1,720,986 research outputs found
How range residency and long-range perception change encounter rates
Get PDFEncounter rates link movement strategies to intra- and inter-specific interactions, and therefore translate individual movement behavior into higher-level ecological processes. Indeed, a large body of interacting population theory rests on the law of mass action, which can be derived from assumptions of Brownian motion in an enclosed container with exclusively local perception. These assumptions imply completely uniform space use, individual home ranges equivalent to the population range, and encounter dependent on movement paths actually crossing. Mounting empirical evidence, however, suggests that animals use space non-uniformly, occupy home ranges substantially smaller than the population range, and are often capable of nonlocal perception. Here, we explore how these empirically supported behaviors change pairwise encounter rates. Specifically, we derive novel analytical expressions for encounter rates under Ornstein-Uhlenbeck motion, which features non-uniform space use and allows individual home ranges to differ from the population range. We compare OU-based encounter predictions to those of Reflected Brownian Motion, from which the law of mass action can be derived. For both models, we further explore how the interplay between the scale of perception and home-range size affects encounter rates. We find that neglecting realistic movement and perceptual behaviors can lead to systematic, non-negligible biases in encounter-rate predictions.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)ICTP South American Institute for Fundamental Research & Instituto de Física Teórica - UNESP, Rua Dr. Bento Teobaldo Ferraz 271, Bloco 2 - Barra Funda 01140-070Center for Advanced Systems Understanding (CASUS) GorlitzHelmholtz Centre for Environmental Research – UFZ Department of Ecological ModellingSmithsonian Conservational Biology Institute, National Zoological Park, 1500 Remount Road, Front RoyalDept. of Biology University of MarylandDept. of Ecology & Evolutionary Biology Princeton UniversityInstitute of Geoscience & Geography Martin-Luther-University Halle-WittenbergHelmholtz-Zentrum Dresden - Rossendorf (HZDR) GermanyDept. of Computational Landscape Ecology Helmholtz Centre for Environmental Research-UFZICTP South American Institute for Fundamental Research & Instituto de Física Teórica - UNESP, Rua Dr. Bento Teobaldo Ferraz 271, Bloco 2 - Barra Funda 01140-070FAPESP: 2016/01343-
Implementing code review in the scientific workflow: insights from ecology and evolutionary biology
Get PDFCode review increases reliability and improves reproducibility of research. As such, code review is an inevitable step in software development and is common in fields such as computer science. However, despite its importance, code review is noticeably lacking in ecology and evolutionary biology. This is problematic as it facilitates the propagation of coding errors and a reduction in reproducibility and reliability of published results. To address this, we provide a detailed commentary on how to effectively review code, how to set up your project to enable this form of review and detail its possible implementation at several stages throughout the research process. This guide serves as a primer for code review, and adoption of the principles and advice here will go a long way in promoting more open, reliable, and transparent ecology and evolutionary biology
LDOS/SNAP data for MALA: Beryllium at high temperatures
No full text# Authors:
- Fiedler, Lenz (HZDR / CASUS)
- Cangi, Attila (HZDR / CASUS)
# Affiliations:
HZDR - Helmholtz-Zentrum Dresden-Rossendorf
CASUS - Center for Advanced Systems Understanding
# Dataset description
- System: Be256
- Temperature(s): 3750K, 7500K, 10000K
- Mass density(ies): 1.915 gcc
- Crystal Structure: bcc (material mp-20 in the materials project)
- Number of atomic snapshots: 50
- 30 (3750K)
- 10 (7500K)
- 10 (10000)
- Contents:
- ideal crystal structure: no
- MD trajectory: no
- Atomic positions: no
- DFT inputs: no
- DFT outputs (energies): yes
- SNAP vectors: no
- LDOS vectors: yes (partially, see below)
- dimensions: 160x80x80x250
- note: LDOS parameters are the same for all sizes of the unit cell
- trained networks: no
# Data generation
Ideal crystal structures were obtained using the Materials Project. (https://materialsproject.org/materials/mp-87/)
DFT-MD calculations were performed using the Vienna Ab initio Simulation Package (https://www.vasp.at/, VASP). DFT calculations were performed using QuantumESPRESSO.
For the VASP calculations, the standard VASP pseudopotentials were used. For Quantum Espresso, pslibrary was used (https://dalcorso.github.io/pslibrary/).
The LDOS was preprocessed using MALA.
# Dataset structure
Each temperature folder contains the following folders:
- ldos: holds the LDOS vectors (LDOS was not calculated for all snapshots!)
- dft_outputs: holds the outputs from the DFT calculations, i.e. energies in the form of a QE output file
Please note that the numbering of the snapshots is contiguous per temperature/mass density/number of atoms, and only data used in publications has been uploaded at this poin
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets
No full textUnderstanding development in living organisms requires following the divisions, movements, and fates of cells across developing systems. While advances in microscopy have enabled whole-embryo imaging at the cellular level, extracting and analyzing cell lineages from these massive datasets remains a significant computational challenge. We present Mastodon, a scalable, extensible software platform for manual, semi-automated, and automated cell tracking in large images. A purpose-built graph model supports responsive performance for datasets with millions of annotations, making Mastodon a future-proof platform for cell lineage analysis. Built as a Fiji plugin, Mastodon enables interactive visualization, editing, and analysis of complex lineage trees, seamlessly integrated with the raw image data
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
A Lagrangian model for drifting ecosystems reveals heterogeneity-driven enhancement of marine plankton blooms
No full textAbstract Marine plankton play a crucial role in carbon storage, global climate, and ecosystem function. Planktonic ecosystems are embedded in patches of water that are continuously moving, stretching, and diluting. These processes drive inhomegeneities on a range of scales, with implications for the integrated ecosystem properties, but are hard to characterize. We present a theoretical framework that accounts for all these aspects; tracking the water patch hosting a drifting ecosystem along with its physical, environmental, and biochemical features. The theory resolves patch dilution and internal physical mixing as a function of oceanic strain and diffusion. Ecological dynamics are parameterized by an idealized nutrient and phytoplankton population and we specifically capture the time evolution of the biochemical spatial variances to represent within-patch heterogeneity. We find that, depending only on the physical processes to which the water patch is subjected, the plankton biomass response to a resource perturbation can vary in size up to six times. This work indicates that we must account for these processes when interpreting and modeling marine ecosystems and provides a framework with which to do so
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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