Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing simulations and test data of a radiation damaged CCD for the Euclid mission

The radiation damage effects from the harsh radiative environment outside the Earth's atmosphere can be a cause for concern for most space missions. With the science goals becoming ever more demanding, the requirements on the precision of the instruments on board these missions also increases, and it is therefore important to investigate how the radiation induced damage affects the Charge-Coupled Devices (CCDs) that most of these instruments rely on. The primary goal of the Euclid mission is to study the nature of dark matter and dark energy using weak lensing and baryonic acoustic oscillation techniques. The weak lensing technique depends on very precise shape measurements of distant galaxies obtained by a large CCD array. It is anticipated that over the 6 year nominal lifetime of mission, the CCDs will be degraded to an extent that these measurements will not be possible unless the radiation damage effects are corrected. We have therefore created a Monte Carlo model that simulates the physical processes taking place when transferring signal through a radiation damaged CCD. The software is based on Shockley-Read-Hall theory, and is made to mimic the physical properties in the CCD as close as possible. The code runs on a single electrode level and takes charge cloud size and density, three dimensional trap position, and multi-level clocking into account. A key element of the model is that it takes device specific simulations of electron density as a direct input, thereby avoiding to make any analytical assumptions about the size and density of the charge cloud. This paper illustrates how test data and simulated data can be compared in order to further our understanding of the positions and properties of the individual radiation-induced traps.
Channel width test data compression under a limited number of test inputs and outputs

A narrow channel width between a circuit under test and a tester increases the testing time. In this paper, we propose a channel width compression method when the channel width is limited. A given test sequence is partitioned into sub-sequences, whose widths can be compressed under the limited width. Each sub-sequence is compressed and expanded by a proposed dynamically re-configurable circuit located between the circuit under test and the tester. Since the hardware overhead depends on the number of partitions for a test sequence, a procedure to partition a given test sequence into a minimum number of sub-sequences under the channel width limitation is proposed. Experimental results show that our method can compress the width of a test sequence into a half through a quarter with a relatively small number of partitions.
A context-aware do-not-disturb service for mobile devices

Modern sensor-equipped smartphones have attracted significant research interest in the pervasive community for recognizing and creating context-aware applications at a personal or community scale level. In this paper, we propose a proof of concept Do-Not-Disturb (DND) service that can a) determine a user's context relevant for DND service from the built-in smartphone sensors and b) correctly predict the DND status based on the given context such as being in a meeting, sleeping, or working at the office. In this preliminary study, we investigate whether sensor data can be clustered to represent user contexts. We use standard machine learning techniques to learn the relationship between a user's context and the corresponding DND status (available or unavailable). Given a user's current context, the DND service predicts a DND status and configures the mobile device accordingly. Our preliminary experiment demonstrates that the proposed system can achieve a prediction accuracy of up to 90% when trained with sufficient data.
Penicillium purpurogenum cultures under ethanol-induced stress and its correlation with fungal adhesion and biodegrading ability

ABSTRACT Fungi are known to be affected by external environmental stimuli, resulting in different stress response effects, which in turn could be used to enhance its biodegrading ability. In a previous study, ethanol was used to manipulate cell–cell and cell–surface interaction to prevent cell loss and maximize the usage of Penicillium purpurogenum cells in the media, a correlation was drawn between ethanol oxidative stress, surface-bound proteins and fungal adhesion. The present study focuses on a more detailed study of the effect of ethanol on the same fungus. The results show that the presence of Yap1p gene and the detection of an oxidized form of glutathione (GSSG) suggest that a stress response might be involved in the adhesion process. The process of adhesion could be described as a signaling process and it is affected by the germ tube formation as an initial step in adhesion. Protein profile showed polymorphism in surface-bound proteins for cultures amended with ethanol when compared to control cultures. Ethanol also affected the DNA polymorphic profile of DNA, rendering the fungus genetically variable. P. purpurogenum produced phenol oxidase enzyme and could be used to degrade total phenols in olive mill waste water without the formation of biofilm on the surface of the containers.
A new mixture ratio of heparin for the cell salvage device

