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At least 415 records · Page 23Linked to original sources
arXiv2018

NeuroStorm: Accelerating Brain Science Discovery in the Cloud

Neuroscientists are now able to acquire data at staggering rates across spatiotemporal scales. However, our ability to capitalize on existing datasets, tools, and intellectual capacities is hampered by technical challenges. The key barriers to accelerating scientific discovery correspond to the FAIR data principles: findability, global access to data, software interoperability, and reproducibility/re-usability. We conducted a hackathon dedicated to making strides in those steps. This manuscript is a technical report summarizing these achievements, and we hope serves as an example of the effectiveness of focused, deliberate hackathons towards the advancement of our quickly-evolving field.

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arXiv2018

Some preliminary results on relation between triplet composition and tissue source in larch total transcriptome

We studied the structuredness ensemble of transcriptome of Siberian larch. The clusters in 64-dimensional space were identified with $K$-means technique, where the objects to be clusterized are the different fragments of the genome. A tetrahedron like structure in distribution of these fragments was found. Chargaff's discrepancy measure was determined for each class, as well as that latter between the classes. It reveals a relative similitude of the classes. The results have been compared to those obtained for specific transcriptome of each tissue. Also, a surrogate transcriptome has been developed comprising the contigs assembled for specific tissues; that latter has been compared with the real total transcriptome, and significant difference has been observed.

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arXiv2018

Sonifying stochastic walks on biomolecular energy landscapes

Translating the complex, multi-dimensional data from simulations of biomolecules to intuitive knowledge is a major challenge in computational chemistry and biology. The so-called "free energy landscape" is amongst the most fundamental concepts used by scientists to understand both static and dynamic properties of biomolecular systems. In this paper we use Markov models to design a strategy for mapping features of this landscape to sonic parameters, for use in conjunction with visual display techniques such as structural animations and free energy diagrams.

cs.HC↗
arXiv2018

Eshel Ben-Jacob: A unique individual in the science of collective phenomena

Eshel Ben-Jacob, one of the co-organizers of this meeting on collective behavior and one of the pioneers in the field of collective behavior in biology, passed away suddenly just before we convened. This article presents a brief glimpse of Eshel's life-long path through science, seen from the perspective of a decades long collaboration on many disparate yet ultimately connected topics. The article attempts to convey how the concept of self-organization of complex interacting objects into higher order functional units, as evidenced so wonderfully by Eshel's experiments on bacterial colony formation, provides a unifying theme for the study of collective behavior. Our entire field will miss his unique ability to "let the complex become simple".

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arXiv2018

Big Data Challenges in Genome Informatics

In recent years, we have witnessed a dramatic data explosion in genomics, thanks to the improvement in sequencing technologies and the drastically decreasing costs. We are entering the era of millions of available genomes. Notably, each genome can be composed of billions of nucleotides stored as plain text files in GigaBytes (GBs). It is undeniable that those genome data impose unprecedented data challenges for us. In this article, we briefly discuss the big data challenges associated with genomics in recent years.

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arXiv2018

Water Bridging Dynamics of Polymerase Chain Reaction in the Gauge Theory Paradigm of Quantum Fields

We discuss the role of water bridging the DNA-enzyme interaction by resorting to recent results showing that London dispersion forces between delocalized electrons of base pairs of DNA are responsible for the formation of dipole modes that can be recognized by \textit{Taq} polymerase. We describe the dynamic origin of the high efficiency and precise targeting of \textit{Taq} activity in PCR. The spatiotemporal distribution of interaction couplings, frequencies, amplitudes, and phase modulations comprise a pattern of fields which constitutes the electromagnetic image of DNA in the surrounding water, which is what the polymerase enzyme actually recognizes in the DNA water environment. The experimental realization of PCR amplification, achieved through replacement of the DNA template by the treatment of pure water with electromagnetic signals recorded from viral and bacterial DNA solutions, is found consistent with the gauge theory paradigm of quantum fields.

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arXiv2018

Can the light be used to treat obesity and diabetes?

The treatment of obesity and diabetes remains a challenge and the biological mechanisms of these diseases are still not fully understood. Diabetes and obesity are associated with increased risk of the development of cardiovascular complications and there is an urgent need to find novel therapeutic approaches for treating obesity and diabetes. Currently there are several approaches to treat these diseases. Among them chemical uncouplers could be used as an effective treatment for obesity but the dangerous side effects of these compounds has limited their use in vivo. Here we propose a novel theoretical model based on the mechanism of action of chemical uncouplers: the thermogenin-like system (TLS). The TLS may be used in vivo to reproduce the mechanism of action of chemical uncouplers but without their dangerous side effects.

