Miracle-dz/UniFAR-FTUs huggingface dataset:
P Particle-Based Stochastic Simulators

Computational simulations are widely used in neuroscience, as in other branches of biology, to explore the implications of quantitative models. They are used to investigate the sequestration of calcium calmodulin kinase II (CamKII) in dendritic spines, the transmission of action potentials through networks of neurons, and the release of heterogeneous synaptic vesicles, among many other topics. Some simulations are used with abstract “toy models” to identify fundamental biological principles, such as which signaling network topologies can transmit information particularly accurately. Others are tightly integrated with experimental work to build better understandings of particular systems. Neuroscience simulation methods can be broadly categorized by the level of detail that they represent. At the coarse end of the scale, one can numerically integrate the differential rate equations that represent the kinetics of biochemical reaction and transport processes (Aldridge et al. 2006). Such integration methods typically assume few spatial compartments and ignore stochasticity. At the other extreme lie molecular dynamics approaches, in which one simulates the intricate motions of individual atoms within potential energy landscapes (Rapaport 2004). In moving along the continuum from coarser to finer levels of detail, these simulation methods typically address smaller total volumes of space, simulate shorter amounts of time, require more simulation parameters, and become more computationally intensive. They also consider space more realistically, such as by moving from a compartment description to a lattice, and then on to continuous space. In addition, the simulators change from using deterministic computations, which are appropriate when enough molecules are considered that their fluctuations become irrelevant, to stochastic computations, which account for natural fluctuations and are essential when there are few molecules. Particle-based simulations lie toward the detailed end of this scale. They track the locations and interactions of all individual molecules of interest, while ignoring water and other molecules
SOFTWARE ARCHITECTURAL STYLES

Growing and executable system architecture has a significant role in successful production of large and distributed systems. Assessing the effect of different decisions in architecture design can decrease the time and cost of software production, especially when these decisions are related to non-functional properties of system. Performance is a non-functional property which relates to timing behaviour of system. In this paper we propose an approach for modelling and analysis of performance in architecture level. To do this, we follow a general process which needs two formal notations for specifying architecture and performance models of system. In this paper we show how Stochastic Process Algebra (SPA) in the form of PEPA language can be used for performance modelling and analysis of software architectures modelled using Graph Transformation System (GTS). To enable architecture model for performance analysis, equivalent PEPA model should be constructed with transformation. Transformed performance model of the architecture has been analysed through PEPA toolkit for some properties like throughput, sensitivity analysis, response time and utilisation rate. The analysis results have been explained with regard to a realistic case study.
MOLECULAR ANALYSIS OF THE INTERACTION BETWEEN POTATO VIRUS X AND THE RESISTANCE GENE NB IN SOLANUM TUBEROSUM

Nb is a single dominant gene in potato that confers hypersensitive resistance to potato virus X group 1 and group 2 (strains ROTH1 and CP2, respectively). Genetic and molecular analysis showed that Nb is located on the upper arm of chromosome V and form part of a cluster of resistance genes encoding specificities to many different pathogens. Part of the strategy for cloning Nb was the construction of a high-resolution genetic map around the Nb locus using amplified fragment length polymorphism (AFLP) technology in conjunction with a bulked segregant approach. We describe the genetical localisation of molecular markers tightly linked to the Nb locus and the development PCR-based markers suitable for isolation of the Nb resistance gene by positional cloning. To characterise the viral elicitor of Nb-mediated resistance we introduced modifications into the genome of the avirulent PVX strain ROTH1 and the virulent PVX strain UK3. We show that the Nb avirulence determinant corresponds to the 25 kDa PVX movement protein and that the isoleucine residue at position 6 in this protein is required for the activation of the Nb response. To study cellular events associated with the Nb response, the 25 kDa proteins of both viral strains were tagged with the green fluorescent protein (GFP). Using laser scanning confocal microscopy we showed that the Nb-mediated response is associated with degradation of subcellular structures.
Dynamics of a bubble rising in gravitational field

Abstract The rising motion in free space of a pulsating spherical bubble of gas and vapour driven by the gravitational force, in an isochoric, inviscid liquid is investigated. The liquid is at rest at the initial time, so that the subsequent flow is irrotational. For this reason, the velocity field due to the bubble motion is described by means of a potential, which is represented through an expansion based on Legendre polynomials. A system of two coupled, ordinary and nonlinear differential equations is derived for the vertical position of the bubble center of mass and for its radius. This latter equation is a modified form of the Rayleigh-Plesset equation, including a term proportional to the kinetic energy associated to the translational motion of the bubble.
Data-Driven Feedforward Learning using Non-Causal Rational Basis Functions: Application to an Industrial Flatbed Printer

