SEARCH · Searcharxiv

Results for “q-bio.OT”

Search indexed arXiv papers on artificial intelligence, large language models, computer vision and robotics. Read source abstracts and follow links to arXiv.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 433 records · Page 24Linked to original sources

arXiv2019

Quantum patterns of genome size variation in angiosperms

The nuclear DNA amount in angiosperms is studied from the eigen-value equation of the genome evolution operator H. The operator H is introduced by physical simulation and it is defined as a function of the genome size N and the derivative with respective to the size. The discontinuity of DNA size distribution and its synergetic occurrence in related angiosperms species are successfully deduced from the solution of the equation. The results agree well with the existing experimental data of Aloe, Clarkia, Nicotiana, Lathyrus, Allium and other genera. It may indicate that the evolutionary constrains on angiosperm genome are essentially of quantum origin.

q-bio.OT↗

arXiv2018

CoHSI II; The average length of proteins, evolutionary pressure and eukaryotic fine structure

The CoHSI (Conservation of Hartley-Shannon Information) distribution is at the heart of a wide-class of discrete systems, defining (amongst other properties) the length distribution of their components. Discrete systems such as the known proteome, computer software and texts are all known to fit this distribution accurately. In a previous paper, we explored the properties of this distribution in detail. Here we will use these properties to show why the average length of components in general and proteins in particular is highly conserved, howsoever measured, demonstrating this on various aggregations of proteins taken from the UniProt database. We will go on to define departures from this equilibrium state, identifying fine structure in the average length of eukaryotic proteins that result from evolutionary processes.

q-bio.OT↗

arXiv2018

The triennial International Pigment Cell Conference (IPCC)

The International Federation of Pigment Cell Societies (IFPCS) held its XXIII triennial International Pigment Cell Conference (IPCC) in Denver, Colorado in August 2017. The goal of the summit was to provide a venue promoting a vibrant interchange among leading basic and clinical researchers working on leading-edge aspects of melanocyte biology and disease. The philosophy of the meeting, entitled Breakthroughs in Pigment Cell and Melanoma Research, was to deliver a comprehensive program in an inclusive environment fostering scientific exchange and building new academic bridges. This document provides an outlook on the history, accomplishments, and sustainability of the pigment cell and melanoma research community. Shared progress in the understanding of cellular homeostasis of pigment cells but also clinical successes and hurdles in the treatment of melanoma and dermatological disorders continue to drive future research activities. A sustainable direction of the societies creates an international forum identifying key areas of imminent needs in laboratory research and clinical care and ensures the future of this vibrant, diverse and unique research community at the same time. Important advances showcase wealth and breadth of the field in melanocyte and melanoma research and include emerging frontiers in melanoma immunotherapy, medical and surgical oncology, dermatology, vitiligo, albinism, genomics and systems biology, precision bench-to-bedside approaches, epidemiology, pigment biophysics and chemistry, and evolution. This report recapitulates highlights of the federate meeting agenda designed to advance clinical and basic research frontiers from melanoma and dermatological sciences followed by a historical perspective of the associated societies and conferences.

q-bio.OT↗

arXiv2018

The Function Transformation Omics - Funomics

There are no two identical leaves in the world, so how to find effective markers or features to distinguish them is an important issue. Function transformation, such as f(x,y) and f(x,y,z), can transform two, three, or multiple input/observation variables (in biology, it generally refers to the observed/measured value of biomarkers, biological characteristics, or other indicators) into a new output variable (new characteristics or indicators). This provided us a chance to re-cognize objective things or relationships beyond the original measurements. For example, Body Mass Index, which transform weight and high into a new indicator BMI=x/y^2 (where x is weight and y is high), is commonly used in to gauge obesity. Here, we proposed a new system, Funomics (Function Transformation Omics), for understanding the world in a different perspective. Funome can be understood as a set of math functions consist of basic elementary functions (such as power functions and exponential functions) and basic mathematical operations (such as addition, subtraction). By scanning the whole Funome, researchers can identify some special functions (called handsome functions) which can generate the novel important output variable (characteristics or indicators). We also start "the Funome project" to develop novel methods, function library and analysis software for Funome studies. The Funome project will accelerate the discovery of new useful indicators or characteristics, will improve the utilization efficiency of directly measured data, and will enhance our ability to understand the world. The analysis tools and data resources about the Funome project can be found gradually at http://www.funome.com.