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arXiv2018

Nonlinear Self-organization Dynamics of a Metabolic Process of the Krebs Cycle

The present work continues studies of the mathematical model of a metabolic process of the Krebs cycle. We study the dependence of its cyclicity on the cell respiration intensity determined by the formation level of carbon dioxide. We constructed the phase-parametric characteristic of the consumption of a substrate by a cell depending on the intensity of the metabolic process of formation of the final product of the oxidation. The scenarios of all possible oscillatory modes of the system are constructed and studied. The bifurcations with period doubling and with formation of chaotic modes are found. Their attractors are constructed. The full spectra of indices and divergencies for the obtained modes, the values of KS-entropies, horizons of predictability, and Lyapunov dimensions of strange attractors are calculated. Some conclusions about the structural-functional connections of the cycle of tricarboxylic acids and their influence on the stability of the metabolic process in a cell are presented.

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arXiv2018

Activit{é} motrice des truies en groupes dans les diff{é}rents syst{è}mes de logement

Assessment of the motor activity of group-housed sows in commercial farms. The objective of this study was to specify the level of motor activity of pregnant sows housed in groups in different housing systems. Eleven commercial farms were selected for this study. Four housing systems were represented: small groups of five to seven sows (SG), free access stalls (FS) with exercise area, electronic sow feeder with a stable group (ESFsta) or a dynamic group (ESFdyn). Ten sows in mid-gestation were observed in each farm. The observations of motor activity were made for 6 hours at the first meal or at the start of the feeding sequence, two consecutive days and at regular intervals of 4 minutes. The results show that the motor activity of group-housed sows depends on the housing system. The activity is higher with the ESFdyn system (standing: 55.7%), sows are less active in the SG system (standing: 26.5%), and FS system is intermediate. The distance traveled by sows in ESF system is linked to a larger area available. Thus, sows travel an average of 362 m $\pm$ 167 m in the ESFdyn system with an average available surface of 446 m${}^2$ whereas sows in small groups travel 50 m $\pm$ 15 m for 15 m${}^2$ available.

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arXiv2018

Identification of Key Proteins Involved in Axon Guidance Related Disorders: A Systems Biology Approach

Axon guidance is a crucial process for growth of the central and peripheral nervous systems. In this study, 3 axon guidance related disorders, namely- Duane Retraction Syndrome (DRS) , Horizontal Gaze Palsy with Progressive Scoliosis (HGPPS) and Congenital fibrosis of the extraocular muscles type 3 (CFEOM3) were studied using various Systems Biology tools to identify the genes and proteins involved with them to get a better idea about the underlying molecular mechanisms including the regulatory mechanisms. Based on the analyses carried out, 7 significant modules have been identified from the PPI network. Five pathways/processes have been found to be significantly associated with DRS, HGPPS and CFEOM3 associated genes. From the PPI network, 3 have been identified as hub proteins- DRD2, UBC and CUL3.

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arXiv2018

When physics meets biology: a less known Feynman

We discuss a less known aspect of Feynman's multifaceted scientific work, centered about his interest in molecular biology, which came out around 1959 and lasted for several years. After a quick historical reconstruction about the birth of molecular biology, we focus on Feynman's work on genetics with Robert S. Edgar in the laboratory of Max Delbruck, which was later quoted by Francis Crick and others in relevant papers, as well as in Feynman's lectures given at the Hughes Aircraft Company on biology, organic chemistry and microbiology, whose notes taken by the attendee John Neer are available. An intriguing perspective comes out about one of the most interesting scientists of the XX century.

physics.hist-ph↗
arXiv2018

Blue-blocking spectacles lenses for retinal damage protection and circadian rhythm: evaluation parameters

There is evidence for the effect of blue light on circadian cycle and ocular pathologies. Moreover, the introduction of LED lamps has increased the presence of blue light. In the last two years, many different blue blocking ophthalmic lenses have been introduced. Due to the different effect of blue light on ocular media and circadian rhythm, we have defined two indices that describe the level of protection of the lenses towards the retina and the circadian cycle under different lighting as for example daylight and tablet. These indexes can help in individuating the right lens for ocular protection.

