjamin, Jennifer R.; Fulbright, Robert K.; Lacadie, Cheryl; Schneider, Karen C.; Katz, Karol H.; Zhang, Heping; Papademetris, Xenophon; Ment, Laura R.

2012-01-01

Preterm (PT) subjects are at risk for developmental delay, and task-based studies suggest that developmental disorders may be due to alterations in neural connectivity. Since emerging data imply the importance of right cerebellar function for language acquisition in typical development, we hypothesized that PT subjects would have alternate areas of cerebellar connectivity, and that these areas would be responsible for differences in cognitive outcomes between PT subjects and term controls at age 20 years. Nineteen PT and 19 term control young adults were prospectively studied using resting-state functional MRI (fMRI) to create voxel-based contrast maps reflecting the functional connectivity of each tissue element in the grey matter through analysis of the intrinsic connectivity contrast degree (ICC-d). Left cerebellar ICC-d differences between subjects identified a region of interest that was used for subsequent seed-based connectivity analyses. Subjects underwent standardized language testing, and correlations with cognitive outcomes were assessed. There were no differences in gender, hand preference, maternal education, age at study, or Peabody Picture Vocabulary Test (PPVT) scores. Functional connectivity (FcMRI) demonstrated increased tissue connectivity in the biventer, simple and quadrangular lobules of the L cerebellum (p<0.05) in PTs compared to term controls; seed-based analyses from these regions demonstrated alterations in connectivity from L cerebellum to both R and L inferior frontal gyri (IFG) in PTs compared to term controls. For PTs but not term controls, there were significant positive correlations between these connections and PPVT scores (R IFG: r=0.555, p=0.01; L IFG: r=0.454, p=0.05), as well as Verbal Comprehension Index (VCI) scores (R IFG: r=0.472, p=0.04). These data suggest the presence of a left cerebellar language circuit in PT subjects at young adulthood. These findings may represent either a delay in maturation or the engagement of alternative neural pathways for language in the developing PT brain. PMID:22982585

Molecular genetic analysis of activation-tagged transcription factors thought to be involved in photomorphogenesis

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

Neff, Michael M.

This is a final report for Department of Energy Grant No. DE-FG02-08ER15927 entitled “Molecular Genetic Analysis of Activation-Tagged Transcription Factors Thought to be Involved in Photomorphogenesis”. Based on our preliminary photobiological and genetic analysis of the sob1-D mutant, we hypothesized that OBP3 is a transcription factor involved in both phytochrome and cryptochrome-mediated signal transduction. In addition, we hypothesized that OBP3 is involved in auxin signaling and root development. Based on our preliminary photobiological and genetic analysis of the sob2-D mutant, we also hypothesized that a related gene, LEP, is involved in hormone signaling and seedling development.

AMD and the alternative complement pathway: genetics and functional implications.

PubMed

Tan, Perciliz L; Bowes Rickman, Catherine; Katsanis, Nicholas

2016-06-21

Age-related macular degeneration (AMD) is an ocular neurodegenerative disorder and is the leading cause of legal blindness in Western societies, with a prevalence of up to 8 % over the age of 60, which continues to increase with age. AMD is characterized by the progressive breakdown of the macula (the central region of the retina), resulting in the loss of central vision including visual acuity. While its molecular etiology remains unclear, advances in genetics and genomics have illuminated the genetic architecture of the disease and have generated attractive pathomechanistic hypotheses. Here, we review the genetic architecture of AMD, considering the contribution of both common and rare alleles to susceptibility, and we explore the possible mechanistic links between photoreceptor degeneration and the alternative complement pathway, a cascade that has emerged as the most potent genetic driver of this disorder.

Eye instability induced by vestibular stimulation in rabbits.

PubMed

Ferraresi, A; Azzena, G B; Troiani, D

2001-07-03

The slow compensatory phases of the vestibulo-ocular reflex (VOR) in the rabbit tend to drift and the drift reverses the direction. This periodic alternating drift (PAD) has two peculiar characteristics: (1) it is induced by sinusoidal vestibular stimulation in naive animals, being evoked immediately after stimulus onset and persisting after the end of stimulation; (2) the peak velocity and period of the drift are dependent on stimulus amplitude. PAD of the rabbit has strong similarities with PAN, a periodic alternating nystagmus observed in humans with cerbellar disorders and in monkeys after nodulo-uvulectomy, although its peak velocity is smaller. It is hypothesized that PAD is due to a slight instability, caused by vestibular stimulation in darkness, of the cerebellar adaptive loop, which exerts a variable gain control on the time constant of the velocity storage integrator.

Relational Motives Reduce Attentional Adhesion to Attractive Alternatives in Heterosexual University Students in China.

PubMed

Zhang, Qiuli; Maner, Jon K; Xu, Yin; Zheng, Yong

2017-02-01

In heterosexual individuals, attention is automatically captured by physically attractive members of the opposite sex. Although helpful for selecting new mates, attention to attractive relationship alternatives can threaten satisfaction with and commitment to an existing romantic relationship. The current study tested the hypothesis that although a mating prime would increase selective attention to attractive opposite-sex targets (relative to less attractive targets) among single participants, this effect would be reduced among people already committed to a long-term romantic partner. Consistent with hypotheses, whereas single participants responded to a mating prime with greater attentional adhesion to physically attractive opposite-sex targets (relative to less attractive targets), participants in a committed romantic relationship showed no such effect. These findings extend previous research suggesting the presence of relationship maintenance mechanisms that operate at early stages of social cognition.

Developmental decoupling of alternative phenotypes: insights from the transcriptomes of horn-polyphenic beetles

PubMed Central

Snell-Rood, Emilie C.; Cash, Amy; Han, Mira V.; Kijimoto, Teiya; Andrews, Justen; Moczek, Armin P.

2010-01-01

Developmental mechanisms play an important role in determining the costs, limits, and evolutionary consequences of phenotypic plasticity. One issue central to these claims is the hypothesis of developmental decoupling, where alternate morphs result from evolutionarily independent developmental pathways. We address this assumption through a microarray study that tests whether differences in gene expression between alternate morphs are as divergent as those between sexes, a classic example of developmental decoupling. We then examine whether genes with morph-biased expression are less conserved than genes with shared expression between morphs, as predicted if developmental decoupling relaxes pleiotropic constraints on divergence. We focus on the developing horns and brains of two species of horned beetles with spectacular sexual- and morph-dimorphism in the expression of horns and fighting behavior. We find that patterns of gene expression were as divergent between morphs as they were between sexes. However, overall patterns of gene expression were also highly correlated across morphs and sexes. Morph-biased genes were more evolutionarily divergent, suggesting a role of relaxed pleiotropic constraints or relaxed selection. Together these results suggest that alternate morphs are to some extent developmentally decoupled, and that this decoupling has significant evolutionary consequences. However, alternative morphs may not be as developmentally decoupled as sometimes assumed and such hypotheses of development should be revisited and refined. PMID:20731717

The Biological Contributions to Gender Identity and Gender Diversity: Bringing Data to the Table.

PubMed

Polderman, Tinca J C; Kreukels, Baudewijntje P C; Irwig, Michael S; Beach, Lauren; Chan, Yee-Ming; Derks, Eske M; Esteva, Isabel; Ehrenfeld, Jesse; Heijer, Martin Den; Posthuma, Danielle; Raynor, Lewis; Tishelman, Amy; Davis, Lea K

2018-03-01

The American Psychological Association defines gender identity as, "A person's deeply-felt, inherent sense of being a boy, a man, or a male; a girl, a woman, or a female; or an alternative gender (e.g., genderqueer, gender nonconforming, gender neutral) that may or may not correspond to a person's sex assigned at birth or to a person's primary or secondary sex characteristics" (American Psychological Association, Am Psychol 70(9):832-864, 2015). Here we review the evidence that gender identity and related socially defined gender constructs are influenced in part by innate factors including genes. Based on the data reviewed, we hypothesize that gender identity is a multifactorial complex trait with a heritable polygenic component. We argue that increasing the awareness of the biological diversity underlying gender identity development is relevant to all domains of social, medical, and neuroscience research and foundational for reducing health disparities and promoting human-rights protections for gender minorities.

Personality traits and environmental choices: On the search for understanding.

PubMed

Farizo, Begoña A; Oglethorpe, David; Soliño, Mario

2016-10-01

In this paper we hypothesize that individuals will choose among alternative courses of action for power generation from wind farms according to their personality profiles. Through a factor analysis we found that certain characteristics of personality do indeed have an effect on environmental choice. The study involves an extensive survey based on the Big Five Traits model to find a pattern of choice that will help to better understand environmental decisions and be useful for policy makers to identify target groups and preview reactions to different courses of action. The research is potentially useful for the better preparation and design of publicity material, awareness raising campaigns and information provision for complex or unpopular policies affecting the environment or in environmental education in general. This research is especially interested in shedding some light on how personality is involved in the processes of environmental decision making, despite the limitations of the present study. Copyright © 2016 Elsevier B.V. All rights reserved.

Payoff-based learning explains the decline in cooperation in public goods games.

PubMed

Burton-Chellew, Maxwell N; Nax, Heinrich H; West, Stuart A

2015-02-22

Economic games such as the public goods game are increasingly being used to measure social behaviours in humans and non-human primates. The results of such games have been used to argue that people are pro-social, and that humans are uniquely altruistic, willingly sacrificing their own welfare in order to benefit others. However, an alternative explanation for the empirical observations is that individuals are mistaken, but learn, during the game, how to improve their personal payoff. We test between these competing hypotheses, by comparing the explanatory power of different behavioural rules, in public goods games, where individuals are given different amounts of information. We find: (i) that individual behaviour is best explained by a learning rule that is trying to maximize personal income; (ii) that conditional cooperation disappears when the consequences of cooperation are made clearer; and (iii) that social preferences, if they exist, are more anti-social than pro-social. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Wastewater disinfection by peracetic acid: assessment of models for tracking residual measurements and inactivation.

PubMed

Santoro, Domenico; Gehr, Ronald; Bartrand, Timothy A; Liberti, Lorenzo; Notarnicola, Michele; Dell'Erba, Adele; Falsanisi, Dario; Haas, Charles N

2007-07-01

With its potential for low (if any) disinfection byproduct formation and easy retrofit for chlorine contactors, peracetic acid (PAA) or use of PAA in combination with other disinfectant technologies may be an attractive alternative to chlorine-based disinfection. Examples of systems that might benefit from use of PAA are water reuse schemes or plants discharging to sensitive receiving water bodies. Though PAA is in use in numerous wastewater treatment plants in Europe, its chemical kinetics, microbial inactivation rates, and mode of action against microorganisms are not thoroughly understood. This paper presents results from experimental studies of PAA demand, PAA decay, and microbial inactivation, with a complementary modeling analysis. Model results are used to evaluate techniques for measurement of PAA concentration and to develop hypotheses regarding the mode of action of PAA in bacterial inactivation. Kinetic and microbial inactivation rate data were collected for typical wastewaters and may be useful for engineers in evaluating whether to convert from chlorine to PAA disinfection.

Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery.

PubMed

Simm, Jaak; Klambauer, Günter; Arany, Adam; Steijaert, Marvin; Wegner, Jörg Kurt; Gustin, Emmanuel; Chupakhin, Vladimir; Chong, Yolanda T; Vialard, Jorge; Buijnsters, Peter; Velter, Ingrid; Vapirev, Alexander; Singh, Shantanu; Carpenter, Anne E; Wuyts, Roel; Hochreiter, Sepp; Moreau, Yves; Ceulemans, Hugo

2018-05-17

In both academia and the pharmaceutical industry, large-scale assays for drug discovery are expensive and often impractical, particularly for the increasingly important physiologically relevant model systems that require primary cells, organoids, whole organisms, or expensive or rare reagents. We hypothesized that data from a single high-throughput imaging assay can be repurposed to predict the biological activity of compounds in other assays, even those targeting alternate pathways or biological processes. Indeed, quantitative information extracted from a three-channel microscopy-based screen for glucocorticoid receptor translocation was able to predict assay-specific biological activity in two ongoing drug discovery projects. In these projects, repurposing increased hit rates by 50- to 250-fold over that of the initial project assays while increasing the chemical structure diversity of the hits. Our results suggest that data from high-content screens are a rich source of information that can be used to predict and replace customized biological assays. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evaluating Nonattachment and Decentering as Possible Mediators of the Link Between Mindfulness and Psychological Distress in a Nonclinical College Sample.

PubMed

Bhambhani, Yash; Cabral, Gail

2016-10-01

Although increasing evidence shows that mindfulness is positively related to mental health, the nature and mechanisms of this relationship are not fully understood. Based on previous research findings and suggestions, the authors of the current study hypothesized that decentering and nonattachment are 2 variables that mediate the relationship between mindfulness and psychological distress. A nonclinical, non-treatment-seeking sample of 308 students and employees from a middle-class, primarily Caucasian university filled out mindfulness, decentering, nonattachment, and mental distress measures online. Mediational analyses failed to support the hypothesis. Results suggest that mindfulness and nonattachment are independent predictors of nonclinical psychological distress and fully explain the effect of decentering on psychological distress. Results should be interpreted with caution and not generalized to clinical issues. A more comprehensive look into the mechanisms of mindfulness, especially with rigorous experimental, longitudinal studies, is warranted. The authors stress the importance of checking alternative, equivalent models in mediation studies. © The Author(s) 2015.

Laboratory simulated transport of microcystin-LR and cylindrospermopsin in groundwater under the influence of stormwater ponds: implications for harvesting of infiltrated stormwater

USGS Publications Warehouse

O'Reilly, Andrew M.; Wanielista, Martin P.; Loftin, Keith A.; Chang, Ni-Bin; Schirmer, Mario; Hoehn, Eduard; Vogt, Tobias

2011-01-01

Water shortages in the southeastern United States have led to a need for more intensive management and usage of stormwater for beneficial uses such as irrigation. Harvesting of infiltrated stormwater from horizontal wells in sandy aquifer sediments beneath stormwater ponds has emerged as an alternative in need of evaluation. Cyanobacteria may proliferate in stormwater ponds; cyanotoxins produced by these organisms represent potential public health concerns. Results of two, saturated flow, sand column experiments indicate breakthrough of microcystin-LR (MCLR) and cylindrospermopsin (CYL) within 1―2 pore volumes indicating little removal attributable to sorption. Concentration-based MCLR removal efficiencies up to 90% were achieved, which we hypothesize were predominantly due to biodegradation. In contrast, CYL removal efficiencies were generally less than 15%. On the basis of these results, removal of sandy soil in the stormwater pond bottom and addition of sorption media with greater binding affinities to cyanotoxins may enhance natural attenuation processes prior to water withdrawal.

Dark matter spin determination with directional direct detection experiments

NASA Astrophysics Data System (ADS)

Catena, Riccardo; Conrad, Jan; Döring, Christian; Ferella, Alfredo Davide; Krauss, Martin B.

2018-01-01

If dark matter has spin 0, only two WIMP-nucleon interaction operators can arise as leading operators from the nonrelativistic reduction of renormalizable single-mediator models for dark matter-quark interactions. Based on this crucial observation, we show that about 100 signal events at next generation directional detection experiments can be enough to enable a 2 σ rejection of the spin 0 dark matter hypothesis in favor of alternative hypotheses where the dark matter particle has spin 1 /2 or 1. In this context, directional sensitivity is crucial since anisotropy patterns in the sphere of nuclear recoil directions depend on the spin of the dark matter particle. For comparison, about 100 signal events are expected in a CF4 detector operating at a pressure of 30 torr with an exposure of approximately 26,000 cubic-meter-detector days for WIMPs of 100 GeV mass and a WIMP-fluorine scattering cross section of 0.25 pb. Comparable exposures require an array of cubic meter time projection chamber detectors.

Limited and time-delayed internal resource allocation generates oscillations and chaos in the dynamics of citrus crops

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

Ye, Xujun, E-mail: yexujun@cc.hirosaki-u.ac.jp; Faculty of Agriculture and Life Sciences, Hirosaki University, Aomori 036-8561; Sakai, Kenshi, E-mail: ken@cc.tuat.ac.jp

Alternate bearing or masting is a yield variability phenomenon in perennial crops. The complex dynamics in this phenomenon have stimulated much ecological research. Motivated by data from an eight-year experiment with forty-eight individual trees, we explored the mechanism inherent to these dynamics in Satsuma mandarin (Citrus unshiu Marc.). By integrating high-resolution imaging technology, we found that the canopy structure and reproduction output of individual citrus crops are mutually dependent on each other. Furthermore, it was revealed that the mature leaves in early season contribute their energy to the fruiting of the current growing season, whereas the younger leaves show amore » delayed contribution to the next growing season. We thus hypothesized that the annual yield variability might be caused by the limited and time-delayed resource allocation in individual plants. A novel lattice model based on this hypothesis demonstrates that this pattern of resource allocation will generate oscillations and chaos in citrus yield.« less

Identification of novel nuclear localization signals of Drosophila myeloid leukemia factor.

PubMed

Sugano, Wakana; Yamaguchi, Masamitsu

2007-01-01

Myeloid leukemia factor 1 (MLF1) was first identified as part of a leukemic fusion protein produced by a chromosomal translocation, and MLF family proteins are present in many animals. In mammalian cells, MLF1 has been described as mainly cytoplasmic, but in Drosophila, one of the dMLF isoforms (dMLFA) localized mainly in the nucleus while the other isoform (dMLFB), that appears to be produced by the alternative splicing, displays both nuclear and cytoplasmic localization. To investigate the difference in subcellular localization between MLF family members, we examined the subcellular localization of deletion mutants of dMLFA isoform. The analyses showed that the C-terminal 40 amino acid region of dMLFA is necessary and sufficient for nuclear localization. Based on amino acid sequences, we hypothesized that two nuclear localization signals (NLSs) are present within the region. Site-directed mutagenesis of critical residues within the two putative NLSs leads to loss of nuclear localization, suggesting that both NLS motifs are necessary for nuclear localization.

Evolution of sprint speed in African savannah herbivores in relation to predation.

PubMed

Bro-Jørgensen, Jakob

2013-11-01

Predator-prey arms races are widely speculated to underlie fast speed in terrestrial mammals. However, due to lack of empirical testing, both the specificity of any evolutionary coupling between particular predator and prey species, and the relevance of alternative food-based hypotheses of speed evolution, remain obscure. Here I examine the ecological links between the sprint speed of African savannah herbivores, their vulnerability to predators, and their diet. I show that sprint speed is strongly predicted by the vulnerability of prey to their main predators; however, the direction of the link depends on the hunting style of the predator. Speed increases with vulnerability to pursuit predators, whereas vulnerability to ambush predators is associated with particularly slow speed. These findings suggest that differential vulnerability to specific predators can indeed drive interspecific variation in speed within prey communities, but that predator hunting style influences the intensity and consistency with which selection on speed is coupled between particular species. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Exposure ages of carbonaceous chondrites, 1

NASA Technical Reports Server (NTRS)

Nishiizumi, K.; Arnold, J. R.; Caffee, M. W.; Finkel, R. C.; Southon, J. R.; Nagai, H.; Honda, M.; Sharma, P.; Imamura, M.; Kobayashi, K.

1993-01-01

The recent exposure histories of carbonaceous chondrites have been investigated using cosmogenic radionuclides. Our results may indicate a clustering of exposure ages of C1 and C2 chondrites into two peaks, 0.2 My and 0.6 My, perhaps implying two collisional events of Earth-crossing parent bodies. Among carbonaceous chondrites are some having short exposure ages which Mazor et al. hypothesized cluster into a small number of families. This hypothesis is based on spallogenic Ne-21 exposure ages, which in some instances are difficult to determine owing to the large amounts of trapped noble gases in carbonaceous chondrites. Also, since Ne-21 is stable, it integrates a sample's entire exposure history, so meteorites with complex exposure histories are difficult to understand using exclusively Ne-21. Cosmogenic radionuclides provide an alternative means of determining the recent cosmic ray exposure duration. To test the hypothesis of Mazor et al. we have begun a systematic investigation of exposure histories of Antarctic and non-Antarctic carbonaceous chondrites especially C2s.

Some controversial multiple testing problems in regulatory applications.

PubMed

Hung, H M James; Wang, Sue-Jane

2009-01-01

Multiple testing problems in regulatory applications are often more challenging than the problems of handling a set of mathematical symbols representing multiple null hypotheses under testing. In the union-intersection setting, it is important to define a family of null hypotheses relevant to the clinical questions at issue. The distinction between primary endpoint and secondary endpoint needs to be considered properly in different clinical applications. Without proper consideration, the widely used sequential gate keeping strategies often impose too many logical restrictions to make sense, particularly to deal with the problem of testing multiple doses and multiple endpoints, the problem of testing a composite endpoint and its component endpoints, and the problem of testing superiority and noninferiority in the presence of multiple endpoints. Partitioning the null hypotheses involved in closed testing into clinical relevant orderings or sets can be a viable alternative to resolving the illogical problems requiring more attention from clinical trialists in defining the clinical hypotheses or clinical question(s) at the design stage. In the intersection-union setting there is little room for alleviating the stringency of the requirement that each endpoint must meet the same intended alpha level, unless the parameter space under the null hypothesis can be substantially restricted. Such restriction often requires insurmountable justification and usually cannot be supported by the internal data. Thus, a possible remedial approach to alleviate the possible conservatism as a result of this requirement is a group-sequential design strategy that starts with a conservative sample size planning and then utilizes an alpha spending function to possibly reach the conclusion early.

