Modelling quarantine effects on SARS-CoV-2 epidemiological dynamics in Chilean communes and their relationship with the Social Priority Index.

Background: An epidemiological model (susceptible, un-quarantined infected, quarantined infected, confirmed infected (SUQC)) was previously developed and applied to incorporate quarantine measures and calculate COVID-19 contagion dynamics and pandemic control in some Chinese regions. Here, we generalized this model to incorporate the disease recovery rate and applied our model to records of the total number of confirmed cases of people infected with the SARS-CoV-2 virus in some Chilean communes. Methods: In each commune, two consecutive stages were considered: a stage without quarantine and an immediately subsequent quarantine stage imposed by the Ministry of Health. To adjust the model, typical epidemiological parameters were determined, such as the confirmation rate and the quarantine rate. The latter allowed us to calculate the reproduction number. Results: The mathematical model adequately reproduced the data, indicating a higher quarantine rate when quarantine was imposed by the health authority, with a corresponding decrease in the reproduction number of the virus down to values that prevent or decrease its exponential spread. In general, during this second stage, the communes with the lowest social priority indices had the highest quarantine rates, and therefore, the lowest effective viral reproduction numbers. This study provides useful evidence to address the health inequity of pandemics. The mathematical model applied here can be used in other regions or easily modified for other cases of infectious disease control by quarantine.

Modelling Quarantine Effects on SARS-CoV-2 Epidemiological Dynamics in Chilean Communes and their Relationship with the Social Priority Index

An epidemiological model [Susceptible, Un-quarantined infected, Quarantined infected, Confirmed infected (SUQC)] has previously been developed and applied to incorporate quarantine measures and calculate COVID-19 contagion dynamics and pandemic control in some Chinese regions. Here, we generalized this model to incorporate the disease recovery rate and applied our model to records of the total number of confirmed cases of people infected with the SARS-CoV-2 virus in some Chilean communes. In each commune, two consecutive stages were considered: a stage without quarantine and an immediately subsequent quarantine stage imposed by the Ministry of Health. To adjust the model, typical epidemiological parameters were determined, such as the confirmation rate and the quarantine rate. The latter allowed us to calculate the reproduction number. The mathematical model adequately reproduced the data, indicating a higher quarantine rate when quarantine was imposed by the health authority, with a corresponding decrease in the reproduction number of the virus down to values that prevent or decrease its exponential spread. In general, during this second stage, the communes with the lowest social priority indices had the highest quarantine rates, and therefore, the lowest effective viral reproduction numbers. This study provides useful evidence to address the health inequity of pandemics. The mathematical model applied here can be used in other regions or easily modified for other cases of infectious disease control by quarantine.

Reimagining Rural: Shifting Paradigms About Health and Well-Being in the Rural United States.

Rural health disparities have attracted increased national attention, compelling an expanded focus on rural health research. In this article, we deconstruct the definitions and narratives of "rural" communities and suggest that a paradigm shift is needed that centers the complexity and strength of rural places. We discuss the relevance of health equity frameworks, implementation science, and community-engaged approaches to promote rural well-being. Focusing on rural in its own right will lead to intervention innovations and reinvention with implications beyond rural areas. We conclude with suggestions for research and practice to inspire renewed interest in partnering with rural communities to promote health equity.

Average and Standard Deviation of the Error Function for Random Genetic Codes with Standard Stop Codons.

The origin of the genetic code has been attributed in part to an accidental assignment of codons to amino acids. Although several lines of evidence indicate the subsequent expansion and improvement of the genetic code, the hypothesis of Francis Crick concerning a frozen accident occurring at the early stage of genetic code evolution is still widely accepted. Considering Crick's hypothesis, mathematical descriptions of hypothetical scenarios involving a huge number of possible coexisting random genetic codes could be very important to explain the origin and evolution of a selected genetic code. This work aims to contribute in this regard, that is, it provides a theoretical framework in which statistical parameters of error functions are calculated. Given a genetic code and an amino acid property, the functional code robustness is estimated by means of a known error function. In this work, using analytical calculations, general expressions for the average and standard deviation of the error function distributions of completely random codes with standard stop codons were obtained. As a possible biological application of these results, any set of amino acids and any pure or mixed amino acid properties can be used in the calculations, such that, in case of having to select a set of amino acids to create a genetic code, possible advantages of natural selection of the genetic codes could be discussed.

