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A Model-Theoretic Approach to Modular Implementation, with Application to Biological SystemsJul 12 2019We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in the actions ... More
Topological Information Data AnalysisJul 06 2019This paper presents methods that quantify the structure of statistical interactions within a given data set, and was first used in \cite{Tapia2018}. It establishes new results on the k-multivariate mutual-informations (I_k) inspired by the topological ... More
Investigating some attributes of periodicity in DNA sequences via semi-Markov modellingJul 06 2019DNA segments and sequences have been studied thoroughly during the past decades. One of the main problems in computational biology is the identification of exon-intron structures inside genes using mathematical techniques. Previous studies have used different ... More
Measuring Time with Minimal ClocksJun 17 2019Being able to measure time, whether directly or indirectly, is a significant advantage for an organism. It allows for the timely reaction to regular or predicted events, reducing the pressure for fast processing of sensory input. Thus, clocks are ubiquitous ... More
Quantifying impacts of the drought 2018 on European ecosystems in comparison to 2003Jun 07 2019In recent decades, an increasing persistence of atmospheric circulation patterns has been observed. In the course of the associated long-lasting anticyclonic summer circulations, heat waves and drought spells often coincide, leading to so-called hotter ... More
Studies on Bone-mass Formation within a Theoretical ModelJun 03 2019Bone-mass formation in human is looked at to understand the underlying dynamics with an eye on healing of bone-fracture and non-unions in non-invasive pathways. Three biological cells osteoblasts, osteoclasts and osteocytes are important players in creating ... More
The behaviour of information flow near criticalityJun 03 2019Recent experiments have indicated that many biological systems self-organise near their critical point, which hints at a common design principle. While it has been suggested that information transmission is optimized near the critical point, it remains ... More
Review: dual benefits, compositions, recommended storage, and intake duration of mother's milkMay 28 2019Breastfeeding benefits both infants and mothers. Nutrients in mother's milk help protect infants from multiple diseases including infections, cancers, diabetes, gastrointestinal and respiratory diseases. We performed literature mining on 31,496 mother's-milk-related ... More
The challenges of purely mechanistic models in biology and the minimum need for a 'mechanism-plus-X' frameworkMay 27 2019Ever since the advent of molecular biology in the 1970s, mechanical models have become the dogma in the field, where a "true" understanding of any subject is equated to a mechanistic description. This has been to the detriment of the biomedical sciences, ... More
A Prerequisite for LifeMay 22 2019The complex physicochemical structures and chemical reactions in living organism have some common features: (1) The life processes take place in the cytosol in the cells, which, from a physicochemical point of view is an emulsion of biomolecules in a ... More
Effect of E-cigarette Use and Social Network on Smoking Behavior Change: An agent-based model of E-cigarette and Cigarette InteractionMay 03 2019Despite a general reduction in smoking in many areas of the developed world, it remains one of the biggest public health threats. As an alternative to tobacco, the use of electronic cigarettes (ECig) has been increased dramatically over the last decade. ... More
Morphogenesis Software based on Epigenetic Code ConceptApr 23 2019The process of morphogenesis is an evolution of shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such as amputation ... More
Base spacing distribution analysis for human genomeApr 16 2019The distribution of bases spacing in human genome was investigated. An analysis of the frequency of occurrence in the human genome of different sequence lengths flanked by one type of nucleotide was carried out showing that the distribution has no self-similar ... More
Detection of Metallo-\b{eta}-Lactamases-Encoding Genes Among Clinical Isolates of Escherichia Coli in a Tertiary Care Hospital, MalaysiaApr 10 2019The multidrug resistant Escherichia coli strains causes multiple clinical infections and has become a rising problem globally. The metallo-\b{eta}-lactamases encoding genes are very severe in gram-negative bacteria especially E. coli. This study was aimed ... More
Revising the Wilks Scoring System for pro RAW PowerliftingMar 22 2019Purpose: In powerlifting the total result is highly dependent on the athletes bodyweight. Powerlifting is divided to equipped and RAW types. Pro RAW powerlifting competitions use the Wilks scoring system to compare and rank powerlifting results across ... More
Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas ProgramMar 18 2019Jun 07 2019Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to ... More
Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas ProgramMar 18 2019Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) aims to develop ... More
Self-Organization and Artificial LifeMar 14 2019Self-organization can be broadly defined as the ability of a system to display ordered spatio-temporal patterns solely as the result of the interactions among the system components. Processes of this kind characterize both living and artificial systems, ... More
Helminth Dynamics: Mean Number of Worms, Reproductive RatesFeb 25 2019We derive formulas to compute mean number of worms in a newly Helminth infected population before secondary infections are started (population is closed). We have proved the two types of growth functions arise in this process as measurable functions.
