Miracle-dz/UniFAR-FTUs huggingface dataset:
Interactive decision making using dissimilarity to visually represented prototypes

To make informed decisions, an expert has to reason with multi-dimensional, heterogeneous data and analysis results of these. Items in such datasets are typically represented by features. However, as argued in cognitive science, features do not yield an optimal space for human reasoning. In fact, humans tend to organize complex information in terms of prototypes or known cases rather than in absolute terms. When confronted with unknown data items, humans assess them in terms of similarity to these prototypical elements. Interestingly, an analogues similarity-to-prototype approach, where prototypes are taken from the data, has been successfully applied in machine learning. Combining such a machine learning approach with human prototypical reasoning in a Visual Analytics context requires to integrate similarity-based classification with interactive visualizations. To that end, the data prototypes should be visually represented to trigger direct associations to cases familiar to the domain experts. In this paper, we propose a set of highly interactive visualizations to explore data and classification results in terms of dissimilarities to visually represented prototypes. We argue that this approach not only supports human reasoning processes, but is also suitable to enhance understanding of heterogeneous data. The proposed framework is applied to a risk assessment case study in Forensic Psychiatry.
Systems toxicology of chemically induced liver and kidney injuries: histopathology‐associated gene co‐expression modules

Organ injuries caused by environmental chemical exposures or use of pharmaceutical drugs pose a serious health risk that may be difficult to assess because of a lack of non‐invasive diagnostic tests. Mapping chemical injuries to organ‐specific histopathology outcomes via biomarkers will provide a foundation for designing precise and robust diagnostic tests. We identified co‐expressed genes (modules) specific to injury endpoints using the Open Toxicogenomics Project‐Genomics Assisted Toxicity Evaluation System (TG‐GATEs) – a toxicogenomics database containing organ‐specific gene expression data matched to dose‐ and time‐dependent chemical exposures and adverse histopathology assessments in Sprague–Dawley rats. We proposed a protocol for selecting gene modules associated with chemical‐induced injuries that classify 11 liver and eight kidney histopathology endpoints based on dose‐dependent activation of the identified modules. We showed that the activation of the modules for a particular chemical exposure condition, i.e., chemical‐time‐dose combination, correlated with the severity of histopathological damage in a dose‐dependent manner. Furthermore, the modules could distinguish different types of injuries caused by chemical exposures as well as determine whether the injury module activation was specific to the tissue of origin (liver and kidney). The generated modules provide a link between toxic chemical exposures, different molecular initiating events among underlying molecular pathways and resultant organ damage. Published 2016. This article is a U.S. Government work and is in the public domain in the USA. Journal of Applied Toxicology published by John Wiley & Sons, Ltd.
Towards memristive crossbar-based neuromorphic HW accelerators for signal processing

Research progress in neuromorphic hardware, capable of biological perception and cognitive information processing, is leading the way towards a revolution in computing technology. Current research efforts have focused mainly on resistive switching devices, the electronic analog of synapses in artificial neural networks (ANNs), and the crossbar nanoarchitecture, for its huge connectivity and maximum integration density. In this context, this work presents the design and simulation of a memristive crossbar-based ANN for text recognition tasks, implementing a novel computing algorithm. In such case study, important issues during the application mapping process are identified and properly addressed at device and circuit level. The computing capabilities of the proposed system are highlighted through SPICE-level circuit simulations, which show excellent agreement with theoretical simulation results.
Inhibition of N-Type Calcium Channels by Fluorophenoxyanilide Derivatives

A set of fluorophenoxyanilides, designed to be simplified analogues of previously reported ω-conotoxin GVIA mimetics, were prepared and tested for N-type calcium channel inhibition in a SH-SY5Y neuroblastoma FLIPR assay. N-type or Cav2.2 channel is a validated target for the treatment of refractory chronic pain. Despite being significantly less complex than the originally designed mimetics, up to a seven-fold improvement in activity was observed.
Reconstructing the Duplication History of a Tandem Repeat

One of the less well understood mutational transformations that act upon DNA is tandem duplication. In this process, a stretch of DNA is duplicated to produce two or more adjacent copies, resulting in a tandem repeat. Over time, the copies undergo additional mutations so that typically, multiple approximate tandem copies are present. An interesting feature of tandem repeats is that the duplicated copies are preserved together, making it possible to do "phylogenetic analysis" on a single sequence. This involves using the pattern of mutations among the copies to determine a minimal or a most likely history for the repeat. A history tries to describe the interwoven pattern of substitutions, indels, and duplication events in such a way as to minimize the number of identical mutations that arise independently. Because the copies are adjacent and ordered, the history problem can not be solved by standard phylogeny algorithms. In this paper, we introduce several versions of the tandem repeat history problem, develop algorithmic solutions and evaluate their performance. We also develop ways to visualize important features of a history with the goal of discovering properties of the duplication mechanism.
Morphology Evolution during Annealing and Electrical Conductivity of Titania Nanotube Films

