Miracle-dz/UniFAR-FTUs huggingface dataset:
Linear feature alignment based on vector potential field

An approach to align a linear feature in one dataset with a corresponding feature in another dataset that is considered more accurate is presented. The approach is based on the active contours (snake) concept, but implements the external force as a vector potential field in which case the source of the force is in vector form; further the snake feature is implemented as a non-closed snake. This is different from the conventional implementation of the snake, where the source of the external force is an image and the force is implemented as a gradient flow and usually as a closed snake. In this approach two conditions: the length and alignment conditions have to be satisfied to obtain a good alignment. Whereas the length condition ensures that the length of the snake feature is nearly equal that of the reference feature, the alignment condition requires that the snake and the reference feature are properly aligned. The length condition is achieved by fixing the end points of the snake feature to those of the reference feature. The alignment condition is achieved by segmenting the reference feature so that there is uniform external force from all parts of the feature. One assumption in this approach is that the snake and the reference feature are matched prior to alignment. An outstanding challenge therefore is to find out how to consider the effects of non-corresponding but neighbouring reference features on a snake feature in circumstances where prior matching has not been undertaken.
Simulating articulated subspace self-contact

We present an efficient new subspace method for simulating the self-contact of articulated deformable bodies, such as characters. Self-contact is highly structured in this setting, as the limited space of possible articulations produces a predictable set of coherent collisions. Subspace methods can leverage this coherence, and have been used in the past to accelerate the collision detection stage of contact simulation. We show that these methods can be used to accelerate the entire contact computation, and allow self-contact to be resolved without looking at all of the contact points. Our analysis of the problem yields a broader insight into the types of non-linearities that subspace methods can efficiently approximate, and leads us to design a pose-space cubature scheme. Our algorithm accelerates self-contact by up to an order of magnitude over other subspace simulations, and accelerates the overall simulation by two orders of magnitude over full-rank simulations. We demonstrate the simulation of high resolution (100K -- 400K elements) meshes in self-contact at interactive rates (5.8 -- 50 FPS).
Angled microfiber arrays as low-modulus, low Poisson's ratio compliant substrates

This paper presents a novel fabrication method for producing high-aspect-ratio, angled polymer microfiber arrays by directional pulling of polyethylene from low-aspect-ratio, microporous polycarbonate templates. These arrays represent a novel substrate for electrostatic sensors and actuators because they are characterized by low stiffness (<24 kPa effective elastic modulus), low Poisson's ratio (effectively zero at low strains), and very low density (<1% of solid polyethylene). Validation of these properties is presented by developing a model based on elastica theory, and by performing experiments using a parallel-plate electrostatic actuator fabricated with a fiber array as the dielectric and return spring.
Article in Press G Model Artificial Intelligence in Medicine a Comparative Analysis of the Density of the Snomed Ct Conceptual Content for Semantic Harmonization

Keywords: Biomedical terminology Semantic interoperability Semantic harmonization Structural methodology SNOMED CT UMLS a b s t r a c t Objectives: Medical terminologies vary in the amount of concept information (the " density ") represented, even in the same sub-domains. This causes problems in terminology mapping, semantic harmonization and terminology integration. Moreover, complex clinical scenarios need to be encoded by a medical terminology with comprehensive content. SNOMED Clinical Terms (SNOMED CT), a leading clinical terminology , was reported to lack concepts and synonyms, problems that cannot be fully alleviated by using post-coordination. Therefore, a scalable solution is needed to enrich the conceptual content of SNOMED CT. We are developing a structure-based, algorithmic method to identify potential concepts for enriching the conceptual content of SNOMED CT and to support semantic harmonization of SNOMED CT with selected other Unified Medical Language System (UMLS) terminologies. Methods: We first identified a subset of English terminologies in the UMLS that have 'PAR' relationship labeled with 'IS A' and over 10% overlap with one or more of the 19 hierarchies of SNOMED CT. We call these " reference terminologies " and we note that our use of this name is different from the standard use. Next, we defined a set of topological patterns across pairs of terminologies, with SNOMED CT being one terminology in each pair and the other being one of the reference terminologies. We then explored how often these topological patterns appear between SNOMED CT and each reference terminology, and how to interpret them. Results: Four viable reference terminologies were identified. Large density differences between terminologies were found. Expected interpretations of these differences were indeed observed, as follows. A random sample of 299 instances of special topological patterns (" 2:3 and 3:2 trapezoids ") showed that 39.1% and 59.5% of analyzed concepts in SNOMED CT and in a reference terminology, respectively, were deemed to be alternative classifications of the same conceptual content. In 30.5% and 17.6% of the cases, it was found that intermediate concepts could be imported into SNOMED CT or into the reference terminology , respectively, to enhance their conceptual content, if approved by a human curator. Other cases included synonymy and errors in one of the terminologies. Conclusion: These results show that structure-based algorithmic methods can be used to identify potential concepts to enrich SNOMED CT and the four reference terminologies. The comparative analysis has the future potential of supporting terminology …
An Information-Geometric Approach to Real-Time Audio Segmentation