DIA-datasnooping and identifiability

NASA Astrophysics Data System (ADS)

Zaminpardaz, S.; Teunissen, P. J. G.

2018-04-01

In this contribution, we present and analyze datasnooping in the context of the DIA method. As the DIA method for the detection, identification and adaptation of mismodelling errors is concerned with estimation and testing, it is the combination of both that needs to be considered. This combination is rigorously captured by the DIA estimator. We discuss and analyze the DIA-datasnooping decision probabilities and the construction of the corresponding partitioning of misclosure space. We also investigate the circumstances under which two or more hypotheses are nonseparable in the identification step. By means of a theorem on the equivalence between the nonseparability of hypotheses and the inestimability of parameters, we demonstrate that one can forget about adapting the parameter vector for hypotheses that are nonseparable. However, as this concerns the complete vector and not necessarily functions of it, we also show that parameter functions may exist for which adaptation is still possible. It is shown how this adaptation looks like and how it changes the structure of the DIA estimator. To demonstrate the performance of the various elements of DIA-datasnooping, we apply the theory to some selected examples. We analyze how geometry changes in the measurement setup affect the testing procedure, by studying their partitioning of misclosure space, the decision probabilities and the minimal detectable and identifiable biases. The difference between these two minimal biases is highlighted by showing the difference between their corresponding contributing factors. We also show that if two alternative hypotheses, say Hi and Hj , are nonseparable, the testing procedure may have different levels of sensitivity to Hi -biases compared to the same Hj -biases.

What Kills the Hindgut Flagellates of Lower Termites during the Host Molting Cycle?

PubMed Central

Nalepa, Christine A.

2017-01-01

Subsocial wood feeding cockroaches in the genus Cryptocercus, the sister group of termites, retain their symbiotic gut flagellates during the host molting cycle, but in lower termites, closely related flagellates die prior to host ecdysis. Although the prevalent view is that termite flagellates die because of conditions of starvation and desiccation in the gut during the host molting cycle, the work of L.R. Cleveland in the 1930s through the 1960s provides a strong alternate hypothesis: it was the changed hormonal environment associated with the origin of eusociality and its concomitant shift in termite developmental ontogeny that instigates the death of the flagellates in termites. Although the research on termite gut microbial communities has exploded since the advent of modern molecular techniques, the role of the host hormonal environment on the life cycle of its gut flagellates has been neglected. Here Cleveland’s studies are revisited to provide a basis for re-examination of the problem, and the results framed in the context of two alternate hypotheses: the flagellate symbionts are victims of the change in host social status, or the flagellates have become incorporated into the life cycle of the eusocial termite colony. Recent work on parasitic protists suggests clear paths for exploring these hypotheses and for resolving long standing issues regarding sexual-encystment cycles in flagellates of the Cryptocercus-termite lineage using molecular methodologies, bringing the problem into the modern era. PMID:29258251

Workplace support, discrimination, and person-organization fit: tests of the theory of work adjustment with LGB individuals.

PubMed

Velez, Brandon L; Moradi, Bonnie

2012-07-01

The present study explored the links of 2 workplace contextual variables--perceptions of workplace heterosexist discrimination and lesbian, gay, and bisexual (LGB)-supportive climates--with job satisfaction and turnover intentions in a sample of LGB employees. An extension of the theory of work adjustment (TWA) was used as the conceptual framework for the study; as such, perceived person-organization (P-O) fit was tested as a mediator of the relations between the workplace contextual variables and job outcomes. Data were analyzed from 326 LGB employees. Zero-order correlations indicated that perceptions of workplace heterosexist discrimination and LGB-supportive climates were correlated in expected directions with P-O fit, job satisfaction, and turnover intentions. Structural equation modeling (SEM) was used to compare multiple alternative measurement models evaluating the discriminant validity of the 2 workplace contextual variables relative to one another, and the 3 TWA job variables relative to one another; SEM was also used to test the hypothesized mediation model. Comparisons of multiple alternative measurement models supported the construct distinctiveness of the variables of interest. The test of the hypothesized structural model revealed that only LGB-supportive climates (and not workplace heterosexist discrimination) had a unique direct positive link with P-O fit and, through the mediating role of P-O fit, had significant indirect positive and negative relations with job satisfaction and turnover intentions, respectively. Moreover, P-O fit had a significant indirect negative link with turnover intentions through job satisfaction.

Updating impairments and the failure to explore new hypotheses following right brain damage.

PubMed

Stöttinger, Elisabeth; Guay, Carolyn Louise; Danckert, James; Anderson, Britt

2018-06-01

We have shown recently that damage to the right hemisphere impairs the ability to update mental models when evidence suggests an old model is no longer appropriate. We argue that this deficit is generic in the sense that it crosses multiple cognitive and perceptual domains. Here, we examined the nature of this updating impairment to determine more precisely the underlying mechanisms. We had right (RBD, N = 12) and left brain damaged (LBD, N = 10) patients perform versions of our picture-morphing task in which pictures gradually morph from one object (e.g., shark) to another (e.g., plane). Performance was contrasted against two groups of healthy older controls, one matched on age (HCO-age-matched, N = 9) and another matched on general level of cognitive ability (HCO-cognitively-matched, N = 9). We replicated our earlier findings showing that RBD patients took longer than LBD patients and HCOs to report seeing the second object in a sequence of morphing images. The groups did not differ when exposed to a morphing sequence a second time, or when responding to ambiguous images outside the morphing context. This indicates that RBD patients have little difficulty alternating between known representations or labeling ambiguous images. Instead, the difficulty lies in generating alternate hypotheses for ambiguous information. Lesion overlay analyses, although speculative given the sample size, are consistent with our fMRI work in healthy individuals in implicating the anterior insular cortex as critical for updating mental models.

Annual Research Review: Transdiagnostic neuroscience of child and adolescent mental disorders--differentiating decision making in attention-deficit/hyperactivity disorder, conduct disorder, depression, and anxiety.

PubMed

Sonuga-Barke, Edmund J S; Cortese, Samuele; Fairchild, Graeme; Stringaris, Argyris

2016-03-01

Ineffective decision making is a major source of everyday functional impairment and reduced quality of life for young people with mental disorders. However, very little is known about what distinguishes decision making by individuals with different disorders or the neuropsychological processes or brain systems underlying these. This is the focus of the current review. We first propose a neuroeconomic model of the decision-making process with separate stages for the prechoice evaluation of expected utility of future options; choice execution and postchoice management; the appraisal of outcome against expectation; and the updating of value estimates to guide future decisions. According to the proposed model, decision making is mediated by neuropsychological processes operating within three domains: (a) self-referential processes involved in autobiographical reflection on past, and prospection about future, experiences; (b) executive functions, such as working memory, inhibition, and planning, that regulate the implementation of decisions; and (c) processes involved in value estimation and outcome appraisal and learning. These processes are underpinned by the interplay of multiple brain networks, especially medial and lateralized cortical components of the default mode network, dorsal corticostriatal circuits underpinning higher order cognitive and behavioral control, and ventral frontostriatal circuits, connecting to brain regions implicated in emotion processing, that control valuation and learning processes. Based on clinical insights and considering each of the decision-making stages in turn, we outline disorder-specific hypotheses about impaired decision making in four childhood disorders: attention-deficit/hyperactivity disorder (ADHD), conduct disorder (CD), depression, and anxiety. We hypothesize that decision making in ADHD is deficient (i.e. inefficient, insufficiently reflective, and inconsistent) and impulsive (biased toward immediate over delayed alternatives). In CD, it is reckless and insensitive to negative consequences. In depression, it is disengaged, perseverative, and pessimistic, while in anxiety, it is hesitant, risk-averse, and self-deprecating. A survey of current empirical indications related to these disorder-specific hypotheses highlights the limited and fragmentary nature of the evidence base and illustrates the need for a major research initiative in decision making in childhood disorders. The final section highlights a number of important additional general themes that need to be considered in future research. © 2015 The Authors. Journal of Child Psychology and Psychiatry published by John Wiley & Sons Ltd on behalf of Association for Child and Adolescent Mental Health.

Combining Theory-Driven Evaluation and Causal Loop Diagramming for Opening the ‘Black Box’ of an Intervention in the Health Sector: A Case of Performance-Based Financing in Western Uganda

PubMed Central

Holvoet, Nathalie; Criel, Bart

2017-01-01

Increased attention on “complexity” in health systems evaluation has resulted in many different methodological responses. Theory-driven evaluations and systems thinking are two such responses that aim for better understanding of the mechanisms underlying given outcomes. Here, we studied the implementation of a performance-based financing intervention by the Belgian Technical Cooperation in Western Uganda to illustrate a methodological strategy of combining these two approaches. We utilized a systems dynamics tool called causal loop diagramming (CLD) to generate hypotheses feeding into a theory-driven evaluation. Semi-structured interviews were conducted with 30 health workers from two districts (Kasese and Kyenjojo) and with 16 key informants. After CLD, we identified three relevant hypotheses: “success to the successful”, “growth and underinvestment”, and “supervision conundrum”. The first hypothesis leads to increasing improvements in performance, as better performance leads to more incentives, which in turn leads to better performance. The latter two hypotheses point to potential bottlenecks. Thus, the proposed methodological strategy was a useful tool for identifying hypotheses that can inform a theory-driven evaluation. The hypotheses are represented in a comprehensible way while highlighting the underlying assumptions, and are more easily falsifiable than hypotheses identified without using CLD. PMID:28869518

The Tongue Map, Real or Not?

ERIC Educational Resources Information Center

Marshall, Pamela A.

2013-01-01

Students need practice in proposing hypotheses, developing experiments that will test these hypotheses, and generating data that they will analyze to support or refute them. I describe a guided-inquiry activity based on the "tongue map" concept, appropriate for middle school and high school students.

Mindfulness in schizophrenia: Associations with self-reported motivation, emotion regulation, dysfunctional attitudes, and negative symptoms.

