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openodc-byFeb 2020View details →

Citation contexts of papers citing Merton's work "Social Theory and Social Structure"

Citation contexts of papers citing Merton's work "Social Theory and Social Structure" based on MAG. Please see also: https://aka.ms/msracad Arnab Sinha, Zhihong Shen, Yang Song, Hao Ma, Darrin Eide, Bo-June (Paul) Hsu, and Kuansan Wang. 2015. An Overview of Microsoft Academic Service (MA) and Applications. In Proceedings of the 24th International Conference on World Wide Web (WWW '15 Companion). ACM, New York, NY, USA, 243-246. DOI=http://dx.doi.org/10.1145/2740908.2742839

opencc-by-4.0Apr 2020View details →

Dataset for Sparse Hashing for Scalable Approximate Model Counting: Theory and Practice

The dataset consists of (1) Benchmark files (2) the logfile (outputs) generated by ApproxMC4 and ApproxMC5 respectively (3) A summary of the results for the files where at least one of ApproxMC4 or ApproxMC5 did not time out and took more than 1 second.  The corresponding paper titled "Scalable Approximate Model Counting via Concentrated Hashing]{Sparse Hashing for Scalable Approximate Model Counting: Theory and Practice" will appear in the Proceedings of Logic in Computer science(LICS), 2020.

opencc-by-4.0Mar 2010View details →

Figure 3. D in Neotypification of Drawida hattamimizu Hatai, 1930 (Annelida, Oligochaeta, Megadrili, Moniligastridae) as a model linking mtDNA (COI) sequences to an earthworm type, with a response to the 'Can of Worms' theory of cryptic species

Figure 3. D. hattamimizu detailed internal anatomy showing the disputed paired nephridial funnels ("n.m.") sketched for only three of the nephridia (after Hatai, 1930: fig. 4).

opencc-by-4.0Apr 2020View details →

Data for "An application of upscaled optimal foraging theory using hidden Markov modelling: year-round behavioural variation in a large arctic herbivore"

Data for the article “An application of upscaled optimal foraging theory using hidden Markov modelling: year-round behavioural variation in a large arctic herbivore” By LT Beumer, J Pohle, NMS Schmidt, M Chimienti, JP Desforges, LH Hansen, R Langrock, SH Pedersen, M Stelvig, FM van Beest   The data set includes three files: A readme file describing the data files and two data files accompanying the above publication. Combined, the two data files represent the dataset collected by GPS collars fitted on 19 female muskoxen in northeast Greenland (28 muskox-years with 153-1062 observation days/animal) and associated extracted covariates, divided into a summer and winter season dataset as modelled in the article. Data here are given as included in the models (for a description of cleaning procedures, see article). All continuous, non-cyclical covariates were standardised to have zero mean and unit standard deviation to improve numerical stability of parameter estimation. This is indicated by “_scaled” in the column name. For further queries please contact nms@bios.au.dk

opencc-by-4.0Apr 2020View details →

Project files provided as supporting information to the manuscript "An information theory-based approach for optimal model reduction of biomolecules"

The dataset contains the following files: <ul> <li>- adenylate.zip</li> <li>- antitrypsin.zip</li> <li>- tamapin.zip</li> <li>- analysis_notebooks.zip</li> </ul> Each of these refers to one of three proteins. For each CG sites number N, each compressed folder contains the following files: <ul> <li>random mappings (random_mappings_${N}.txt) </li> <li>random mapping entropies (random_smaps_${N}.txt) [fig1]</li> <li>optimal mappings (lowest_mappings_${N}.txt) [fig3, fig4, figS2]</li> <li>optimal mapping entropies (lowest_smaps_${N}.txt) [fig1]</li> <li>pdb files with conservations probabilities in the beta factor column (${N}_probs.pdb) [fig4, figs2]</li> <li>SASA values (${protein_name}_SASA_residues.xvg </li> <li>transition mapping entropies (${protein_name}_transition_smaps.txt) [fig2]</li> <li>additional transition mapping entropies (${protein_name}_transition_smaps*) [figs3]</li> </ul> The file analysis_notebooks.zip contains the python3 notebooks employed to perform all the analysis present in the paper: <ul> <li>paper_analysis_adenylate.ipynb</li> <li>paper_analysis_antitrypsin.ipynb</li> <li>paper_analysis_tamapin.ipynb</li> </ul> Packages required for the usage of these python 3 scripts: - numpy - pandas - matplotlib - seaborn

opencc-by-4.0Jun 2020View details →

Whistler-mode waves excited by anisotropic hot electrons with a drift velocity in Earth's magnetosphere: Linear theory

