Quantitative Biology

The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an experimental science. These examples show how the development of theoretical biological models generates experimentally verifiable computer hypotheses, which necessarily must be validated by experiments in vitro or in vivo.

Soil organic carbon (SOC) plays an important role on improving soil conditions and soil functions. Increasing land use changes have induced an important decline of SOC content at global scale. Increasing SOC in agricultural soils has been proposed as a strategy to mitigate climate change. Animal manure has the characteristic of enriching SOC, when applied to crop fields, while, in parallel, it could constitute a natural fertilizer for the crops. In this paper, a simulation is performed using the area of Catalonia, Spain as a case study for the characteristic low SOC in the Mediterranean, to examine whether animal manure can improve substantially the SOC of agricultural fields, when applied as organic fertilizers. Our results show that the policy goals of the 4x1000 strategy can be achieved only partially by using manure transported to the fields. This implies that the proposed approach needs to be combined with other strategies.

The registration of tremor was performed in two groups of subjects (15 people in each group) with different physical fitness at rest and at a static loads of 3N. Each subject has been tested 15 series (number of series N=15) in both states (with and without physical loads) and each series contained 15 samples (n=15) of tremorogramm measurements (500 elements in each sample, registered coordinates x1(t) of the finger position relative to eddy current sensor) of the finger. Using non-parametric Wilcoxon test of each series of experiment a pairwise comparison was made forming 15 tables in which the results of calculation of pairwise comparison was presented as a matrix (15x15) for tremorogramms are presented. The average number of hits random pairs of samples (<k>) and standard deviation {\sigma} were calculated for all 15 matrices without load and under the impact of physical load (3N), which showed an increase almost in twice in the number k of pairs of matching samples of tremorogramms at conditions of a static load. For all these samples it was calculated special quasi-attractor (this square was presented the distinguishes between physical load and without it. All samples present the stochastic unstable state.

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

Incubation with noradrenaline (norepinephrine) of isolated membranes of rat's brain corpus striatum and cortex, showed that ionic-magnesium (Mg2+) is required for the neurotransmitter activatory response of Adenylate Cyclase [ATP pyrophosphate-lyase (cyclizing), (EC this http URL)], this http URL Mg2+-dependent response to the activatory effects of adrenaline, and subsequent inhibition by calcium, suggest capability for a turnover, associated with cyclic changes in membrane potential and participation in a short term-memory this http URL the cell, the neurotransmitter by activating AC generates intracellular cyclic AMP. Calcium entrance in the cell inhibits the enzyme. The increment of cyclic AMP activates kinaseA and their protein phosphorylating activity, allowing a long term memory pathway. Hence, consolidating neuronal circuits, related to emotional learning and memory affirmation.The activatory effect relates to an enzyme-noradrenaline complex which may participate on the physiology of the fight or flight response, by prolonged exposure. However, the persistence of an unstable enzyme complex turns the enzyme inactive. Effect concordant, with the observation that prolonged exposure to adrenaline, participate in the etiology of stress triggered pathologies. At the cell physiological level AC responsiveness to hormones could be modulated by the concentration of Chelating Metabolites. These ones produce the release of free ATP4-, a negative modulator of AC and the Mg2+ activated insulin receptor tyrosine kinase (IRTK). Thus, allowing an integration of the hormonal response of both enzymes by ionic controls. This effect could supersede the metabolic feedback control by energy-charge. Accordingly, maximum hormonal response of both enzymes, to high Mg2+ and low free ATP4-, allows a correlation with the known effects of low caloric intake increasing average life expectancy.

