Qualitative Hypotheses Research Articles

Current oscillations in the course of birnessite electrodeposition as related to resulting microstructure: experimental manifestations and qualitative hypotheses

Current oscillations in the course of birnessite electrodeposition as related to resulting microstructure: experimental manifestations and qualitative hypotheses

Vascular Cambium—Between the Hammer and the Anvil: A Tensile Stress Hypothesis on the Mechanism of Radial Growth of Broadleaved Trees

The vascular cambium is the main lateral meristem responsible for the secondary growth of trees. There are a number of explicit and implicit assumptions behind this statement which allow questions to be raised about the mechanism underlying the radial growth of trees. Based on the hypothesis of the diurnal strains of plant organs, it is anticipated that the process of radial growth can be understood as an adaptation to the cyclically changing mechanical stress in the radial direction generated by the phloem during the 24 h day cycle. This qualitative hypothesis treats cambium as a tissue subjected to nighttime stretching and daytime compression in the radial direction. The proposed osmo-mechanical hypothesis of the radial growth of vascular cambium links the daily change in water status and the considerable daily strains in the xylem and phloem with the radial net expansion of a tree trunk. We highlight transpiration as a major factor influencing the secondary growth of woody plants. Thus, we indirectly relate all the biotic (e.g., insect infestation, fungi infections, injuries, shadowing, intra- and interspecies competition, parasitism, symbiosis, etc.) and abiotic (e.g., humidity, water availability, wind, injuries, shadowing, day length in a vegetative season, altitude, temperature, insolation, etc.) processes influencing transpiration with radial growth. In the proposed hypothesis, we also infer that differences in the strains in phloem and xylem are the direct source of tensile stress, tensile stress relaxation, compressive stress, and compressive stress relaxation in the vascular cambium. This sequence appears to be crucial in understanding both the process of the radial growth of trees and the formation of differential wood patterns, within the same genotype as well as in different genotypes. It also provides arguments for the discussion on the mechanisms regulating processes in the vascular cambium. It points out the important role of the variable mechanical stresses in the radial, circumferential, and axial directions and their interference in the development of this lateral meristem. Thus, this hypothesis supports the concept of the epigenetic and systemic regulation of intrinsic wood patterns and tree forms by environmental factors. The hypothesis is focused exclusively on broadleaved trees and symplastic growth. This limitation of the scope is due to a concern for clarity. In this form, the hypothesis provides an alternative explanation for a pure process of radial growth and paves the way for a better interpretation of such phenomena as earlywood and latewood formation. At the same time, this approach to the vascular cambium provides answers to many questions related to the generation of the mechanical conditions necessary for the occurrence of intrusive growth between tangential cell walls; this is of fundamental importance for fusiform initials readjustment, vessel element and fibre formation, ring-porous wood formation, etc.

Abstract P650: Addressing Cardiovascular Disease Inequities: Qualitative Process Evaluation From a Co-Investigation With Im/Migrants Exploring How to Sustain a Community-Driven, Social Network Intervention Using a Racism-Conscious Approach

Introduction: Health promotion programs focused on cardiovascular disease are underutilized with im/migrants. The one-time referral to group-based interventions model ignores (1) the complex sociocultural influences on behavior change and (2) the socio-historical context of migration, racialization of immigrants and refugees, and the roles these play in differential social integration of refugees. One solution may be to apply community-based participatory research (CBPR) and Public Health Critical Race Praxis (PHCRP) to social network interventions with opinion leaders. Yet, these interventions are challenging to scale. There is a critical need to understand how to scale community-driven social network interventions to effectively address cardiovascular disease inequities resulting from systemic racism experienced by im/migrant populations. Developed using CBPR and informed by PHCRP, this work builds upon Healthy Immigrant Community (HIC), a collaborative effort between Latinx and Somali im/migrant partners and Rochester Healthy Community Partnership. Our aim is to explore opinion leader recruitment, their characteristics, and expectations for HIC scale-up. Qualitative Hypothesis: Learning more about the opinion leaders’ background and experience in the Healthy Immigrant Community social network intervention will prepare us for a future efficacy study. Methods: We conducted a process evaluation by: (1) interviewing community partners who recruited opinion leaders (n=8) and (2) conducting three pre-intervention focus groups with opinion leaders (Latinx n=4; Somali women n=8; Somali men n=8). We used PHCRP to deductively form codes yet allowed for new ideas that arose from the data by inductively generating additional codes. Results: Interview participants described their decision-making process, qualities considered, recruitment strategies, and expectations for an implementation study. Focus group participants discussed their personal motivations for participation, how they hoped the study would help their community, and the barriers to health they experience because of structural determinism (macro-level forces that sustain inequities). Conclusions: This work will enhance our ability to translate HIC to other communities by expanding our knowledge of opinion leader characteristics that are important in a community-driven, social network intervention. Because social network interventions have been demonstrated to cause positive behavior change, further adapting these interventions in a community setting would be expected to provide a more effective approach compared to individually targeted behavior change strategies. Additionally, selecting OLs is neither time nor resource intensive and could enhance organizational strategies for implementing health promotion programming.