Exploring the structure-function relationship in a hypothetical membrane protein from a nucleotide sequence.

An educational activity is proposed that uses software for proteomic analysis and databases available for free on the Internet to estimate the structure and function of a hypothetical protein from its coding nucleotide sequence. This bioinformatics activity is recommended for integrated introductory courses that address the structure function relationship in proteins.

Controls on the size distributions of shallow landslides.

Rainfall-triggered shallow landslides are destructive hazards and play an important role in landscape processes. A theory explaining the size distributions of such features remains elusive. Prior work connects size distributions to topography, but field-mapped inventories reveal pronounced similarities in the form, mode, and spread of distributions from diverse landscapes. We analyze nearly identical distributions occurring in the Oregon Coast Range and the English Lake District, two regions of strikingly different topography, lithology, and vegetation. Similarity in minimum sizes at these sites is partly explained by theory that accounts for the interplay of mechanical soil strength controls resisting failure. Maximum sizes, however, are not explained by current theory. We develop a generalized framework to account for the entire size distribution by unifying a mechanistic slope stability model with a flexible spatial-statistical description for the variability of hillslope strength. Using hillslope-scale numerical experiments, we find that landslides can occur not only in individual low strength areas but also across multiple smaller patches that coalesce. We show that reproducing observed size distributions requires spatial strength variations to be strongly localized, of large amplitude, and a consequence of multiple interacting factors. Such constraints can act together with the mechanical determinants of landslide initiation to produce size distributions of broadly similar character in widely different landscapes, as found in our examples. We propose that size distributions reflect the systematic scale dependence of the spatially averaged strength. Our results highlight the critical need to constrain the form, amplitude, and wavelength of spatial variability in material strength properties of hillslopes.

Experimental induction and mathematical modeling of Ca2+ dynamics in rat round spermatids.

Cytosolic Ca2+ concentration ([Ca2+ ]) has an important role in spermatozoa and hence it regulates fertilization. In male germinal cells, there are indirect evidences that this ion could regulate physiological processes in spermatogenesis. Since little is known about Ca2+ homeostasis in spermatogenic cells, in this work we propose a mathematical model that accounts for experimental [Ca2+ ] dynamics triggered by blockade of the SERCA transport ATPase with thapsigargin in round rat spermatids, without external Ca2+ and with different extracellular lactate concentrations. The model included three homogeneous calcium compartments and Ca2+-ATPase activities sensitive and insensitive to thapsigargin, and it adjusted satisfactorily the experimental calcium dynamic data. Moreover, an extended version of the model satisfactorily adjusted the stationary states of calcium modulated by extracellular lactate, which is consistent with the participation of a low affinity lactate transporter and further lactate metabolism in these cells. Further studies and modeling would be necessary to shed some light into the relation between Ca2+-lactate-ATP homeostasis and cell-cell interactions in the seminiferous tubules that are expected to modulate Ca2+ dynamics by hormonal factors or energetic substrates in meiotic and postmeiotic spermatogenic cells.

Local conditions for global stability in the space of codons of the genetic code.

The polar requirement is an attribute of amino acids that is a major determinant of the structure and function of the proteins, and it plays a role in the flexibility and robustness of the genetic code. The viability of an organism depends on flexibility, which allows the exploration of new functions. However, robustness is necessary to protect the organism from deleterious changes derived from misreading errors and single-point mutations. Compared with random codes, the standard genetic code is one of the most robust against such errors. Here, using analytical and numerical calculations and the set of amino acid-encoding codons, we have proposed some local conditions that are necessary for the optimal robustness of the genetic code, and we explored the association between the local conditions and the robustness. The localness of the proposed conditions and the underlying evolutionary mechanism, which begins with a random code and progresses toward more efficient codes (e.g., the standard code), might be biologically plausible.

Flux theory for Poisson distributed pores with Gaussian permeability.

The mean of the solute flux through membrane pores depends on the random distribution and permeability of the pores. Mathematical models including such randomness factors make it possible to obtain statistical parameters for pore characterization. Here, assuming that pores follow a Poisson distribution in the lipid phase and that their permeabilities follow a Gaussian distribution, a mathematical model for solute dynamics is obtained by applying a general result from a previous work regarding any number of different kinds of randomly distributed pores. The new proposed theory is studied using experimental parameters obtained elsewhere, and a method for finding the mean single pore flux rate from liposome flux assays is suggested. This method is useful for pores without requiring studies by patch-clamp in single cells or single-channel recordings. However, it does not apply in the case of ion-selective channels, in which a more complex flux law combining the concentration and electrical gradient is required.