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arXiv2018

Analyzing counterintuitive data

Purpose: To explore the issue of counterintuitive data via analysis of a representative case and further discussion of those situations in which the data appear to be inconsistent with current knowledge. Case: 844 postoperative CABG patients, who were extubated within 24 hours of surgery were identified in a critical care database (MIMIC-III). Nurse elicited pain scores were documented throughout their hospital stay on a scale of 0 to 10. Levels were tracked as mean, median, and maximum values, and categorized as no (0/10), mild (1-3), moderate (4-6) and severe pain (7-10). Regression analysis was employed to analyze the relationship between pain scores and outcomes of interest (mortality and hospital LOS). After covariate adjustment, increased levels of pain were found to be associated with lower mortality rates and reduced hospital LOS. Conclusion: These counterintuitive results for post-CABG pain related outcomes have not been previously reported. While not representing strong enough evidence to alter clinical practice, confirmed and reliable results such as these should serve as a research trigger and prompt further studies into unexpected associations between pain and patient outcomes. With the advent of frequent secondary analysis of electronic health records, such counterintuitive data results are likely to become more frequent. We discuss the issue of counterintuitive data in extended fashion, including possible reasons for, and approaches to, this phenomenon.

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arXiv2018

CoHSI I; Detailed properties of the Canonical Distribution for Discrete Systems such as the Proteome

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.

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arXiv2018

Mineralogical Characteristics of Harmattan Dust Across Jos North Central and Potiskum North Earthern Cities of Nigeria

The trace metals and mineralogical composition of harmattan dust carried out on the samples collected at Jos ((9 55'N, 8 55'E)) and Potiskum ((11 43'N, 11 02'E) as revealed by PIXE and AAS machine using clean Petri Dishes and Plastic bowls of 10 cm in diameter aimed on the characteristics of the mineralogical and elemental composition of the harmattan dust carried out in Nigeria. Thirteen trace elements, Na, K, Ca, Mg, Fe, Cd, Zn, Mn, Cu, Si, Al, Ti, and Zr were determined and their concentrations were evaluated in different proportion. Minerals such as Quartz [SiO2], Corundum [Al2O3], Hematite [Fe2O3], Lime [CaO], Periclase [MgO], Rutile [TiO2], Zincite [MnO], Bunsenite [NiO], Cuprite [Cu2O], Zincite [ZnO], Baddeleyite [ZrO2], Litharge [PbO], Monazite [P2O5], Montrodydite [HgO] and Petzite [Au2O3] were also determined in different concentrations. The particle weight of the sample for the residential and commercial areas were calculated to be Jos (18.95g/m2, 19.25g/m2), Potiskum (24.24 g/m2, 2515g/m2) respectively. The results shows that the harmattan dust that blows across the two stations in Nigeria comprise of high elements and more minerals.

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arXiv2018

Observations and perspectives on the diversification of genomes

Rich information on the prebiotic evolution is still stored in contemporary genomic data. The statistical mechanism at the sequence level may play a significant role in the prebiotic evolution. Based on statistical analysis of genome sequences, it has been observed that there is a close relationship between the evolution of the genetic code and the organisation of genomes. A biodiversity space for species is constructed based on comparing the distributions of codons in genomes for different species according to recruitment order of codons in the prebiotic evolution, by which a closely relationship between the evolution of the genetic code and the tree of life has been confirmed. On one hand, the three domain tree of life can be reconstructed according to the distance matrix of species in this biodiversity space, which supports the three-domain tree rather than the eocyte tree. On the other hand, an evolutionary tree of codons can be obtained by comparing the distributions of the 64 codons in genomes, which agrees with the recruitment order of codons on the roadmap. This is a simple phylogenomic method to study the origins of metazoan, the evolution of primates, etc. This study should be regarded as an exploratory attempt to explain the diversification of the three domains of life by statistical mechanism in prebiotic sequence evolution. It is indicated that the number of bases in the triplet codons might be explained statistically by the number of strands in the triplex DNAs. The adaptation of life to the changing environment might be due to assembly of redundant genomes at the sequence level.

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arXiv2018

Observations and perspectives on the prebiotic sequence evolution

The post-genomic era has brought opportunities to bridge traditionally separate fields of early history of life and brought new insight into origin and evolution of biodiversity. According to distributions of codons in genome sequences, I found a relationship between the genetic code and the tree of life. This remote and profound relationship involves the origin and evolution of the genetic code and the diversification and expansion of genomes. Here, a prebiotic picture of the triplex nucleic acid evolution is proposed to explain the origin of the genetic code, where the transition from disorder to order in the origin of life might be due to the increasing stabilities of triplex base pairs. The codon degeneracy can be obtained in detail based on the coevolution of the genetic code with amino acids, or equivalently, the coevolution of tRNAs with aaRSs. This theory is based on experimental data such as the stability of triplex base pairs and the statistical features of genomic codon distributions. Several experimentally testable proposals have been developed. This study should be regarded as an exploratory attempt to reveal the early evolution of life based on sequence information in a statistical manner.

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