The data used to generate the figures in this paper.

opencc-zeroJun 2020View details →

Verifiability of genus-level classification under quantification and parsimony theories: a case study of follicucullid radiolarians

The classical taxonomy of fossil invertebrates is based on subjective judgments of morphology, which can cause confusion since there are no codified standards for the classification of genera. Here, we explore the validity of the genus taxonomy of 75 species and morphospecies of the Follicucullidae, a Late Paleozoic family of radiolarians, using a new method, <a name="_Hlk41571699">Hayashi's quantification theory II</a> (HQT-II), a general multivariate statistical method for categorical datasets relevant to discriminant analysis. We identify a scheme of ten genera rather than the currently accepted three genera (Follicucullus, Ishigaconus and Parafollicucullus). As HQT-II cannot incorporate stratigraphic data, a phylogenetic tree of Follicucullidae was reconstructed for 38 species using maximum parsimony. Six lineages emerged, roughly in concordance with the results of HQT-II. Combined with parsimony ancestral state reconstruction, the ancestral group of this family is Haplodiacanthus. Five other groups were discriminated, the Parafollicucullus, Curvalbaillella, Pseudoalbaillella, Longtanella, and Follicucullus–Cariver lineages. The morphological evolution of these lineages comprises a minimum essential list of eight states of four traits. <a name="_Hlk41488876">HQT-II is a novel discriminant analytical multivariate method that may be of value in other taxonomic problems of paleobiology.</a>

opencc-by-4.0Aug 2018View details →

3D Models from Morales, J. I., et al. (2015). "Measuring Retouch Intensity in Lithic Tools: A New Proposal Using 3D Scan Data." Journal of Archaeological Method and Theory 22(2): 543-558.

This document compiles the complete set of 3D models and the measurements used for the experimental work of the paper: Morales, J. I., et al. (2015). "Measuring Retouch Intensity in Lithic Tools: A New Proposal Using 3D Scan Data." Journal of Archaeological Method and Theory 22(2): 543-558.   It includes 3D scans from both unmodified and modified flakes (X & Xb). All the flakes produced in this experiment were produced by freehand hard hammer percussion and no specific flaking method was followed. Diferents types of tertiary evaporitic flint described in Soto, M., et al. (2017). "The chert abundance ratio (CAR): a new parameter for interpreting Palaeolithic raw material procurement." J. Archaeol Anthropol Sci. (https://doi.org/10.1007/s12520-017-0516-3) were used.

Data from: A theory for polymicrogyria and brain arteriovenous malformations in HHT

Hereditary hemorrhagic telangiectasia (HHT) is generally considered a disorder of endothelial dysfunction, characterized by the development of multiple systemic arteriovenous malformations (AVMs), including within the brain. However, there have recently been a number of reports correlating HHT with malformations of cortical development, of which polymicrogyria is the most common type. Here we present seven new cases demonstrating polymicrogyria in HHT, six of which demonstrate a brain AVM (bAVM) in close spatial proximity, with the aim of providing a common origin for the association. Upon reviewing patient genetics and imaging data and comparing with previously reported findings, we form two new conclusions: i) polymicrogyria in HHT appears exclusively associated with a subset of mutations in the transmembrane protein endoglin that is involved with blood flow related mechanotransduction signaling during angiogenesis, and ii) the polymicrogyria is characteristically unilateral, typically focal, and correlates with vascular regions experiencing low fluid shear stress during corticogenesis in utero. Integrating these with findings in the literature from genetics and molecular biology experiments, we propose a theory suggesting dominant-negative endoglin mutations may predispose focal, aberrant hypersprouting angiogenesis during corticogenesis that leads to the production of polymicrogyria. This hypoxic insult may further serve as the revealing trigger for later development of a spatially coincident bAVM. This hypothesis suggests an essential role for endoglin-mediated hemodynamic mechanotransduction in normal corticogenesis.