PubMed

Tabak, Naomi T; Horan, William P; Green, Michael F

2015-10-01

Mindfulness-based interventions are gaining empirical support as alternative or adjunctive treatments for a variety of mental health conditions, including anxiety, depression, and substance use disorders. Emerging evidence now suggests that mindfulness-based treatments may also improve clinical features of schizophrenia, including negative symptoms. However, no research has examined the construct of mindfulness and its correlates in schizophrenia. In this study, we examined self-reported mindfulness in patients (n=35) and controls (n=25) using the Five-Facet Mindfulness Questionnaire. We examined correlations among mindfulness, negative symptoms, and psychological constructs associated with negative symptoms and adaptive functioning, including motivation, emotion regulation, and dysfunctional attitudes. As hypothesized, patients endorsed lower levels of mindfulness than controls. In patients, mindfulness was unrelated to negative symptoms, but it was associated with more adaptive emotion regulation (greater reappraisal) and beliefs (lower dysfunctional attitudes). Some facets of mindfulness were also associated with self-reported motivation (behavioral activation and inhibition). These patterns of correlations were similar in patients and controls. Findings from this initial study suggest that schizophrenia patients may benefit from mindfulness-based interventions because they (a) have lower self-reported mindfulness than controls and (b) demonstrate strong relationships between mindfulness and psychological constructs related to adaptive functioning. Copyright © 2015 Elsevier B.V. All rights reserved.

Testing a bioenergetics-based habitat choice model: bluegill (Lepomis macrochirus) responses to food availability and temperature

USGS Publications Warehouse

2011-01-01

Using an automated shuttlebox system, we conducted patch choice experiments with 32, 8–12 g bluegill sunfish (Lepomis macrochirus) to test a behavioral energetics hypothesis of habitat choice. When patch temperature and food levels were held constant within patches but different between patches, we expected bluegill to choose patches that maximized growth based on the bioenergetic integration of food and temperature as predicted by a bioenergetics model. Alternative hypotheses were that bluegill may choose patches based only on food (optimal foraging) or temperature (behavioral thermoregulation). The behavioral energetics hypothesis was not a good predictor of short-term (from minutes to weeks) patch choice by bluegill; the behavioral thermoregulation hypothesis was the best predictor. In the short-term, food and temperature appeared to affect patch choice hierarchically; temperature was more important, although food can alter temperature preference during feeding periods. Over a 19-d experiment, mean temperatures occupied by fish offered low rations did decline as predicted by the behavioral energetics hypothesis, but the decline was less than 1.0 °C as opposed to a possible 5 °C decline. A short-term, bioenergetic response to food and temperature may be precluded by physiological costs of acclimation not considered explicitly in the behavioral energetics hypothesis.

CFTR-dependent defect in alternatively-activated macrophages in cystic fibrosis.

PubMed

Tarique, Abdullah A; Sly, Peter D; Holt, Patrick G; Bosco, Anthony; Ware, Robert S; Logan, Jayden; Bell, Scott C; Wainwright, Claire E; Fantino, Emmanuelle

2017-07-01

The role of the macrophages in cystic fibrosis (CF) lung disease has been poorly studied. We hypothesized that alternatively activated M2 macrophages are abnormal in CF lung disease. Blood samples were collected from adults (n=13) children (n=27) with CF on admission for acute pulmonary exacerbation and when clinically stable. Monocytes were differentiated into macrophages and polarized into classical (M1) and alternatively-activated (M2) phenotypes, function determined ex-vivo and compared with healthy controls. In the absence of functional cystic fibrosis trans-membrane conductance regulator (CFTR), either naturally in patients with CF or induced with CFTR inhibitors, monocyte-derived macrophages do not respond to IL-13/IL-4, fail to polarize into M2s associated with a post-transcriptional failure to produce and express IL-13Rα1 on the macrophage surface Polarization to the M1 phenotype was unaffected. CFTR-dependent imbalance of macrophage phenotypes and functions could contribute to the exaggerated inflammatory response seen in CF lung disease. Copyright © 2017 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Testing Hypotheses on Risk Factors for Scientific Misconduct via Matched-Control Analysis of Papers Containing Problematic Image Duplications.

PubMed

Fanelli, Daniele; Costas, Rodrigo; Fang, Ferric C; Casadevall, Arturo; Bik, Elisabeth M

2018-02-19

It is commonly hypothesized that scientists are more likely to engage in data falsification and fabrication when they are subject to pressures to publish, when they are not restrained by forms of social control, when they work in countries lacking policies to tackle scientific misconduct, and when they are male. Evidence to test these hypotheses, however, is inconclusive due to the difficulties of obtaining unbiased data. Here we report a pre-registered test of these four hypotheses, conducted on papers that were identified in a previous study as containing problematic image duplications through a systematic screening of the journal PLoS ONE. Image duplications were classified into three categories based on their complexity, with category 1 being most likely to reflect unintentional error and category 3 being most likely to reflect intentional fabrication. We tested multiple parameters connected to the hypotheses above with a matched-control paradigm, by collecting two controls for each paper containing duplications. Category 1 duplications were mostly not associated with any of the parameters tested, as was predicted based on the assumption that these duplications were mostly not due to misconduct. Categories 2 and 3, however, exhibited numerous statistically significant associations. Results of univariable and multivariable analyses support the hypotheses that academic culture, peer control, cash-based publication incentives and national misconduct policies might affect scientific integrity. No clear support was found for the "pressures to publish" hypothesis. Female authors were found to be equally likely to publish duplicated images compared to males. Country-level parameters generally exhibited stronger effects than individual-level parameters, because developing countries were significantly more likely to produce problematic image duplications. This suggests that promoting good research practices in all countries should be a priority for the international research integrity agenda.

Resource Limitation Issues In Real-Time Intelligent Systems

NASA Astrophysics Data System (ADS)

Green, Peter E.

1986-03-01

This paper examines resource limitation problems that can occur in embedded AI systems which have to run in real-time. It does this by examining two case studies. The first is a system which acoustically tracks low-flying aircraft and has the problem of interpreting a high volume of often ambiguous input data to produce a model of the system's external world. The second is a robotics problem in which the controller for a robot arm has to dynamically plan the order in which to pick up pieces from a conveyer belt and sort them into bins. In this case the system starts with a continuously changing model of its environment and has to select which action to perform next. This latter case emphasizes the issues in designing a system which must operate in an uncertain and rapidly changing environment. The first system uses a distributed HEARSAY methodology running on multiple processors. It is shown, in this case, how the com-binatorial growth of possible interpretation of the input data can require large and unpredictable amounts of computer resources for data interpretation. Techniques are presented which achieve real-time operation by limiting the combinatorial growth of alternate hypotheses and processing those hypotheses that are most likely to lead to meaningful interpretation of the input data. The second system uses a decision tree approach to generate and evaluate possible plans of action. It is shown how the combina-torial growth of possible alternate plans can, as in the previous case, require large and unpredictable amounts of computer time to evalu-ate and select from amongst the alternative. The use of approximate decisions to limit the amount of computer time needed is discussed. The use of concept of using incremental evidence is then introduced and it is shown how this can be used as the basis of systems that can combine heuristic and approximate evidence in making real-time decisions.

Nuclear Physicists in Finance

NASA Astrophysics Data System (ADS)

Mattoni, Carlo

2017-01-01

The financial services industry presents an interesting alternative career path for nuclear physicists. Careers in finance typically offer intellectual challenge, a fast pace, high caliber colleagues, merit-based compensation with substantial upside, and an opportunity to deploy skills learned as a physicist. Physicists are employed at a wide range of financial institutions on both the ``buy side'' (hedge fund managers, private equity managers, mutual fund managers, etc.) and the ``sell side'' (investment banks and brokerages). Historically, physicists in finance were primarily ``quants'' tasked with applying stochastic calculus to determine the price of financial derivatives. With the maturation of the field of derivative pricing, physicists in finance today find work in a variety of roles ranging from quantification and management of risk to investment analysis to development of sophisticated software used to price, trade, and risk manage securities. Only a small subset of today's finance careers for physicists require the use of advanced math and practically none provide an opportunity to tinker with an apparatus, yet most nevertheless draw on important skills honed during the training of a nuclear physicist. Intellectually rigorous critical thinking, sophisticated problem solving, an attention to minute detail and an ability to create and test hypotheses based on incomplete information are key to both disciplines.

Environmental regulation of sex determination in oil palm: current knowledge and insights from other species.

PubMed

Adam, Hélène; Collin, Myriam; Richaud, Frédérique; Beulé, Thierry; Cros, David; Omoré, Alphonse; Nodichao, Leifi; Nouy, Bruno; Tregear, James W

2011-12-01

The African oil palm (Elaeis guineensis) is a monoecious species of the palm subfamily Arecoideae. It may be qualified as 'temporally dioecious' in that it produces functionally unisexual male and female inflorescences in an alternating cycle on the same plant, resulting in an allogamous mode of reproduction. The 'sex ratio' of an oil palm stand is influenced by both genetic and environmental factors. In particular, the enhancement of male inflorescence production in response to water stress has been well documented. This paper presents a review of our current understanding of the sex determination process in oil palm and discusses possible insights that can be gained from other species. Although some informative phenological studies have been carried out, nothing is as yet known about the genetic basis of sex determination in oil palm, nor the mechanisms by which this process is regulated. Nevertheless new genomics-based techniques, when combined with field studies and biochemical and molecular cytological-based approaches, should provide a new understanding of the complex processes governing oil palm sex determination in the foreseeable future. Current hypotheses and strategies for future research are discussed.

On the role of general system theory for functional neuroimaging.

PubMed

Stephan, Klaas Enno

2004-12-01

One of the most important goals of neuroscience is to establish precise structure-function relationships in the brain. Since the 19th century, a major scientific endeavour has been to associate structurally distinct cortical regions with specific cognitive functions. This was traditionally accomplished by correlating microstructurally defined areas with lesion sites found in patients with specific neuropsychological symptoms. Modern neuroimaging techniques with high spatial resolution have promised an alternative approach, enabling non-invasive measurements of regionally specific changes of brain activity that are correlated with certain components of a cognitive process. Reviewing classic approaches towards brain structure-function relationships that are based on correlational approaches, this article argues that these approaches are not sufficient to provide an understanding of the operational principles of a dynamic system such as the brain but must be complemented by models based on general system theory. These models reflect the connectional structure of the system under investigation and emphasize context-dependent couplings between the system elements in terms of effective connectivity. The usefulness of system models whose parameters are fitted to measured functional imaging data for testing hypotheses about structure-function relationships in the brain and their potential for clinical applications is demonstrated by several empirical examples.