q-bio.OT↗

arXiv2018

From Natural to Artificial Camouflage: Components and Systems

We identify the components of bio-inspired artificial camouflage systems including actuation, sensing, and distributed computation. After summarizing recent results in understanding the physiology and system-level performance of a variety of biological systems, we describe computational algorithms that can generate similar patterns and have the potential for distributed implementation. We find that the existing body of work predominately treats component technology in an isolated manner that precludes a material-like implementation that is scale-free and robust. We conclude with open research challenges towards the realization of integrated camouflage solutions.

cs.RO↗

arXiv2019

Solving a non-linear model of HIV infection for CD4+T cells by combining Laplace transformation and Homotopy analysis method

The aim of this paper is to find the approximate solution of HIV infection model of CD4+T cells. For this reason, the homotopy analysis transform method (HATM) is applied. The presented method is combination of traditional homotopy analysis method (HAM) and the Laplace transformation. The convergence of presented method is discussed by preparing a theorem which shows the capabilities of method. The numerical results are shown for different values of iterations. Also, the regions of convergence are demonstrated by plotting several h-curves. Furthermore in order to show the efficiency and accuracy of method, the residual error for different iterations are presented.

q-bio.OT↗

arXiv2018

CoHSI III: Long proteins and implications for protein evolution

The length distribution of proteins measured in amino acids follows the CoHSI (Conservation of Hartley-Shannon Information) probability distribution. In previous papers we have verified various predictions of this using the Uniprot database but here we explore a novel predicted relationship between the longest proteins and evolutionary time. We demonstrate from both theory and experiment that the longest protein and the total number of proteins are intimately related by Information Theory and we give a simple formula for this. We stress that no evolutionary explanation is necessary; it is an intrinsic property of a CoHSI system. While the CoHSI distribution favors the appearance of proteins with fewer than 750 amino acids (characteristic of most functional proteins or their constituent domains) its intrinsic asymptotic power-law also favors the appearance of unusually long proteins; we predict that there are as yet undiscovered proteins longer than 45,000 amino acids. In so doing, we draw an analogy between the process of protein folding driven by favorable pathways (or funnels) through the energy landscape of protein conformations, and the preferential information pathways through which CoHSI exerts its constraints in discrete systems. Finally, we show that CoHSI predicts the recent appearance in evolutionary time of the longest proteins, specifically in eukaryotes because of their richer unique alphabet of amino acids, and by merging with independent phylogenetic data, we confirm a predicted consistent relationship between the longest proteins and documented and potential undocumented mass extinctions.

q-bio.OT↗

arXiv2018

Wanted Dead or Alive Extraterrestrial Life Forms (Thermodynamic criterion for life is a growing open system that performs self-assembly processes)

For more than 100 years, humanity (both specialists and enthusiastic laics) has been searching for extraterrestrial life hoping we are not alone. The first step in the quest for extraterrestrial life is to define what and where exactly to look for. Thus, the basic definition of living matter is a conditio sine qua non for the quest. The diversity of species on Earth is so large that our quest for extraterrestrial life cannot be limited to forms and shapes present and known to us from our environment. However, there are two formal conditions that must be fulfilled in order for something to be assumed as living matter. First, it should represent a growing open thermodynamic system (in biological terms - a cell), and thus be a system out of equilibrium. Second, it must perform synthesis, self-assembly and accumulation processes (in biological terms to grow, maintain homeostasis, respond to environment, reproduce, exchange matter and energy, evolve). Populated planets are consisted of two components: biosphere and its environment (geosphere, hydrosphere and atmosphere). Living matter and its environment are out of equilibrium. Thus, the candidate planets are dynamic inhomogeneous systems for two reasons. First, a planet receives energy from its star, which leads to disequilibrium for external reasons. Animate matter contributes to disequilibrium for internal reasons: accumulation of matter and self-assembly. In practice, for a screening, an astrobiologist should search for increase in inhomogeneity on a candidate planet.