Data from: When to monitor and when to act: value of information theory for multiple management units and limited budgets

1.The question of when to monitor and when to act is fundamental to applied ecology, and notoriously difficult to answer. Value of information (VOI) theory holds great promise to help answer this question for many management problems. However, VOI theory in applied ecology has only been demonstrated in single-decision problems, and has lacked explicit links between monitoring and management costs. 2.Here, we present an extension of VOI theory for solving multi-unit decisions of whether to monitor before managing, while explicitly accounting for monitoring costs. Our formulation helps to choose the optimal monitoring/management strategy among groups of management units (e.g. species, habitat patches), and can be used to examine the benefits of partial and repeat monitoring. 3.To demonstrate our approach, we use case simulated studies of single-species protection that must choose among potential habitat areas, and classification and management of multiple species threatened with extinction. We provide spreadsheets and code to illustrate the calculations and facilitate application. Our case studies demonstrate the utility of predicting the number of units with a given outcome for problems with probabilities of discrete states, and the efficiency of having a flexible approach to manage according to monitoring outcomes. 4.Synthesis and applications. The decision to act or gather more information can have serious consequences for management. No decision, including the decision to monitor, is risk-free. Our multi-unit expansion of Value of Information (VOI) theory can reduce the risk in monitoring/acting decisions for many applied ecology problems. While our approach cannot account for the potential value of discovering previously unknown threats or ecological processes via monitoring programs, it can provide quantitative guidance on whether to monitor before acting, and which monitoring/management actions are most likely to meet management objectives.

opencc-zeroDec 2015View details →

Data from: Weaponry and defenses in fighting animals: how allometry can alter predictions from contest theory

Theoretical models have been developed to understand how animals decide to withdraw from a contest. They provide testable predictions regarding the relationship between resource holding potential (RHP) and contest duration that assume linear relationships among RHP traits. However, RHP traits might scale with body size according to power laws. Furthermore, investment across different RHP traits may vary. Herein, we provide a model that encompasses the allometric relationship between body size and other RHP traits. First, we partition RHP traits into "offensive" traits (i.e., the ability to inflict damage) and "defensive" traits (i.e., persistence in a contest). Defensive traits may in turn be subdivided into "damage endurance" (DE) or the ability to absorb damage and "stamina." We then model scenarios where: 1) there are power relationships among RHP traits; 2) individuals invest differently in defensive and offensive traits; 3) offensive traits and DE have a positive/negative relationship with body size. We modeled sized-matched injurious contests where 1) offensive capacity (OC) increases superlinearly with body size, 2) DE increases superlinearly, and 3) OC increases superlinearly but DE increases sublinearly. Our analyses indicate that if RHP traits scale linearly current predictions are upheld for injurious contests—contest duration increases with body size. However, with power relationships we can expect nonlinear relationships. Here, contest duration increased with body size until a maximum, decreasing afterwards. Thus, considering allometric relationships between body size and RHP traits may lead to new insights in animal contest theory and may help to solve discrepancies between current theory and empirical data.

opencc-zeroDec 2014View details →

Data from: A spatial theory for characterizing predator–multiprey interactions in heterogeneous landscapes

Trophic interactions in multiprey systems can be largely determined by prey distributions. Yet, classic predator–prey models assume spatially homogeneous interactions between predators and prey. We developed a spatially informed theory that predicts how habitat heterogeneity alters the landscape-scale distribution of mortality risk of prey from predation, and hence the nature of predator interactions in multiprey systems. The theoretical model is a spatially explicit, multiprey functional response in which species-specific advection–diffusion models account for the response of individual prey to habitat edges. The model demonstrates that distinct responses of alternative prey species can alter the consequences of conspecific aggregation, from increasing safety to increasing predation risk. Observations of threatened boreal caribou, moose and grey wolf interacting over 378 181 km2 of human-managed boreal forest support this principle. This empirically supported theory demonstrates how distinct responses of apparent competitors to landscape heterogeneity, including to human disturbances, can reverse density dependence in fitness correlates.

opencc-zeroDec 2016View details →

Data from: Wolf in sheep's clothing: model misspecification undermines tests of the neutral theory for life histories