On the role of general system theory for functional neuroimaging

PubMed Central

Stephan, Klaas Enno

2004-01-01

One of the most important goals of neuroscience is to establish precise structure–function relationships in the brain. Since the 19th century, a major scientific endeavour has been to associate structurally distinct cortical regions with specific cognitive functions. This was traditionally accomplished by correlating microstructurally defined areas with lesion sites found in patients with specific neuropsychological symptoms. Modern neuroimaging techniques with high spatial resolution have promised an alternative approach, enabling non-invasive measurements of regionally specific changes of brain activity that are correlated with certain components of a cognitive process. Reviewing classic approaches towards brain structure–function relationships that are based on correlational approaches, this article argues that these approaches are not sufficient to provide an understanding of the operational principles of a dynamic system such as the brain but must be complemented by models based on general system theory. These models reflect the connectional structure of the system under investigation and emphasize context-dependent couplings between the system elements in terms of effective connectivity. The usefulness of system models whose parameters are fitted to measured functional imaging data for testing hypotheses about structure–function relationships in the brain and their potential for clinical applications is demonstrated by several empirical examples. PMID:15610393

Twenty-eight Days to a Climax community: A Succession Laboratory Using Periphyton

NASA Astrophysics Data System (ADS)

Denicola, D. M.

2005-05-01

Succession in benthic algal communities (periphyton) occurs in a relatively short time scale because of the rapid reproductive rates of algae. To examine primary succession of periphyton in a lake and stream, unglazed tiles are placed in the respective habitats and sampled on days 4, 8, 16 and 28. Students count the preserved samples at 400X and identify taxa to genera based on customized picture keys (does not require a high degree of instructor expertise). Genera also are categorized according to algal growth forms, based on the size, shape, motility and attachment mechanism. After pooling the class data, students present the change in community structure, contrast succession between the lake and stream, and hypothesize which mechanisms may apply (facilitation, inhibition, tolerance). Successional sequences also are examined to see whether they agree with published growth form models for periphyton succession in lotic and lentic habitats. The laboratory uses the more intuitive method of repeated measures to study succession as an alternative to the often infeasible chronosequence method traditionally done for terrestrial communities. Additional outcomes include, reinforcement of the concept of species guilds (growth forms), an introduction into the use of empirical models, and an increased awareness of microorganism communities.

Estimation of parameter uncertainty for an activated sludge model using Bayesian inference: a comparison with the frequentist method.

PubMed

Zonta, Zivko J; Flotats, Xavier; Magrí, Albert

2014-08-01

The procedure commonly used for the assessment of the parameters included in activated sludge models (ASMs) relies on the estimation of their optimal value within a confidence region (i.e. frequentist inference). Once optimal values are estimated, parameter uncertainty is computed through the covariance matrix. However, alternative approaches based on the consideration of the model parameters as probability distributions (i.e. Bayesian inference), may be of interest. The aim of this work is to apply (and compare) both Bayesian and frequentist inference methods when assessing uncertainty for an ASM-type model, which considers intracellular storage and biomass growth, simultaneously. Practical identifiability was addressed exclusively considering respirometric profiles based on the oxygen uptake rate and with the aid of probabilistic global sensitivity analysis. Parameter uncertainty was thus estimated according to both the Bayesian and frequentist inferential procedures. Results were compared in order to evidence the strengths and weaknesses of both approaches. Since it was demonstrated that Bayesian inference could be reduced to a frequentist approach under particular hypotheses, the former can be considered as a more generalist methodology. Hence, the use of Bayesian inference is encouraged for tackling inferential issues in ASM environments.

Mode of action human relevance (species concordance) framework: Evolution of the Bradford Hill considerations and comparative analysis of weight of evidence

PubMed Central

Meek, M E (Bette); Palermo, Christine M; Bachman, Ammie N; North, Colin M; Jeffrey Lewis, R

2014-01-01

The mode of action human relevance (MOA/HR) framework increases transparency in systematically considering data on MOA for end (adverse) effects and their relevance to humans. This framework continues to evolve as experience increases in its application. Though the MOA/HR framework is not designed to address the question of “how much information is enough” to support a hypothesized MOA in animals or its relevance to humans, its organizing construct has potential value in considering relative weight of evidence (WOE) among different cases and hypothesized MOA(s). This context is explored based on MOA analyses in published assessments to illustrate the relative extent of supporting data and their implications for dose–response analysis and involved comparisons for chemical assessments on trichloropropane, and carbon tetrachloride with several hypothesized MOA(s) for cancer. The WOE for each hypothesized MOA was summarized in narrative tables based on comparison and contrast of the extent and nature of the supporting database versus potentially inconsistent or missing information. The comparison was based on evolved Bradford Hill considerations rank ordered to reflect their relative contribution to WOE determinations of MOA taking into account increasing experience in their application internationally. This clarification of considerations for WOE determinations as a basis for comparative analysis is anticipated to contribute to increasing consistency in the application of MOA/HR analysis and potentially, transparency in separating science judgment from public policy considerations in regulatory risk assessment. Copyright © 2014. The Authors. Journal of Applied Toxicology Published by John Wiley & Sons Ltd. The potential value of the mode of action (MOA)/human relevance (species concordance) framework in considering relative weight of evidence (WOE) amongst different cases and hypothesized MOA(s) is explored based on the content of several published assessments. The comparison is based on evolved Bradford Hill considerations rank ordered to reflect their relative contribution to WOE determinations for MOA based on experience internationally. PMID:24777878

Role of predation in short-term population fluctuations of some birds and mammals in Fennoscandia.

PubMed

Angelstam, P; Lindström, E; Widén, P

1984-05-01

We tested the hypothesis that synchronous fluctuations in small game species in boreal Fennoscandia are caused by varying predation pressure. The main prey of predators are the cyclically superabundant voles. Small game species (alternative prey) are rare compared to voles. The following 4 predictions were checked: (1) Predators should shift their diet from main prey to alternative prey as main prey decline. - This was confirmed using data on red fox (Vulpes vulpes L.) diet.; (2) The mortality rate of alternative prey should be inversely correlated to the abundance of main prey. - This was true for mountain hare (Lepus timidus L.) mortality rates and the rate of nest predation on black grouse (Tetrao tetrix L.).; (3) The total consumption of prey by all the predators should at least equal the critical losses in alternative prey during a decline year. - A tentative estimate of predator consumption amounted to 10 times the losses in grouse and hare.; and (4) The absence of synchrony between the species in the boreonemoral region should be associated with a more diverse diet of predators. - This was the case for red fox diets throughout Sweden. Although all 4 predictions were confirmed, we could not necessarily exclude other hypotheses involving changes in quality or quantity of plant food.

Culture, Cross-Role Consistency, and Adjustment: Testing Trait and Cultural Psychology Perspectives

PubMed Central

Church, A. Timothy; Anderson-Harumi, Cheryl A.; del Prado, Alicia M.; Curtis, Guy J.; Tanaka-Matsumi, Junko; Valdez Medina, José L.; Mastor, Khairul A.; White, Fiona A.; Miramontes, Lilia A.; Katigbak, Marcia S.

2008-01-01

Trait and cultural psychology perspectives on cross-role consistency and its relation to adjustment were examined in two individualistic cultures, the United States (N = 231) and Australia (N = 195), and four collectivistic cultures, Mexico (N = 199), Philippines (N = 195), Malaysia (N = 217), and Japan (N = 180). Cross-role consistency in trait ratings was evident in all cultures, supporting trait perspectives. Cultural comparisons of mean consistency provided support for cultural psychology perspectives as applied to East Asian cultures (i.e., Japan), but not collectivistic cultures more generally. Some but not all of the hypothesized predictors of consistency were supported across cultures. Cross-role consistency predicted aspects of adjustment in all cultures, but prediction was most reliable in the American sample and weakest in the Japanese sample. Alternative constructs proposed by cultural psychologists—personality coherence, social appraisal, and relationship harmony—predicted adjustment in all cultures, but were not, as hypothesized, better predictors of adjustment in collectivistic cultures than in individualistic cultures. PMID:18729706

Adaptive significance of natural variations in maternal care in rats: a translational perspective

PubMed Central

Beery, Annaliese K.; Francis, Darlene D.

2011-01-01

A wealth of data from the last fifty years documents the potency of early life experiences including maternal care on developing offspring. A majority of this research has focused on the developing stress axis and stress-sensitive behaviors in hopes of identifying factors impacting resilience and risk-sensitivity. The power of early life experience to shape later development is profound and has the potential to increase fitness of individuals for their environments. Current findings in a rat maternal care paradigm highlight the complex and dynamic relation between early experiences and a variety of outcomes. In this review we propose adaptive hypotheses for alternate maternal strategies and resulting offspring phenotypes, and ways to distinguish between these hypotheses. We also provide evidence underscoring the critical role of context in interpreting the adaptive significance of early experiences. If our goal is to identify risk-factors relevant to humans, we must better explore the role of the social and physical environment in our basic animal models. PMID:21458485

Culture, cross-role consistency, and adjustment: testing trait and cultural psychology perspectives.

PubMed

Church, A Timothy; Anderson-Harumi, Cheryl A; del Prado, Alicia M; Curtis, Guy J; Tanaka-Matsumi, Junko; Valdez Medina, José L; Mastor, Khairul A; White, Fiona A; Miramontes, Lilia A; Katigbak, Marcia S

2008-09-01

Trait and cultural psychology perspectives on cross-role consistency and its relation to adjustment were examined in 2 individualistic cultures, the United States (N=231) and Australia (N=195), and 4 collectivistic cultures, Mexico (N=199), the Philippines (N=195), Malaysia (N=217), and Japan (N=180). Cross-role consistency in trait ratings was evident in all cultures, supporting trait perspectives. Cultural comparisons of mean consistency provided support for cultural psychology perspectives as applied to East Asian cultures (i.e., Japan) but not collectivistic cultures more generally. Some but not all of the hypothesized predictors of consistency were supported across cultures. Cross-role consistency predicted aspects of adjustment in all cultures, but prediction was most reliable in the U.S. sample and weakest in the Japanese sample. Alternative constructs proposed by cultural psychologists--personality coherence, social appraisal, and relationship harmony--predicted adjustment in all cultures but were not, as hypothesized, better predictors of adjustment in collectivistic cultures than in individualistic cultures.

Strategies to intervene on causal systems are adaptively selected.

PubMed

Coenen, Anna; Rehder, Bob; Gureckis, Todd M

2015-06-01

How do people choose interventions to learn about causal systems? Here, we considered two possibilities. First, we test an information sampling model, information gain, which values interventions that can discriminate between a learner's hypotheses (i.e. possible causal structures). We compare this discriminatory model to a positive testing strategy that instead aims to confirm individual hypotheses. Experiment 1 shows that individual behavior is described best by a mixture of these two alternatives. In Experiment 2 we find that people are able to adaptively alter their behavior and adopt the discriminatory model more often after experiencing that the confirmatory strategy leads to a subjective performance decrement. In Experiment 3, time pressure leads to the opposite effect of inducing a change towards the simpler positive testing strategy. These findings suggest that there is no single strategy that describes how intervention decisions are made. Instead, people select strategies in an adaptive fashion that trades off their expected performance and cognitive effort. Copyright © 2015 Elsevier Inc. All rights reserved.