A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime integer quaternion of norm 7 and involves a function that associates with each codon, represented by three of these quaternions, another integer quaternion (amino acid type quaternion) in such a way that the essentials of the standard genetic code (particulaty its degeneration) are preserved. To show the advantages of such a quaternionic representation we have, in turn, associated with each amino acid of a given protein, besides of the type quaternion, another real one according to its order along the protein (order quaternion) and have designed an algorithm to go from the primary to the tertiary structure of the protein by using type and order quaternions. In this context, we incorporate chirality in our representation by observing that the set of eight integer quaternions of norm 7 can be partitioned into a pair of subsets of cardinality four each with their elements mutually conjugates and by putting they in correspondence one to one with the two sets of enantiomers (D and L) of the four nucleotide bases adenine, cytosine, guanine and uracil, respectively. Thus, guided by two diagrams proposed for the codes evolution, we define functions that in each case assign a L- (D-) amino acid type integer quaternion to the triplets of D- (L-) bases. The assignation is such that for a given D-amino acid, the associated integer quaternion is the conjugate of that one corresponding to the enantiomer L. The chiral type quaternions obtained for the amino acids are used, together with a common set of order quaternions, to describe the folding of the two classes, L and D, of homochiral proteins.

Mammalian offspring require parental care, at least in the form of suckling during their early development. While mothers need to invest considerable time and energy in ensuring the survival of their current offspring, they also need to optimize their investment in one batch of offspring in order to ensure future reproduction and hence lifetime reproductive success. Free-ranging dogs live in small social groups, mate promiscuously, and lack the cooperative breeding biology of other group living canids. They face high early life mortality, which in turn reduces fitness benefits of the mother from a batch of pups. We carried out a field based study on free-ranging dogs in India to understand the nature of parental care provided by mothers at different stages of pup development. Using behavioural patterns of mother-pup interactions, we draw up a timeline of pup ontogeny. Our analysis reveals that mothers cleverly reduce investment in energy intensive active care and increase passive care as the pups grow older, thereby keeping overall levels of parental care more or less constant over pup age.

The coronavirus disease 2019 (COVID-19) pandemic has spread rapidly across the world, leading to enormous amounts of human death and economic loss. Until definitive preventive or curative measures are developed, policies regarding testing, contact tracing, and quarantine remain the best public health tools for curbing viral spread. Testing is a crucial component of these efforts, enabling the identification and isolation of infected individuals. Differences in testing methodologies, time frames, and outcomes can have an impact on their overall efficiency, usability and efficacy. In this early draft, we draw a comparison between the various types of diagnostic tests including PCR, antigen, and home tests in relation to their relative advantages, disadvantages, and use cases. We also look into alternative and unconventional methods. Further, we analyze the short-term and long-term impacts of the virus and its testing on various verticals such as business, government laws, policies, and healthcare.

In this paper, we provide guidance on how standard safety analyses and reporting of clinical trial safety data may need to be modified, given the potential impact of the COVID-19 pandemic. The impact could include missed visits, alternative methods for assessments (such as virtual visits), alternative locations for assessments (such as local labs), and study drug interruptions. We focus on safety planning for Phase 2-4 clinical trials and integrated summaries for submissions. Starting from the recommended safety analyses proposed in white papers and a workshop, created as part of an FDA/PHUSE collaboration (PHUSE 2013, 2015, 2017, 2019), we assess what modifications might be needed. Impact from COVID-19 will likely affect treatment arms equally, so analyses of adverse events from controlled data can, to a large extent, remain unchanged. However, interpretation of summaries from uncontrolled data (summaries that include open-label extension data) will require even more caution than usual. Special consideration will be needed for safety topics of interest, especially events expected to have a higher incidence due to a COVID-19 infection or due to quarantine or travel restrictions (e.g., depression). Analyses of laboratory measurements may need to be modified to account for the combination of measurements from local and central laboratories.

The CoHSI (Conservation of Hartley-Shannon Information) distribution is at the heart of a wide-class of discrete systems, defining the length distribution of their components amongst other global properties. Discrete systems such as the known proteome where components are proteins, computer software, where components are functions and texts where components are books, are all known to fit this distribution accurately. In this short paper, we explore its solution and its resulting properties and lay the foundation for a series of papers which will demonstrate amongst other things, why the average length of components is so highly conserved and why long components occur so frequently in these systems. These properties are not amenable to local arguments such as natural selection in the case of the proteome or human volition in the case of computer software, and indeed turn out to be inevitable global properties of discrete systems devolving directly from CoHSI and shared by all. We will illustrate this using examples from the Uniprot protein database as a prelude to subsequent studies.