Learning about solubility.

Qualitative questions are proposed to assess the understanding of solubility and some of its applications. To improve those results, a simple quantitative problem on the precipitation of proteins is proposed.

Fluxes theory in experiments with random distributed channels on vesicles.

When channels are randomly distributed in a population of vesicles, disregarding the number of channels per vesicle, these channels follow a Poisson distribution. This has been verified in many cases, determining the average of channels per vesicle. However, to determine kinetic parameters in population studies, a mathematical expression for the mean flux of solute through channels per vesicle is necessary. Hence, here, this mean flux is calculated, assuming Poisson distributed channels in a population of vesicle. Moreover, this result has been generalized to any number of different kinds of channels (i.e., channels with different permeabilities). These results, useful for in vitro experiments with mixed both channels and vesicles, can be supplemented with those from other techniques, in order to understanding how the nature of the lipid membrane affects kinetic parameters of channel.

Probable relationship between partitions of the set of codons and the origin of the genetic code.

Here we study the distribution of randomly generated partitions of the set of amino acid-coding codons. Some results are an application from a previous work, about the Stirling numbers of the second kind and triplet codes, both to the cases of triplet codes having four stop codons, as in mammalian mitochondrial genetic code, and hypothetical doublet codes. Extending previous results, in this work it is found that the most probable number of blocks of synonymous codons, in a genetic code, is similar to the number of amino acids when there are four stop codons, as well as it could be for a primigenious doublet code. Also it is studied the integer partitions associated to patterns of synonymous codons and it is shown, for the canonical code, that the standard deviation inside an integer partition is one of the most probable. We think that, in some early epoch, the genetic code might have had a maximum of the disorder or entropy, independent of the assignment between codons and amino acids, reaching a state similar to "code freeze" proposed by Francis Crick. In later stages, maybe deterministic rules have reassigned codons to amino acids, forming the natural codes, such as the canonical code, but keeping the numerical features describing the set partitions and the integer partitions, like a "fossil numbers"; both kinds of partitions about the set of amino acid-coding codons.

Application of the Sequential Organ Failure Assessment Score to predict outcome in critically ill dogs: preliminary results.

In human medicine the Sequential Organ Failure Assessment (SOFA) score is one of the most commonly organ dysfunction scoring systems used to assess critically ill patients and to predict the outcome in Intensive Care Units (ICUs). It is composed of scores from six organ systems (respiratory, cardiovascular, hepatic, coagulation, renal, and neurological) graded according to the degree of the dysfunction. The aim of the current study was to describe the applicability of the SOFA score in assessing the outcome of critically ill dogs. A total of 45 dogs admitted to the ICU was enrolled. Among these, 40 dogs completed the study: 50 % survived and left the veterinary clinic. The SOFA score was computed for each dog every 24 hours for the first 3 days of ICU stay, starting on the day of admission. A statistically significant correlation between SOFA score and death or survival was found. Most of the dogs showing an increase of the SOFA score in the first 3 days of hospitalization died, whereas the dogs with a decrease of the score survived. These results suggest that the SOFA score system could be considered a useful indicator of prognosis in ICUs hospitalized dogs.

The most probable number of blocks for the partitions of the set of codons could have determined the number of standard amino acids.

Given a genetic code formed by 64 codons, we calculate the number of partitions of the set of encoding amino acid codons. When there are 0-3 stop codons, the results indicate that the most probable number of partitions is 19 and/or 20. Then, assuming that in the early evolution the genetic code could have had random variations, we suggest that the most probable number of partitions of the set of encoding amino acid codons determined the actual number 20 of standard amino acids.

Lipid metabolizing enzyme activities modulated by phospholipid substrate lateral distribution.

