Compositional Modeling with Stock and Flow Diagrams

Stock and flow diagrams are widely used in epidemiology to model the dynamics of populations. Although tools already exist for building these diagrams and simulating the systems they describe, we have created a new package called StockFlow, part of the AlgebraicJulia ecosystem, which uses ideas from category theory to overcome notable limitations of existing software. Compositionality is provided by the theory of decorated cospans: stock and flow diagrams can be composed to form larger ones in an intuitive way formalized by the operad of undirected wiring diagrams. Our approach also cleanly separates the syntax of stock and flow diagrams from the semantics they can be assigned. We consider semantics in ordinary differential equations, although others are possible. As an example, we explain code in StockFlow that implements a simplified version of a COVID-19 model used in Canada.Comment: In Proceedings ACT 2022, arXiv:2307.1551

Spontaneous circadian rhythms in a cold-Adapted natural isolate of Aureobasidium pullulans

Indexación: Scopus.Circadian systems enable organisms to synchronize their physiology to daily and seasonal environmental changes relying on endogenous pacemakers that oscillate with a period close to 24 h even in the absence of external timing cues. The oscillations are achieved by intracellular transcriptional/translational feedback loops thoroughly characterized for many organisms, but still little is known about the presence and characteristics of circadian clocks in fungi other than Neurospora crassa. We sought to characterize the circadian system of a natural isolate of Aureobasidium pullulans, a cold-Adapted yeast bearing great biotechnological potential. A. pullulans formed daily concentric rings that were synchronized by light/dark cycles and were also formed in constant darkness with a period of 24.5 h. Moreover, these rhythms were temperature compensated, as evidenced by experiments conducted at temperatures as low as 10 °C. Finally, the expression of clock-essential genes, frequency, white collar-1, white collar-2 and vivid was confirmed. In summary, our results indicate the existence of a functional circadian clock in A. pullulans, capable of sustaining rhythms at very low temperatures and, based on the presence of conserved clock-gene homologues, suggest a molecular and functional relationship to well-described circadian systems.https://www.nature.com/articles/s41598-017-14085-

An Algebraic Framework for Stock & Flow Diagrams and Dynamical Systems Using Category Theory

Mathematical modeling of infectious disease at scale is important, but challenging. Some of these difficulties can be alleviated by an approach that takes diagrams seriously as mathematical formalisms in their own right. Stock & flow diagrams are widely used as broadly accessible building blocks for infectious disease modeling. In this chapter, rather than focusing on the underlying mathematics, we informally use communicable disease examples created by the implemented software of StockFlow.jl to explain the basics, characteristics, and benefits of the categorical framework. We first characterize categorical stock & flow diagrams, and note the clear separation between the syntax of stock & flow diagrams and their semantics, demonstrating three examples of semantics already implemented in the software: ODEs, causal loop diagrams, and system structure diagrams. We then establish composition and stratification frameworks and examples for stock & flow diagrams. Applying category theory, these frameworks can build large diagrams from smaller ones in a modular fashion. Finally, we introduce the open-source ModelCollab software for diagram-centric real-time collaborative modeling. Using the graphical user interface, this web-based software allows the user to undertake the types of categorically-rooted operations discussed above, but without any knowledge of their categorical foundations

Polymorphism of viral dsRNA in Xanthophyllomyces dendrorhous strains isolated from different geographic areas