Understanding the processes behind change in reproductive state along life-history trajectories is a salient research program in evolutionary ecology. Two processes, state dependence and heterogeneity, can drive the dynamics of change among states. Both processes can operate simultaneously, begging the difficult question of how to tease them apart in practice. The Neutral Theory for Life Histories (NTLH) holds that the bulk of variations in life-history trajectories is due to state dependence and is hence neutral: Once previous (breeding) state is taken into account, variations are mostly random. Lifetime reproductive success (LRS), the number of descendants produced over an individual's reproductive life span, has been used to infer support for NTLH in natura. Support stemmed from accurate prediction of the population-level distribution of LRS with parameters estimated from a state dependence model. We show with Monte Carlo simulations that the current reliance of NTLH on LRS prediction in a null hypothesis framework easily leads to selecting a misspecified model, biased estimates and flawed inferences. Support for the NTLH can be spurious because of a systematic positive bias in estimated state dependence when heterogeneity is present in the data but ignored in the analysis. This bias can lead to spurious positive covariance between fitness components when there is in fact an underlying trade-off. Furthermore, neutrality implied by NTLH needs a clarification because of a probable disjunction between its common understanding by evolutionary ecologists and its translation into statistical models of life-history trajectories. Irrespective of what neutrality entails, testing hypotheses about the dynamics of change among states in life histories requires a multimodel framework because state dependence and heterogeneity can easily be mistaken for each other.

Data from: Locally and systemically induced glucosinolates follow optimal defence allocation theory upon root herbivory

1. Herbivore-induced defences in plants are considered a strategy to manage multiple interactions while saving resources. The optimal defence theory (ODT) is one of the most prominent theoretical frameworks to explain the defence allocation patterns within plants. It was recently shown that the ODT generally applies to constitutive glucosinolate (GSL) allocation in shoot and root organs. Previous studies showed that both root and shoot herbivore feeding may alter defence allocation over plant organs. For shoots, the effect depends on where the herbivores feed. It is as yet unknown whether similar principles apply to root-herbivore induced GSLs. 2. To analyse the effects of root localized herbivore feeding on GSL allocation, we conducted a pot experiment using Anomala cuprea grubs and four Brassicaceae; Brassica rapa, B. nigra, B. oleracea, and Sinapis alba. Individuals of these four plant species were grown in dedicated mesocosms. The grubs were confined either to the bottom soil, the middle section, or to the top soil. Plants grown in the same set-ups but without root herbivores served as controls. Glucosinolate levels of the leaf lamina, petiole, and stem as well as of the taproot, lateral roots, and fine roots were measured after eight days of herbivory. 3. Plant biomass reduction due to herbivory was the largest when herbivores were confined to the top soil. In the three Brassica species, taproot GSL levels increased upon herbivory independent of where the root herbivores were feeding. Glucosinolate levels in fine roots and shoots, on the other hand, hardly responded to root herbivory. Indole GSLs, which are more effective to pathogens than to herbivores, were more strongly induced than aliphatic and aromatic GSLs, especially in the taproots. Sinapis alba did not show remarkable increments in any GSL level upon herbivory. 4. These results show that locally and systemically induced defences in roots are consistent with the ODT: the taproot which is the most vulnerable and valuable to plant performance shows the highest increase in defence induction. The induced GSL profiles suggest that the response may not only target herbivores, but may also help to prevent secondary infection by microbial pathogens.

Data from: Integrating encounter theory with decision analysis to evaluate collision risk and determine optimal protection zones for wildlife

1. Better understanding human-wildlife interactions and their links with management can help improve the design of wildlife protection zones. One important example is the problem of wildlife collisions with vehicles or human-built structures (e.g. power lines, wind farms). In fact, collisions between marine wildlife and watercraft are among the major threats faced by several endangered species of marine mammals. Natural resource managers are therefore interested in finding cost-effective solutions to mitigate these threats. 2. We combined abundance estimators with encounter rate theory to estimate relative lethal collision risk of the Florida manatee (Trichechus manatus latirostris) from watercraft. We first modeled seasonal abundance of watercraft and manatees using a Bayesian analysis of aerial survey count data. We then modeled relative lethal collision risk in space and across seasons. Finally, we applied decision analysis and Linear Integer Programming to determine the optimal design of speed zones in terms of relative risk to manatees and costs to waterway users. We used a Pareto efficient frontier approach to evaluate the performance of alternative zones, which included additional practical considerations (e.g. spatial aggregation of speed zones) in relation to the optimal zone configurations. 3. Under the various relationships for probability of death given strike speed that we considered, the current speed zones reduced the relative lethal collision risk by an average of 51.5% to 70% compared to the scenario in which all speed regulations were removed (i.e. the no-protection scenario). We identified optimal zones and near-optimal zones with additional management considerations that improved upon the current zones in terms of cost or relative risk. 4. Policy Implications: Our analytical framework combines encounter rate theory and decision analysis to quantify the effectiveness of speed zones protecting manatees while accounting for uncertainty. Our approach can be used to optimize the design of protection zones intended to reduce conflicts between human waterborne activity and marine mammals. This framework could be extended to address many other problems of human-wildlife interactions, such as the optimal placement of wind farms to minimize collisions with wildlife or the optimal allocation of ranger effort to mitigate poaching threats.