CoHSI V: Identical multiple scale-independent systems within genomes and computer softwareFeb 25 2019A mechanism-free and symbol-agnostic conservation principle, the Conservation of Hartley-Shannon Information (CoHSI) is predicted to constrain the structure of discrete systems regardless of their origin or function. Despite their distinct provenance, ... More
Biophysics at the coffee shop: lessons learned working with George OsterFeb 20 2019Mar 28 2019Over the past 50 years, the use of mathematical models, derived from physical reasoning, to describe molecular and cellular systems has evolved from an art of the few to a cornerstone of biological inquiry. George Oster stood out as a pioneer of this ... More
Biophysics at the coffee shop: lessons learned working with George OsterFeb 20 2019Over the past 50 years, the use of mathematical models, derived from physical reasoning, to describe molecular and cellular systems has evolved from an art of the few to a cornerstone of biological inquiry. George Oster stood out as a pioneer of this ... More
Towards peptide strings pharmacologyFeb 18 2019Peptide strings have been developed as a concept for the past fourteen years. They are proposed to basically entail various quantum states engendered by the physical interactions of proteins containing peptide portions that are similar to one another ... More
Comparison of SVM and Spectral Embedding in Promoter Biobricks' Categorizing and ClusteringFeb 15 2019Feb 18 2019Background: 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. ... More
A clinical update on Antibiotic Resistance Gram-negative bacteria in Malaysia- a reviewFeb 13 2019Antibiotics are the wonder discoveries to combat microbes. For decades, multiple varieties of antibiotics have been used for therapeutic purposes in hospital settings and communities throughout the world. Unfortunately, bacteria have become resistant ... More
Detection of virulence factors and beta-lactamase encoding genes among the clinical isolates of Pseudomonas aeruginosaFeb 06 2019Background: Pseudomonas aeruginosa has emerged as a significant opportunistic bacterial pathogen that causes nosocomial infections in healthcare settings resulting in treatment failure throughout the world. This study was carried out to compare the relatedness ... More
Biogenic magnetic nanoparticles in plantsJan 22 2019The 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 ... More
Single cell data explosion: Deep learning to the rescueJan 18 2019Mar 11 2019The 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.
Single cell data explosion: Deep learning to the rescueJan 18 2019The 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.
Moonshots for agingJan 13 2019As the global population ages, there is increased interest in living longer and improving quality of life in later years. However studying aging is expensive and time-consuming. And despite successes in extending lifespan in model organisms there still ... More
Measurement of trace elements in five popular medicinal plants using Instrumental Neutron Activation Analysis method (INAA) in Arak, IranJan 05 2019In this work, the specific mass of twelve elements were determined in five of the most commonly used medicinal plants as Caraway (Carum carvi), Savory (Satureia hortensis), Purslane (Portulaca oleracea), Fenugreek (Trigonella foenum-graecum) and Milk ... More
Chaotic dynamics of movements stochastic instability and the hypothesis of N.A. Bernstein about "repetition without repetition"Dec 21 2018The 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 ... More
Low-temperature marginal ferromagnetism explains anomalous scale-free correlations in natural flocksDec 18 2018We introduce a new ferromagnetic model capable of reproducing one of the most intriguing properties of collective behaviour in starling flocks, namely the fact that strong collective order of the system coexists with scale-free correlations of the modulus ... More
La fauna de mamíferos fósiles del depósito paleontológico "El Abrón" (nivel ix), Pinar del Río, CubaDec 14 2018"El Abr\'on" 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 ... More
Thermoregulation in mice, rats and humans: An insight into the evolution of human hairlessnessDec 04 2018The 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 ... More
The need for an integrative thinking to fight against emerging infectious diseasesNov 13 2018We present here the proceedings of the 5th seminar on emerging infectious diseases (EIDs), held in Paris on March 22nd, 2016, with seven priority proposals that can be outlined as follows:$\bullet$Encourage research on the prediction, screening and early ... More
CoHSI IV: Unifying Horizontal and Vertical Gene Transfer - is Mechanism Irrelevant ?Nov 05 2018In 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, ... More
Proofs of life: molecular-biology reasoning simulates cell behaviors from first principlesOct 30 2018Jan 22 2019We axiomatize the molecular-biology reasoning style, verify compliance of the standard reference: Ptashne, A Genetic Switch, and present proof-theory-induced technologies to predict phenotypes and life cycles from genotypes. The key is to note that `reductionist ... More
Proofs of life: molecular-biology reasoning simulates cell behaviors from first principlesOct 30 2018Mar 18 2019We 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 ... More
Why Abeta42 Is Much More Toxic Than Abeta40Oct 25 2018Amyloid 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 ... More
Wanted Dead or Alive Extraterrestrial Life Forms (Thermodynamic criterion for life is a growing open system that performs self-assembly processes)Oct 23 2018For 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, ... More