Adequate cell salvage for extracorporeal circulation requires anticoagulants such as heparin. The guideline of the American Association of Blood Banks recommends that 1 L of 0.9% saline containing 30,000 units of heparin should be mixed with aspirated blood at a ratio of 15 ml per 100 ml of collected blood [1]. If we maintain the ratio of heparinized saline to blood at 15 : 100, we need 2 vials of the Korean heparin product because its maximum amount of heparin in a vial is 25,000 units [2]. Therefore, we developed an alternative method of anticoagulation using only 1 vial of heparin. For extracorporeal circulation, the dose of heparin, which maintains an ACT of longer than 400-450 seconds, is 300-400 U/kg body weight [3]. To simplify calculation, we assume blood volume to be 70 ml/kg because the average blood volume of men is 75 ml/kg and that of women is 65 ml/kg. Since 70 ml of blood requires 300 units of heparin, 100 ml of blood requires 428 units of heparin. According to the guideline, 15 ml of heparinized saline contains 450 units of heparin because 1 L of heparinzed saline contains 30,000 units of heparin. If we mix 25,000 units of heparin with 1 L of 0.9% saline, we need 18 ml of heparinized saline to maintain the same amount of heparin because the new concentration of heparin is 25 units/ml. If we apply this method to a continuous autotransfusion system (CATS®), we should set the infusion rate at 234 drops per minute because 13 drops make 1 ml in the CATS. In summary, we can use 1 vial of heparin (25,000 units) to prevent coagulation in the cell salvage device using our mixture ratio.
Space‐time planning in changing environments : using dynamic objects for accessibility

Navigation is a critical task for agents populating virtual worlds. In the last years, numerous solutions have been proposed to solve the path planning problem in order to enhance the autonomy of virtual agents. Those solutions mainly focused on static environments, eventually populated with dynamic obstacles. However, dynamic objects are usually more than just obstacles as they can be used by an agent to reach new locations. In this paper, we propose an online path planning algorithm in dynamically changing environments with unknown evolution such as physically based‐environments. Our method represents objects in terms of obstacles but also in terms of navigable surfaces. This representation allows our algorithm to find temporal paths through disconnected and moving platforms. We will also show that the proposed method also enables several kinds of adaptations such as avoiding moving obstacles or adapting the agent postures to environmental constraints. Copyright © 2012 John Wiley & Sons, Ltd.
Towards a theory of document learning

In a bibliographic information system the database consists of a set of document representatives. Part of each document representative is a list of index terms whose function is to identify the content of the document represented. These index terms can be derived using an automated process. It is argued that automatic methods do not result in the best set of index terms being assigned to a document representative. A mathematical model is proposed which describes an information system which includes a method, document learning, of improving the set of index terms assigned to a document representative.
Sung 1 Feature Selection for Intrusion Detection using Neural Networks and Support Vector Machines

Computational Intelligence (CI) methods are increasingly being used for problem solving. This paper concerns using CI-type learning machines for intrusion detection, which is a problem of general interest to transportation infrastructure protection since a necessary task thereof is to protect the computers responsible for the infrastructure’s operational control, and an effective Intrusion Detection System (IDS) is essential for ensuring network security. Two classes of learning machines for IDSs are studied: Artificial Neural Networks (ANNs) and Support Vector Machines (SVMs). We show that SVMs are superior to ANNs in three critical respects of IDSs: SVMs train and run an order of magnitude faster; SVMs scale much better; and SVMs give higher classification accuracy. We also address the related issue of ranking the importance of input features, which is itself a problem of great interest. Since elimination of the insignificant and/or useless inputs leads to a simplified problem and possibly faster and more accurate detection, feature selection is very important in intrusion detection. Two methods for feature ranking are presented: the first one is independent of the modeling tool, while the second method is specific to SVMs. The two methods are applied to identify the important features in the 1999 DARPA intrusion data set. It is shown that the two methods produce results that are largely consistent. We present experimental results that indicate that SVM-based IDSs using a reduced number of features can deliver enhanced or comparable performance. Finally, an SVM-based IDS for class-specific detection is proposed.
Mitochondrial Pathway Thymocytes Independently of the Glucocorticoid-Induced Apoptosis of Sphingosine Contributes to

During the selection process in the thymus, most thymocytes are eliminated by apoptosis through signaling via TCR or glucocorticoids. The involvement of ceramide (Cer) and sphingosine (SP), important apoptotic mediators, remains poorly deﬁned in glucocorticoid-induced apoptosis. We report that, in mouse thymocytes, apoptosis triggered by 10 (cid:1) 6 M dexamethasone (DX) was preceded by a caspase-dependent Cer and SP generation, together with activation of acidic and neutral ceramidases. Apoptosis was drastically reduced by blocking either sphingolipid production (by acid sphingomyelinase inhibitor) or SP production (by ceramidase inhibitors), but not by inhibition of de novo Cer synthesis. Thus, SP generated through acid sphingomyelinase and ceramidase activity would contribute to the apoptotic effect of DX. Consistent with this hypothesis, SP addition or inhibition of SP kinase induced thymocyte apoptosis. DX induced a proteasome-dependent loss of mitochondrial membrane potential ( (cid:2)(cid:3) m ) and caspase-8, -3, and -9 processing. Apoptosis was abolished by inhibition of (cid:2)(cid:3) m loss or caspase-8 or -3, but not caspase-9. (cid:2)(cid:3) m loss was independent of SP production and caspase-8, -3, and -9 activation. However, inhibition of SP production reduced caspase-8 and -3, but not caspase-9 processing. Proteasome inhibition impaired activation of the three caspases, whereas inhibition of (cid:2)(cid:3) m loss solely blocked caspase-9 activation. These data indicate that DX-induced apoptosis
Promoter-proximal pausing of RNA polymerase II: an opportunity to regulate gene transcription