Titania nanotube films were produced by anodization of titanium foil. The titania nanotube films were annealed at different temperatures. Morphology evolution, phase transformation and electrical conductivity of the titania nanotubes were studied. Results showed that the nanotube walls became rough, porous and even collapsed after annealed at 400, 500 and 600 °C respectively. Titania anatase phase formed after annealed at 400 °C; the amount of anatase phase increased as the annealing temperature increased. The conductivity of the nanotube film annealed at 400 °C was improved greatly compared with the conductivity of the as-anodized nanotube film. However, the conductivity of the nanotube films annealed at higher temperatures decreased. The effect of the morphology on the electronic conductivity of the titania nanotube films was discussed.
ORMOCER Coated Fiber-Optic Bragg Grating Sensors at Cryogenic Temperatures

ORMOCER coated Fiber-Bragg-Gratings (FBGs) were investigated at cryogenic temperatures. Below the Bragg wavelength of uncoated FBG is nearly independent on temperature. ORMOCER coated FBG are temperature dependent over the whole temperature range investigated from 10 to 300 K. For 50-300 K, the ORMOCER coating contributes to an additional linear temperature shift of the Bragg wavelength of 2.4 pm/K. Below 40 K the temperature dependence decreases to 1.0 pm/K. ORMOCER coated FBGs can be used as sensor at cryogenic temperatures.
First-Principles Study on Electronic and Optical Properties in Pr-Doped Anatase TiO2

The crystal structures, band structures, density of states, charge density, overlap population and optical properties of pure anatase TiO2 and Pr-doped anatase TiO2 were studied by using the plane-wave pseudopotential method based on the first-principles. After Pr doping, the valence band and the conduction band moved down and became dense, energy gap became narrow and a impurity band which consists of Pr 4f states appeared. And the dipole moment got improved, which is good for the separate of the electron-hole pairs. These effectively overcome two huge shortcomings of TiO2. Besides, Pr-doped anatase TiO2 produced more carriers which have good transport properties and the absorption spectra of Pr-O bond appear in the region that the wavelength is longer. The calculation results of optical properties show that the absorption edge occured red shift, which means the photocatalytic activity of anatase TiO2 got remarkable improved during visible-light region. This conforms to the previous analysis. So the photocatalytic activity of anatase TiO2 got remarkable improved after Pr doping.
Intrathecal morphine and inflammatory masses.

between of inﬂammatory masses in with high-dose morphine sulfate delivered by continuous infusion causes inﬂammatory masses and neurologic injury in a high percentage of at-risk research animals, well as in an unknown percentage of patients receiving this therapy. time course and frequency of this complication in provides a for study and development of effective analgesics with a proﬁle than only Catheter-associated masses have the potential to cause devastating permanent neurologic injury in animal models and patients receiving intrathecal therapy. It has now been shown that occult lesions may be detected in asymptomatic patients using readily available radiographic screening methods and that noninvasive interventions may be undertaken to reverse or arrest the progression of these masses without additional surgery or catheter explantation. Termination of infusion, initiation of infusion, or in or minimally symptomatic have been to result in spontaneous regression of lesions the development of neurologic injury, changing to a different analgesic drug may arrest the progression In Reply:— Despite the lack of large epidemiologic studies to date, increased reporting of the inﬂammatory mass phenomenon as a consequence of scientiﬁc presentations and “Dear Doctor” letters to physicians, as well as the availability of new preclinical data, motivated the organization of a consensus panel. This panel’s goal was to formulate hypotheses about the etiology of catheter-tip masses and to provide recommendations for clinicians about the detection and treatment of this complication. 1,2 Together, these papers provide a comprehensive review of the preclinical and clinical data available regarding the incidence, etiology, and clinical features of inﬂammatory masses associated with intrathecal drug infusion and provide recommendations for screening, detection, diagnosis, treatment, and prevention of these masses. These recommendations emphasize the need for physician awareness, attentive patient follow-up, and maintaining intrathecal opioid dose and concentration as low as possible for as long as possible while still achieving adequate analgesia.
Dynamic Signature Verification System Based on One Real Signature

The dynamic signature is a biometric trait widely used and accepted for verifying a person’s identity. Current automatic signature-based biometric systems typically require five, ten, or even more specimens of a person’s signature to learn intrapersonal variability sufficient to provide an accurate verification of the individual’s identity. To mitigate this drawback, this paper proposes a procedure for training with only a single reference signature. Our strategy consists of duplicating the given signature a number of times and training an automatic signature verifier with each of the resulting signatures. The duplication scheme is based on a sigma lognormal decomposition of the reference signature. Two methods are presented to create human-like duplicated signatures: the first varies the strokes’ lognormal parameters (stroke-wise) whereas the second modifies their virtual target points (target-wise). A challenging benchmark, assessed with multiple state-of-the-art automatic signature verifiers and multiple databases, proves the robustness of the system. Experimental results suggest that our system, with a single reference signature, is capable of achieving a similar performance to standard verifiers trained with up to five signature specimens.
PIGEA-14, a Novel Coiled-coil Protein Affecting the Intracellular Distribution of Polycystin-2*