Biological membranes contain many domains enriched in phospholipid lipids and there is not yet clear explanation about how these domains can control the activity of phospholipid metabolizing enzymes. Here we used the surface dilution kinetic theory to derive general equations describing how complex substrate distributions affect the activity of enzymes following either the phospholipid binding kinetic model (which assumes that the enzyme molecules directly bind the phospholipid substrate molecules), or the surface-binding kinetic model (which assumes that the enzyme molecules bind to the membrane before binding the phospholipid substrate). Our results strongly suggest that, if the enzyme follows the phospholipid binding kinetic model, any substrate redistribution would increase the enzyme activity over than observed for a homogeneous distribution of substrate. Besides, enzymes following the surface-binding model would be independent of the substrate distribution. Given that the distribution of substrate in a population of micelles (each of them a lipid domain) should follow a Poisson law, we demonstrate that the general equations give an excellent fit to experimental data of lipases acting on micelles, providing reasonable values for kinetic parameters--without invoking special effects such as cooperative phenomena. Our theory will allow a better understanding of the cellular-metabolism control in membranes, as well as a more simple analysis of the mechanisms of membrane acting enzymes.

Applying community-based participatory research principles to the development of a smoking-cessation program for American Indian teens: telling our story

Community-based participatory research provides communities and researchers with opportunities to develop interventions that are effective as well as acceptable and culturally competent. The present project responds to the voices of the North Carolina American Indian (AI) community and the desire for their youth to recognize tobacco addiction and commercial cigarette smoking as debilitating to their health and future. Seven community-based participatory principles led to the AI adaptation of the Not On Tobacco teen-smoking-cessation program and fostered sound research and meaningful results among an historically exploited population. Success was attributed to values-driven, community-based principles that (a) assured recognition of a community-driven need, (b) built on strengths of the tribes, (c) nurtured partnerships in all project phases, (d) integrated the community's cultural knowledge, (e) produced mutually beneficial tools/products, (f) built capacity through co-learning and empowerment, (g) used an iterative process of development, and (h) shared findings/ knowledge with all partners. (AU)

Changes of enzyme activity in lipid signaling pathways related to substrate reordering.

The static fluid mosaic model of biological membranes has been progressively complemented by a dynamic membrane model that includes phospholipid reordering in domains that are proposed to extend from nanometers to microns. Kinetic models for lipolytic enzymes have only been developed for homogeneous lipid phases. In this work, we develop a generalization of the well-known surface dilution kinetic theory to cases where, in a same lipid phase, both domain and nondomain phases coexist. Our model also allows understanding the changes in enzymatic activity due to a decrease of free substrate concentration when domains are induced by peptides. This lipid reordering and domain dynamics can affect the activity of lipolytic enzymes, and can provide a simple explanation for how basic peptides, with a strong direct interaction with acidic phospholipids (such as beta-amyloid peptide), may cause a complex modulation of the activities of many important enzymes in lipid signaling pathways.

A 2-year efficacy study of Not On Tobacco in Florida: an overview of program successes in changing teen smoking behavior.

BACKGROUND: Adolescent smoking has been an issue of major concern in the United States. This has led to a need for the development, evaluation, and dissemination of effective youth cessation programs. The purpose of this paper is to report the results of a 2-year demonstration study (1999-2000) of the American Lung Association's teen smoking cessation program, the Not On Tobacco (NOT) program. METHODS: The study used a "matched" design wherein each NOT school was matched to a brief intervention (BI) school. The study consisted of 20 NOT and 20 BI Florida high schools encompassing 627 students. The primary outcome measures were carbon monoxide-validated quit and reduction rates for NOT and BI schools at 5.2 months postprogram. RESULTS: NOT smoking cessation and reduction outcomes were significantly better than those of the brief intervention. Further, data indicate that NOT was more effective than the brief intervention for females compared with males; males showed successful quit attempts in both intervention groups. Overall, more NOT youth either quit or reduced smoking than did BI youth. CONCLUSIONS: These positive smoking behavior changes suggest that NOT is an effective teen smoking cessation option.

Teen smoking cessation: making it work through school and community partnerships.

For the past several years, the West Virginia University Prevention Research Center has been collaborating with state and national partners to design, evaluate, and disseminate the American Lung Association's new teen smoking cessation program, Not On Tobacco (N-O-T). This article describes a process that began with a field-identified need followed by a formal needs assessment and literature review. It also details how partners worked together to identify important program components, implementation strategies, and the evaluation protocol. Finally, it describes the process by which the American Lung Association adopted and disseminated N-O-T across West Virginia and the United States.