q-bio.OT↗

arXiv2018

Why Abeta42 Is Much More Toxic Than Abeta40

Amyloid precursor with 770 amino acids dimerizes and aggregates, as do its c terminal 99 amino acids and amyloid 40,42 amino acids fragments. The titled question has been discussed extensively, and here it is addressed further using thermodynamic scaling theory to analyze mutational trends in structural factors and kinetics. Special attention is given to Family Alzheimer's Disease mutations outside amyloid 42. The scaling analysis is connected to extensive docking simulations which included membranes, thereby confirming their results and extending them to Amyloid precursor.

q-bio.OT↗

arXiv2019

Proofs of life: molecular-biology reasoning simulates cell behaviors from first principles

We axiomatize the molecular-biology reasoning style, show compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to help infer phenotypes and to predict life cycles from genotypes. The key is to note that `reductionist discipline' entails constructive reasoning: any proof of a compound property can be decomposed to proofs of constituent properties. Proof theory makes explicit the inner structure of the axiomatized reasoning style and allows the permissible dynamics to be presented as a mode of computation that can be executed and analyzed. Constructivity and execution guarantee simulation when working over domain-specific languages. Here, we exhibit phenotype properties for genotype reasons: a molecular-biology argument is an open-system concurrent computation that results in compartment changes and is performed among processes of physiology change as determined from the molecular programming of given DNA. Life cycles are the possible sequentializations of the processes. A main implication of our construction is that formal correctness provides a complementary perspective on science that is as fundamental there as for pure mathematics. The bulk of the presented work has been verified formally correct by computer.

q-bio.OT↗

arXiv2018

CoHSI IV: Unifying Horizontal and Vertical Gene Transfer - is Mechanism Irrelevant ?

In previous papers we have described with strong experimental support, the organising role that CoHSI (Conservation of Hartley-Shannon Information) plays in determining important global properties of all known proteins, from defining the length distribution, to the natural emergence of very long proteins and their relationship to evolutionary time. Here we consider the insight that CoHSI might bring to a different problem, the distribution of identical proteins across species. Horizontal and Vertical Gene Transfer (HGT/VGT) both lead to the replication of protein sequences across species through a diversity of mechanisms some of which remain unknown. In contrast, CoHSI predicts from fundamental theory that such systems will demonstrate power law behavior independently of any mechanisms, and using the Uniprot database we show that the global pattern of protein re-use is emphatically linear on a log-log plot (adj. $R^{2} = 0.99, p < 2.2 \times 10^{-16}$ over 4 decades); i.e. it is extremely close to the predicted power law. Specifically we show that over 6.9 million proteins in TrEMBL 18-02 are re-used, i.e. their sequence appears identically in between 2 and 9,812 species, with re-used proteins varying in length from 7 to as long as 14,596 amino acids. Using (DL+V) to denote the three domains of life plus viruses, 21,676 proteins are shared between two (DL+V); 22 between three (DL+V) and 5 are shared in all four (DL+V). Although the majority of protein re-use occurs between bacterial species those proteins most frequently re-used occur disproportionately in viruses, which play a fundamental role in this distribution. These results suggest that diverse mechanisms of gene transfer (including traditional inheritance) are irrelevant in determining the global distribution of protein re-use.

q-bio.OT↗

arXiv2018

Thermoregulation in mice, rats and humans: An insight into the evolution of human hairlessness

The thermoregulation system in animals removes body heat in hot temperatures and retains body heat in cold temperatures. The better the animal removes heat, the worse the animal retains heat and visa versa. It is the balance between these two conflicting goals that determines the mammal's size, heart rate and amount of hair. The rat's loss of tail hair and human's loss of its body hair are responses to these conflicting thermoregulation needs as these animals evolved to larger size over time.

q-bio.OT↗

arXiv2018

La fauna de mamíferos fósiles del depósito paleontológico "El Abrón" (nivel ix), Pinar del Río, Cuba

