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At least 361 records · Page 20Linked to original sources
arXiv2017

Improving institutional memory on challenges and methods for estimation of pig herd antimicrobial exposure based on data from the Danish Veterinary Medicines Statistics Program (VetStat)

With the increasing occurrence of antimicrobial resistance, more attention has been directed towards surveillance of both human and veterinary antimicrobial use. Since the early 2000s, several research papers on Danish pig antimicrobial usage have been published, based on data from the Danish Veterinary Medicines Statistics Program (VetStat). VetStat was established in 2000, as a national database containing detailed information on purchases of veterinary medicine. This paper presents a critical set of challenges originating from static system features, which researchers must address when estimating antimicrobial exposure in Danish pig herds. Most challenges presented are followed by at least one robust solution. A set of challenges requiring awareness from the researcher, but for which no immediate solution was available, were also presented. The selection of challenges and solutions was based on a consensus by a cross-institutional group of researchers working in projects using VetStat data. No quantitative data quality evaluations were performed, as the frequency of errors and inconsistencies in a dataset will vary, depending on the period covered in the data. Instead, this paper focuses on clarifying how VetStat data may be translated to an estimation of the antimicrobial exposure at herd level, by suggesting uniform methods of extracting and editing data, in order to obtain reliable and comparable estimates on pig antimicrobial consumption for research purposes.

q-bio.OT↗
arXiv2025

Transverse contributions to the longitudinal stiffness of the human foot

Humans rely on foot stiffness to withstand the propulsive forces of walking and running. Skeletal adaptations that increase foot stiffness include the medial longitudinal arch (MLA) and the transverse tarsal arch (TTA). The TTA has been hypothesized to stiffen the foot through cross-axis coupling of transverse intermetatarsal stiffness with sagittal-plane midfoot stiffness, but this has been tested only in cadaveric specimens. In vivo testing is essential because muscle contraction substantially modulates MLA function and may similarly affect the TTA's cross-axis coupling. Here we provide in vivo evidence for the TTA's contribution to foot stiffness by externally increasing intermetatarsal stiffness and measuring its effects on midfoot elasticity during walking. As predicted by the cross-axis coupling hypothesis, increasing intermetatarsal stiffness with an elastic tape wrapped around the forefoot reduced the energy absorbed in midfoot flattening and increased sagittal-plane midfoot stiffness concomitantly (mean,$\pm$,standard error of the mean (SEM): $13.9\% \pm 3\%$ and $16.8\% \pm 5.8\%$, respectively). However, taping did not change the curvature of the TTA, thereby isolating the effects of cross-axis coupling from morphological changes to the TTA. Thus, forefoot taping modulates midfoot stiffness through cross-axis coupling and could provide a non-invasive means to manage pathological foot flexibility or enhance athletic performance.

physics.bio-ph↗
arXiv2017

Analysis of Bacteriostatic Effect of Chinese Herbal Medicine Against E.coli

To analyze the bacteriostatic effect of Chinese traditional herbal medicines on E. coli, total 35 different preparations (decoction, volatile oil and distillate) of Chinese traditional herbal medicines were tested using plate culture method. The results showed that 18 preparations of traditional Chinese herbal medicines have different inhibition effect on E. coli in vitro. The results also revealed that different process and combination affect the bacteriostatic effect and different medicines could be used in singles or combined to treat E.coli disease

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arXiv2017

Time as it could Be measured in Artificial Living Systems

Being able to measure time, whether directly or indirectly, is a significant advantage for an organism. It permits it to predict regular events, and prepare for them on time. Thus, clocks are ubiquitous in biology. In the present paper, we consider the most minimal abstract pure clocks and investigate their characteristics with respect to their ability to measure time. Amongst other, we find fundamentally diametral clock characteristics, such as oscillatory behaviour for local time measurement or decay-based clocks measuring time periods in scales global to the problem. We include also cascades of independent clocks ("clock bags") and composite clocks with controlled dependency; the latter show various regimes of markedly different dynamics.

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arXiv2017

The lunar cycle's influence on sex determination at conception in humans

The lunar cycle has long been suspected to influence biological phenomena. Folklore alludes to such a relationship, but previous scientific analyses have failed to find significant associations. It has been shown that lunar cycles indeed have effects on animals; significant associations between human circadian rhythms and lunar cycles have also been reported. We set out to determine whether a significant statistical correlation exists between the lunar phase and sex determination during conception. We found that significant associations (\textit{p}-value $< 5 \times 10^{-5}$) exist between the average sex ratio (male:female) and the lunar month. The likelihood of conception of a male is at its highest point five days after the full moon, whereas the highest likelihood of female conception occurs nineteen days after the full moon. Furthermore, we found that the strength of this influence is correlated with the amount of solar radiation (which is proportional to moonlight). Our results suggest that sex determination may be influenced by the moon cycle, which suggests the possibility of lunar influence on other biological phenomena. We suggest for future research the exploration of similar effects in other phenomena involving humans and other species.

q-bio.OT↗
arXiv2017

Implications of the Trivers-Willard Sex Ratio Hypothesis for Avian Species and Poultry Production, And a Summary of the Historic Context of this Research

At a theoretical level, the Trivers-Willard Sex Ratio Hypothesis applies to both avian species and mammals. This article, however, conjectures that at the statistical level, sex ratio effects are likely to produce sharper numerical variations among birds than among mammals. We explain this greater statistical variation should likely have beneficial implications for increasing the efficiency of world-wide poultry egg (and perhaps also meat) production.