We present a generic approach to real-time audio segmentation in the framework of information geometry for exponential families. The proposed system detects changes by monitoring the information rate of the signals as they arrive in time. We also address shortcomings of traditional cumulative sum approaches to change detection, which assume known parameters before change. This is done by considering exact generalized likelihood ratio test statistics, with a complete estimation of the unknown parameters in the respective hypotheses. We derive an efficient sequential scheme to compute these statistics through convex duality. We finally provide results for speech segmentation in speakers, and polyphonic music segmentation in note slices.
Depletion of the co-chaperone CDC-37 reveals two modes of PAR-6 cortical association in C. elegans embryos

PAR proteins play roles in the establishment and maintenance of polarity in many different cell types in metazoans. In C. elegans, polarity established in the one-cell embryo determines the anteroposterior axis of the developing animal and is essential to set the identities of the early blastomeres. PAR-1 and PAR-2 colocalize at the posterior cortex of the embryo. PAR-3, PAR-6 and PKC-3 (aPKC) colocalize at the anterior cortex of the embryo. A process of mutual exclusion maintains the anterior and posterior protein domains. We present results indicating that a homolog of the Hsp90 co-chaperone Cdc37 plays a role in dynamic interactions among the PAR proteins. We show that CDC-37 is required for the establishment phase of embryonic polarity; that CDC-37 reduction allows PAR-3-independent cortical accumulation of PAR-6 and PKC-3; and that CDC-37 is required for the mutual exclusion of the anterior and posterior group PAR proteins. Our results indicate that CDC-37 acts in part by maintaining PKC-3 levels and in part by influencing the activity or levels of other client proteins. Loss of the activities of these client proteins reveals that there are two sites for PAR-6 cortical association, one dependent on CDC-42 and not associated with PAR-3, and the other independent of CDC-42 and co-localizing with PAR-3. We propose that, in wild-type embryos, CDC-37-mediated inhibition of the CDC-42-dependent binding site and PAR-3-mediated release of this inhibition provide a key mechanism for the anterior accumulation of PAR-6.
A high order sliding mode control scheme based on adaptive radial basis function neural network

A high order sliding mode control algorithm for uncertain nonlinear systems is presented. This problem can be considered as finite time stabilization of higher order input-output dynamic systems with bounded uncertainties. The algorithm developed is based on the concept of integral sliding mode and includes two steps. One is the controller for nominal system using geometric homogeneity. The other is one compensating for uncertainties utilizing sliding mode control. In addition, to overcome the difficulty in determining the boundaries of uncertainties, the adaptive radial basis function neural network is designed to estimate bounded uncertainties. The proposed procedure ensures establishment of high order sliding mode and provides easy implementation. An illustrative example of a car control shows feasibility of the approach.
Comparison of genetic polymorphisms of the NAT2 gene between Korean and four other ethnic groups

Background and objective: N‐acetyltransferase 2 (NAT2) is responsible for the acetylation of numerous drugs and in the transformation of aromatic and heterocyclinc amines into carcinogenic intermediates. Polymorphism of NAT2 may contribute to interindividual variability in such acetylation. The aim of this study was to determine the allele frequencies of polymorphisms of the NAT2 gene, analyse linkage disequilibrium (LD) block and haplotypes in Koreans and compare them with those of other ethnic groups.
On-line efficiency estimation for DC/DC converter cluster by dedicated software

