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DNA coding and Gödel numbering

Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we encounter the biological "atoms", the four nucleotide molecules. At the same time these four nucleotides may be considered as the "letters" of an alphabet. These four "letters", through a genetic code, generate biological "words", "phrases", "sentences" (aminoacids, proteins, cells, living organisms). In this spirit we may consider equally well a DNA strand as a mathematical statement. Inspired by the work of Kurt Gödel, we attach to each DNA strand a Gödel's number, a product of prime numbers raised to appropriate powers. To each DNA chain corresponds a single Gödel's number $G$, and inversely given a Gödel's number $G$, we can specify the DNA chain it stands for. Next, considering a single DNA strand composed of $N$ bases, we study the statistical distribution of $g$, the logarithm of $G$. Our assumption is that the choice of the $m$-th term is random and with equal probability for the four possible outcomes. The "experiment", to some extent, appears as throwing $N$ times a four-faces die. Through the moment generating function we obtain the discrete and then the continuum distribution of $g$. There is an excellent agreement between our formalism and simulated data. At the end we compare our formalism to actual data, to specify the presence of traces of non-random dynamics.

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Possible traces of resonance signaling in the genome

Although theories regarding the role of sequence-specific DNA resonance in biology have abounded for over 40 years, the published evidence for it is lacking. Here, the authors reasoned that for sustained resonance signaling, the number of oscillating DNA sequences per genome should be exceptionally high and that, therefore, genomic repeats of various sizes are good candidates for serving as resonators. Moreover, it was suggested that for the two DNA sequences to resonate, they do not necessarily have to be identical. Therefore, the existence of sequences differing in the primary sequence but having similar resonating sub-structures was proposed. It was hypothesized that such sequences, named HIDERs, would be enriched in the genomes of multicellular species. Specifically, it was hypothesized that delocalized electron clouds of purine-pyrimidine sequences could serve as the basis of HIDERs. The consequent genomic analysis confirmed the enrichment of purine-pyrimidine HIDERs in a few selected genomes of mammals, an insect, and a plant, compared to randomized sequence controls. Similarly, it was suggested that hypothetical delocalized proton clouds of the hydrogen bonds of multiple stacked bases could serve as sequence-dependent hydrogen-bond-based HIDERs. Similarly, the enrichment of such HIDERs was observed. It is suggested that these enrichments are the first evidence in support of sequence-specific resonance signaling in the genome.

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Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body

Several ongoing international efforts are developing methods of localizing single cells within organs or mapping the entire human body at the single cell level, including the Chan Zuckerberg Initiative's Human Cell Atlas (HCA), and the Knut and Allice Wallenberg Foundation's Human Protein Atlas (HPA), and the National Institutes of Health's Human BioMolecular Atlas Program (HuBMAP). Their goals are to understand cell specialization, interactions, spatial organization in their natural context, and ultimately the function of every cell within the body. In the same way that the Human Genome Project had to assemble sequence data from different people to construct a complete sequence, multiple centers around the world are collecting tissue specimens from a diverse population that varies in age, race, sex, and body size. A challenge will be combining these heterogeneous tissue samples into a 3D reference map that will enable multiscale, multidimensional Google Maps-like exploration of the human body. Key to making alignment of tissue samples work is identifying and using a coordinate system called a Common Coordinate Framework (CCF), which defines the positions, or "addresses", in a reference body, from whole organs down to functional tissue units and individual cells. In this perspective, we examine the concept of a CCF based on the vasculature and describe why it would be an attractive choice for mapping the human body.

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Effect of Copper Chemical Form on The Growth of Pseudomonas aeruginosa Isolated from Burned Patients and on Its Cu Uptake

The main object of this investigation was to shed light on the information on the level of Cu uptake by Pseudomonas aeruginosa that has been previously isolated from patients using Gram-negative E. aerogenes ans a Gram-positive Bacillus thuringiensis as a control for Cu uptake measurements. Cu uptake data showed that maximum Cu uptake was obtained by the Pseudomonas aeruginosa. The metal uptake was dependent on the type of biosorbent with different accumulation affinities toward the tested chemical form of the copper. Cells harvested at exponential growth phase showed slightly higher Cu uptake than at stationary phase, which reflect that the Cu uptake is metabolism dependent-process. The increasing order of affinity of the cupric chloride and cupric sulphate towards the three genera were almost constant. However, where cupric nitrate was used, the copper uptake behavior in Pseudomonas aeroginosa was not changed from those results with the other two chemical forms, whereas with E. aerogenes & B. thuringiensis, different Cu uptake behaviors were observed. In B. thuengenesis, the copper uptake rate as a function of initial Cu concentration were shown to increase with increasing the initial concentration of Cu, constantly above 320 ppm as compared with others. In Enterobacter with cupric nitrate, different bahavior was also shown in which the copper uptake decline sharply beyond the 320 ppm. These results reflect that the Cu uptake in P. aeruginosa is with different mechanisms as compared with other tested bacteria.

