Computer Simulations of Biological Growth Patterns: Tree Modeling Success and Applications

The purpose of this investigation was to explore the depiction of trees in three dimensions on a microcomputer. While the use of computer-aided design in landscape architecture is increasing, imagery for plant materials is found to be at a more or less symbolic level. The literature concerning previous inquiries into the mechanisms of tree growth and differentiation provide a good deal of information ranging from physiological basics to sophisticated structural and mathematical growth models. This forms the basis from which programming work proceeded. In this context, the body of work reported here emphasizes the development of a programming methodology for achieving better tree images, rather than the sophistication of the images them-selves. A major goal in this effort was simplicity in the resulting algorithms. This is significant in both minimizing use of computer memory, and in aiding the transfer of the algorithms to other devices and uses. Discussed are the developmental steps taken from an initial tree model requiring a digitizing tablet and the internal storage of coordinates, to a tree model in which machine memory and algorithm complexity are minimized. The methodology deemed most useful is that of storing the tr:es as a general set of rules for image generation, rather than a lengthy data file for each tree. The operational value of this process is intrinsic to future applications; whether six discrete tree types are to be used or sixty types, the computer is working vii with the same amount of data -- the tree generation algorithm. Further applications of this approach could offer savings in both storage requirements and data input for a variety of complex graphic images

Optimizing Traffic Lights in a Cellular Automaton Model for City Traffic

We study the impact of global traffic light control strategies in a recently proposed cellular automaton model for vehicular traffic in city networks. The model combines basic ideas of the Biham-Middleton-Levine model for city traffic and the Nagel-Schreckenberg model for highway traffic. The city network has a simple square lattice geometry. All streets and intersections are treated equally, i.e., there are no dominant streets. Starting from a simple synchronized strategy we show that the capacity of the network strongly depends on the cycle times of the traffic lights. Moreover we point out that the optimal time periods are determined by the geometric characteristics of the network, i.e., the distance between the intersections. In the case of synchronized traffic lights the derivation of the optimal cycle times in the network can be reduced to a simpler problem, the flow optimization of a single street with one traffic light operating as a bottleneck. In order to obtain an enhanced throughput in the model improved global strategies are tested, e.g., green wave and random switching strategies, which lead to surprising results.Comment: 13 pages, 10 figure

Development of a lyophilization process for Campylobacter bacteriophage storage and transport

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Bacteriophages are a sustainable alternative to control pathogenic bacteria in the post-antibiotic era. Despite promising reports, there are still obstacles to phage use, notably titer stability and transport‐associated expenses for applications in food and agriculture. In this study, we have developed a lyophilization approach to maintain phage titers, ensure efficacy and reduce transport costs of Campylobacter bacteriophages. Lyophilization methods were adopted with various excipients to enhance stabilization in combination with packaging options for international transport. Lyophilization of Eucampyvirinae CP30A using tryptone formed a cake that limited processing titer reduction to 0.35 ± 0.09 log10 PFU mL‐1. Transmission electron microscopy revealed the initial titer reduction was associated with capsid collapse of a subpopulation. Freeze‐dried phages were generally stable under refrigerated vacuum conditions and showed no significant titer changes over 3 months incubation at 4 °C (p = 0.29). Reduced stability was observed for lyophilized phages that were incubated either at 30 °C under vacuum or at 4 °C at 70% or 90% relative humidity. Refrigerated international transport and rehydration of the cake resulted in a total phage titer reduction of 0.81 ± 0.44 log10 PFU mL‐1. A significantly higher titer loss was observed for phages that were not refrigerated during transport (2.03 ± 0.32 log10 PFU mL‐1). We propose that lyophilization offers a convenient method to preserve and transport Campylobacter phages, with minimal titer reduction after the drying process

Collective Efficacy: Development and Validation of a Measurement Scale for Use in Public Health and Development Programmes.

Impact evaluations of water, sanitation, and hygiene interventions have demonstrated lower than expected health gains, in some cases due to low uptake and sustained adoption of interventions at a community level. These findings represent common challenges for public health and development programmes relying on collective action. One possible explanation may be low collective efficacy (CE)-perceptions regarding a group's ability to execute actions related to a common goal. The purpose of this study was to develop and validate a metric to assess factors related to CE. We conducted this research within a cluster-randomised sanitation and hygiene trial in Amhara, Ethiopia. Exploratory and confirmatory factor analyses were carried out to examine underlying structures of CE for men and women in rural Ethiopia. We produced three CE scales: one each for men and women that allow for examinations of gender-specific mechanisms through which CE operates, and one 26-item CE scale that can be used across genders. All scales demonstrated high construct validity. CE factor scores were significantly higher for men than women, even among household-level male-female dyads. These CE scales will allow implementers to better design and target community-level interventions, and examine the role of CE in the effectiveness of community-based programming

A manganese photosensitive tricarbonyl molecule [Mn(CO)3(tpa-κ(3)N)]Br enhances antibiotic efficacy in a multi-drug-resistant Escherichia coli

