Miracle-dz/UniFAR-FTUs huggingface dataset:
Outline of a Genome Navigation System Based on the Properties of GA-Sequences and Their Flanks

Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GA-sequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments. Although not integral parts of them, Alu-elements were found immediately upstream of all human and chimpanzee GA-sequences with an upstream poly(A)-segment. The article hypothesizes that genome navigation uses these properties of GA-sequences in the following way. (1) Poly(A) binding proteins interact with the upstream poly(A)-segments and arrange adjacent GA-sequences side-by-side (‘GA-ribbon’), while folding the intervening DNA sequences between them into loops (‘associated DNA-loops’). (2) Genome navigation uses the GA-ribbon as a search path for specific target genes that is up to 730-fold shorter than the full-length chromosome. (3) As to the specificity of the search, each molecule of a target protein is assumed to catalyze the formation of specific oligomers from a set of transcription factors that recognize tetra-GA-motifs. Their specific combinations of tetra-GA motifs are assumed to be present in the particular GA-sequence whose associated loop contains the gene for the target protein. As long as the target protein is abundant in the cell it produces sufficient numbers of such oligomers which bind to their specific GA-sequences and, thereby, inhibit locally the transcription of the target protein in the associated loop. However, if the amount of target protein drops below a certain threshold, the resultant reduction of specific oligomers leaves the corresponding GA-sequence ‘denuded’. In response, the associated DNA-loop releases its nucleosomes and allows transcription of the target protein to proceed. (4) The Alu-transcripts may help control the general background of protein synthesis proportional to the number of transcriptionally active associated loops, especially in stressed cells. (5) The model offers a new mechanism of co-regulation of protein synthesis based on the shared segments of different GA-sequences.
Soft shadow rendering using spherical reparameterization scheme

Rendering realistic soft shadow under all-frequency lighting environment is receiving more and more attention in recent years. 2D Haar wavelet has been recognized superior at approximation of all-frequency signals such as very keen-edged shadows. Nevertheless, rotating scene objects efficiently under wavelet basis has yet remained a troublesome problem. In this paper, we present a spherical reparameterization scheme under which spherical functions, as lighting, BRDF and visibility, are mapped onto the spherical polar coordinates. Rotating scene objects can thus be eased by a single linear transformation in our approach. Furthermore, a technique for efficiently projecting visibility is proposed. To accelerate shadow computation, we make full use of the computational resources of modern graphical hardware to perform our algorithm.
Mice Lacking Niemann-Pick Type C1 Protein Trafficking and NKT Cell Development in Cutting Edge: Impaired Glycosphingolipid

Niemann-Pick Type C1 (NPC1) is a late endosomal/lyso-somal transmembrane protein involved in the cellular transport of glycosphingolipids and cholesterol that is mu-tated in a majority of patients with Niemann-Pick C neurodegenerative disease. We found that NPC1-deficient mice lacked V (cid:1) 14-J (cid:1) 18 NKT cells, a major population of CD1d-restricted T cells that is conserved in humans. NPC1-deficient mice also exhibited marked defects in the presentation of Sphingomonas cell wall Ags to NKT cells and in bacterial clearance in vivo. A synthetic fluorescent (cid:1) -glycosylceramide analog of the Sphingomonas Ag traf-ficked to the lysosome of wild-type cells but accumulated in the late endosome of NPC1-deficient cells. These findings reveal a blockade of lipid trafficking between endosome and lysosome as a consequence of NPC1 deficiency and suggest a common mechanism for the defects in lipid presentation and development of V (cid:1) 14-J (cid:1) 18 NKT cells. The Journal of Immunology, 2006, 177: 26–30. iemann-Pick is large endosomal/ lysosomal glycoprotein from yeast to mam-mals with 13 predicted membrane-spanning domains that include a potential sterol-sensing domain (1, 2). Mutations in the NPC-1 are found in 95% of patients with NPC disease, a neurodegenerative disorder associated with lipid storage (3).
Multilayer infrared-based face identification system for security vehicle-robot vision

Recently, vehicle robots are often deployed in critical situations as part of industrial operations, law enforcement or antiterror measures; such as identifying suspicious objects or identifying individuals in rescuing situations. Therefore, owing to the extreme circumstances, these vehicle robots have to meet particular requirements. Other than the size of vehicle robots, decision making algorithm within vehicle robots have to be kept simple yet effective in order to lessen the power usage since vehicle robots are normally powered by lead gel batteries. Most decision making in identifying individuals or objects rely on what is acquired from vehicle robots’ vision, therefore, an efficient, low-level technique mainly focused for facial identifications is presented in this paper.
Continuous Speech Recognition at LIMSI