Exposure to and fear of terror as predictors of self-rated health among apparently healthy employees.

PubMed

Shirom, Arie; Toker, Sharon; Shapira, Itzhak; Berliner, Shlomo; Melamed, Samuel

2008-05-01

The effects of exposure to terror on physical health were investigated by relating objective exposure to terror and fear of terror to self-rated health (SRH), a proxy measure of health status. Our respondents were apparently healthy (N=4,877, 38% women) adults who completed self-report questionnaires. Objective exposure was assessed by the number of terrorist attacks and their casualties in a respondent's urban area prior to her/his completion of the questionnaire. Using several alternative assessments, objective exposure to terror did not predict SRH for both the genders. As hypothesized, fear of terror negatively predicted SRH for both females and males (beta=-0.04, -0.05, respectively). The effects of subjective and objective exposure were not found to be more pronounced among women relative to men, thus disconfirming our hypotheses in this regard. Our findings suggest that living under continuous fear of terror may adversely influence physical health irrespective of objective exposure.

Adaptive management for soil ecosystem services

USGS Publications Warehouse

Birge, Hannah E.; Bevans, Rebecca A.; Allen, Craig R.; Angeler, David G.; Baer, Sara G.; Wall, Diana H.

2016-01-01

Ecosystem services provided by soil include regulation of the atmosphere and climate, primary (including agricultural) production, waste processing, decomposition, nutrient conservation, water purification, erosion control, medical resources, pest control, and disease mitigation. The simultaneous production of these multiple services arises from complex interactions among diverse aboveground and belowground communities across multiple scales. When a system is mismanaged, non-linear and persistent losses in ecosystem services can arise. Adaptive management is an approach to management designed to reduce uncertainty as management proceeds. By developing alternative hypotheses, testing these hypotheses and adjusting management in response to outcomes, managers can probe dynamic mechanistic relationships among aboveground and belowground soil system components. In doing so, soil ecosystem services can be preserved and critical ecological thresholds avoided. Here, we present an adaptive management framework designed to reduce uncertainty surrounding the soil system, even when soil ecosystem services production is not the explicit management objective, so that managers can reach their management goals without undermining soil multifunctionality or contributing to an irreversible loss of soil ecosystem services.

Fusarium musae infected banana fruits as potential source of human fusariosis: May occur more frequently than we might think and hypotheses about infection

PubMed Central

Triest, David; Piérard, Denis; De Cremer, Koen; Hendrickx, Marijke

2016-01-01

ABSTRACT The banana fruit infecting fungus Fusarium musae was originally known as a distinct population within Fusarium verticillioides. However, recently, Fusarium musae was installed as a separate species and the first cases of human infection associated with Fusarium musae were found. In this article, we report an additional survey indicating that human pathogenic Fusarium musae infections may occur more frequently than we might think. Moreover, we evaluate the hypotheses on how infection can be acquired. A first hypothesis is that banana fruits act as carriers of Fusarium musae spores and thereby be the source of human infection with Fusarium musae. Acquisition is likely to be caused through contact with Fusarium musae contaminated banana fruits, either being imported or after traveling of the patient to a banana-producing country. An alternative hypothesis is that Fusarium musae is not only present on banana fruits, but also on other plant hosts or environmental sources. PMID:27195070

Continental monophyly of cichlid fishes and the phylogenetic position of Heterochromis multidens.

PubMed

Keck, Benjamin P; Hulsey, C Darrin

2014-04-01

The incredibly species-rich cichlid fish faunas of both the Neotropics and Africa are generally thought to be reciprocally monophyletic. However, the phylogenetic affinity of the African cichlid Heterochromis multidens is ambiguous, and this distinct lineage could make African cichlids paraphyletic. In past studies, Heterochromis has been variously suggested to be one of the earliest diverging lineages within either the Neotropical or the African cichlid radiations, and it has even been hypothesized to be the sister lineage to a clade containing all Neotropical and African cichlids. We examined the phylogenetic relationships among a representative sample of cichlids with a dataset of 29 nuclear loci to assess the support for the different hypotheses of the phylogenetic position of Heterochromis. Although individual gene trees in some instances supported alternative relationships, a majority of gene trees, integration of genes into species trees, and hypothesis testing of putative topologies all supported Heterochromis as belonging to the clade of African cichlids. Copyright © 2014 Elsevier Inc. All rights reserved.

Melanosomes or Microbes: Testing an Alternative Hypothesis for the Origin of Microbodies in Fossil Feathers

PubMed Central

Moyer, Alison E.; Zheng, Wenxia; Johnson, Elizabeth A.; Lamanna, Matthew C.; Li, Da-qing; Lacovara, Kenneth J.; Schweitzer, Mary H.

2014-01-01

Microbodies associated with fossil feathers, originally attributed to microbial biofilm, have been reinterpreted as melanosomes: pigment-containing, eukaryotic organelles. This interpretation generated hypotheses regarding coloration in non-avian and avian dinosaurs. Because melanosomes and microbes overlap in size, distribution and morphology, we re-evaluate both hypotheses. We compare melanosomes within feathers of extant chickens with patterns induced by microbial overgrowth on the same feathers, using scanning (SEM), field emission (FESEM) and transmission (TEM) electron microscopy. Melanosomes are always internal, embedded in a morphologically distinct keratinous matrix. Conversely, microbes grow across the surface of feathers in continuous layers, more consistent with published images from fossil feathers. We compare our results to both published literature and new data from a fossil feather ascribed to Gansus yumenensis (ANSP 23403). ‘Mouldic impressions’ were observed in association with both the feather and sediment grains, supporting a microbial origin. We propose criteria for distinguishing between these two microbodies. PMID:24595214

Process tracing in political science: What's the story?

PubMed

Crasnow, Sharon

2017-04-01

Methodologists in political science have advocated for causal process tracing as a way of providing evidence for causal mechanisms. Recent analyses of the method have sought to provide more rigorous accounts of how it provides such evidence. These accounts have focused on the role of process tracing for causal inference and specifically on the way it can be used with case studies for testing hypotheses. While the analyses do provide an account of such testing, they pay little attention to the narrative elements of case studies. I argue that the role of narrative in case studies is not merely incidental. Narrative does cognitive work by both facilitating the consideration of alternative hypotheses and clarifying the relationship between evidence and explanation. I consider the use of process tracing in a particular case (the Fashoda Incident) in order to illustrate the role of narrative. I argue that process tracing contributes to knowledge production in ways that the current focus on inference tends to obscure. Copyright © 2017 Elsevier Ltd. All rights reserved.

Towards an Enhanced Understanding of Plant–Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism

PubMed Central

Thijs, Sofie; Sillen, Wouter; Rineau, Francois; Weyens, Nele; Vangronsveld, Jaco

2016-01-01

Phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. However, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant–microbe interactions is needed. A number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely understood. Moreover, current approaches that target the plant host, and environment separately to improve phytoremediation, potentially overlook microbial functions and properties that are part of the multiscale complexity of the plant-environment wherein biodegradation takes place. In contrast, in situ studies of phytoremediation research at the metaorganism level (host and microbiome together) are lacking. Here, we discuss a competition-driven model, based on recent evidence from the metagenomics level, and hypotheses generated by microbial community ecology, to explain the establishment of a catabolic rhizosphere microbiome in a contaminated soil. There is evidence to ground that if the host provides the right level and mix of resources (exudates) over which the microbes can compete, then a competitive catabolic and plant-growth promoting (PGP) microbiome can be selected for as long as it provides a competitive superiority in the niche. The competition-driven model indicates four strategies to interfere with the microbiome. Specifically, the rhizosphere microbiome community can be shifted using treatments that alter the host, resources, environment, and that take advantage of prioritization in inoculation. Our model and suggestions, considering the metaorganism in its natural context, would allow to gain further knowledge on the plant–microbial functions, and facilitate translation to more effective, and predictable phytotechnologies. PMID:27014254

Dementia: treating patients and caregivers with complementary and alternative medicine--results of a clinical expert conference using the World Café method.

PubMed

Teut, Michael; Bloedt, Susanne; Baur, Roland; Betsch, Frederik; Elies, Michael; Fruehwald, Maria; Fuesgen, Ingo; Kerckhoff, Annette; Krüger, Eckard; Schimpf, Dorothee; Schnabel, Katharina; Walach, Harald; Warme, Britta; Warning, Albercht; Wilkens, Johannes; Witt, Claudia M

2013-01-01

In Germany the number of inhabitants with dementia is expected to increase from 1.2 million at present to 2.3 million in 2050. Our aim was to investigate which treatments complementary and alternative medicine (CAM) experts consider to be of therapeutic use in developing treatment strategies and hypotheses for further clinical studies. In a participatory group workshop the 'World Café' method was used. As questions we asked: 1) 'Based on your clinical experience, which CAM therapies are effective in the treatment of patients with dementia? 2) Based on your clinical experience, which CAM therapies are effective in the treatment of lay and professional caregivers of patients with dementia?, and 3) How should a CAM treatment program look like?' Further Delphi rounds were used to reach consensus and summarize the results. The 2-day workshop took place in January 2012 in Berlin. A total of 17 experts participated. The most important subject in the treatment was the need to understand patients' biographies in order to individualize the therapy. Therapy itself consists of the therapeutic relationship, nonmedical therapies such as sports, massage, music and arts therapy as well as medical treatment such as herbal or homeopathic medicines. With regard to caregivers the most important aim is to prevent or reduce psychological distress, e.g., by mind-body programs. Instead of single treatments, more general elements such as understanding the patients' biographies, therapeutic relationships, individualizing, networking, and self-care emerged as main results. An integrative treatment program should connect outpatient and inpatient care as well as all experts. CAM training courses should be offered to doctors, nurses, and caregivers. Future clinical studies should focus on complex intervention programs integrating these key elements. © 2013 S. Karger GmbH, Freiburg.

Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation

PubMed Central

Romero-Severson, Ethan O.; Bulla, Ingo; Hengartner, Nick; Bártolo, Inês; Abecasis, Ana; Azevedo-Pereira, José M.; Taveira, Nuno; Leitner, Thomas

2017-01-01

Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections, there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods, and the reconstruction of epidemiologic histories. To infer who-infected-whom, and to compute the probability of alternative transmission scenarios while explicitly taking phylogenetic uncertainty into account, we created an approximate Bayesian computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity. We applied our method to a suspected heterosexual transmission case involving three individuals, showing a complex monophyletic-paraphyletic-polyphyletic phylogenetic topology. We detected that seven phylogenetic lineages had been transmitted between two of the individuals based on the available samples, implying that many more unsampled lineages had also been transmitted. Testing whether the lineages had been transmitted at one time or over some length of time suggested that an ongoing superinfection process over several years was most likely. While one individual was found unlinked to the other two, surprisingly, when evaluating two competing epidemiological priors, the donor of the two that did infect each other was not identified by the host root-label, and was also not the primary suspect in that transmission. This highlights that it is important to take epidemiological information into account when analyzing support for one transmission hypothesis over another, as results may be nonintuitive and sensitive to details about sampling dates relative to possible infection dates. Our study provides a formal inference framework to include information on infection and sampling times, and to investigate ancestral node-label states, transmission direction, transmitted genetic diversity, and frequency of transmission. PMID:28912340

Satellite image-based maps: Scientific inference or pretty pictures?