Hominin evolution was caused by introgression from GorillaOct 02 2018The discovery of Paranthropus deyiremeda in 3.3-3.5 million year old fossil sites in Afar, together with 30% of the gorilla genome showing lineage sorting between humans and chimpanzees, and a NUMT ("nuclear mitochondrial DNA segment") on chromosome 5 ... More
An Inductive Logic Programming Approach to Validate Hexose Binding Biochemical KnowledgeOct 02 2018Hexoses are simple sugars that play a key role in many cellular pathways, and in the regulation of development and disease mechanisms. Current protein-sugar computational models are based, at least partially, on prior biochemical findings and knowledge. ... More
Time to Stop Telling Biophysics Students that Light is Primarily a WaveSep 15 2018Standard pedagogy introduces optics as though it were a consequence of Maxwell's equations, and only grudgingly admits, usually in a rushed aside, that light has a particulate character that can somehow be reconciled with the wave picture. Recent revolutionary ... More
Solving a non-linear model of HIV infection for CD4+T cells by combining Laplace transformation and Homotopy analysisSep 13 2018The 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) ... More
From Natural to Artificial Camouflage: Components and SystemsSep 11 2018We 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 ... More
True Epidemic Growth Construction Through Harmonic AnalysisAug 29 2018Sep 04 2018In this paper, we have proposed a two phase procedure (combining discrete graphs and wavelets) for constructing a true epidemic growth. In the first phase graph theory based approach was developed to update partial data available and in the second phase ... More
Fluid-Structure Interaction for the Classroom: Interpolation, Hearts, and Swimming!Aug 23 2018While students may find spline interpolation easily digestible, based on their familiarity with continuity of a function and its derivatives, some of its inherent value may be missed when students only see it applied to standard data interpolation exercises. ... More
The Function Transformation Omics - FunomicsAug 17 2018There 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 ... More
The triennial International Pigment Cell Conference (IPCC)Aug 15 2018Aug 24 2018The 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 ... More
How dark can it get at night? Examining how clouds darken the sky via all-sky differential photometryJul 27 2018Artificial light at night has affected most of the natural nocturnal landscapes worldwide and the subsequent light pollution has diverse effects on flora, fauna and human well-being. To evaluate the environmental impacts of light pollution, it is crucial ... More
Quantum patterns of genome size variation in angiospermsJul 16 2018The discontinuous DNA distribution in angiosperms is deduced from the eigen-value equation of the genome evolution operator H . The results agree well with the existing experimental data of Aloe, Nicotiana, Lathyrus and other genera. It may indicate that ... More
Ten Simple Rules When Considering RetirementJul 13 2018This is an article submitted to the Ten Simple Rules series of professional development articles published by PLOS Computational Biology.
Observations and perspectives on the prebiotic sequence evolutionJul 12 2018The 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 ... More
Observations and perspectives on the diversification of genomesJul 10 2018Rich 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 ... More
Attack and defence in cellular decision-making: lessons from machine learningJul 10 2018Jan 30 2019Machine learning algorithms are sensitive to meaningless (or "adversarial") perturbations. This is reminiscent of cellular decision-making where ligands (called "antagonists") prevent correct signalling, like in early immune recognition. We draw a formal ... More
Classification of red blood cell shapes in flow using outlier tolerant machine learningJun 21 2018The manual evaluation, classification and counting of biological objects demands for an enormous expenditure of time and subjective human input may be a source of error. Investigating the shape of red blood cells (RBCs) in microcapillary Poiseuille flow, ... More
Mineralogical Characteristics of Harmattan Dust Across Jos North Central and Potiskum North Earthern Cities of NigeriaJun 19 2018The 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 ... More
Analyzing counterintuitive dataJun 12 2018Purpose: 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 ... More
Blue-blocking spectacles lenses for retinal damage protection and circadian rhythm: evaluation parametersJun 11 2018There 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 ... More
Reproducible research using biomodelsJun 04 2018Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area of research ... More
Effects of forest fire severity on terrestrial carbon emission and ecosystem production in the Himalayan region, IndiaMay 27 2018Remote sensing techniques have been used effectively for measuring the overall loss of terrestrial ecosystem production and biodiversity due to the forest fire. The current research focuses on assessing the impact of forest fire severity on terrestrial ... More
When physics meets biology: a less known FeynmanMay 10 2018We 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, ... More
A Dynamical Systems Perspective on Chimeric Antigen Receptor T-Cell DosingMay 08 2018Chimeric antigen receptor T cells (CAR T cells) are dosed similarly to donor lymphocyte infusions following hematopoietic cell transplantation. In this perspective paper a mathematical basis for personalized dosing of CAR T cells is introduced.