Employing a yeast two-hybrid screen with the COOH terminus of polycystin-2, one of the proteins mutated in patients with polycystic kidney disease, we were able to isolate a novel protein that we call PIGEA-14 (polycystin-2 interactor, Golgi- and endoplasmic reticulum-associated protein with a molecular mass of 14 kDa). Molecular modeling only predicts a coiled-coil motif, but no other functional domains, in PIGEA-14. In a subsequent two-hybrid screen using PIGEA-14 as a bait, we found GM130, a component of the cis-compartment of the Golgi apparatus. Co-expression of the PIGEA-14 and PKD2 cDNAs in LLC-PK1 and HeLa cells resulted in a redistribution of PIGEA-14 and polycystin-2 to the trans-Golgi network, which suggests that PIGEA-14 plays an important role in regulating the intracellular location of polycystin-2 and possibly other intracellular proteins. Our results also indicate that the intracellular trafficking of polycystin-2 is regulated both at the level of the endo-plasmic reticulum and that of the trans-Golgi network.
Resilience of Natural Gas Networks during Conflicts, Crises and Disruptions

Human conflict, geopolitical crises, terrorist attacks, and natural disasters can turn large parts of energy distribution networks offline. Europe's current gas supply network is largely dependent on deliveries from Russia and North Africa, creating vulnerabilities to social and political instabilities. During crises, less delivery may mean greater congestion, as the pipeline network is used in ways it has not been designed for. Given the importance of the security of natural gas supply, we develop a model to handle network congestion on various geographical scales. We offer a resilient response strategy to energy shortages and quantify its effectiveness for a variety of relevant scenarios. In essence, Europe's gas supply can be made robust even to major supply disruptions, if a fair distribution strategy is applied.
A PRELIMINARY ASSESSMENT OF THE EFFECTS OF DIFFERENT CONSTANT TEMPERATURES ON THE , REPRODUCTION OF ELDANA SACCHARINA ( LEPIDOPTERA : PYRALIDAE ) MJWAY South

Studies on newly emerged adults held at constant temperatures of 15°e, 20 25°e and 35°e provided information on the reproductive biology of Eldana saccharina Walker. The following aspects were investigated: • adult female longevity • mating success • oviposition • egg development. Female longevity was highest at the lower temperatures and mating was recorded at all temperatures. Fecundity was greatest at 20 and 25°e, and eggs hatched at both temperatures. At 15°e eggs were fertile but failed to hatch after one month incubation. Eggslaid at 35°e were infertile. Some implications for the distribution of eldana are discussed.
Harmonics elimination in multilevel inverter with unequal DC sources by fuzzy-ABC algorithm

The harmonious appearance in multilevel inverter output voltage is more for the case of unequal DC sources. In this paper, a hybrid technique incorporating fuzzy inference system (FIS) and artificial bee's colony (ABC) algorithm is proposed. FIS is a rule-based artificial intelligent technique which is used for generating the data set in terms of switching angle, harmonic voltage and harmonic distortion. The data set is generated as per the behaviour of the multilevel inverter without using any harmonic elimination technique. In the generated data set, the switching angle and the harmonic voltage are categorised as SMALL, MEDIUM and LARGE. Then, the ABC algorithm is used to optimise the selection of switching angles from the training data set. The performance of the proposed hybrid technique is tested on a 7-level cascade H-bridge inverter for different voltage levels of unequal DC sources using MATLAB/SIMULINK platform. The effectiveness and superiority of the proposed technique is evaluated by comparing the reduction capacity of total harmonic distortion for different voltage levels of unequal DC sources with particle swarm optimisation (PSO) algorithm and fuzzy-PSO algorithm.
Dependence in Classification of Aluminium Waste

Based on the dependence between edge and colour intensity of aluminium waste image, the aim of this paper is to classify the aluminium waste into three types; pure aluminium, not pure aluminium type-1 (mixed iron/lead) and not pure aluminium type 2 (unrecycle). Principal Component Analysis (PCA) was employed to reduction the dimension of image data, while Bayes’ theorem with the Gaussian copula was applied to classification. The copula was employed to handle dependence between edge and colour intensity of aluminium waste image. The results showed that the classifier has been correctly classifiable by 88.33%.
Integrating genome assemblies with MAIA