A novel specimen-based mid-Paleozoic dataset of antiarch placoderms (the most basal jawed vertebrates)

Abstract. Antiarcha data are essential to quantitative studies of basal jawed vertebrates. The absence of structured data on key groups of early vertebrates, such as Antiarcha, has lagged in understanding their diversity and distribution patterns. Previous works of early vertebrates usually focused on anatomy and phylogeny, given their significant impacts on the evolution of key characters, but lacked comprehensive structured data. Here, we contribute an unprecedented open-access Antiarcha dataset covering 60 genera of 6025 specimens from the Ludfordian to the Famennian globally. We have organized an expert team to collect and curate 142 publications spanning from 1939 to 2021. Additionally, we have two-stage quality controls in the process: domain experts examined the literature and senior experts reviewed the results. In this paper, we give details of the data storage structure and visualize these antiarch fossil sites on the paleogeographic map. The novel Antiarcha dataset has tremendous research potential, including testing previous qualitative hypotheses in biodiversity changes, spatiotemporal distribution, evolution, and community composition. It is now an essential part of the DeepBone database and will be updated with the latest publication, also available on https://doi.org/10.5281/zenodo.6536446 (Pan and Zhu, 2021).

NETWORK DIFFERENTIAL CONNECTIVITY ANALYSIS.

Identifying differences in networks has become a canonical problem in many biological applications. Existing methods try to accomplish this goal by either directly comparing the estimated structures of two networks, or testing the null hypothesis that the covariance or inverse covariance matrices in two populations are identical. However, estimation approaches do not provide measures of uncertainty, e.g., p-values, whereas existing testing approaches could lead to misleading results, as we illustrate in this paper. To address these shortcomings, we propose a qualitative hypothesis testing framework, which tests whether the connectivity structures in the two networks are the same. our framework is especially appropriate if the goal is to identify nodes or edges that are differentially connected. No existing approach could test such hypotheses and provide corresponding measures of uncertainty. Theoretically, we show that under appropriate conditions, our proposal correctly controls the type-I error rate in testing the qualitative hypothesis. Empirically, we demonstrate the performance of our proposal using simulation studies and applications in cancer genomics.

Multiphase Coexistences in Rod-Polymer Mixtures.

Using recently derived analytical equations of state for hard rod dispersions, we predict the phase behavior of athermal rod–polymer mixtures with free volume theory. The rods are modeled as hard spherocylinders, while the nonadsorbing polymer chains are described as penetrable hard spheres. It is demonstrated that all of the different types of phase states that are stable for pure colloidal rod dispersions can coexist with any combination of these phases if polymers are added, depending on the concentrations, rod aspect ratio, and polymer–rod size ratio. This includes novel two-, three-, and four-phase coexistences and isostructural coexistences between dilute and concentrated phases of the same kind, even for the more ordered (liquid) crystal phases. This work provides insight into the conditions at which particular multiphase coexistences are expected for well-defined model colloidal rod–polymer mixtures. We provide a quantitative map detailing the various types of isostructural coexistences, which confirms an early qualitative hypothesis by Bolhuis et al. (J. Chem. Phys.107, 19971551).