The measurement of the efficiency of power electronics converters is a special challenge, because it is difficult to perform it accurately using electrical methods (especially in the high efficiency range or in low power applications). Therefore in many applications, where accuracy is crucial, engineers resort to calorimetric approaches. These in turn are extremely slow and special conditions need to be created to obtain good results. In other applications, where the accuracy is not the primary goal, but rather the fast, on-line, comparative estimation governs the demand for realizing the final aim. As a result, a solution to effectively determine the efficiency of the converters while working, is still sought for. The current paper aims at presenting a possible alternative, calculating the efficiency on-line with satisfactory accuracy at a low cost.
Sub-Nyquist SAR via Fourier Domain Range-Doppler Processing

Conventional synthetic aperture radar (SAR) systems are limited in their ability to satisfy the increasing requirement for improved spatial resolution and wider coverage. The demand for high resolution requires high sampling rates, while coverage is limited by the pulse repetition frequency. Consequently, sampling rate reduction is of high practical value in SAR imaging. In this paper, we introduce a new algorithm, equivalent to the well-known range-Doppler method, to process SAR data using the Fourier series coefficients of the raw signals. We then demonstrate how to exploit the algorithm features to reduce sampling rate in both range and azimuth axes and process the signals at sub-Nyquist rates, by using compressive sensing (CS) tools. In particular, we demonstrate recovery of an image using only a portion of the received signal’s bandwidth and also while dropping a large percentage of the transmitted pulses. The complementary pulses may be used to capture other scenes within the same coherent processing interval. In addition, we propose exploiting the ability to reconstruct the image from narrow bands in order to dynamically adapt the transmitted waveform energy to vacant spectral bands, paving the way to cognitive SAR. The proposed recovery algorithms form a new CS-SAR imaging method that can be applied to high-resolution SAR data acquired at sub-Nyquist rates in range and azimuth. The performance of our method is assessed using simulated and real data sets. Finally, our approach is implemented in hardware using a previously suggested Xampling radar prototype.
A well-separated pairs decomposition algorithm for k-d trees implemented on multi-core architectures

Variations of k-d trees represent a fundamental data structure used in Computational Geometry with numerous applications in science. For example particle track fitting in the software of the LHC experiments, and in simulations of N-body systems in the study of dynamics of interacting galaxies, particle beam physics, and molecular dynamics in biochemistry. The many-body tree methods devised by Barnes and Hutt in the 1980s and the Fast Multipole Method introduced in 1987 by Greengard and Rokhlin use variants of k-d trees to reduce the computation time upper bounds to O(n log n) and even O(n) from O(n2). We present an algorithm that uses the principle of well-separated pairs decomposition to always produce compressed trees in O(n log n) work. We present and evaluate parallel implementations for the algorithm that can take advantage of multi-core architectures.
Berberine Is a Novel Type Efflux Inhibitor Which Attenuates the MexXY-Mediated Aminoglycoside Resistance in Pseudomonas aeruginosa

The emergence and spread of multidrug-resistant P. aeruginosa infections is of great concern, as very few agents are effective against strains of this species. Methanolic extracts from the Coptidis Rhizoma (the rhizomes of Coptis japonica var. major Satake) or Phellodendri Cortex (the bark of Phellodendron chinense Schneider) markedly reduced resistance to anti-pseudomonal aminoglycosides (e.g., amikacin) in multidrug-resistant P. aeruginosa strains. Berberine, the most abundant benzylisoquinoline alkaloid in the two extracts, reduced aminoglycoside resistance of P. aeruginosa via a mechanism that required the MexXY multidrug efflux system; berberine also reduced aminoglycoside MICs in Achromobacter xylosoxidans and Burkholderia cepacia, two species that harbor intrinsic multidrug efflux systems very similar to the MexXY. Furthermore this compound inhibited MexXY-dependent antibiotic resistance of other classes including cephalosporins (cefepime), macrolides (erythromycin), and lincosamides (lincomycin) demonstrated using a pseudomonad lacking the four other major Mex pumps. Although phenylalanine-arginine beta-naphthylamide (PAβN), a well-known efflux inhibitor, antagonized aminoglycoside in a MexXY-dependent manner, a lower concentration of berberine was sufficient to reduce amikacin resistance of P. aeruginosa in the presence of PAβN. Moreover, berberine enhanced the synergistic effects of amikacin and piperacillin (and vice versa) in multidrug-resistant P. aeruginosa strains. Thus, berberine appears to be a novel type inhibitor of the MexXY-dependent aminoglycoside efflux in P. aeruginosa. As aminoglycosides are molecules of choice to treat severe infections the clinical impact is potentially important.
Impact of granules from crushed expanded polystyrene package on properties of thermo-insulating plaster