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arXiv2017

Interactions of Fungi with Concrete: Significant Importance for Bio-Based Self-Healing Concrete

The goal of this study is to explore a new self-healing concept in which fungi are used as a self-healing agent to promote calcium mineral precipitation to fill the cracks in concrete. An initial screening of different species of fungi has been conducted. Fungal growth medium was overlaid onto cured concrete plate. Mycelial discs were aseptically deposited at the plate center. The results showed that, due to the dissolving of Ca(OH)2 from concrete, the pH of the growth medium increased from its original value of 6.5 to 13.0. Despite the drastic pH increase, Trichoderma reesei (ATCC13631) spores germinated into hyphal mycelium and grew equally well with or without concrete. X-ray diffraction (XRD) and scanning electron microscope (SEM) confirmed that the crystals precipitated on the fungal hyphae were composed of calcite. These results indicate that T. reesei has great potential to be used in bio-based self-healing concrete for sustainable infrastructure.

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arXiv2017

When rule-based models need to count

Rule-based modelers dislike direct enumeration of cases when more efficient means of enumeration are available. We present an extension of the Kappa language which attaches to agents a notion of level. We detail two encodings that are more concise than the former practice.

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arXiv2017

Information Theory and the Length Distribution of all Discrete Systems

We begin with the extraordinary observation that the length distribution of 80 million proteins in UniProt, the Universal Protein Resource, measured in amino acids, is qualitatively identical to the length distribution of large collections of computer functions measured in programming language tokens, at all scales. That two such disparate discrete systems share important structural properties suggests that yet other apparently unrelated discrete systems might share the same properties, and certainly invites an explanation. We demonstrate that this is inevitable for all discrete systems of components built from tokens or symbols. Departing from existing work by embedding the Conservation of Hartley-Shannon information (CoHSI) in a classical statistical mechanics framework, we identify two kinds of discrete system, heterogeneous and homogeneous. Heterogeneous systems contain components built from a unique alphabet of tokens and yield an implicit CoHSI distribution with a sharp unimodal peak asymptoting to a power-law. Homogeneous systems contain components each built from just one kind of token unique to that component and yield a CoHSI distribution corresponding to Zipf's law. This theory is applied to heterogeneous systems, (proteome, computer software, music); homogeneous systems (language texts, abundance of the elements); and to systems in which both heterogeneous and homogeneous behaviour co-exist (word frequencies and word length frequencies in language texts). In each case, the predictions of the theory are tested and supported to high levels of statistical significance. We also show that in the same heterogeneous system, different but consistent alphabets must be related by a power-law. We demonstrate this on a large body of music by excluding and including note duration in the definition of the unique alphabet of notes.

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arXiv2020

The rules of long DNA-sequences and tetra-groups of oligonucleotides

The article represents a new class of hidden symmetries in long sequences of oligonucleotides of single stranded DNA from their representative set. These symmetries are an addition to symmetries described by the second parity rule of Chargaff. These new symmetries and their rules concern collective probabilities of oligonucleotides from special tetra-groups and their subgroups in long DNA-texts including complete sets of chromosomes of human and some model organisms. These rules of tetra-group probabilities are considered as possible candidacies for the role of universal rules of long DNA-sequences. A quantum-informational model of genetic symmetries of these collective probabilities is proposed on the basis of the known quantum-mechanic statement that quantum state of a multicomponent system is defined by the tensor product of quantum states of its subsystems. In this model, nitrogenous bases C, T, G, A of DNA are represented as computational basis states of 2-qubit quantum CTGA-systems. The biological meaning of these new quantum-information symmetries of long DNA texts is associated with the common ability of all living organisms to grow and develop on the basis of incorporation into their body of new and new molecules of nutrients becoming new quantum-mechanic subsystems of the united quantum-mechanic organism. An important role of resonances, photons and photonic crystals in quantum information genetics is noted.

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arXiv2018

An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

We demonstrate that the algorithmic information content of a system is deeply connected to its potential dynamics, thus affording an avenue for moving systems in the information-theoretic space and controlling them in the phase space. To this end we performed experiments and validated the results on (1) a very large set of small graphs, (2) a number of larger networks with different topologies, and (3) biological networks from a widely studied and validated genetic network (e.coli) as well as on a significant number of differentiating (Th17) and differentiated human cells from high quality databases (Harvard's CellNet) with results conforming to experimentally validated biological data. Based on these results we introduce a conceptual framework, a model-based interventional calculus and a reprogrammability measure with which to steer, manipulate, and reconstruct the dynamics of non- linear dynamical systems from partial and disordered observations. The method consists in finding and applying a series of controlled interventions to a dynamical system to estimate how its algorithmic information content is affected when every one of its elements are perturbed. The approach represents an alternative to numerical simulation and statistical approaches for inferring causal mechanistic/generative models and finding first principles. We demonstrate the framework's capabilities by reconstructing the phase space of some discrete dynamical systems (cellular automata) as case study and reconstructing their generating rules. We thus advance tools for reprogramming artificial and living systems without full knowledge or access to the system's actual kinetic equations or probability distributions yielding a suite of universal and parameter-free algorithms of wide applicability ranging from causation, dimension reduction, feature selection and model generation.