Transcription of eukaryotic genes by RNA polymerase II (pol II) is a complex, highly regulated multiphasic process. Pol II pauses in the proximity of the promoter on a large fraction of transcribed genes. Transcription initiation and elongation of transcripts are under distinct control. Induced gene expression can thus be due to enhanced initiation and/or stimulated elongation. Pausing and resumption of the elongation of transcripts is under the control of transcription elongation factors. Three of them, P-TEFb, DSIF, and NELF have been well characterized as protein complexes with multiple general but also gene specific functions. Elongation factors execute checkpoint functions but serve also as targets for signaling processes which regulate gene expression. Due to the general importance of transcription elongation factors, it is difficult to delineate the mechanisms by which elongation of specific genes is regulated by specific intracellular signals. However, it is clear that the controlled pausing of pol II provides an opportunity to finely control timing and quantity of transcriptional output.
Recognizers for extracting architectural features from source code

Architectural representation can play a pivotal role throughout the life cycle of any software program. In particular, we are interested in the role it plays in the maintenance/evolution of legacy programs. During these phases, analysts often describe programs using architectural terminology (e.g., "interfaces", "interprocess communication", "layers", "objects"). Our research and development goals center on supporting such activities through architectural recovery tools that are based on reverse engineering technology. These tools start with existing source code and extract architecture-level descriptions. We have implemented a framework for architectural recovery and our experience leads us to several observations about the representational needs of a library that is populated with families of architecture recognition rules. This paper characterizes the kinds of recognizers we have developed and describes an approach for rule parameterization and retrieval.
Olfactory Reinforcement of a Paired Associate Learning Task

Acquisition of factual knowledge is a necessary skill in any educational setting. This type of learning requires a great deal of deliberate practice (Ericsson, Krampe, & Tesch-Romer, 1993), much of which relies on the learner's motivation to regularly expend the effort required to attain long-term retention, and timely recall. Individuals fail to acquire factual information (and other kinds of content for that matter) for reasons that may include low levels of interest (Cameron, or lack of strategies required for effective self-coaching (Mondria, & Mondria-De Vries, 1994). As such, learners who endeavor to learn new content may feel, and actually be, unqualified to effectively manage their own learning. Researchers point to time on task as one of the fundamental features of achieving expert levels of performance. Depending on the content, some learners may feel less motivated than others to spend the time on task that is required to learn a new language, or other kinds of factual knowledge. As such, research findings point to the value of extrinsic rewards for the Learners who do not have the financial means to acquire expensive learning technologies (i.e., the computer), may be unaware of non-electronic technologies that could contribute to 2 more effective acquisition of factual content. This product is tailored primarily to individuals who want to enhance their learning, but are limited in resources. Another potential set of users could be learners who do have the means of purchasing a computer, but who want to use a non-electronic means for content mastery. A product such as the one described herein may present alternatives to self-study not previously available, or widely publicized. The purpose of this project is to design an instructional product that promotes effective presentation of factual content, and incorporates motivation-enhancing extrinsic rewards that promote retention. The product constitutes Leitner's hand computer (as described by Mondria and Mondria-De Vries, 1994), and also includes a system for scheduled delivery of olfactory-based reinforcement that aims to augment retention through recreation of the original learning environment. Literature to support the chosen approaches for designing the product is ducumented in the Scientific Principles section of this paper. The majority of the research regarding learning, memory and reinforcement is found in the literature reviewed during the course of the semester. Research literature on the use of olfactory cues to enhance learning has been conducted through Utah State University Library online journal searches. Primary search databases include Wilson …
Vibrational and Spectroscopic Analysis on 2,3-Dimercapto-1- Propanol by HF and DFT Calculations

A combined experimental and theoretical study on molecular and vibrational structure of 2,3-Dimercapto-1-propanol have been undertaken in the present work. The FTIR Spectrum and FT-Raman spectrum of the molecule have been recorded in the region of 4000-400 cm-1 and 4000-100 cm-1. The optimized geometry, frequency and intensity of the vibrational bands of the molecule were obtained at HF and DFT (B3LYP) levels using 6-31G (d,p) basis set. A Complete vibrational assignments for the theoretical harmonic frequency were made and compared with the experimental frequencies recorded. HOMO-LUMO study confirms the charge transfer within the molecule. Mulliken population analysis and thermodynamic properties of the molecule were tabulated.
The tangled bank of amino acids