Host-pathogen immune feedbacks can explain widely divergent outcomes from similar infections.

A long-standing question in infection biology is why two very similar individuals, with very similar pathogen exposures, may have very different outcomes. Recent experiments have found that even isogenic Drosophila melanogaster hosts, given identical inoculations of some bacterial pathogens at suitable doses, can experience very similar initial bacteria proliferation but then diverge to either a lethal infection or a sustained chronic infection with much lower pathogen load. We hypothesized that divergent infection outcomes are a natural result of mutual negative feedbacks between pathogens and the host immune response. Here, we test this hypothesis in silico by constructing process-based dynamic models for bacterial population growth, host immune induction and the feedbacks between them, based on common mechanisms of immune system response. Mathematical analysis of a minimal conceptual model confirms our qualitative hypothesis that mutual negative feedbacks can magnify small differences among hosts into life-or-death differences in outcome. However, explaining observed features of chronic infections requires an extension of the model to include induced pathogen modifications that shield themselves from host immune responses at the cost of reduced proliferation rate. Our analysis thus generates new, testable predictions about the mechanisms underlying bimodal infection outcomes.

Mechanisms of Partial Melting of Metasomatized Mantle Ultramafic Rocks beneath Avacha Volcano, Kamchatka, and the Growth of Minerals from a Gas Phase in Fractures

Data on xenoliths carried by lavas of Avacha volcano and ejected during eruptions are used in discussing the partial melting of metasomatized rocks of the lithospheric mantle (which were tectonically reformed by seismic events beneath the frontal zone of Avacha volcano) and the associated growth of minerals from a gas phase in open fractures above the magma chamber feeding the volcano. Based on a comprehensive study of representative mantle xenoliths from explosions of the volcano, we developed and numerically studied a mathematical model of convective heat and mass transfer in the permeable zone above the feeding magma chamber. The model enables analysis of the area of active seismic destruction of rocks at depths of 30–70 km beneath Avacha volcano. This analysis involves (1) current qualitative genetic hypotheses concerning the nature of the identified textural and structural relationships between the xenoliths and lavas transporting them, (2) data on the composition of mineral-hosted fluid and melt inclusions, (3) estimated homogenization temperatures of the inclusions, and (4) hypothetical melting mechanisms of metasomatized ultramafics and the associated growth mechanism of minerals in open fractures. It is demonstrated that fractured porous seismogenic regions above magma chambers are coupled with a set of convective processes of fluid-mediated heterophase heat and mass transfer in the lithosphere: infiltration metasomatism at the spinel depth facies and the sublimation and condensation of major components from a gas phase. It is hypothesized that local partial decompression melting of highly heated ultramafic and mafic rocks may be followed by major seismic events. It is shown that spinel-facies infiltration metasomatism in fractured mantle rocks may be associated with the growth of crystal crusts and clusters of clinopyroxene and amphibole from a gas phase in open fractures. There are two paths by which decompression partial melting takes place: (1) the melting of spinel aggregates with the host crystals of “metasomatic” orthopyroxene, which replaced olivine in harzburgites, and (2) the development of clinopyroxene, amphibole, and relict orthopyroxene vein fillings. To test these hypotheses, physical experiments were conducted with the use of convective heating of samples of natural xenoliths. The experiments were carried out in a flow-through reactor capable of reproducing the partial melting phenomena and in an electron gun with a power unit for a welding system with a dense electron beam. The latter experiments simulated the sublimation and deposition of major components from a gas phase over the solidus boundary for all petrographic types of mantle ultramafic rocks. Neither structural nor mineralogical indications of the infiltration of magmatic fluid were detected in the experiments, and no traces of diffusion–reaction zoning of the “melt–rock” type were found in the xenoliths.