AbstractThe paper deals with the use of lightweight porous aggregate, i.e. crushed expanded polystyrene package crumbs (EPSC) in the composition of thermo-insulating plaster. Its effectiveness is compared to that of spherical granules of expanded polystyrene – white coloured (EPS) and grey coloured (NEOPOR). The content of lightweight aggregate changed from 1.25 to 1.75 l/kg of dry mix. The investigation focused on properties of modified plaster, such as density, compressive strength, thermal conductivity and water vapour permeability. It was established that EPSC reduce density of plaster from 1350 to 530 kg/m3, improving such properties as thermal conductivity and water vapour permeability but decreasing compressive strength. In addition, the paper established the adhesion force of plaster (content of lightweight aggregate was 1.25 l/kg of dry mix) to ceramics, silicate and autoclaved aerated concrete masonry elements. The character of macrostructure of plaster was considered, as well as bonding with a .
Quantifying motion in video recordings of neonatal seizures by robust motion trackers based on block motion models

This paper introduces a methodology for the development of robust motion trackers for video based on block motion models. According to this methodology, the motion of a site between two successive frames is estimated by minimizing an error function defined in terms of the intensities at these frames. The proposed methodology is used to develop robust motion trackers that rely on fractional block motion models. The motion trackers developed in this paper are utilized to extract motor activity signals from video recordings of neonatal seizures. The experimental results reveal that the proposed motion trackers are more accurate and reliable than existing motion tracking methods relying on pure translation and affine block motion models.
Answering the endocrine test questions.

Evidence suggesting that certain chemicals may bind to endogenous hormone receptors and disturb normal endocrine functioning, thereby increasing the risk of reproductive problems and cancer in humans, has led to international efforts to screen chemicals for endocrine activity and potential health effects. The U.S. Environmental Protection Agency (EPA) has recommended that some 87,000 commercial chemicals for which there currently are inadequate toxicity data be evaluated. In December 1998, the EPA's Endocrine Disruptor Screening and Testing Advisory Committee (EDSTAC) recommended the use of a tiered system of screening and testing assays to sequentially eliminate chemicals for which further testing is deemed unnecessary. The first step toward implementing such a system-validation of the tests to be used-is presenting some challenges, however, with stakeholders disagreeing over which tests to validate, how extensively to validate them, and how much it will cost.
Ultrasound-Induced Phase Change of Emulsion Droplets for Targeted Gene and Drug Delivery