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Characteristics Of Post Partum Perineum Wounds With Infra Red Therapy

Perineal wounds other than their localization in humid feminine areas and can pose a risk of infection. This quantitative study aims to see a description of the characteristics of post partum maternal perineal wounds with infrared therapy twice a day for three consecutive days with a descriptive analytic analysis design. Sample selection technique with purposive sampling in post partum mothers with spontaneous parturition, 1-2 degrees of perineal wounds in the amount of 20 people. Perineal wound characteristics were assessed and observed using the Southampton instrument with the results of the instrument trial r = 0.99 (Karl Pearson correlation coefficient), and the reliability value of 0.99 (brown spearman). The results of this study showed that degeneration of wounds was found only until the first day of post-intervention (1.95 ), poor wound regeneration occurred until the second day of pre-intervention (1.95), and wound regeneration was being encountered changes from the first day to the second day pre-intervention (1.05). These results indicate that infrared therapy does not show significant changes if only done for one day. Key Words: localization, parturition, regeneration

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Venue-based HIV testing at sex work hotspots to reach adolescent girls and young women living with HIV: a cross-sectional study in Mombasa, Kenya

Background: We estimated the potential number of newly diagnosed HIV infections among adolescent girls and young women (AGYW) using a venue-based approach to HIV testing at sex work hotspots. Methods: We used hotspot enumeration and cross-sectional bio-behavioural survey data from the 2015 Transitions Study of AGYW aged 14-24 years who frequented hotspots in Mombasa, Kenya. We compared the HIV cascade among AGYW who sell sex (YSW, N=408) versus those who do not (NSW, N=891); and triangulated the potential (100% test acceptance and accuracy) and feasible (accounting for test acceptance and sensitivity) number of AGYW that could be newly diagnosed via hotspot-based HIV rapid testing in Mombasa. We identified the profile of AGYW recently tested for HIV (in the past year) using multivariable logistic regression. Results: N=37/365 (10.1%) YSW and N=30/828 (3.6%) NSW were living with HIV, of whom 27.0% (N=10/37) and 30.0% (N=9/30) were diagnosed and aware (p=0.79). Rapid test acceptance was 89.3% and sensitivity was 80.4%. Hotspot enumeration estimated 15,635 (range: 12,172-19,097) AGYW in hotspots in Mombasa. The potential and feasible number of new diagnosis were 627 (310-1,081), and 450 (223-776), respectively. Thus, hotspot-based testing could feasibly reduce the undiagnosed fraction from 71.6% to 20.2%. The profile of AGYW who recently tested was similar among YSW and NSW. YSW were two-fold more likely to report a recent HIV test after adjusting for other determinants [odds ratio (95% CI): 2.1 (1.6-3.1)]. Conclusion: Reaching AGYW via hotspot-based HIV testing could fill gaps left by traditional, clinic-based HIV prevention and testing services.

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On the Order of Gene Distribution on Chromosomes Across the Animal Kingdom

Background. The large-scale pattern of distribution of genes on the chromosomes in the known animal genomes is not well characterized. We hypothesized that individual genes will be distributed on chromosomes in a mathematically ordered manner across the animal kingdom. Results. Twenty-one animal genomes reported in the NCBI database were examined. Numerically, there was a trend towards increasing overall gene content with increasing size of the genome as reflected by the chromosomal complement. Gene frequency on individual chromosomes in each animal genome was analyzed and demonstrated uniformity of proportions within each animal with respect to both average gene frequency on individual chromosomes and gene distribution across the unique genomes. Further, average gene distribution across animal species followed a relationship whereby it was, approximately, inversely proportional to the square root of the number of chromosomes in the unique animal genomes, consistent with the notion that there is an ordered increase in gene dispersion as the complexity of the genome increased. To further corroborate these findings a derived measure, termed gene spacing on chromosomes correlated with gene frequency and gene distribution. Conclusion. As animal species have evolved, the distribution of their genes on individual chromosomes and within their genomes, when viewed on a large scale is not random, but follows a mathematically ordered process, such that as the complexity of the organism increases, the genes become less densely distributed on the chromosomes and more dispersed across the genome.