Activit{é} motrice des truies en groupes dans les diff{é}rents syst{è}mes de logementMay 02 2018Assessment 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 ... More
Evolution of macromolecular structure: a 'double tale' of biological accretionApr 30 2018The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that are responsible ... More
Water Bridging Dynamics of Polymerase Chain Reaction in the Gauge Theory Paradigm of Quantum FieldsMar 29 2018We 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 ... More
Big Data Challenges in Genome InformaticsMar 20 2018In 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 ... More
Eshel Ben-Jacob: A unique individual in the science of collective phenomenaMar 18 2018Eshel 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 ... More
Sonifying stochastic walks on biomolecular energy landscapesMar 15 2018Translating 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 ... More
Nutritionally recommended food for semi- to strict vegetarian diets based on large-scale nutrient composition dataMar 12 2018Sep 06 2018Diet design for vegetarian health is challenging due to the limited food repertoire of vegetarians. This challenge can be partially overcome by quantitative, data-driven approaches that utilise massive nutritional information collected for many different ... More
Some preliminary results on relation between triplet composition and tissue source in larch total transcriptomeMar 09 2018We 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 ... More
NeuroStorm: Accelerating Brain Science Discovery in the CloudMar 09 2018Mar 20 2018Neuroscientists 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 ... More
Sensitivity and Bifurcation Analysis of a DAE Model for a Microbial Electrolysis CellFeb 18 2018Microbial electrolysis cells (MECs) are a promising new technology for producing hydrogen cheaply, efficiently, and sustainably. However, to scale up this technology, we need a better understanding of the processes in the devices. In this effort, we present ... More
Telling apart <I>Felidae</I> and <I>Ursidae</I> from the distribution of nucleotides in mitochondrial DNAFeb 07 2018Rank--frequency distributions of nucleotide sequences in mitochondrial DNA are defined in a way analogous to the linguistic approach, with the highest-frequent nucleobase serving as a whitespace. For such sequences, entropy and mean length are calculated. ... More
Reactive species involved in higher seeds germination and shoots vigor through direct plasma exposure and plasma-activated liquidsFeb 06 2018Cold atmospheric plasma treatments have been applied on lenses seeds and shoots to improve their germination and vigor rates. Two approaches have been considered: direct plasma exposure and plasma activation of liquids (tap water, demineralized water ... More
Hierarchical evolutive systems, fuzzy categories and the living single cellJan 31 2018In this article, the theory of hierarchical evolutive systems of Ehresmann and Vandremeersch [Bull. Math. Bio. 49, 13-50 (1987)] is improved by considering the categories of the theory as fuzzy sets whose elements are the composite objects formed by the ... More
A mathematical model of the metabolism of a cell. Self-organization and chaosJan 31 2018Using the classical tools of nonlinear dynamics, we study the process of self-organization and the appearance of the chaos in the metabolic process in a cell with the help of a mathematical model of the transformation of steroids by a cell Arthrobacter ... More
Nerve impulse propagation and wavelet theoryJan 24 2018A luminous stimulus which penetrates in a retina is converted to a nerve message. Ganglion cells give a response that may be approximated by a wavelet. We determine a function PSI which is associated with the propagation of nerve impulses along an axon. ... More
When Streams of Optofluidics Meet the Sea of LifeJan 10 2018Luke P. Lee is a Tan Chin Tuan Centennial Professor at the National University of Singapore. In this contribution he describes the power of optofluidics as a research tool and reviews new insights within the areas of single cell analysis, microphysiological ... More
Microfluidics for Chemical Synthesis: Flow ChemistryJan 10 2018Klavs F. Jensen is Warren K. Lewis Professor in Chemical Engineering and Materials Science and Engineering at the Massachusetts Institute of Technology. Here he describes the use of microfluidics for chemical synthesis, from the early demonstration examples ... More
Centrifugal Microfluidics for Biomedical ApplicationsJan 10 2018Yoon-Kyoung Cho is a full professor in Biomedical Engineering at UNIST. In this contribution she describes a fully integrated and automated lab-on-a-disc using centrifugal microfluidics to provide a "sample-in and answer-out" type of biochemical analysis ... More
Microfluidic tools for assaying immune cell functionJan 10 2018Joel Voldman is a professor in the Electrical Engineering and Computer Science Department at MIT. Here he describes his labs efforts to develop microfluidic devices for cell manipulation and analysis.