3D hindlimb joint mobility of the stem-archosaur Euparkeria capensis with implications for postural evolution within Archosauria

Triassic archosaurs and stem-archosaurs show a remarkable disparity in their ankle and pelvis morphologies. However, the implications of these different morphologies for specific functions are still poorly understood. Here, we present the first quantitative analysis into the locomotor abilities of a stem-archosaur applying 3D modelling techniques. μCT scans of multiple specimens of Euparkeria capensis enabled the reconstruction and three-dimensional articulation of the hindlimb. The joint mobility of the hindlimb was quantified in 3D to address previous qualitative hypotheses regarding the stance of Euparkeria. Our range of motion analysis implies the potential for an erect posture, consistent with the hip morphology, allowing the femur to be fully adducted to position the feet beneath the body. A fully sprawling pose appears unlikely but a wide range of hip abduction remained feasible—the hip appears quite mobile. The oblique mesotarsal ankle joint in Euparkeria implies, however, a more abducted hindlimb. This is consistent with a mosaic of ancestral and derived osteological characters in the hindlimb, and might suggest a moderately adducted posture for Euparkeria. Our results support a single origin of a pillar-erect hip morphology, ancestral to Eucrocopoda that preceded later development of a hinge-like ankle joint and a more erect hindlimb posture.

Addressing Quantitative and Qualitative Hypotheses Using Regression Models with Equality Restrictions and Predictors Measured in Common Units

In regression, some or all of the predictors may be measured in common units: e.g. X 1 = carbohydrate calories, X2 = protein calories, X3 = fat calories. Such predictors can occur in disciplines as diverse as business, economics, education, medicine, nutrition, psychology, sport science, etc. Predictors in common units can lead to unique quantitative and qualitative hypotheses that can be addressed by imposing equality restrictions on the regression weights (e.g. ). A simple device, total score substitution, is available for constraining regression coefficients to be equal in a variety of regression applications. Applications to linear, moderated linear, and polynomial models are described, but extensions to generalized linear models and multilevel linear models are also possible. Total score substitution in linear and moderated regression is illustrated using high school coursework and mathematics achievement data. Data, code (R, SPSS, SAS), and output are publicly available.

Learning to use benefit-cost arguments: A microgenetic study of argument-counterargument integration in an undergraduate seminar course.

This microgenetic case study explores how an undergraduate student (Nolan) in a second-year seminar mastered an argument weighing scheme and used it to organize his writing. The students in this seminar completed argumentation vee diagrams (AVDs) prior to discussing controversial issues. Students also completed preessays and postessays on a different topic without using AVDs. Through the AVDs, students were provided with critical, evaluative questions related to designing solutions and weighing arguments against counterarguments. In separate work, we report that the intervention was effective in increasing the number of refutations related to the critical questions (Nussbaum & Dove, 2018). Nolan showed particularly strong growth, and this case study analyzes his discourse to generate qualitative insights and hypotheses into his development. Using the conceptual framework of argument-counterargument integration (Nussbaum, 2008b), we analyzed Nolan’s written artifacts and discussions to better understand how his proficiency with using the argument scheme developed over time. Our results suggest that Nolan initially displayed piecemeal use of the scheme, but over time, Nolan learned to articulate general principles and to integrate these with specific points regarding benefits and costs, as well as with solution-oriented design statements that further reduced disadvantages. Use of the scheme spontaneously transferred to a novel topic. Extensive engagement in ethical discussions, along with studying ethical theory and answering critical questions on AVDs, may have contributed to his development. Theoretical and practical implications related to teaching argumentative writing in conjunction with oral discourse are discussed. (PsycINFO Database Record (c) 2020 APA, all rights reserved)

Reliance on small samples and the value of taxing reckless behaviors

AbstractNew technology can be used to enhance safety by imposing costs, or taxes, on certain reckless behaviors. The current paper presents two pre-registered experiments that clarify the impact of taxation of this type on decisions from experience between three alternatives. Experiment 1 focuses on an environment in which safe choices maximize expected returns and examines the impact of taxing the more attractive of two risky options. The results reveal a U-shaped effect of taxation: some taxation improves safety, but too much taxation impairs safety. Experiment 2 shows a clear negative effect of high taxation even when the taxation eliminates the expected benefit from risk-taking. Comparison of alternative models suggests that taxing reckless behaviors backfires when it significantly increases the proportion of experiences in which a more dangerous behavior leads to better outcomes than the taxed behavior. Qualitative hypotheses derived from naïve sampling models assuming small samples were only partially supported by the data.