<p>Abstract</p> <p>Background</p> <p>Strains of the astaxanthin producing yeast <it>Xanthophyllomyces dendrorhous </it>have been isolated from different cold regions around the earth, and the presence of double stranded RNA (dsRNA) elements was described in some isolates. This kind of viruses is widely distributed among yeasts and filamentous fungi and, although generally are cryptic in function, their studies have been a key factor in the knowledge of important fungi. In this work, the characterization and genetic relationships among dsRNA elements were determined in strains representatives of almost all regions of the earth where <it>X. dendrorhous </it>have been isolated.</p> <p>Results</p> <p>Almost all strains of <it>X. dendrorhous </it>analyzed carry one, two or four dsRNA elements, of molecular sizes in the range from 0.8 to 5.0 kb. Different dsRNA-patterns were observed in strains with different geographic origin, being L1 (5.0 kb) the common dsRNA element. By hybridization assays a high genomic polymorphism was observed among L1 dsRNAs of different <it>X. dendrorhous </it>strains. Contrary, hybridization was observed between L1 and L2 dsRNAs of strains from same or different regions, while the dsRNA elements of minor sizes (M, S1, and S2) present in several strains did not show hybridization with neither L1 or L2 dsRNAs. Along the growth curve of UCD 67-385 (harboring four dsRNAs) an increase of L2 relative to L1 dsRNA was observed, whiles the S1/L1 ratio remains constant, as well as the M/L1 ratio of Patagonian strain. Strains cured of S2 dsRNA were obtained by treatment with anisomycin, and comparison of its dsRNA contents with uncured strain, revealed an increase of L1 dsRNA while the L2 and S1 dsRNA remain unaltered.</p> <p>Conclusion</p> <p>The dsRNA elements of <it>X. dendrorhous </it>are highly variable in size and sequence, and the dsRNA pattern is specific to the geographic region of isolation. Each L1 and L2 dsRNA are viral elements able to self replicate and to coexist into a cell, and L1 and S2 dsRNAs elements could be part of a helper/satellite virus system in <it>X. dendrorhous</it>.</p

Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae

Interspecific hybrids are commonplace in agriculture and horticulture; bread wheat and grapefruit are but two examples. The benefits derived from interspecific hybridisation include the potential of generating advantageous transgressive phenotypes. This paper describes the generation of a new breed of wine yeast by interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast strain and Saccharomyces mikatae, a species hitherto not associated with industrial fermentation environs. While commercially available wine yeast strains provide consistent and reliable fermentations, wines produced using single inocula are thought to lack the sensory complexity and rounded palate structure obtained from spontaneous fermentations. In contrast, interspecific yeast hybrids have the potential to deliver increased complexity to wine sensory properties and alternative wine styles through the formation of novel, and wider ranging, yeast volatile fermentation metabolite profiles, whilst maintaining the robustness of the wine yeast parent. Screening of newly generated hybrids from a cross between a S. cerevisiae wine yeast and S. mikatae (closely-related but ecologically distant members of the Saccharomyces sensu stricto clade), has identified progeny with robust fermentation properties and winemaking potential. Chemical analysis showed that, relative to the S. cerevisiae wine yeast parent, hybrids produced wines with different concentrations of volatile metabolites that are known to contribute to wine flavour and aroma, including flavour compounds associated with non-Saccharomyces species. The new S. cerevisiae x S. mikatae hybrids have the potential to produce complex wines akin to products of spontaneous fermentation while giving winemakers the safeguard of an inoculated ferment.Jennifer R. Bellon, Frank Schmid, Dimitra L. Capone, Barbara L. Dunn, Paul J. Chamber

Extremophilic Patagonian Microorganisms Working in Biomining

The microorganisms known as extremophiles have become a powerful tool in the field of biotechnology. Among them, acidophilic and thermophilic microorganisms capable of oxidizing iron(II) or sulfur compounds are very important in ore-processing operations as they are able to enhance the dissolution of sulfide ores. The aim of this chapter is to describe the physiological and phylogenetic characteristics of the main acidophilic species and communities found in geothermal and mining environments in Neuquen Province, Patagonia Argentina, and the advances done by our research group in their application to biomining and bioremediation of heavy metals. Additionally, the chapter includes the description of a novel thermoacidophilic archaeon from the genus Acidianus (Acidianus copahuensis) autochthonous of the Copahue geothermal area isolated and characterized by our research group.Centro de Investigación y Desarrollo en Fermentaciones IndustrialesUniversidad Nacional del Comahu

The Scrounge-atron: a phased approach to the Advanced Hydrotest Facility utilizing proton radiography