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Process simulation and optimization of agro-systems by DNDC model

Many people are still facing hunger and the global food shortages is still an urgent problem. Meanwhile, global warming is still severe. Therefore, we propose a simulation-based optimization approach for improving crop yield and reducing the greenhouse gas emissions (GHG) of agriculture system. We simulated and verified the crop yield and carbon/nitrogen cycle with Denitrification-Decomposition (DNDC) model. A set of empirical equations of DNDC model were selected and implemented in gPROMS for obtaining the optimal solution of fertilizer usage. A case study shows that the optimized framework improves crop yield by 18%, when 72.42kg N/ha urea was used. Meanwhile the GHG emission of the system was reduced by 10%. The results show the necessity of optimal planning and usage of fertilizer in agriculture system.

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Simple mathematical model of aging

A simple mathematical model of the aging process for long-lived organisms is considered. The key point in this model is the assumption that the body does not have internal clocks that count out the chronological time at scales of decades. At these scales, we may limit ourselves by empirical consideration only the background (smoothed, averaged) processes. The body is dealing with internal biological factors, which can be considered as the biological clocks in suitable parameterization of corresponding variables. The dynamics of these variables is described using a system of autonomous ODEs. A particular representation of the right-hand side of equations in the form of quadratic polynomials is considered. In the simplest case of one variable we deal with a logistic equation, which has an analytical solution. Such quadratic model is justified if it is used to predict the dynamic of aging process for relatively small time intervals. However, since a well-defined biological interpretation can be given for the quadratic right-hand side of the equations, we can expect that the area of applicability of this simplified empirical model can extend to relatively large time intervals. The considered model is, in our opinion, a good and simple mathematical framework for organizing experimental data. The model may be useful to quantify and arrange the chains of causal relationships that may appear significant for the development of the aging process.

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The Hoare-fol Tool

This document presents the tool named ''Application of Hoare Logic and Dijkstra's Weakest Proposition Calculus to Biological Regulatory Networks Using Path Programs with Branching First-Order Logic Operators'' or Hoare-fol for short. This tool consists in an implementation of the theoretical work developed in [Bernot et al., 2019] and contains the following features: (1) computation of the weakest precondition of a Hoare triple, (2) simplification of this weakest precondition using De Morgan laws and partial knowledge on the initial state, and (3) translation into Answer Set Programming to allow a solving of all compatible solutions.

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A framework for parsing heritable information

Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here I develop a framework for heredity and development that includes the cycling regulators parsed in terms of what an organism can sense about itself and its environment by defining entities, their sensors, and the sensed properties. Entities include small molecules (ATP, ions, metabolites, etc.), macromolecules (individual proteins, RNAs, polysaccharides, etc.), and assemblies of molecules. While concentration may be the only relevant property measured by sensors for small molecules, multiple properties that include concentration, sequence, conformation, and modification may all be measured for macromolecules and assemblies. Each configuration of these entities and sensors that is recreated in successive generations in a given environment thus specifies a potentially vast amount of information driving complex development in each generation. This Entity-Sensor-Property framework explains how sensors limit the number of distinguishable states, how distinct molecular configurations can be functionally equivalent, and how regulation of sensors prevents detection of some perturbations. Overall, this framework is a useful guide for understanding how life evolves and how the storage of information has itself evolved with complexity since before the origin of life.

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Open Source Software Sustainability Models: Initial White Paper from the Informatics Technology for Cancer Research Sustainability and Industry Partnership Work Group

The Sustainability and Industry Partnership Work Group (SIP-WG) is a part of the National Cancer Institute Informatics Technology for Cancer Research (ITCR) program. The charter of the SIP-WG is to investigate options of long-term sustainability of open source software (OSS) developed by the ITCR, in part by developing a collection of business model archetypes that can serve as sustainability plans for ITCR OSS development initiatives. The workgroup assembled models from the ITCR program, from other studies, and via engagement of its extensive network of relationships with other organizations (e.g., Chan Zuckerberg Initiative, Open Source Initiative and Software Sustainability Institute). This article reviews existing sustainability models and describes ten OSS use cases disseminated by the SIP-WG and others, and highlights five essential attributes (alignment with unmet scientific needs, dedicated development team, vibrant user community, feasible licensing model, and sustainable financial model) to assist academic software developers in achieving best practice in software sustainability.

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AI and Medicine

Which part of medicine, if any, can and should be entrusted to AI, now or at some moment in the future? That both medicine and AI will continue to change goes without saying.