ULTRASOUND INDUCED PHASE CHANGE OF EMULSION DROPLETS FOR TARGETED GENEAND DRUG-DELIVERY James R. Lattin Department of Chemical Engineering, BYU Doctor of Philosophy This dissertation explores the potential of using perfluorocarbon emulsion droplets to add an ultrasound-sensitive element to drug delivery systems. These emulsion droplets may be induced to vaporize with ultrasound; during the rarefactional phase of an ultrasound wave, the pressure around the droplets may fall below the vapor pressure of the liquid forming the emulsion, providing a thermodynamic potential for vaporization. This ultrasound-induced phase change of the emulsion droplet could release therapeutics attached to the droplet surface or aid in drug delivery due to mechanical effects associated with vaporization and expansion, similar to the ability of cavitating bubbles to aid in drug delivery. In contrast to bubbles, stable emulsions can be formed at nano-scale sizes, allowing them to extravasate into tissues and potentially be endocytosed into cells. Perfluorohexane and perfluoropentane were selected to form the emulsions due to their relatively high vapor pressure, low water solubility, and biocompatibility. Acoustic droplet vaporization was explored for its potential to increase ultrasoundinduced drug release from liposomes. Liposomes have proven to be versatile and effective drug carriers, but are not inherently responsive to ultrasound. eLiposomes, defined as a liposome with encapsulated emulsion droplets, were developed due to the potential of the expanding vapor phase to disrupt bilayer membranes. The resulting vesicle retains the advantages of liposomes for drug delivery, while adding an ultrasound-sensitive element. eLiposomes were loaded with calcein, a fluorescent molecule, as a model drug in order to quantify ultrasound-mediated drug release compared to release from conventional liposomes. Upon exposure to ultrasound, eLiposomes typically released 3 to 5 times as much of the encapsulated load compared to conventional liposomes, with some eLiposome samples approaching 100% release. Emulsion droplets were also added to the outside of conventional liposomes, but resulted in little to no increase compared to control samples without emulsions. Lastly, in vitro experiments were performed with HeLa cells to explore the ability of emulsion droplets and eLiposomes to deliver calcein inside of cells. Calcein delivery to the cytosol was accomplished, and the emulsion-containing samples demonstrated the ability to aid in endosomal escape.
On a Formal Model of Safe and Scalable Self-driving Cars

In recent years, car makers and tech companies have been racing towards self driving cars. It seems that the main parameter in this race is who will have the first car on the road. The goal of this paper is to add to the equation two additional crucial parameters. The first is standardization of safety assurance --- what are the minimal requirements that every self-driving car must satisfy, and how can we verify these requirements. The second parameter is scalability --- engineering solutions that lead to unleashed costs will not scale to millions of cars, which will push interest in this field into a niche academic corner, and drive the entire field into a "winter of autonomous driving". In the first part of the paper we propose a white-box, interpretable, mathematical model for safety assurance, which we call Responsibility-Sensitive Safety (RSS). In the second part we describe a design of a system that adheres to our safety assurance requirements and is scalable to millions of cars.
Visual pathway morphometry in visual field defects

Het gezichtsvermogen is een cruciale sensorische functie voor de mens. Mensen hebben een gezichtsveld dat van boven naar beneden en van links naar rechts bijna een gebied van 180 graden omvat. Hierdoor zijn zij zich constant bewust van hun omgeving. Het centrale deel van het gezichtsveld, de fovea of macula, wordt gebruikt voor nauwkeurige visuele taken zoals lezen, het waarnemen van details van een object of het herkennen van kleuren. De rest van het gezichtsveld, ook wel het perifere gezichtsveld genoemd, geeft ons overzicht en stelt ons in staat om beweging waar te nemen. Het stelt ons ook in staat om nog wat zien wanneer er weinig licht is. Het netvlies is een laag met zenuwcellen aan de achterkant van het oog. Het netvlies vangt het licht op dat binnenvalt in het oog en zet dit om in een neuraal signaal. Net als andere lichaamsfuncties kan het netvlies, en daarmee het gezichtsveld, worden aangetast door ziektes. Het centrale gezichtsveld kan aangetast worden door maculadegeneratie, waarbij de zenuwcellen in het centrale deel van het netvlies beschadigd worden. Bij de oogziekte glaucoom wordt vooral het perifere deel van het netvlies aangetast. Met behulp van MRI (magnetic resonance imaging) hebben we beelden gemaakt van de hersenen van patienten met deze oogziekten. Na een uitgebreide bewerking van deze beelden konden we de inhoud van delen van de hersenen van verschillende patienten- en controlegroepen vergelijken. Hierbij hebben we specifiek gekeken naar de visuele banen. Dat is het deel van de hersenen waar de visuele informatie van het oog wordt doorgegeven naar het deel van de hersenen dat betrokken is bij het zien (de visuele cortex). URL for Chapter 2: http://brain.oxfordjournals. org/content/132/7/1898.