Motivation: De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for assembly projects. We introduce an assembly integrator that makes use of all available data, i.e. multiple de novo assemblies and mappings against multiple related genomes, by optimizing a weighted combination of criteria. Results: The developed algorithm was applied on the de novo sequencing of the Saccharomyces cerevisiae CEN.PK 113-7D strain. Using Solexa and 454 read data, two de novo and three comparative assemblies were constructed and subsequently integrated, yielding 29 contigs, covering more than 12 Mbp; a drastic improvement compared with the single assemblies. Availability: MAIA is available as a Matlab package and can be downloaded from http://bioinformatics.tudelft.nl Contact: j.f. nijkamp@tudelft.nl
JMB: scaling wireless capacity with user demands

We present joint multi-user beamforming (JMB), a system that enables independent access points (APs) to beamform their signals, and communicate with their clients on the same channel as if they were one large MIMO transmitter. The key enabling technology behind JMB is a new low-overhead technique for synchronizing the phase of multiple transmitters in a distributed manner. The design allows a wireless LAN to scale its throughput by continually adding more APs on the same channel. JMB is implemented and tested with both software radio clients and off-the-shelf 802.11n cards, and evaluated in a dense congested deployment resembling a conference room. Results from a 10-AP software-radio testbed show a linear increase in network throughput with a median gain of 8.1 to 9.4x. Our results also demonstrate that JMB's joint multi-user beamforming can provide throughput gains with unmodified 802.11n cards.
Versatile near-field scanning optical microscope

As a branch of scanning probe microscopy, near field scanning optical microscopy (NSOM) has been the most intensively developed for the past few years. A wide variety of types of NSOM have been created of recent years. However, a versatile NSOM that allow to investigate a same with different near field microscopy is not worked out up to now. In our lab a new versatile NSOM for biological application have been developed. The microscope can be operated in all known modes, viz., scanning optical, photon tunneling and aperture less photon tunneling modes. The basic element of the NSOM design is a coarse adjustment unit on which various scanners and sample holders are mounted. The maximal displacement of the coarse adjustment unit is 1 mm the approach step is about 50 micrometers . The NSOM scanner consists of a mechanical scanner with large displacement range on which is mounted a fine piezoscanner with t a scanning range about 2 micrometers . The maximal scanning range of the NSOM is about 1 mm laterally and 4 micrometers in perpendicular to sample surface direction with rough selection of area for study in the total are about 3 X 3 mm under conventional optical microscopy observation. As a sample holder are used either a glass prism in photon tunneling mode or a flat glass in scanning optical mode. The microscope has a digital control unit connected with IBM PC through a parallel interface. Different biological samples were investigated by means of the NSOM with resolution better than 15 nm. The NSOM high rigidity makes it possible to operate in ordinary laboratory without any additional vibration isolation devices.
Universal Voting Protocol Tweaks to Make Manipulation Hard

Voting is a general method for preference aggregation in multiagent settings, but seminal results have shown that all (nondictatorial) voting protocols are manipulable. One could try to avoid manipulation by using voting protocols where determining a beneficial manipulation is hard computationally. A number of recent papers study the complexity of manipulating existing protocols. This paper is the first work to take the next step of designing new protocols that are especially hard to manipulate. Rather than designing these new protocols from scratch, we instead show how to tweak existing protocols to make manipulation hard, while leaving much of the original nature of the protocol intact. The tweak studied consists of adding one elimination preround to the election. Surprisingly, this extremely simple and universal tweak makes typical protocols hard to manipulate! The protocols become NP-hard, NP-hard, or PSPACE-hard to manipulate, depending on whether the schedule of the preround is determined before the votes are collected, after the votes are collected, or the scheduling and the vote collecting are interleaved, respectively. We prove general sufficient conditions on the protocols for this tweak to introduce the hardness, and show that the most common voting protocols satisfy those conditions. These are the first results in voting settings where manipulation is in a higher complexity class than NP (presuming PSPACE ≠ NP).
Efficient Contact Modeling using Compliance Warping

Contact handling is the key of deformable objects simulation, since without it, objects can not interact with their environment nor with the user. In this paper, we propose a novel and very efficient approach for precise computation of contact response between various types of objects commonly used in computer animation. Being constraint based, this method ensures physical correctness, and respects Singorini s law. It can be used with any deformation model, and is based on the use of the initial compliance matrix and contact warping. Thus, the contact response can be computed efficiently, and the object deformation can still be done in a physically plausible way provided the underlying model is physical.
Measurement of Frequency Dependent Dielectric Properties by the Capacitance Technique

Measurement model of a capacitor designed for nondestructive testing (NDT) of dielectric materials in a frequency range is proposed. The capacitor, which is a source of electric field, fulfills also functions of a sensor. Proposed design involves electrodes, which are placed on the surface of a test objects, and therefore, secures unilateral access for testing. Particular case with electrodes of the capacitor located in one plane is discussed more in details.