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Natural intelligence and anthropic reasoning

This paper aims to justify the concept of natural intelligence, the type of intelligence wider than human intelligence and its derivative, AI. I will argue that the process of life is a cognitive process and that organisms, from bacteria to animals, are cognitive agents. To justify these arguments, the neural intelligence represented by the form of reasoning known as anthropic reasoning will be compared and contrasted with types of intelligence explicated by four disciplines of biology, relational biology, evolutionary epistemology, biosemiotics and the systems view of life, not biased towards neural intelligence. The comparison will be achieved by asking several questions that probe the concepts of observers and true observers. To answer the questions I will rely on a range of established concepts including SETI, Fermi's paradox, bacterial cognition, versions of the panspermia theory, and some newly introduced concepts including biocivilisations, cognitive universes, and the cognitive multiverse. The key point emerging from the answers is that the process of cognition, the essence of natural intelligence, is a biological universal.

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Recommendations to enhance rigor and reproducibility in biomedical research

Computational methods have reshaped the landscape of modern biology. While the biomedical community is increasingly dependent on computational tools, the mechanisms ensuring open data, open software, and reproducibility are variably enforced by academic institutions, funders, and publishers. Publications may present academic software for which essential materials are or become unavailable, such as source code and documentation. Publications that lack such information compromise the role of peer review in evaluating technical strength and scientific contribution. Incomplete ancillary information for an academic software package may bias or limit any subsequent work produced with the tool. We provide eight recommendations across four different domains to improve reproducibility, transparency, and rigor in computational biology - precisely on the main values which should be emphasized in life science curricula. Our recommendations for improving software availability, usability, and archival stability aim to foster a sustainable data science ecosystem in biomedicine and life science research.

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New method for evaluating fitness using the waist-to-height ratio among Korean adults

Objectives: This paper introduces a new method for evaluating fitness and determining effective exercises for reducing abdominal obesity in Korean adults using the new kind of waist-to-height ratio (WHT2R). Materials and Methods: The body mass index (BMI), body shape index (ABSI), and two other waist-to-height ratios (WHT.5R, WHTR) were considered as possible contenders for the WHT2R. The correlation coefficients were calculated by correlation analyses between the indices and four fitness tests for comparison. The LMV (lump mean value) and FSPW (fitness sensitivity percentage to WHT2R) were introduced to find the association between fitness and abdominal obesity using a linear regression method and to use as an indicator for the effective control of abdominal obesity. Results: The WHT2R is more suitable for assessing fitness than the other indices and can be controlled effectively by decreasing the 10-m shuttle run score for both males and females. Conclusions: The WHT2R can be used as a possible contender for evaluating fitness and is an effective indicator for the reduction of abdominal obesity. The LMV and FSPW can be used to establish personal exercise aims.

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Artificial Intelligence Forecasting of Covid-19 in China

BACKGROUND An alternative to epidemiological models for transmission dynamics of Covid-19 in China, we propose the artificial intelligence (AI)-inspired methods for real-time forecasting of Covid-19 to estimate the size, lengths and ending time of Covid-19 across China. METHODS We developed a modified stacked auto-encoder for modeling the transmission dynamics of the epidemics. We applied this model to real-time forecasting the confirmed cases of Covid-19 across China. The data were collected from January 11 to February 27, 2020 by WHO. We used the latent variables in the auto-encoder and clustering algorithms to group the provinces/cities for investigating the transmission structure. RESULTS We forecasted curves of cumulative confirmed cases of Covid-19 across China from Jan 20, 2020 to April 20, 2020. Using the multiple-step forecasting, the estimated average errors of 6-step, 7-step, 8-step, 9-step and 10-step forecasting were 1.64%, 2.27%, 2.14%, 2.08%, 0.73%, respectively. We predicted that the time points of the provinces/cities entering the plateau of the forecasted transmission dynamic curves varied, ranging from Jan 21 to April 19, 2020. The 34 provinces/cities were grouped into 9 clusters. CONCLUSIONS The accuracy of the AI-based methods for forecasting the trajectory of Covid-19 was high. We predicted that the epidemics of Covid-19 will be over by the middle of April. If the data are reliable and there are no second transmissions, we can accurately forecast the transmission dynamics of the Covid-19 across the provinces/cities in China. The AI-inspired methods are a powerful tool for helping public health planning and policymaking.

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Mass spectrometry for semi-experimental protein structure determination and modeling

The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an overview about experimental structure determination methods with their pros and cons is given. Then we describe how mass spectrometry is useful for semi-experimental integrative protein structure determination. We review the methodology and describe software programs supporting such integrated protein structure prediction approaches, making use of distance constraints got from mass spectrometry cross-linking experiments

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