"El Abrón" is a fossil deposit located in Pinar del Rio, Cuba, and whose age is only reference level VII (17 406 years BP), it is classified as the largest collection of fossils accumulated for our archipelago, produced by trophic action of barn owls for thousands of years. The aim of this study was to determine the living taxonomic composition of the fauna of extinct mammals, and throughout the paleontological study of the deeper level of said tank (Level IX). The extracted material which it is currently stored in the warehouse of paleontological collections of the National Museum of Natural History in Havana, Cuba (MNHNCu) was analyzed. We proceeded to clean the bones, to classify and to identify them from the species and also the taphonomic analysis of the condition of the remains. It was found that the mammal fauna of the paleontological deposit under study is composed essentially of 3 orders, 7 families and 14 species. The most significative order is Chiroptera (bat fauna), represented by 4 families, 9 genus and 9 species of the total which were identified. There were reported four species of bats Erophylla sezecorni, Monophyllus redmani, Pteronotus parnelli and Tadarida brasiliensis in the location. The results are the basis of the future paleoecological studies in order to reconstruct the natural history of these species. Moreover, the discovery of new species in this area is a contribution to the knowledge about the distribution of these species in the Cuban archipelago and the age of them. Finally, the taphonomic analysis of the conservation status of these remains permitted the understanding of the processes that gave rise to the tank and its characteristics, and also it contribute to an adequate estimation of the species present in it and the relationship between spatiotemporal with the fossil.

q-bio.OT↗

arXiv2018

Chaotic dynamics of movements stochastic instability and the hypothesis of N.A. Bernstein about "repetition without repetition"

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 ( ) and standard deviation σ 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.

q-bio.OT↗

arXiv2019

Moonshots for aging

As the global population ages, there is increased interest in living longer and improving one's quality of life in later years. However, studying aging - the decline in body function - is expensive and time-consuming. And despite research success to make model organisms live longer, there still aren't really any feasible solutions for delaying aging in humans. With space travel, scientists couldn't know what it would take to get to the moon. They had to extrapolate from theory and shorter-range tests. Perhaps with aging, we need a similar moonshot philosophy. And though "shot" might imply medicine, perhaps we need to think beyond biological interventions. Like the moon, we seem a long way away from provable therapies to increase human healthspan (the healthy period of one's life) or lifespan (how long one lives). This review therefore focuses on radical proposals. We hope it might stimulate discussion on what we might consider doing significantly differently than ongoing aging research.

q-bio.OT↗

arXiv2019

Single cell data explosion: Deep learning to the rescue

The plethora of single-cell multi-omics data is getting treatment with deep learning, a revolutionary method in artificial intelligence, which has been increasingly expanding its reign over the bioscience frontiers.

q-bio.OT↗

arXiv2019

Biogenic magnetic nanoparticles in plants

The genetic programming of biosynthesis of biogenic magnetic nanoparticles (BMNs) in plants was revealed by methods of comparative genomics. The samples of leaves and the root of Nicotiana tabacum, the stems and tubers of Solanum tuberosum and the stems of pea Pisum sativum were examined by scanning probe microscopy (in atomic force and magnetic power modes), and it was found that the BMNs are located in the form of chains in the wall of the phloem sieve tubes (ie, the vascular tissue of plants). Such a localization of BMNs supports the idea that the chains of BMNs in different organs of plants have common metabolic functions. Stray gradient magnetic fields about several thousand Oe, which are created by chains of BMNs, can significantly affect the processes of mass transfer near the membrane of vesicles, granules, organelles, structural elements of the membrane, and others. This process is enhanced in plants when artificial magnetite is added to the soil.

q-bio.OT↗

arXiv2019

Comparison of SVM and Spectral Embedding in Promoter Biobricks' Categorizing and Clustering

Background: In organisms' genomes, promoters are short DNA sequences on the upstream of structural genes, with the function of controlling genes' transcription. Promoters can be roughly divided into two classes: constitutive promoters and inducible promoters. Promoters with clear functional annotations are practical synthetic biology biobricks. Many statistical and machine learning methods have been introduced to predict the functions of candidate promoters. Spectral Eigenmap has been proved to be an effective clustering method to classify biobricks, while support vector machine (SVM) is a powerful machine learning algorithm, especially when dataset is small. Methods: The two algorithms: spectral embedding and SVM are applied to the same dataset with 375 prokaryotic promoters. For spectral embedding, a Laplacian matrix is built with edit distance, followed by K-Means Clustering. The sequences are represented by numeric vector to serve as dataset for SVM trainning. Results: SVM achieved a high predicting accuracy of 93.07% in 10-fold cross validation for classification of promoters' transcriptional functions. Laplacian eigenmap (spectral embedding) based on editing distance may not be capable for extracting discriminative features for this task.

q-bio.OT↗