FORMAL QUALITATIVE PROBABILITY

AbstractChoices rarely deal with certainties; and, where assertoric logic and modal logic are insufficient, those seeking to be reasonable turn to one or more things called “probability.” These things typically have a shared mathematical form, which is an arithmetic construct. The construct is often felt to be unsatisfactory for various reasons. A more general construct is that of a preordering, which may even be incomplete, allowing for cases in which there is no known probability relation between two propositions or between two events. Previous discussion of incomplete preorderings has been as if incidental, with researchers focusing upon preorderings for which quantifications are possible. This article presents formal axioms for the more general case. Challenges peculiar to some specific interpretations of the nature of probability are brought to light in the context of these propositions. A qualitative interpretation is offered for probability differences that are often taken to be quantified. A generalization of Bayesian updating is defended without dependence upon coherence. Qualitative hypothesis testing is offered as a possible alternative in cases for which quantitative hypothesis testing is shown to be unsuitable.

Multiscale Inference and Long-Run Variance Estimation in Non-Parametric Regression with Time Series Errors

SummaryWe develop new multiscale methods to test qualitative hypotheses about the function m in the non-parametric regression model Yt, T = m(t/T) + ɛt with time series errors ɛt. In time series applications, m represents a non-parametric time trend. Practitioners are often interested in whether the trend m has certain shape properties. For example, they would like to know whether m is constant or whether it is increasing or decreasing in certain time intervals. Our multiscale methods enable us to test for such shape properties of the trend m. To perform the methods, we require an estimator of the long-run error variance σ2=Σl=−∞∞cov(ε0,εl). We propose a new difference-based estimator of σ2 for the case that {ɛt} belongs to the class of auto-regressive AR(∞) processes. In the technical part of the paper, we derive asymptotic theory for the proposed multiscale test and the estimator of the long-run error variance. The theory is complemented by a simulation study and an empirical application to climate data.

Scaling the interactive effects of attractive and repellent odours for insect search behaviour

Insects searching for resources are exposed to a complexity of mixed odours, often involving both attractant and repellent substances. Understanding how insects respond to this complexity of cues is crucial for understanding consumer-resource interactions, but also to develop novel tools to control harmful pests. To advance our understanding of insect responses to combinations of attractive and repellent odours, we formulated three qualitative hypotheses; the response-ratio hypothesis, the repellent-threshold hypothesis and the odour-modulation hypothesis. The hypotheses were tested by exposing Drosophila melanogaster in a wind tunnel to combinations of vinegar as attractant and four known repellents; benzaldehyde, 1-octen-3-ol, geosmin and phenol. The responses to benzaldehyde, 1-octen-3-ol and geosmin provided support for the response-ratio hypothesis, which assumes that the behavioural response depends on the ratio between attractants and repellents. The response to phenol, rather supported the repellent-threshold hypothesis, where aversion only occurs above a threshold concentration of the repellent due to overshadowing of the attractant. We hypothesize that the different responses may be connected to the localization of receptors, as receptors detecting phenol are located on the maxillary palps whereas receptors detecting the other odorants are located on the antennae.

Modeling trade to discover lost cities

Economics The locations and characteristics of ancient cities are often disputed. Barjamovic et al. developed a comprehensive dataset of trading routes among cities in the Bronze Age originally recorded by Assyrian merchants. They then used the data to build a model that captures the locations and trade flows among those cities, which can be extrapolated to provide probable locations of undiscovered cities. In some cases, the model corroborates qualitative hypotheses by historians, while in others, the model supports one hypothesis over another. They are also able to model the likely size, density, and network importance of these cities. These results have implications for our understanding of ancient trade and how cities have changed over time. Q. J. Econ. 134 , 1455 (2019).

MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network.