q-bio.OT↗
arXiv2017

Quantum origin of life: methodological, epistemological and ontological issues

The aim of this essay is to analyze the role of quantum mechanics as an inherent characteristic of life. During the last ten years the problem of the origin of life has become an innovative research subject approached by many authors. The essay is divided in to three parts: the first deals with the problem of life from a philosophical and biological perspective. The second presents the conceptual and methodological basis of the essay which is founded on the Information Theory and the Quantum Theory. This basis is then used, in the third part, to discuss the different arguments and conjectures of a quantum origin of life. There are many philosophical views on the problem of life, two of which are especially important at the moment: reductive physicalism and biosystemic emergentism. From a scientific perspective, all the theories and experimental evidences put forward by Biology can be summed up in to two main research themes: the RNA world and the vesicular theory. The RNA world, from a physicalist point of view, maintains that replication is the essence of life while the vesicular theory, founded on biosystemic grounds, believes the essence of life can be found in cellular metabolism. This essay uses the Information Theory to discard the idea of a spontaneous emergency of life through replication. Understanding the nature and basis of quantum mechanics is fundamental in order to be able to comprehend the advantages of using quantum computation to be able increase the probabilities of existence of auto replicative structures. Different arguments are set forth such as the inherence of quantum mechanics to the origin of life. Finally, in order to try to resolve the question of auto replication, three scientific propositions are put forward: Q-life, the quantum combinatory library and the role of algorithms in the origin of genetic language.

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arXiv2017

The epistemological status of Astrobiology: a problematic case of integration of scientific disciplines

Astrobiology is a scientific discipline that studies life in the Universe. We call it a discipline and not a science because some authors have cast doubts over its epistemological status by calling it 'a science without an object of study'. As with astrophysics, the scientific nature of astrobiology is related to historical-narrative sciences and nomothetic sciences. This discipline also integrates complex methodological and conceptual problems which originate from the methodological and epistemological differences that exist between physics and biology. This is why it is so important to evidence the different philosophical approaches from which its results are interpreted. After a brief historical introduction, we will consider the problem of life and we will analyse the influence that different philosophical approaches have on astrobiology. Subsequently, we will introduce ontological and epistemological questions that originate from interdisciplinarity, for example, their role in a physicalistic type of reductionism and in teleology.

astro-ph.IM↗
arXiv2017

Essential Facts on the History of Hyperthermia and their Connections with Electromedicine

The term hyperthermia is a combination of two Greek words: HYPER (rise) and THERME (heat) and refers to the increasing of body temperature or selected tissues in order to achieve a precise therapeutic effect. This paper reviews the development of thermotherapy by describing the most important moments in its history. For decades, the development of hyperthermia ran parallel with the development of cancer treatment and had numerous connections with electromedicine. Throughout its history, hyperthermia evoked a number of hopes, brought spectacular successes, but also was the subject of many disappointments.

physics.med-ph↗
arXiv2017

Adapting a Formal Model Theory to Applications in Augmented Personalized Medicine

The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal multi-agents. Our first step is to provide foundations for modelling of emergent and evolving dynamic multi-level organic complexes and their sustentative processes in artificial and natural life systems. Main applications are in life sciences, medicine, ecology and astrobiology, as well as robotics, industrial automation and man-machine interface. Since 2011 over 100 scientists from a number of disciplines have been exploring a substantial set of theoretical frameworks for a comprehensive theory of life known as Integral Biomathics. That effort identified the need for a robust core model of organisms as dynamic wholes, using advanced and adequately computable mathematics. The work described here for that core combines the advantages of a situation and context aware multivalent computational logic for active self-organizing networks, Wandering Logic Intelligence (WLI), and a multi-scale dynamic category theory, Memory Evolutive Systems (MES), hence WLIMES. This is presented to the modeller via a formal augmented reality language as a first step towards practical modelling and simulation of multi-level living systems. Initial work focuses on the design and implementation of this visual language and calculus (VLC) and its graphical user interface. The results will be integrated within the current methodology and practices of theoretical biology and (personalized) medicine to deepen and to enhance the holistic understanding of life.

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arXiv2017

Mathematics at the eve of a historic transition in biology

A century ago physicists and mathematicians worked in tandem and established quantum mechanism. Indeed, algebras, partial differential equations, group theory, and functional analysis underpin the foundation of quantum mechanism. Currently, biology is undergoing a historic transition from qualitative, phenomenological and descriptive to quantitative, analytical and predictive. Mathematics, again, becomes a driving force behind this new transition in biology.

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