The Department of Energy has initiated its Stockpile Stewardship and Management Program (SSMP) to provide a single, integrated technical program for maintaining the continued safety and reliability of the nation's nuclear weapons stockpile in the absence of nuclear testing. Consistent with the SSMP, the Advanced Hydrotest Facility (AHF) has been conceived to provide improved radiographic imaging with multiple axes and multiple time frames. The AHF would be used to better understand the evolution of nuclear weapon primary implosion shape under normal and accident scenarios. There are three fundamental technologies currently under consideration for use on the AHF. These include linear induction acceleration, inductive-adder pulsed-power technology (both technologies using high current electron beams to produce an intense X-ray beam) and high-energy proton accelerators to produce a proton beam. The Scrounge-atron (a proton synchrotron) was conceived to be a relatively low cost demonstration of the viability of the third technology using bursts of energetic protons, magnetic lenses, and particle detectors to produce the radiographic image. In order for the Scrounge-atron to provide information useful for the AHF technology decision, the accelerator would have to be built as quickly and as economically as possible. These conditions can be met by "scrounging" parts from decommissioned accelerators across the country, especially the Main Ring at Fermilab. The Scrounge-atron is designed to meet the baseline parameters for single axis proton radiography: a 20 GeV proton beam of ten pulses, 10 degrees protons each, spaced 250 ns apart. (2 refs)

On the complexity of the Saccharomyces bayanus taxon: hybridization and potential hybrid speciation

Although the genus Saccharomyces has been thoroughly studied, some species in the genus has not yet been accurately resolved; an example is S. bayanus, a taxon that includes genetically diverse lineages of pure and hybrid strains. This diversity makes the assignation and classification of strains belonging to this species unclear and controversial. They have been subdivided by some authors into two varieties (bayanus and uvarum), which have been raised to the species level by others. In this work, we evaluate the complexity of 46 different strains included in the S. bayanus taxon by means of PCR-RFLP analysis and by sequencing of 34 gene regions and one mitochondrial gene. Using the sequence data, and based on the S. bayanus var. bayanus reference strain NBRC 1948, a hypothetical pure S. bayanus was reconstructed for these genes that showed alleles with similarity values lower than 97% with the S. bayanus var. uvarum strain CBS 7001, and of 99¿100% with the non S. cerevisiae portion in S. pastorianus Weihenstephan 34/70 and with the new species S. eubayanus. Among the S. bayanus strains under study, different levels of homozygosity, hybridization and introgression were found; however, no pure S. bayanus var. bayanus strain was identified. These S. bayanus hybrids can be classified into two types: homozygous (type I) and heterozygous hybrids (type II), indicating that they have been originated by different hybridization processes. Therefore, a putative evolutionary scenario involving two different hybridization events between a S. bayanus var. uvarum and unknown European S. eubayanus-like strains can be postulated to explain the genomic diversity observed in our S. bayanus var. bayanus strains

First observations of separated atmospheric nu_mu and bar{nu-mu} events in the MINOS detector

The complete 5.4 kton MINOS far detector has been taking data since the beginning of August 2003 at a depth of 2070 meters water-equivalent in the Soudan mine, Minnesota. This paper presents the first MINOS observations of nuµ and [overline nu ]µ charged-current atmospheric neutrino interactions based on an exposure of 418 days. The ratio of upward- to downward-going events in the data is compared to the Monte Carlo expectation in the absence of neutrino oscillations, giving Rup/downdata/Rup/downMC=0.62-0.14+0.19(stat.)±0.02(sys.). An extended maximum likelihood analysis of the observed L/E distributions excludes the null hypothesis of no neutrino oscillations at the 98% confidence level. Using the curvature of the observed muons in the 1.3 T MINOS magnetic field nuµ and [overline nu ]µ interactions are separated. The ratio of [overline nu ]µ to nuµ events in the data is compared to the Monte Carlo expectation assuming neutrinos and antineutrinos oscillate in the same manner, giving R[overline nu ][sub mu]/nu[sub mu]data/R[overline nu ][sub mu]/nu[sub mu]MC=0.96-0.27+0.38(stat.)±0.15(sys.), where the errors are the statistical and systematic uncertainties. Although the statistics are limited, this is the first direct observation of atmospheric neutrino interactions separately for nuµ and [overline nu ]µ