Analysis of differential expression of genes is often performed to understand how the metabolic activity of an organism is impacted by a perturbation. However, because the system of metabolic regulation is complex and all changes are not directly reflected in the expression levels, interpreting these data can be difficult. In this work, we present a new algorithm and computational tool that uses a genome-scale metabolic reconstruction to infer metabolic changes from differential expression data. Using the framework of constraint-based analysis, our method produces a qualitative hypothesis of a change in metabolic activity. In other words, each reaction of the network is inferred to have increased, decreased, or remained unchanged in flux. In contrast to similar previous approaches, our method does not require a biological objective function and does not assign on/off activity states to genes. An implementation is provided and it is available online. We apply the method to three published datasets to show that it successfully accomplishes its two main goals: confirming or rejecting metabolic changes suggested by differentially expressed genes based on how well they fit in as parts of a coordinated metabolic change, as well as inferring changes in reactions whose genes did not undergo differential expression. github.com/htpusa/moomin. Supplementary data are available at Bioinformatics online.

Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning.

Discrete stochastic models of gene regulatory network models are indispensable tools for biological inquiry since they allow the modeler to predict how molecular interactions give rise to nonlinear system output. Model exploration with the objective of generating qualitative hypotheses about the workings of a pathway is usually the first step in the modeling process. It involves simulating the gene network model under a very large range of conditions, due to the large uncertainty in interactions and kinetic parameters. This makes model exploration highly computational demanding. Furthermore, with no prior information about the model behavior, labor-intensive manual inspection of very large amounts of simulation results becomes necessary. This limits systematic computational exploration to simplistic models. We have developed an interactive, smart workflow for model exploration based on semi-supervised learning and human-in-the-loop labeling of data. The workflow lets a modeler rapidly discover ranges of interesting behaviors predicted by the model. Utilizing that similar simulation output is in proximity of each other in a feature space, the modeler can focus on informing the system about what behaviors are more interesting than others by labeling, rather than analyzing simulation results with custom scripts and workflows. This results in a large reduction in time-consuming manual work by the modeler early in a modeling project, which can substantially reduce the time needed to go from an initial model to testable predictions and downstream analysis. A python-package is available at https://github.com/Wrede/mio.git. Supplementary data are available at Bioinformatics online.

Visually Hypothesising in Scientific Paper Writing: Confirming and Refuting Qualitative Research Hypotheses Using Diagrams

Qualitative research involves scientific narratives and the analysis and interpretation of textual or numerical data (or both), mostly from conversations and discussions, to uncover meaningful patterns that describe a particular phenomenon. It is important to know other ways of framing and explaining these nuanced scientific narratives so that they can convey scientific knowledge. A qualitative hypothesis can play this role. The testing of hypotheses in qualitative research—which does not strictly mean the same thing as testing of hypotheses in quantitative research—always comes with challenges that provoke concerns. The questions that scholars, especially undergraduate and postgraduate students, have had to deal with are: Is it possible to “test” hypotheses using a qualitative method? If it is possible, how can this be done? This study deconstructs the concept, notion, and use of the hypotheses. It presents the “how-to” aspect of hypothesising (in qualitative research and inquiries) by using creative diagramming within post-positivist research, and also contributes to the literature on visual communication and qualitative research. The study is a guide to early career scholars (including undergraduate and post-graduate students) on how to formulate and “test” hypotheses qualitatively using visual or diagrammatical approaches.

Modeling the formation of soil microaggregates

The functions of soils are intimately linked to its aggregated structure. Microaggregates formed during pedogenesis from a vast variety of mineral, organic, and biotic materials are the smallest conceivable compounds at the basis of soil structural hierarchy. Qualitative hypotheses and concepts on how aggregates form are quite elaborate, but the consistent quantitative application within a mechanistic and physically rigorous framework is still missing. This is partly caused by the fact that such an endeavor requires the combination of synergistic concepts on the transport of particles and their interactions affected by shape, size, and surface properties in aqueous suspension. Here we present a novel quantitative approach for the formation of soil microaggregates in silico that integrates diffusion-limited cluster-cluster aggregation with a probabilistic attachment following the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of particle interactions. To represent universal mineral shapes found in soils, we implemented spherical, plate-like as well as rod-like particle morphologies inspired by weathered silicates, secondary clay minerals and pedogenic iron oxides. In this way, we developed a model that produces an explicit three-dimensional structure of aggregates emerging from hetero- as well as homo-aggregation in response to the chemical milieu. We then exploited the 3D morphology to assess functional properties of aggregates exemplified with the water retention curve and pore size distribution.