opencc-zeroDec 2010View details →

Data from: Experimental tests of sex allocation theory with two species of simultaneously hermaphroditic acorn barnacles

Sex allocation theory for simultaneous hermaphrodites predicts increases in relative allocation to male-specific function as competition for fertilizations increases. Theoretical models developed specifically for competing acorn barnacles predict that the proportional allocation to male function increases towards an asymptote of 50% as the number of competitors for fertilizations increases. Experimental manipulations were used to investigate how mate competition affected both relative and absolute allocation to the sex functions for two species of acorn barnacle: Semibalanus balanoides and Balanus glandula. The ratio of male to female allocation did not increase with the number of competitors for either species. However, both species showed increased allocation to male function (estimated as total mass of sex-specific tissues) with increased crowding. Allocation to female function seemed to be limited by other factors and did not vary with mating group size as predicted. Allocation to male and female function were both positively related to body size, but a trade-off between male and female function, a key assumption of prior models, was not observed.

Data from: Testing the heat dissipation limit theory in a breeding passerine

The maximum work rate of animals has recently been suggested to be determined by the rate at which excess metabolic heat generated during work can be dissipated (heat dissipation limitation theory; HDL). As a first step towards testing this theory in wild animals, we experimentally manipulated brood size in breeding marsh tits (Poecile palustris) to change their work rate. Parents feeding nestlings generally operated at above-normal body temperatures. Body temperature in both males and females increased with maximum ambient temperature and with manipulated work rate, sometimes even exceeding 45 °C, which is close to suggested lethal levels for birds. Such high body temperatures have previously only been described for birds living in hot and arid regions. Thus, reproductive effort in marsh tits may potentially be limited by the rate of heat dissipation. Females had lower body temperatures, a possible consequence of their brood patch serving as a thermal window facilitating heat dissipation. Because increasing body temperatures are connected to somatic costs, we suggest that the HDL theory may constitute a possible mediator of the trade-off between current and future reproduction. It follows that globally increasing, more stochastic, ambient temperatures may restrict the capacity for sustained work of animals in the future.

opencc-zeroDec 2016View details →

Data from: Multiresponse algorithms for community-level modeling: review of theory, applications, and comparison to species distribution models

1.Community-level models (CLMs) consider multiple, co-occurring species in model fitting and are lesser known alternatives to species distribution models (SDMs) for analyzing and predicting biodiversity patterns. CLMs simultaneously model multiple species, including rare species, while reducing overfitting and implicitly considering drivers of co-occurrence. Many CLMs are direct extensions of well-known SDMs and therefore should be familiar to ecologists. However, CLMs remain underutilized, and there have been few tests of their potential benefits and no systematic reviews of their assumptions and implementations. Here we review this emerging field and provide examples in R to fit common CLMs. Our goal is to introduce CLMs to a broader audience, and discuss their attributes, benefits, and limitations relative to SDMs. 2.We review i) statistical implementations and applications of CLMs, ii) their advantages and limitations, and iii) comparative analyses of CLMs and SDMs. We also suggest directions for future research. 3.We identify seven CLM algorithms with similar data structures and predictive outputs as SDMs that should be most accessible to ecologists familiar with species-level modeling, including five methods that predict assemblage composition and individual species distributions and two methods that model compositional turnover along environmental gradients. CLMs have been applied to numerous taxa, regions, and spatial scales, and a variety of topics (e.g., studying drivers of community structure or assessing relationships between community composition and functional traits). Studies suggest that the relative benefits of CLMs and SDMs may be case specific, especially in terms of predicting species distributions and community composition. However, CLMs may offer advantages in terms of computational efficiency, modeling rare species, and projecting to no-analog climates. A major shortcoming of CLMs is their reliance on presence-absence community composition data. 4.Studies are needed to assess the relative merits of SDMs and CLMs, and different CLM algorithms, with a focus on three key areas: i) under which circumstances CLMs improve predictions for rare species, ii) how CLMs perform under different community compositions (e.g. relative abundance of rare vs. common species), including the extent to which co-occurrence patterns are structured by biotic interactions, and iii) ability to project across time/space.