This paper presents some of the recent research on speaker-independent continuous speech recognition at LIMSI including efforts in phone and word recognition for both French and English. Evaluation of an HMMbased phone recognizer on a subset of the BREF corpus, gives a phone accuracy of 67.1% with 35 context-independent phone models and 74.2% with 428 context-dependent phone models. The word accuracy is 88% for a 1139 word lexicon and 86% for a 2716 word lexicon, using a word pair grammar with respective perplexities of 101 and 160. Phone recognition is also shown to be effective for language, sex, and speaker identification. The second part of the paper describes the recognizer used for the September-92 Resource Management evaluation test. The HMM-based word recognizer is built by concatenation of the phone models for each word, where each phone model is a 3-state left-to-right HMM with Gaussian mixture observation densities. Separate male and female models are run in parallel. The lexicon is represented with a reduced set of 36 phones so as to permit additional sharing of contexts. Intraand inter-word phonological rules are optionally applied during training and recognition. These rules attempt to account for some of the phonological variations observed in fluent speech. The speaker-independent word accuracy on the Sep92 test data was 95.6%. On the previous test materials which were used for development, the word accuracies are: 96.7% (Jun88), 97.5% (Feb89), 96.7% (Oct89) and 97.4% (Feb91).
X3D in Radiation Therapy Procedure Planning

Radiation therapy, an increasingly available and effective cancer treatment solution, involves sophisticated machinery as well as careful planning. Interactive 3D simulations combined with accurate 3D patient specific data can improve the planning process saving time and resources in generating the optimal treatment plan. We illustrate the potential of X3D in radiation therapy, specifically radiation treatment planning. Embedding patient specific data (2D CT scans) in the interactive virtual setup improves the radiation therapy planning by early detection of collision cases. The X3D system may be used to support the decision making process as well as innovations in medical planning and training.
Transcultural believability in embodied agents: a matter of consistent adaptation

In this contribution, we propose some reflections on how an Embodied Animated Agent might be designed so as to adapt its behavior to the cultural context to which it applies. We start from a discussion of the meaning of the term ‘culture’, to then analyse the literature findings about the way human beings’ behavior (natural language expression, affect feeling and display, verbal and nonverbal components of their communication and so on) varies according to the culture. The description of a context-adaptable Embodied Animated Agent is a departure point to suggest how adaptation might be extended to cultural factors. Finally, the problem of how to insure that the agent behaviour does not loose in consistency while acquiring adaptation abilities is examined: consistency is considered, at present, as an essential constituent of an agent ‘believability’ and should therefore guide the setting of values for adaptation parameters.
Image Segmentation Using Region Merging Combined with a Multi-class Spectral Method

In this paper we propose an image segmentation algorithm that combines region merging with spectral-based techniques. An initial partitioning of the image into primitive regions is produced by applying a region merging approach which produces a chunk graph that takes in attention the image gradient magnitude. This initial partition is the input to a computationally efficient region segmentation process that produces the final segmentation. The latter process uses a multi-class partition that minimizes the normalized cut value for the region graph. We have efficiently applied the proposed approach with good visual and objective segmentation quality results.
On the influence of the underlying network topology on optical telecommunication network availability under shared risk link group failures

Network availability is of paramount importance in optical telecommunication networks. Their rising connectivity and consequently their availability is compromised by link and node failures, usually due to physical force (e.g. digging, earthquake or fire). Single link failures can in turn cause multiple failures in case a failure hits a shared risk link group (SRLG), which is a group of logically distinct links sharing a common physical resource, be it a cable or a conduit. The number and length of SRLGs, as well as the characteristics of the underlying physical topology can significantly affect network availability. Especially, the physical topology can be represented by realistic synthetic graphs which are created by numerous geographic graph generators. This work describes the implementation and usage of six different physical topology models (Random Geometric, Gabriel, Relative Neighborhood, K-Nearest Neighbor, Waxman and Spatial Barabási-Albert) for investigation of the influence of the underlying topology on the optical telecommunication network availability. Network availability is estimated using Monte Carlo simulations based on a model of optical telecommunication network implemented by network simulator ns-3. Scenarios utilizing six topology models both in absence and presence of SRLGs are studied, and the optical network availability sensitivity to the underlying physical network topology is presented as the main result.
From Local Behaviors to the Dynamics in an Agent Network