Data-driven feedforward learning enables high performance for industrial motion systems based on measured data from previous motion tasks. The key aspect herein is the chosen feedforward parametrization, which should parsimoniously model the inverse system. At present, high performance comes at the cost of parametrizations that are nonlinear in the parameters and consequences thereof. A linear parametrization is proposed that enables parsimonious modeling of inverse systems for feedforward through the use of non-causal rational orthonormal basis functions. The benefits of the proposed parametrization are experimentally demonstrated on an industrial printer, including pre-actuation and cyclic pole repetition.
Developing Distributed Hard-Real Time Software Systems Using FPGAs and Soft Cores

Hard real-time systems guarantee by design that no deadline is ever missed. In a distributed environment such as particle accelerators, there is often the extra requirement of having diverse real-time systems synchronize to each other. Implementations on top of general purpose multitasking operating systems such as Linux generally suer from lack of full control of the platform. On the other hand, solutions based on logic inside FPGAs can result in long development cycles. A mid-way approach is presented which allows fast software development yet guarantees full control of the timing of the execution. The solution involves using soft cores inside FPGAs, running single tasks without interrupts and without an operating system underneath. Two CERN developments are presented, both based on a unique free and open source HDL core comprising a parameterizable number of CPUs, logic to synchronize them and message queues to communicate with the local host and with remote systems. This development environment is being oered as a service to fill the gap between Linux-based solutions and full-hardware implementations. BACKGROUND
Site-Specific M utagenesis in H um an C ells by Bulky Exocyclic A m ino-Substituted G uanine and A denine Derivatives

P urpose: 7-Bromomethylbenz[a ]anthracene is a wellknown mutagen and carcinogen. The a im of this study is to determine the mutagenic potency of its two major D NA adducts [N -(benz[a ]anthracen-7-ylmethyl)-2 ’-deoxyguanosine (b[a ]a G ) and N -(benz[a ]anthracen-7ylmethyl)-2 ’-deoxyadenosine (b[a ]a A)] and the simpler benzyla ted analogs [N -benzyl-2 ’-deoxyguanosine (bnG ) and N -benzyl-2 ’-deoxyadenosine (bnA)] in Ad293 human cells and to compare to their mutagenicity in human cells and E . coli. M ateria ls and M ethods: The shuttle vector pG P 50 is capable of replicating in E. coli and human cells. M odified nucleotides were positioned in the plasmid pG P 50 in a manner similar to pG P 10 as described (8). Adenovirus transformed human embryonic kidney cells (line 293) were transfected with a shuttle vector containing an adduct. Two days later, the plasmids were recovered and treated with DpnI to remove unreplicated DN A. DH 10B E. coli were transformed with the plasmids. Bacteria were cultured with the media conta ining X -gal, IP TG and ampicillin. Bacteria transformed by the plasmid with the adduct-induced mutation in the initiation codon of lacZ’ form white colonies whereas bacteria transformed by the plasmid without mutation form blue colonies. R esults: In the human cell site-specific mutagenesis system, bnG exhibited weak mutagenicity and bnA was not mutagenic, a lthough b[a ]a G or b[a ]a A produced 8% and 7% mutant colonies, respectively. At the site of the adduct, b[a ]a G induced the G→T transversion mutation while b[a ]a A produced the A→G transition mutation. Conclusion: These data indicate that bulkier b[a ]aG and b[a ]a A exhibit significantly greater mutagenicity in human cells than in E. coli. (C ancer R esearch and Treatment 2004;36:151-156) 󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏 Key W ords: M utagenesis, M utagen
Should We Treat Data as Labor? Moving Beyond “Free”

In the previous paper in this session and in a forthcoming book (Posner and Weyl, 2018), one of us argues that by creating or strengthening absent markets, we can simultaneously address the inequality, stagnation and sociopolitical conflict afflicting developed countries. He calls such cases “radical markets” because of their transformative emancipatory potential. A promising example was suggested years earlier by another of us, who wrote a book (Lanier, 2013) highlighting the social problems with the culture of “free” online, in which users are neither paid for their data contributions to digital services nor pay directly for the value they receive from these services. While free data for free services is a barter, he argued that the lack of targeting of incentives undermines market principles of evaluation, skews distribution of financial returns from the data economy and stops users from developing themselves into “first-class digital citizens”. In this paper we explore whether and how treating the market for data like a labor market could serve as a radical market that is practical in the near term.
COLICINE K VII. THE TRANS~V.R OF TYPE K COLICmOGENY

