1,720,974 research outputs found
Data accompanying "Shaping the Growth Behaviour of Biofilms Initiated from Bacterial Aggregates, 2013-2016" (Submitted paper).
No full textBacterial biofilms are usually assumed to originate from individual cells deposited on a surface. However, many biofilm-forming bacteria tend to aggregate in the planktonic phase so that it is possible that many natural and infectious biofilms originate wholly or partially from pre-formed cell aggregates. Here, we use agent-based computer simulations to investigate the role of pre-formed aggregates in biofilm development. Focusing on the initial shape the aggregate forms on the surface, we find that the degree of spreading of an aggregate on a surface can play an important role in determining its eventual fate during biofilm development. Specifically, initially spread aggregates perform better when competition with surrounding unaggregated bacterial cells is low, while initially rounded aggregates perform better when competition with surrounding unaggregated cells is high. These contrasting outcomes are governed by a trade-off between aggregate surface area and height. Our results provide new insight into biofilm formation and development, and reveal new factors that may be at play in the social evolution of biofilm communities.1. Fig2.zip contains image files used to create Fig 2 of manuscript.
2. Fig3.zip contains all agent_State files for generating Fig 3 of manuscript.
3. Fig4.zip contains image files used to create Fig 4 of manuscript.
4. Fig5.zip contains nutrient concentration field data for the spread aggregate in the absence of competition along with corresponding agent_State files.
5. Fig6.zip contains all agent_State files used to create Fig 6.
6. Fig7_to_9.zip contains all agent_Sum files for all densities used to create figures 7 to 9.
7. SI_morphologies_different_concs_densities.zip contains all simulation output files used for Fig S4.
8. SI_high_conc_data.zip contains the final agent_Sum files from the high concentration runs for the spread and rounded aggregate used for Fig S7.
9. SI_3D_data_dens_0_03_aggregate_conf1.zip contains all simulations output from the aggregate simulations in 3D (section J of SI) at density 0.03 cells per micron squared for aggregate configuration 1.
10. SI_3D_data_dens_0_03_aggregate_conf2.zip contains all simulations output from the aggregate simulations in 3D (section J of SI) at density 0.03 cells per micron squared for aggregate configuration 2.
11. SI_3D_data_dens_0_03_aggregate_conf3.zip contains all simulations output from the aggregate simulations in 3D (section J of SI) at density 0.03 cells per micron squared for aggregate configuration 3.
12. SI_3D_data_dens_0_002_aggregate_conf1.zip contains all simulations output from the aggregate simulations in 3D (section J of SI) at density 0.002 cells per micron squared for aggregate configuration 1.
13. SI_3D_data_dens_0_002_aggregate_conf2.zip contains all simulations output from the aggregate simulations in 3D (section J of SI) at density 0.002 cells per micron squared for aggregate configuration 2.
14. SI_3D_data_dens_0_002_aggregate_conf3.zip contains all simulations output from the aggregate simulations in 3D (section J of SI) at density 0.002 cells per micron squared for aggregate configuration 3
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
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
Computer simulations of liquids with intrinsic microporosity
No full textDesigning porous materials capable of hosting molecular species in cavities of molecular dimensions is an important goal in materials science and engineering. Contrary to the small, transient cavities that exist in the interstitial voids between the molecules of any conventional liquid, a "porous liquid" possesses well-defined, permanent voids inherent to the molecular architecture of the liquid molecules. The efficacy of such a microporous liquid lies in the ability of these intramolecular cavities to selectively house molecular guests. In this thesis we use computer simulations to embark on the first investigation into the microporous nature of potential "porous liquids", and establish whether this novel concept is viable. Simulations studies, using models as an approximation to the geometry of cage-like molecules, suggest that it is possible to design a system that exhibits permanent microporosity in the liquid phase. By calculating the distribution of cavity sizes in the liquid samples and simulating gas absorption experiments, we also establish that an existing system (synthesised by our experimental collaborators) is a potential candidate as the first microporous liquid.EThOS - Electronic Theses Online ServiceGBUnited Kingdo
Dynamics of polymers embedded in nematic and active fluids
Get PDFComplex fluids—including suspensions of polymers, colloids, and liquid crystals—
exhibit fascinating rheological properties that vary with time, stress, and
temperature. Their inherent versatility enables a broad spectrum of applications
in both biology (e.g., lubrication, protection and digestion via mucus and saliva)
and manufacturing (e.g., shear-thinning behaviour in extrusion-based additive
manufacturing and injectable hydrogels for controlled drug delivery). Extensive
research has provided a detailed understanding of these materials, paving the
way for the development of composite or hypercomplex systems that combine
multiple complex fluids to yield emergent properties not present in the individual
components.
This thesis investigates hypercomplex polymeric materials, focusing on systems
in which polymers are embedded in rheologically complex or active backgrounds.
Simulating such systems requires a versatile computational framework capable of
capturing thermal fluctuations, hydrodynamic interactions, and spatiotemporally
varying active forces—features that become critical on mesoscopic length scales
and energy scales comparable to thermal energy. To this end, a hybrid coarsegrained
simulation approach is employed: the background fluid is modelled via
multi-particle collision dynamics, while the polymer dynamics are resolved using
molecular dynamics. This framework enables the exploration of passive polymeric
suspensions in hypercomplex environments.
The first part of this work examines polymers embedded in nematic liquid
crystalline media. Despite extensive studies on both liquid crystals and polymers
individually, the behaviour of a single polymer in a nematic background remains
largely uncharted. Here, we explore the coupling between the polymer backbone
and the orientational order of a passive nematic fluid. We show that the polymer
adopts conformations featuring hairpins—sudden kinks along the backbone—that
allow it to conform to the nematic symmetry while maintaining a diverse range of
configurations. These hairpins are responsible for inducing anisotropic diffusivity
in the polymer.
The second part addresses systems in which passive polymers are immersed
in an active nematic fluid, with activity introduced via locally injected energy
through force dipoles. In this scenario, active, self-organised coherent flows advect
the polymer, resulting in a thousand-fold increase in diffusivity compared to
equilibrium conditions. This dramatic enhancement is governed by the interplay
of key dimensionless numbers—the Peclet number and the Weissenberg number,
which are intrinsically linked through the Ericksen number that characterises the
ratio of fundamental length scales in the system.
The third part investigates how flexible polymers respond to active nematic flows
and uncovers a length-dependent transition in their conformations. Depending on
the balance between polymer size and the emergent flow scale, chains either compress
or stretch: short polymers collapse due to asymmetric, transient interactions
with motile defects, while long polymers align and elongate along coherent flow
structures. This behaviour reflects a general principle—conformational control
through competition between intrinsic polymer dimensions and the structural
length scale of the active medium—offering a unified framework for interpreting
polymer conformational dynamics in diverse active environments.
In summary, this work demonstrates how hypercomplex environments—formed
by embedding polymers in structured or active fluids—can fundamentally reshape
polymer dynamics and conformations. By tuning parameters, such as the
coupling to the nematic orientation, active length scale or polymer length, it
becomes possible to drive transitions between compact and extended states, or to
control transport. This perspective provides a foundation for the rational design
of responsive soft materials and offers a unifying framework for understanding the
interplay between structure and dynamics in non-equilibrium polymeric systems.
In doing so, it opens new directions for exploring self-organisation and functional
behaviour in active and biologically relevant environments
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
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
- …