The use of amino acid substitution matrices to model protein evolution has yielded important insights into both the evolutionary process and the properties of specific protein families. In order to make these models tractable, standard substitution matrices represent the average results of the evolutionary process rather than the underlying molecular biophysics and population genetics, treating proteins as a set of independently evolving sites rather than as an integrated biomolecular entity. With advances in computing and the increasing availability of sequence data, we now have an opportunity to move beyond current substitution matrices to more interpretable mechanistic models with greater fidelity to the evolutionary process of mutation and selection and the holistic nature of the selective constraints. As part of this endeavour, we consider how epistatic interactions induce spatial and temporal rate heterogeneity, and demonstrate how these generally ignored factors can reconcile standard substitution rate matrices and the underlying biology, allowing us to better understand the meaning of these substitution rates. Using computational simulations of protein evolution, we can demonstrate the importance of both spatial and temporal heterogeneity in modelling protein evolution.
A pipeline for identifying integration sites of mobile elements in the genome using next-generation sequencing

Next Generation Sequencing (NGS) reads obtained by sequencing of the junction of a mobile element and the host flanking region from individuals in a population are typically mapped to a reference genome to determine the location of the mobile element-host junction. We propose a clustering pipeline for grouping such NGS data into clusters corresponding to the locations of integration sites in the genome. Our pipeline relies on the UCLUST clustering software, which clusters reads into groups using a clustering threshold, to cluster the integration sites NGS reads into groups based on their site of origin. An optimal clustering threshold is chosen based on a proposed clustering measure, I − index. We evaluate our pipeline on simulated integration sites data from the human genome and compare its performance to UCLUST clustering. Our pipeline is more accurate in recovering both the number and the correct sequence of the integration sites when compared to the other method. This pipeline can be beneficial in detecting the mobile element-host junctions in a population for species with no reference genome.
Design of State-Based Schedulers for a Network of Control Loops

For a closed-loop system with a contention-based multiple access network on its sensor link, the medium access controller (MAC) may discard some packets when the traffic on the link is high. We use a local state-based scheduler to select a few critical data packets to send to the MAC. In this paper, we analyze the impact of such a scheduler on the closed-loop system in the presence of traffic, and show that there is a dual effect with state-based scheduling. In general, this makes the optimal scheduler and controller hard to find. However, by removing past controls from the scheduling criterion, we find that certainty equivalence holds. This condition is related to the classical result of Bar-Shalom and Tse, and it leads to the design of an innovations-based scheduler with a certainty equivalent controller. However, this controller is not an equivalent design for the optimal controller, in the sense of Witsenhausen. The computation of the estimate can be simplified by introducing a symmetry constraint on the scheduler. Based on these findings, we propose a dual predictor architecture for the closed-loop system, which ensures separation between scheduler, observer and controller. We present an example of this architecture, which illustrates a network-aware event-triggering mechanism.
Sample-Size Invariance of LNRE Model Parameters: Problems and Opportunities

Abstract A well‐known problem in the domain of lexical statistics concerns the dependence of measures of lexical richness on the text size. To avoid this dependence, Large Number of Rare Event (LNRE) models have been developed, the parameters of which are, in theory, sample‐size invariant. In practice, however, the parameters of LNRE models may nevertheless reveal considerable dependence on the text size. We show that for LNRE models this dependence is a direct consequence of two factors: the non‐random use of words in texts on the one hand, and a theoretical lack of goodness‐of‐fit on the other hand. We describe how we can use this dependence to our advantage to enhance the interpolation and extrapolation accuracy of LNRE models. In addition, we outline methods for carrying out cross‐text comparisons using the empirical developmental profiles of LNRE parameters.
Picking statistically valid and early simulation points

Modern architecture research relies heavily on detailed pipeline simulation. Simulating the full execution of an industry standard benchmark can take weeks to months to complete. To address this issue we have recently proposed using simulation points (found by only examining basic block execution frequency profiles) to increase the efficiency and accuracy of simulation. Simulation points are a small set of execution samples that when combined represent the complete execution of the program. We present a statistically driven algorithm for forming clusters from which simulation points are chosen, and examine algorithms for picking simulation points earlier in a program's execution-in order to significantly reduce fast-forwarding time during simulation. In addition, we show that simulation points can be used independent of the underlying architecture. The points are generated once for a program/input pair by only examining the code executed. We show the points accurately track hardware metrics (e.g., performance and cache miss rates) between different architecture configurations. They can therefore be used across different architecture configurations to allow a designer to make accurate trade-off decisions between different configurations.