There can be but little doubt that the bactericidal activity of the colieine K which is elaborated by F~cherichia coli K235 resides in the protein portion of the bacterial somatic antigen (1). In its native state this component is firmly bound to a lipopolysaccharide and the two cannot be separated by the usual chemical or physical techniques. The question has arisen, however, as to what might happen were colicinogeny transferred from E. coli to another microorganism such as Shigella sonnei. Would the colicine again be produced as a protein-lipopolysaccharide complex or would it be released as an unconjugated protein? If the latter were true, our studies on the active site of the colicine molecule would be greatly simplified. On the other hand, were the new colicine to be released as a somatic antigen, one could now compare its properties with those of the somatic antigen of the noncolicinogenic parent strain used as the recipient. Such a study might reveal the changes which are brought about when a microorganism becomes colicinogenic. The investigation was therefore undertaken and evidence will be presented to show that type K colicinogeny can be transferred to Sh. sonnei. The new colicine is elaborated as a somatic antigen and, though its chemical and serological properties are strikingly different from those of colicine K, it will be seen that the two colicines do indeed possess certain properties in common.
The Use of Single-Subject Research to Identify Evidence-Based Practice in Special Education

Single-subject research plays an important role in the development of evidence-based practice in special education. The defining features of single-subject research are presented, the contributions of single-subject research for special education are reviewed, and a specific proposal is offered for using single-subject research to document evidence-based practice. This article allows readers to determine if a specific study is a credible example of single-subject research and if a specific practice or procedure has been validated as “evidence-based” via single-subject research.
STABILITY ANALYSIS OF MULTIRATE MODEL PREDICTIVE CONTROL

Abstract This paper proposes a multirate Model Predictive Control (MPC) algorithm for constrained systems where the control effort is adjusted several times during one sampling interval. Stability criterion for this new proposed algorithm is established. The test of the stability condition, the estimation of stability regions and the choice of the terminal weighting term are discussed.
Corrupt Bandits

We study a variant of the stochastic multi-armed bandit (MAB) problem in which the rewards are corrupted. In this framework, motivated by privacy preserving in online recommender systems, the goal is to maximize the sum of the (unobserved) rewards, based on the observation of transformation of these rewards through a stochastic corruption process with known parameters. We provide a lower bound on the expected regret of any bandit algorithm in this corrupted setting, and devise two upper conﬁdence bound algorithms, UCB-CF and KLUCB-CF. We provide upper bounds on their regret and present some experimental results which conﬁrm our analysis.
Surface chemistry and morphology in single particle optical imaging

Abstract Biological nanoparticles such as viruses and exosomes are important biomarkers for a range of medical conditions, from infectious diseases to cancer. Biological sensors that detect whole viruses and exosomes with high specificity, yet without additional labeling, are promising because they reduce the complexity of sample preparation and may improve measurement quality by retaining information about nanoscale physical structure of the bio-nanoparticle (BNP). Towards this end, a variety of BNP biosensor technologies have been developed, several of which are capable of enumerating the precise number of detected viruses or exosomes and analyzing physical properties of each individual particle. Optical imaging techniques are promising candidates among broad range of label-free nanoparticle detectors. These imaging BNP sensors detect the binding of single nanoparticles on a flat surface functionalized with a specific capture molecule or an array of multiplexed capture probes. The functionalization step confers all molecular specificity for the sensor’s target but can introduce an unforeseen problem; a rough and inhomogeneous surface coating can be a source of noise, as these sensors detect small local changes in optical refractive index. In this paper, we review several optical technologies for label-free BNP detectors with a focus on imaging systems. We compare the surface-imaging methods including dark-field, surface plasmon resonance imaging and interference reflectance imaging. We discuss the importance of ensuring consistently uniform and smooth surface coatings of capture molecules for these types of biosensors and finally summarize several methods that have been developed towards addressing this challenge.
Thermal Design of Refridgerated Hexapole 18 GHZ ECRIS HIISI

A project is underway for constructing a new 18 GHz ECR ion source HIISI at University of Jyvaskyla. An innovative plasma chamber structure with grooves at magnetic poles for larger chamber radius at poles. The hexapole will be refridgerated to sub-zero temperatures to boost the coercivity and the remanence of the permanent magnet material and to allow the use of high remanence, low intrinsic coersivity permanent magnet materials. The hexapole structure is insulated from high temperature solenoid coils and plasma chamber by vacuum. The thermal design of the structure has been made using a thermal diffusion code taking in account radiative, conductive and convective heat transfer processes. The heat flux distribution from plasma has been estimated using electron trajectory simulations. The electron simulations are verified by comparing the distribution to plasma chamber patterns from 14 GHz ECR. Thermal design efforts are presented together with an analysis of the demagnetizing H-field in the permanent magnets.
Raman optical activity comes of age