Carbon monoxide-releasing molecules (CORMs) are a promising class of new antimicrobials, with multiple modes of action that are distinct from those of standard antibiotics. The relentless increase in antimicrobial resistance, exacerbated by a lack of new antibiotics, necessitates a better understanding of how such novel agents act and might be used synergistically with established antibiotics. This work aimed to understand the mechanism(s) underlying synergy between a manganese-based photoactivated carbon monoxide-releasing molecule (PhotoCORM), [Mn(CO)3(tpa-κ(3)N)]Br [tpa=tris(2-pyridylmethyl)amine], and various classes of antibiotics in their activities towards Escherichia coli EC958, a multi-drug-resistant uropathogen. The title compound acts synergistically with polymyxins [polymyxin B and colistin (polymyxin E)] by damaging the bacterial cytoplasmic membrane. [Mn(CO)3(tpa-κ(3)N)]Br also potentiates the action of doxycycline, resulting in reduced expression of tetA, which encodes a tetracycline efflux pump. We show that, like tetracyclines, the breakdown products of [Mn(CO)3(tpa-κ(3)N)]Br activation chelate iron and trigger an iron starvation response, which we propose to be a further basis for the synergies observed. Conversely, media supplemented with excess iron abrogated the inhibition of growth by doxycycline and the title compound. In conclusion, multiple factors contribute to the ability of this PhotoCORM to increase the efficacy of antibiotics in the polymyxin and tetracycline families. We propose that light-activated carbon monoxide release is not the sole basis of the antimicrobial activities of [Mn(CO)3(tpa-κ(3)N)]Br

Comparison of 2D and 3D calculation of left ventricular torsion as circumferential-longitudinal shear angle using cardiovascular magnetic resonance tagging

<p>Abstract</p> <p>Purpose</p> <p>To compare left ventricular (LV) torsion represented as the circumferential-longitudinal (CL) shear angle between 2D and 3D quantification, using cardiovascular magnetic resonance (CMR).</p> <p>Methods</p> <p>CMR tagging was performed in six healthy volunteers. From this, LV torsion was calculated using a 2D and a 3D method. The cross-correlation between both methods was evaluated and comparisons were made using Bland-Altman analysis.</p> <p>Results</p> <p>The cross-correlation between the curves was <it>r</it>²= 0.97 ± 0.02. No significant time-delay was observed between the curves. Bland-Altman analysis revealed a significant positive linear relationship between the difference and the average value of both analysis methods, with the 2D results showing larger values than the 3D. The difference between both methods can be explained by the definition of the 2D method.</p> <p>Conclusion</p> <p>LV torsion represented as CL shear quantified by the 2D and 3D analysis methods are strongly related. Therefore, it is suggested to use the faster 2D method for torsion calculation.</p

PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

The PhosPhAt database of Arabidopsis phosphorylation sites was initially launched in August 2007. Since then, along with 10-fold increase in database entries, functionality of PhosPhAt (phosphat.mpimp-golm.mpg.de) has been considerably upgraded and re-designed. PhosPhAt is now more of a web application with the inclusion of advanced search functions allowing combinatorial searches by Boolean terms. The results output now includes interactive visualization of annotated fragmentation spectra and the ability to export spectra and peptide sequences as text files for use in other applications. We have also implemented dynamic links to other web resources thus augmenting PhosPhAt-specific information with external protein-related data. For experimental phosphorylation sites with information about dynamic behavior in response to external stimuli, we display simple time-resolved diagrams. We have included predictions for pT and pY sites and updated pS predictions. Access to prediction algorithm now allows ‘on-the-fly’ prediction of phosphorylation of any user-uploaded protein sequence. Protein Pfam domain structures are now mapped onto the protein sequence display next to experimental and predicted phosphorylation sites. Finally, we have implemented functional annotation of proteins using MAPMAN ontology. These new developments make the PhosPhAt resource a useful and powerful tool for the scientific community as a whole beyond the plant sciences

Transformative Materials to Create 3D Functional Human Tissue Models In Vitro in a Reproducible Manner

Recreating human tissues and organs in the petri dish to establish models as tools in biomedical sciences has gained momentum. These models can provide insight into mechanisms of human physiology, disease onset, and progression, and improve drug target validation, as well as the development of new medical therapeutics. Transformative materials play an important role in this evolution, as they can be programmed to direct cell behavior and fate by controlling the activity of bioactive molecules and material properties. Using nature as an inspiration, scientists are creating materials that incorporate specific biological processes observed during human organogenesis and tissue regeneration. This article presents the reader with state-of-the-art developments in the field of in vitro tissue engineering and the challenges related to the design, production, and translation of these transformative materials. Advances regarding (stem) cell sources, expansion, and differentiation, and how novel responsive materials, automated and large-scale fabrication processes, culture conditions, in situ monitoring systems, and computer simulations are required to create functional human tissue models that are relevant and efficient for drug discovery, are described. This paper illustrates how these different technologies need to converge to generate in vitro life-like human tissue models that provide a platform to answer health-based scientific questions.</p