Treesearch

Ronald E. McRoberts

2011-01-01

The scientific method has been characterized as having two distinct components, Discovery and Justification. Discovery emphasizes ideas and creativity, focuses on conceiving hypotheses and constructing models, and is generally regarded as lacking a formal logic. Justification begins with the hypotheses and models and ends with a...

How Quickly Do They React?

ERIC Educational Resources Information Center

Ortolano, Girolamo; Finn, Julia; Ortolano, Leonard

2017-01-01

In this activity, students learned scientific practices and evidence-based reasoning by formulating and testing hypotheses about factors affecting human reaction time and examining those hypotheses with data from ruler-drop tests. The project aligns with all eight of the science and engineering practices (SEP) embodied in the "Next Generation…

Darwinism, not mutationism, explains the design of organisms.

PubMed

Gardner, Andy

2013-04-01

Shapiro claims that advances in molecular genetics have undermined Darwinism, leading him to advocate mutationism. However, this extreme view is bourne out of conceptual error. He has misunderstood the distinction between gradualism and saltationism, which do not concern the rate of genetic change, but rather the emergence of complex design. And he has misunderstood the relationship between the dynamics of natural selection and the agency of individual organisms: these are not competing hypotheses, but rather alternative conceptualizations of the same phenomenon. Copyright © 2012 Elsevier Ltd. All rights reserved.

Forgiveness and justice: a research agenda for social and personality psychology.

PubMed

Exline, Julie Juola; Worthington, Everett L; Hill, Peter; McCullough, Michael E

2003-01-01

Forgiveness and related constructs (e.g., repentance, mercy, reconciliation) are ripe for study by social and personality psychologists, including those interested in justice. Current trends in social science, law, management, philosophy, and theology suggest a need to expand existing justice frameworks to incorporate alternatives or complements to retribution, including forgiveness and related processes. In this article, we raise five challenging empirical questions about forgiveness. For each question, we briefly review representative research, raise hypotheses, and suggest specific ways in which social and personality psychologists could make distinctive contributions.

A Systems Approach to the Physiology of Weightlessness

NASA Technical Reports Server (NTRS)

White, Ronald J.; Leonard, Joel I.; Rummel, John A.; Leach, Carolyn S.

1991-01-01

A systems approach to the unraveling of the complex response pattern of the human subjected to weightlessness is presented. The major goal of this research is to obtain an understanding of the role that each of the major components of the human system plays following the transition to and from space. The cornerstone of this approach is the utilization of a variety of mathematical models in order to pose and test alternative hypotheses concerned with the adaptation process. An integrated hypothesis for the human physiological response to weightlessness is developed.

Adaptive displays and controllers using alternative feedback.

PubMed

Repperger, D W

2004-12-01

Investigations on the design of haptic (force reflecting joystick or force display) controllers were conducted by viewing the display of force information within the context of several different paradigms. First, using analogies from electrical and mechanical systems, certain schemes of the haptic interface were hypothesized which may improve the human-machine interaction with respect to various criteria. A discussion is given on how this interaction benefits the electrical and mechanical system. To generalize this concept to the design of human-machine interfaces, three studies with haptic mechanisms were then synthesized and analyzed.

Switching skeletons: hydrostatic support in molting crabs

NASA Technical Reports Server (NTRS)

Taylor, Jennifer R A.; Kier, William M.; Walker, I. D. (Principal Investigator)

2003-01-01

Skeletal support systems are essential for support, movement, muscular antagonism, and locomotion. Crustaceans shed their rigid exoskeleton at each molt yet are still capable of forceful movement. We hypothesize that the soft water-inflated body of newly molted crabs may rely on a hydrostatic skeleton, similar to that of worms and polyps. We measured internal hydrostatic pressure and the force exerted during claw adduction and observed a strong correlation between force and hydrostatic pressure, consistent with hydrostatic skeletal support. This alternation between the two basic skeletal types may be widespread among arthropods.

Involvement of the arcuate nucleus of the hypothalamus in interleukin-1-induced anorexia.

PubMed

Reyes, Teresa M; Sawchenko, Paul E

2002-06-15

Cytokine-mediated anorexia is a component of "sickness behavior" and presents a significant obstacle in the treatment of chronic illnesses. We hypothesized an involvement of the hypothalamic arcuate nucleus (ARH) in mediating the anorexic effects of a systemic interleukin-1 (IL-1) challenge based on its content of peptidergic neurons involved in feeding, its expression of IL-1 receptors and its sensitivity to systemic IL-1. IL-1 (6 microg/kg, i.v.) was found to induce Fos expression in both pro-opiomelanocortin- and neuropeptide Y-expressing neurons in and around the ARH. Contrary to expectations, rats that had sustained lesions of the arcuate nucleus, produced by neonatal monosodium glutamate treatment, displayed a more pronounced suppression (by 25%) of food intake than nonlesioned controls when treated with IL-1 after a 20 hr fast. To confirm and further characterize this unexpected result, a second ablation method was used in a similar paradigm. Animals bearing knife cuts designed to sever major ARH projections displayed an even more accentuated loss of appetite (by 60%, relative to controls) in response to systemic IL-1. This effect exhibited at least some degree of specificity, because the knife cuts did not alter either IL-1 effects on another centrally mediated acute phase response (fever) or the anorexia produced by an alternate agent, fenfluramine. These results fail to support the hypothesized ARH mediation of IL-1-induced anorexia and may suggest rather that the net output of this cell group may serve normally to restrain cytokine-induced reductions in food intake.

The three-hit concept of vulnerability and resilience: towards understanding adaptation to early-life adversity outcome

PubMed Central

Daskalakis, Nikolaos P.; Bagot, Rosemary C.; Parker, Karen J.; Vinkers, Christiaan H.; de Kloet, E. R.

2013-01-01

Stressful experiences during early-life can modulate the genetic programming of specific brain circuits underlying emotional and cognitive aspects of behavioral adaptation to stressful experiences later in life. Although this programming effect exerted by experience-related factors is an important determinant of mental health, its outcome depends on cognitive inputs and hence the valence an individual assigns to a given environmental context. From this perspective we will highlight, with studies in rodents, non-human primates and humans, the three-hit concept of vulnerability and resilience to stress-related mental disorders, which is based on gene-environment interactions during critical phases of perinatal and juvenile brain development. The three-hit (i.e., hit-1: genetic predisposition, hit-2: early-life environment, and hit-3: later-life environment) concept accommodates the cumulative stress hypothesis stating that in a given context vulnerability is enhanced when failure to cope with adversity accumulates. Alternatively, the concept also points to the individual’s predictive adaptive capacity, which underlies the stress inoculation and match/mismatch hypotheses. The latter hypotheses propose that the experience of relatively mild early-life adversity prepares for the future and promotes resilience to similar challenges in later-life; when a mismatch occurs between early and later-life experience, coping is compromised and vulnerability is enhanced. The three-hit concept is fundamental for understanding how individuals can either be prepared for coping with life to come and remain resilient or are unable to do so and succumb to a stress-related mental disorder, under seemingly identical circumstances. PMID:23838101

Thumbs down: a molecular-morphogenetic approach to avian digit homology.

PubMed

Capek, Daniel; Metscher, Brian D; Müller, Gerd B

2014-01-01

Avian forelimb digit homology remains one of the standard themes in comparative biology and EvoDevo research. In order to resolve the apparent contradictions between embryological and paleontological evidence a variety of hypotheses have been presented in recent years. The proposals range from excluding birds from the dinosaur clade, to assignments of homology by different criteria, or even assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail: the frame shift hypothesis and the pyramid reduction hypothesis. While the former postulates a homeotic shift of digit identities, the latter argues for a gradual bilateral reduction of phalanges and digits. Here we present a new model that integrates elements from both hypotheses with the existing experimental and fossil evidence. We start from the main feature common to both earlier concepts, the initiating ontogenetic event: reduction and loss of the anterior-most digit. It is proposed that a concerted mechanism of molecular regulation and developmental mechanics is capable of shifting the boundaries of hoxD expression in embryonic forelimb buds as well as changing the digit phenotypes. Based on a distinction between positional (topological) and compositional (phenotypic) homology criteria, we argue that the identity of the avian digits is II, III, IV, despite a partially altered phenotype. Finally, we introduce an alternative digit reduction scheme that reconciles the current fossil evidence with the presented molecular-morphogenetic model. Our approach identifies specific experiments that allow to test whether gene expression can be shifted and digit phenotypes can be altered by induced digit loss or digit gain. © 2013 Wiley Periodicals, Inc.

Pollinator shifts as triggers of speciation in painted petal irises (Lapeirousia: Iridaceae)

PubMed Central

Forest, Félix; Goldblatt, Peter; Manning, John C.; Baker, David; Colville, Jonathan F.; Devey, Dion S.; Jose, Sarah; Kaye, Maria; Buerki, Sven

2014-01-01

Background and Aims Adaptation to different pollinators has been hypothesized as one of the main factors promoting the formation of new species in the Cape region of South Africa. Other researchers favour alternative causes such as shifts in edaphic preferences. Using a phylogenetic framework and taking into consideration the biogeographical scenario explaining the distribution of the group as well as the distribution of pollinators, this study compares pollination strategies with substrate adaptations to develop hypotheses of the primary factors leading to speciation in Lapeirousia (Iridaceae), a genus of corm-bearing geophytes well represented in the Cape and presenting an important diversity of pollination syndromes and edaphic preferences. Methods Phylogenetic relationships are reconstructed within Lapeirousia using nuclear and plastid DNA sequence data. State-of-the-art methods in biogeography, divergence time estimation, character optimization and diversification rate assessments are used to examine the evolution of pollination syndromes and substrate shifts in the history of the group. Based on the phylogenetic results, ecological factors are compared for nine sister species pairs in Lapeirousia. Key Results Seventeen pollinator shifts and ten changes in substrate types were inferred during the evolution of the genus Lapeirousia. Of the nine species pairs examined, all show divergence in pollination syndromes, while only four pairs present different substrate types. Conclusions The available evidence points to a predominant influence of pollinator shifts over substrate types on the speciation process within Lapeirousia, contrary to previous studies that favoured a more important role for edaphic factors in these processes. This work also highlights the importance of biogeographical patterns in the study of pollination syndromes. PMID:24323246

The three-hit concept of vulnerability and resilience: toward understanding adaptation to early-life adversity outcome.