The theory and applications of Raman optical activity (ROA), which measures vibrational optical activity by means of a small difference in the intensity of Raman scattering from chiral molecules in right- and left-circularly polarized incident light or, equivalently, a small circularly polarized component in the scattered light, are briefly reviewed. Thanks to new developments in instrumentation, ROA may be applied to a wide range of chiral molecular species. As well as providing the absolute configuration of small chiral molecules, the application of ab initio methods to the analysis of experimental ROA spectra holds great promise for the determination of the three-dimensional structure and conformational distribution in unprecedented detail. The many structure-sensitive bands in the ROA spectra of aqueous solutions of biomolecules provide detailed structural information including, in the case of proteins, the tertiary fold in addition to secondary structure elements such as helix and sheet. ROA studies of unfolded and partially folded proteins are providing new insight into the residual structure in denatured proteins and the aberrant behaviour of proteins responsible for misfolding diseases. It is even possible to measure the ROA spectra of most intact viruses, from which information about the folds of the major coat proteins and the structure of the nucleic acid core may be obtained. Hopefully this review will stimulate interest in the molecular physics aspects of the subject, and will encourage further theoretical work aimed at extracting maximum information from the plethora of structure-sensitive bands in typical ROA spectra.
Alternating Direction Implicit (ADI) schemes for a PDE-based image osmosis model

We consider Alternating Direction Implicit (ADI) splitting schemes to compute efficiently the numerical solution of the PDE osmosis model considered by Weickert et al. in [10] for several imaging applications. The discretised scheme is shown to preserve analogous properties to the continuous model. The dimensional splitting strategy traduces numerically into the solution of simple tridiagonal systems for which standard matrix factorisation techniques can be used to improve upon the performance of classical implicit methods, even for large time steps. Applications to the shadow removal problem are presented.
Elucidating the Phylogeny and Taxonomic Position of the genus Chrysodidymus Prowse (Chrysophyceae, Synurales)

Abstract Chrysodidymus represents a monotypic genus of silica-scaled chrysophytes, with well characterised morphology and ultrastructure, as well as pretty known ecology. However, the taxonomic status of this genus remains ambiguous due to the absence of relevant sequence data. In this study, we have aimed to genetically characterize a newly established C. synuroideus culture to elucidate the taxonomy of Chrysodidymus. Our multigene SSU rDNA + LSU rDNA + rbcL phylogenetic analysis inferred C. synuroideus to be significantly nested deeply inside the genus Synura. This convincing evidence led us to propose a new combination for this taxon — Synura synuroidea (Prowse) Pusztai et al., comb. nov.
Image Segmentation using Improved Bacterial Foraging Algorithm

Bacterial foraging optimization algorithm (BFOA) has been widely accepted as a global optimization algorithm of current interest for distributed optimization and control. BFOA is inspired by the social foraging behavior of Escherichia coli. BFOA has already drawn the attention of researchers because of its efficiency in solving real-world optimization problems arising in several application domains. The underlying biology behind the foraging strategy of Escherichia coli is emulated in an extraordinary manner and used as a simple optimization algorithm. The cross entropy function works well in case of bi-level thresholding problem. However, if there is a need of the multi-thresholding in image processing application, a global and generic objective function is desired so that each threshold could be tested for its best performance statistically. The maxima of the selected threshold is optimized by using the BFO algorithm based on constant chemo taxis length, constant rate of elimination and dispersion of bacteria and constant swim and tumbling of bacteria. The constant rate of swim, tumbling and rate of elimination and dispersion does not provide a natural optimization of the maxima of the threshold level from the given threshold levels.
COST -EFFECTIVE STEREO VISION SYSTEM FOR MOBILE ROBOT NAVIGATION AND 3D MAP RECONSTRUCTION

The key component of a mobile robot system is the ability to localize itself accurately in an unknown environment and simultaneously build the map of the environment. Majority of the existing navigation systems are based on laser range finders, sonar sensors or artificial landmarks. Navigation systems using stereo vision are rapidly developing technique in the field of autonomous mobile robots. But they are less advisable in replacing the conventional approaches to build small scale autonomous robot because of their high implementation cost. This paper describes an experimental approach to build a cost- effective stereo vision system for autonomous mobile robots that avoid obstacles and navigate through indoor environments. The mechanical as well as the programming aspects of stereo vision system are documented in this paper. Stereo vision system adjunctively with ultrasound sensors was implemented on the mobile robot, which successfully navigated through different types of cluttered environments with static and dynamic obstacles. The robot was able to create two dimensional topological maps of unknown environments using the sensor data and three dimensional model of the same using stereo vision system.