Microfluidic methods to form artificial cells and to study basic functions of membranesJan 10 2018Petra S. Dittrich is associate professor for Bioanalytics at the Department of Biosystems Science and Engineering at ETH Z\"urich. Here she describes the microfluidic devices that her lab develops to facilitate comprehensive studies on membranes with ... More
Adventures with Micro- and Nanofabricated Devices for Chemical and Biochemical Measurements; Early Days to Present!Jan 10 2018J. Michael Ramsey holds the Minnie N. Goldby Distinguished Professor of Chemistry Chair at the University of North Carolina - Chapel Hill. Here he describes the development of micro- and nanofabricated devices in his lab from the early developments that ... More
Electrochemical conversions in a microfluidic chip for xenobiotic metabolism and proteomicsJan 10 2018Albert van den Berg is a full professor on Miniaturized Systems for (Bio)Chemical Analysis at at the University of Twente. In this contribution he describes how microfluidic techniques can be used to mimic xenobiotic metabolism in vitro. Similar devices ... More
Theoretical aspects of microscale acoustofluidicsJan 10 2018Henrik Bruus is professor of lab-chip systems and theoretical physics at the Technical University of Denmark. In this contribution, he summarizes some of the recent results within theory and simulation of microscale acoustofluidic systems that he has ... More
Order and Chaos: Collective Behavior of Crowded Drops in Microfluidic SystemsJan 10 2018Sindy Tang is assistant professor at in the Department of Mechanical Engineering at Stanford University. In this contribution she describes how her team uses droplet microfluidics to identify bacteria that could increase the efficiency of generation of ... More
Thermodynamic Mechanism of Life and AgingJan 09 2018Life is a complex biological phenomenon represented by numerous chemical, physical and biological processes performed by a biothermodynamic system/cell/organism. Both living organisms and inanimate objects are subject to aging, a biological and physicochemical ... More
Mean squared displacement and sinuosity of three-dimensional random search movementsJan 08 2018Correlated random walks (CRW) have been used for a long time as a null model for animal's random search movement in two dimensions (2D). An increasing number of studies focus on animals' movement in three dimensions (3D), but the key properties of CRW, ... More
Seeded Ising Model and Statistical Natures of Human Iris TemplatesJan 03 2018We propose a variant of Ising model, called the Seeded Ising Model, to model probabilistic nature of human iris templates. This model is an Ising model in which the values at certain lattice points are held fixed throughout Ising model evolution. Using ... More
Porous translucent electrodes enhance current generation from photosynthetic biofilmsDec 25 2017We tested the enhancement of electrical current generated from photosynthetically active bacteria by use of electrodes with porosity on the nano- and micrometer length-scale. For two cyanobacteria on structured indium-tin-oxide electrodes, current generation ... More
Nobel Symposium 162 - MicrofluidicsDec 22 2017Feb 22 2018The Nobel Foundation's Symposium programme was initiated in 1965 and since then over 160 symposia have taken place. With the Nobel symposium summarized in this proceedings volume, we had the ambition to cover the past, current and future developments ... More
Traveling pulse emerges from individuals coordinating their stop-and-go motion: a case study in sheepDec 15 2017Jul 06 2018Monitoring small groups of sheep in spontaneous evolution in the field, we decipher behavioural rules that sheep follow at the individual scale in order to sustain collective motion. Individuals alternate grazing mode at null speed and moving mode at ... More
Encoding DNA sequences by integer chaos game representationDec 12 2017Dec 19 2017DNA sequences are fundamental for encoding genetic information. The genetic information may not only be understood by symbolic sequences but also from the hidden signals inside the sequences. The symbolic sequences need to be transformed into numerical ... More
Missing and spurious interaction in additive, multiplicative and odds ratio modelsDec 12 2017Additive, multiplicative, and odd ratio neutral models for interactions are for long advocated and controversial in epidemiology. We show here that these commonly advocated models are biased, leading to spurious interactions, and missing true interactions. ... More
Optimizing colormaps with consideration for color vision deficiency to enable accurate interpretation of scientific dataNov 29 2017Aug 01 2018Color vision deficiency (CVD) affects more than 4% of the population and leads to a different visual perception of colors. Though this has been known for decades, colormaps with many colors across the visual spectra are often used to represent data, leading ... More
Sequencing single-stranded libraries on the Illumina NextSeq 500 platformNov 29 2017Single-stranded libraries generated from ancient DNA extracts have specific sequencing requirements. The short library molecules typically associated with ancient DNA templates are expected to behave differently during the annealing to the flow cell and ... More