PubMed

Daskalakis, Nikolaos P; Bagot, Rosemary C; Parker, Karen J; Vinkers, Christiaan H; de Kloet, E R

2013-09-01

Stressful experiences during early-life can modulate the genetic programming of specific brain circuits underlying emotional and cognitive aspects of behavioral adaptation to stressful experiences later in life. Although this programming effect exerted by experience-related factors is an important determinant of mental health, its outcome depends on cognitive inputs and hence the valence an individual assigns to a given environmental context. From this perspective we will highlight, with studies in rodents, non-human primates and humans, the three-hit concept of vulnerability and resilience to stress-related mental disorders, which is based on gene-environment interactions during critical phases of perinatal and juvenile brain development. The three-hit (i.e., hit-1: genetic predisposition, hit-2: early-life environment, and hit-3: later-life environment) concept accommodates the cumulative stress hypothesis stating that in a given context vulnerability is enhanced when failure to cope with adversity accumulates. Alternatively, the concept also points to the individual's predictive adaptive capacity, which underlies the stress inoculation and match/mismatch hypotheses. The latter hypotheses propose that the experience of relatively mild early-life adversity prepares for the future and promotes resilience to similar challenges in later-life; when a mismatch occurs between early and later-life experience, coping is compromised and vulnerability is enhanced. The three-hit concept is fundamental for understanding how individuals can either be prepared for coping with life to come and remain resilient or are unable to do so and succumb to a stress-related mental disorder, under seemingly identical circumstances. Copyright © 2013 Elsevier Ltd. All rights reserved.

Conflicting patterns of genetic structure produced by nuclear and mitochondrial markers in the Oregon Slender Salamander (Batrachoseps wrighti): implications for conservation efforts and species management

USGS Publications Warehouse

Miller, Mark; Haig, Susan M.; Wagner, R.S.

2005-01-01

Endemic to Oregon in the northwestern US, the Oregon slender salamander (Batrachoseps wrighti) is a terrestrial plethodontid found associated with late successional mesic forests. Consequently, forest management practices such as timber harvesting may impact their persistence. Therefore, to infer possible future effects of these practices on population structure and differentiation, we used mitochondrial DNA sequences (cytochrome b) and RAPD markers to analyze 22 populations across their range. Phylogenetic analyses of sequence data (774 bp) revealed two historical lineages corresponding to northern and southern-distributed populations. Relationships among haplotypes and haplotype diversity within lineages suggested that the northern region may have more recently been colonized compared to the southern region. In contrast to the mitochondrial data, analyses of 46 RAPD loci suggested an overall pattern of isolation-by-distance in the set of populations examined and no particularly strong clustering of populations based on genetic distances. We propose two non-exclusive hypotheses to account for discrepancies between mitochondrial and nuclear data sets. First, our data may reflect an overall ancestral pattern of isolation-by-distance that has subsequently been influenced by vicariance. Alternately, our analyses may suggest that male-mediated gene flow and female philopatry are important contributors to the pattern of genetic diversity. We discuss the importance of distinguishing between these two hypotheses for the purposes of identifying conservation units and note that, regardless of the relative contribution of each mechanism towards the observed pattern of diversity, protection of habitat will likely prove critical for the long-term persistence of this species.

Activation of plantar flexor muscles is constrained by multiple muscle synergies rather than joint torques

PubMed Central

Suzuki, Takahito; Kinugasa, Ryuta; Fukashiro, Senshi

2017-01-01

Behavioral evidence has suggested that a small number of muscle synergies may be responsible for activating a variety of muscles. Nevertheless, such dimensionality reduction may also be explained using the perspective of alternative hypotheses, such as predictions based on linear combinations of joint torques multiplied by corresponding coefficients. To compare the explanatory capacity of these hypotheses for describing muscle activation, we enrolled 12 male volunteers who performed isometric plantar flexor contractions at 10–100% of maximum effort. During each plantar flexor contraction, the knee extensor muscles were isometrically contracted at 0%, 50%, or 100% of maximum effort. Electromyographic activity was recorded from the vastus lateralis, medial gastrocnemius (MG), lateral gastrocnemius (LG), and soleus muscles and quantified using the average rectified value (ARV). At lower plantar flexion torque, regression analysis identified a clear linear relationship between the MG and soleus ARVs and between the MG and LG ARVs, suggesting the presence of muscle synergy (r2 > 0.65). The contraction of the knee extensor muscles induced a significant change in the slope of this relationship for both pairs of muscles (MG × soleus, P = 0.002; MG × LG, P = 0.006). Similarly, the slope of the linear relationship between the plantar flexion torque and the ARV of the MG or soleus changed significantly with knee extensor contraction (P = 0.031 and P = 0.041, respectively). These results suggest that muscle synergies characterized by non-mechanical constraints are selectively recruited according to whether contraction of the knee extensor muscles is performed simultaneously, which is relatively consistent with the muscle synergy hypothesis. PMID:29107958

An analytical approach for estimating fossil record and diversification events in sharks, skates and rays.

PubMed

Guinot, Guillaume; Adnet, Sylvain; Cappetta, Henri

2012-01-01

Modern selachians and their supposed sister group (hybodont sharks) have a long and successful evolutionary history. Yet, although selachian remains are considered relatively common in the fossil record in comparison with other marine vertebrates, little is known about the quality of their fossil record. Similarly, only a few works based on specific time intervals have attempted to identify major events that marked the evolutionary history of this group. Phylogenetic hypotheses concerning modern selachians' interrelationships are numerous but differ significantly and no consensus has been found. The aim of the present study is to take advantage of the range of recent phylogenetic hypotheses in order to assess the fit of the selachian fossil record to phylogenies, according to two different branching methods. Compilation of these data allowed the inference of an estimated range of diversity through time and evolutionary events that marked this group over the past 300 Ma are identified. Results indicate that with the exception of high taxonomic ranks (orders), the selachian fossil record is by far imperfect, particularly for generic and post-Triassic data. Timing and amplitude of the various identified events that marked the selachian evolutionary history are discussed. Some identified diversity events were mentioned in previous works using alternative methods (Early Jurassic, mid-Cretaceous, K/T boundary and late Paleogene diversity drops), thus reinforcing the efficiency of the methodology presented here in inferring evolutionary events. Other events (Permian/Triassic, Early and Late Cretaceous diversifications; Triassic/Jurassic extinction) are newly identified. Relationships between these events and paleoenvironmental characteristics and other groups' evolutionary history are proposed.

Moving away from a cultural deficit to a holistic perspective: Traditional gender role values, academic attitudes, and educational goals for Mexican descent adolescents.

PubMed

Piña-Watson, Brandy; Lorenzo-Blanco, Elma I; Dornhecker, Marianela; Martinez, Ashley J; Nagoshi, Julie L

2016-04-01

Latina/o youth lag behind Asian American and non-Latina/o White youth in many academic areas. Previous research has taken a deficit approach to understand the factors that affect academic outcomes for Latina/o youth often neglecting to highlight both the potential positive and negative contributions of gender role values. The present study took a holistic perspective to understand the affect of traditional Latina/o gender role values (i.e., marianismo, machismo, and caballerismo) on the academic attitudes and educational goals of Mexican descent youth. Structural equation models were tested to examine the associations of "positive" and "negative" gender role values on educational goals using 524 Mexican descent adolescents from a mid-sized city in southern Texas. We hypothesized that positive aspects of traditional Latina/o gender role values (i.e., "positive marianismo" and caballerismo) would be associated with more positive attitudes toward academics and higher educational goals. We further expected negative gender role values (i.e., "negative marianismo" and machismo) to have the opposite effect. Additionally, based on the theory of planned behavior and gender schema theory, academic attitudes were hypothesized to mediate the relation between gender role values and educational goals. An alternative model was tested in which educational goals mediated the relation between gender roles and academic attitudes. Results indicated that both models fit the data well, and recommendations are made for future longitudinal research aimed at disentangling the directionality of the relations in the model. Implications for research and practice are discussed. (c) 2016 APA, all rights reserved).

Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship.

PubMed

Brunet, Marie A; Levesque, Sébastien A; Hunting, Darel J; Cohen, Alan A; Roucou, Xavier

2018-05-01

Technological advances promise unprecedented opportunities for whole exome sequencing and proteomic analyses of populations. Currently, data from genome and exome sequencing or proteomic studies are searched against reference genome annotations. This provides the foundation for research and clinical screening for genetic causes of pathologies. However, current genome annotations substantially underestimate the proteomic information encoded within a gene. Numerous studies have now demonstrated the expression and function of alternative (mainly small, sometimes overlapping) ORFs within mature gene transcripts. This has important consequences for the correlation of phenotypes and genotypes. Most alternative ORFs are not yet annotated because of a lack of evidence, and this absence from databases precludes their detection by standard proteomic methods, such as mass spectrometry. Here, we demonstrate how current approaches tend to overlook alternative ORFs, hindering the discovery of new genetic drivers and fundamental research. We discuss available tools and techniques to improve identification of proteins from alternative ORFs and finally suggest a novel annotation system to permit a more complete representation of the transcriptomic and proteomic information contained within a gene. Given the crucial challenge of distinguishing functional ORFs from random ones, the suggested pipeline emphasizes both experimental data and conservation signatures. The addition of alternative ORFs in databases will render identification less serendipitous and advance the pace of research and genomic knowledge. This review highlights the urgent medical and research need to incorporate alternative ORFs in current genome annotations and thus permit their inclusion in hypotheses and models, which relate phenotypes and genotypes. © 2018 Brunet et al.; Published by Cold Spring Harbor Laboratory Press.

Reflective questions in health counseling.

PubMed

Poskiparta, M; Kettunen, T; Liimatainen, L

1998-09-01

This study explores questions that nurses ask patients in order to awaken reflection on their health behavior in health counseling. Thirty-eight counseling situations were videotaped in a hospital. The data were analyzed using conversation analysis which was adapted for the purpose of this study. Nonverbal communication supported speech and was interpreted alongside it. This study found that nurses used only a few reflective questions, most of which were future-oriented or introduced hypotheses. In a nonreflective discussion, nurses used only check-up and alternative questions to get information about patients' illnesses and health care measures. Findings indicated that reflective conversation began with check-up questions about patients' immediate situation, followed by questions about patients' feelings in the past, present, or future. On the third level of questioning, the structure might vary between embedded questions, check-up, alternative, or feeling questions. Nonverbal communication supported the discussion. Reflective questions tended to ensure patient-centered conversation and might improve the effectiveness of health counselling.