A social network can be modelled by a multi-agent system, in which the interaction among agents is represented as a service transaction process. In this paper, we present a service-based agent network to simulate and study the dynamics of social networks. In the network, the profiles of agents and service-based interactions are defined deliberately. Autonomy is emphasized as the ability of agents to manage their behaviors according to the local environment and their profiles. The experimental results reveal that network performance, network topology and the profiles of agents all evolve along with local behaviors. The over-shoot phenomenon in the evolution of network is discovered and analyzed. The discoveries are meaningful for understanding the relationship between network dynamics and local behaviors
Are you “phubbing” me? The Determinants of Phubbing Behavior and Assessment of Measurement Invariance across Sex Differences

Phubbing behavior is pervasive but the examination of the determinants and measurement invariance remain deficient. The present study aims to investigate: (1) relationships between Big Five personality traits (i.e., open-mindedness, conscientiousness, extraversion, agreeableness, and negative emotionality), coping styles (i.e., problem-focused and emotional-focused), Internet addiction and phubbing behavior; (2) the mediating role of Internet addiction among these relationships; and (3) measurement invariance across sex groups. A total of 405 responses were included in the final analyses. Participants were sampled using a probability-proportionate-to-size (PPS) method. Data were collected using paper-and-pencil survey: Phubbing Scale, Internet Addiction Test, Big Five Inventory, and Simplified Coping Styles Questionnaire. Negative emotionality, open-mindedness, and Internet addiction were the significant determinants of phubbing behavior. Internet addiction partially mediates open-mindedness and phubbing behavior. As for measurement invariance across sex groups, conscientiousness, extraversion, negative emotionality, Internet addiction, and phubbing behavior constructs achieved full measurement invariance. The agreeableness construct showed partial measurement invariance. Three constructs (i.e., open-mindedness, problem-focused and emotional-focused coping) failed to achieve partial measurement invariance, signifying that male and female participants had different interpretations on the items of these constructs. This pervasive culture could be gradually weakened if in-person interaction is intensely promoted.
An Evolutionary Monte Carlo algorithm for identifying short adjacent repeats in multiple sequences

Evolutionary Monte Carlo (EMC) algorithm is an effective and powerful method to sample complicated distributions. Short adjacent repeats identification problem (SARIP), i.e., searching for the common sequence pattern in multiple DNA sequences, is considered as one of the key challenges in the field of bioinformatics. A recently proposed Markov chain Monte Carlo (MCMC) algorithm has demonstrated its effectiveness in solving SARIP. However, high computation time and inevitable local optima hinder its wide application. In this paper, we apply EMC to parallelize the MCMC algorithm to solve SARIP. Our proposed EMC scheme is implemented on a parallel platform and the simulation results show that, compared with the conventional MCMC algorithm, EMC not only improves the quality of final solution but also reduces the computation time.
An effective overload control algorithm to Parlay gateway of electric power communication networks

This paper studies the Parlay gateway traffic overload control problems in electric power communication networks. A traffic overload control algorithm with energy efficiency is proposed to solve it. Firstly, the fairness and effectiveness of the Parlay gateway is analyzed. Then we can establish the constraints about fairness and effectiveness. The electric power communication network energy efficiency is taken as the optimal objective function. The multi-constraint energy-efficient traffic overload control model about the Parlay gateway is successfully built. Finally, the genetic algorithm is used to solve the model. By the iterative process, an optimal solution to this model can be attained. Simulation results show that our algorithm is feasible and promising.
Transactions on Computers : regular paper log number 114410 ED 4 I : Error Detection by Diverse Data and Duplicated Instructions

Errors in computing systems can cause abnormal behavior and degrade data integrity and system availability. Errors should be avoided especially in embedded systems for critical applications. However, as the trend in VLSI technologies has been towards smaller feature sizes, lower supply voltages, and higher frequencies, there is a growing concern about temporary errors as well as permanent errors in embedded systems; thus, it is very essential to detect those errors. Software Implemented Hardware Fault Tolerance (SIHFT) is a low-cost alternative to hardware fault tolerance techniques for embedded processors: it does not require any hardware modification of Commercial Off-The-Shelf (COTS) processors. EDI is a SIHFT technique that detects both permanent and temporary errors by executing two “different” programs (with the same functionality) and comparing their outputs. EDI maps each number, x in the original program into a new number x′, and then transforms the program so that it operates on the new numbers so that the results can be mapped backwards for comparison with the results of the original program. The mapping in the transformation of ED I is x′ = k⋅x for integer numbers, where k determines the fault detection probability and data integrity of the system. For floating point numbers, we find a value of kf for the fraction andke for the exponent separately and use k = e k f k 2 × for the value ofk. We have demonstrated how to choose an optimal value of k for the transformation. This paper shows that for integer programs, the transformation with k = -2 was the most desirable choice in six out of seven benchmark programs we simulated. It maximizes fault detection probability under the condition that data integrity is highest. For programs that use floating point numbers in the IEEE standard 754 format, we need two transformed programs: the first one with 2 10101010 2 3 1 2 × − = k and the second one with 2 01010101 2 3 2 2 × − = k .
A Qualitative Study on the Impact of Sexual Assault and Its Approach to Cope with in Female Teenage Victims in Surakarta, Central Java

Background: Studies have shown that sexual assault can lead to the profound impact on the victims. It may last short or long, and can even generate a "ripple effect" of negative symptoms in the affected workplace or living environment. This study aimed to explore the psychological and biological impacts of sexual assault and approach to cope with the trauma in female adolescent victims in Surakarta. Subjects and Method: This was a qualitative study conducted in Surakarta, Central Java. The informants were social workers working at Yayasan KAKAK, a non-government organization dealing with sexual harassment issues. The data were collected by in-depth interview. The informants provided information about psychological and biological impacts of sexual harassment as well as the approach to cope with the trauma in female adolescent victims in Surakarta. Results: The psychological impacts of sexual harassment included anger, fear, self-consciousness or embarrassment, difficulty sleeping, loss of appetite. According to the information provided by the informants, the victim’s life turned into a misery, and school became a place to be avoided. The sexual attacks led to feelings of demoralization and humiliation, causing loss of self-confidence and self-esteem. The victims were reported as having trouble studying or paying attention, less able to perform well, participating less, no longer going to study group, thinking about dropping a class or even leaving the school. Victims experienced symptoms such as headaches, stomach aches, nightmares and anxiety attacks. Yayasan KAKAK assisted victims by supporting and guiding about steps to be taken to protect victims and to cope with the aftermath. Conclusion: Sexual harassment has serious emotional and biological effects on adolescent victims. According to this research finding, one of the greatest mitigating factors to trauma is the acknowledgment that it is happening. Victims of sexual harassment should be assisted to find support and guidance about what steps can be taken to protect themselves and how to cope with the aftermath. Keywords: sexual harassment, female adolescent, coping Correspondence: Nila Widya Keswara. Diploma Program in Midwifery, School of Health Polytechnics Dr. Soepraoen Hospital, Malang. Email: nilakeswara_purwanto@yahoo.com. Mobile: +6281235555056. https://doi.org/10.26911/thejhpb.2017. 02.04. 06
Towards the development of a learning analytics extension in open edX

The emergence of platforms to support MOOCs (Massive Open Online Courses) strengthens the need of a powerful learning analytics support since teachers cannot be aware of so many students. However, the learning analytics support in MOOC platforms is in an early stage nowadays. The edX platform, one of the most important MOOC platforms, has few learning analytics functionalities at present. In this paper, we analyze the learning analytics support given by the edX platform, and the main initiatives to implement learning analytics in edX. We also present our initial steps to implement a learning analytics extension in edX. We review technical aspects, difficulties, solutions, the architecture and the different elements involved. Finally, we present some new visualizations in the edX platform for teachers and students to help them understand the learning process.
PAT workbench: Annotation and Evaluation of Text and Pictures in Multimodal Instructions

This paper presents a tool to investigate the design of multimodal instructions (MIs), i.e., instructions that contain both text and pictures. The benefit of including pictures in information presentation has been established, but the characteristics of those pictures and of their textual counterparts and the rela-tion(s) between them have not been researched in a systematic manner. We present the PAT Work-bench, a tool to store, annotate and retrieve MIs based on a validated coding scheme with currently 42 categories that describe instructions in terms of textual features, pictorial elements, and relations be-tween text and pictures. We describe how the PAT Workbench facilitates collaborative annotation and inter-annotator agreement calculation. Future work on the tool includes expanding its functionality and usability by (i) making the MI annotation scheme dynamic for adding relevant features based on empirical evaluations of the MIs, (ii) implementing algorithms for automatic tagging of MI features, and (iii) implementing automatic MI evaluation algorithms based on results obtained via e.g. crowdsourced assessments of MIs.
View interpolation sensitive to pixel positions

Theoretical analysis and an optimization scheme to solve the basic problem with view interpolation are presented. Two error factors, i.e., disparity error and pixel interpolation error, are considered. I found that the method of view interpolation should change according to which error factor is dominant. When disparity information is very accurate, the method of view interpolation should be especially sensitive to pixel positions, which has rarely been noticed in previous studies.