Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of immunotoxicity using precision-cut tissue slices

1. When the immune system encounters incoming infectious agents, this generally leads to immunity. The evoked immune response is usually robust, but can be severely perturbed by potentially harmful environmental agents such as chemicals, pharmaceuticals and allergens. 2. Immunosuppression, hypersensitivity and autoimmunity may occur due to changed immune activity. Evaluation of the immunotoxic potency of agents as part of risk assessment is currently established in vivo with animal models and in vitro with cell lines or primary cells. 3. Although in vivo testing is usually the most relevant situation for many agents, more and more in vitro models are being developed for assessment of immunotoxicity. In this context, hypersensitivity and immunosuppression are considered to be a primary focus for developing in vitro methods. Three-dimensional organotypic tissue models are also part of current research in immunotoxicology. 4. In recent years, there has been a revival of interest in organotypic tissue models. In the context of immunotoxicity testing, precision-cut lung slices in particular have been intensively studied. Therefore, this review is very much focused on pulmonary immunotoxicology. Respiratory hypersensitivity and inflammation are further highlighted aspects of this review. Immunotoxicity assessment currently is of limited use in other tissue models, which are therefore described only briefly within this review.
Mass‐Dependent Integral Curves in Unsteady Vector Fields

Recent research in flow visualization is focusing on the analysis of time‐dependent, but mass‐less particles. However, in many application scenarios, the mass of particles – and their resulting inertia – is essential in understanding fluid mechanics. This includes critical processes, such as dust particles interacting with aircraft (e.g., brown‐or white‐out effects) and particle separation based on density variation. In this paper, we contribute a generalized description of mass‐dependent particle trajectories and apply existing unsteady flow visualization methods to the mass‐dependent case. This comprises the extension of common concepts, i.e., path lines, streak lines, and time lines. Furthermore, we introduce a new class of integral curves, called mass lines that effectively visualizes mass separation and captures mass‐related features in unsteady flow fields that are inaccessible using traditional methods. We demonstrate the applicability of our method, using a number of real‐world and artificial data sets, in which mass is a crucial parameter. In particular, we focus on the analysis of brown‐out conditions, introduced by a helicopter in forward flight close to the ground.
Localization of gene expression regions in Drosophila embryonic images

Automatic localization of gene expression regions in Drosophila embryonic images is an important step in a computational system for the discovery of patterns of gene-gene interaction. In this paper, we propose a thresholding framework that selects an optimal threshold via a consistency criterion on good candidate thresholds provided by multiple response functions, including intensity histograms. In experiments, we test the proposed framework, being compared with four well-known methods, on images in Berkley Drosophila Genome Project (BDGP) dataset, and obtain promising results.
A Parallel GPU Implementation of the Timber Wolf Placement Algorithm

GPUs have been gaining acceptance in the electronic design automation field as attractive platforms for implementing and accelerating computationally extensive applications. Researchers agree that it is critical that EDA algorithms exploit future platforms and explore the use of parallel algorithms as we move to the many core era. This paper describes the implementation of the Timber Wolf placement algorithm using CUDA and demonstrates the applicability of GPUs in accelerating electronic design automation tools. The algorithm has been implemented on a Xeon Workstation using C, and achieved a substantial acceleration on an Nvidia Tesla C2070 card.
Effects of System's and User's Characteristics on E-Learning Use: A Study at Universiti Malaysia Sarawak.

The benefits of an e-learning system will not be maximised if learners do not use the system. This study was conducted with 26 postgraduate students at a faculty in Universiti Malaysia Sarawak taking an on-campus course supplemented with an e-learning system. The purpose of the study was to determine which factors were related to intention to use an e-learning system as a supplementary learning tool. The factors investigated were system characteristics such as functionality, interactivity and response rates; user characteristics incorporating computer self-efficacy and Internet experience; perceived usefulness and perceived ease of use. The findings of the study showed that the participants viewed the e-learning system characteristics positively especially in terms of functionality and interactiveness. However, the response rate for the e-learning system was not up to expectations. Most of the participants believed that they were capable of using the e-learning system to accomplish their learning tasks and have adequate Internet use experience. Intention to use the e-learning system for supplementary learning was positively related to the participants' computer self-efficacy. Computer 2 self-efficacy was also positively related to perceive usefulness of an e-learning system and perceived ease of use. All three systems characteristics of functionality, interactivity and response rate were related to perceived usefulness. Therefore, in developing an e-learning system, the system developers have to consider ensuring the system is easy for the user to handle and improve the system's functionality, interactivity and response rates. Developers, designers, and institutional purchasers of e-learning systems should also ensure compatibility between system features and user requirements to enhance technology adoption for e-learning. Furthermore, to maximize the benefits of e-learning system, educational institution should demonstrate the use of the technology and provide instructional material to ease students' learning of the technology. In addition, it should describe how the technology would benefit students and assist them learn the course content or achieve other learning goals. Recommendations for future studies are also included in the conclusion of the paper.
Designing Usable Localised Websites : Differences between Western and Arab Cultures

This paper presents a case study from a western country (UK) and an Arab country (Oman) to extract the views of Web designers in both countries regarding web usability. The purpose is to determine the most important issues that should be considered when designing for a particular culture. To obtain a deeper and more detailed knowledge on how designers work in each country, it necessitated that the researchers get closer to the designers environment. In such a way the researchers can enquire, observe and converse with them in an open-ended style of discussion. This can best be done through a case study in each of the two countries (Oman and UK). The specific aims of conducting these case studies in the two selected countries were to: 1) investigate the extent of the usage of the published usability guidelines and tools in the design of the user interface of a website; 2) Explore the differences and similarities in designing websites for each of the two cultures; 3) Discover whether they design for different cultures; if they do what considerations they take into account when designing for different cultures? and 4) Investigate whether the designers in both countries consider using Cultural User Interface (CUI) profile or something similar to capture the target culture preferences and expectations, and whether it would fit into the way they normally do business. The data collection instrument consisted questionnaire for the designers and in many cases, this was followed with an interview or an email to the surveyed design companies to clarify their responses. In addition to the questionnaire, the researchers made use of available documentation or archival data that could provide any help to the current research. The researchers also investigated the usability tools and guidelines used as well as other specific design tools which the company found helpful in designing usable websites. The main outcome of this study was that the designers in both countries believed that although the users share similar preferences and perceptions about many website usability issues, however, they differ in the importance they give to certain usability elements such as the adherence to local language, culture and religious beliefs. The results of this study proved that onesize-for-all is not the right approach for a successful website. It highlighted the need to consider the customers’ cultural background and their real world experience.
Health insurance : treatment vs. compensation

In this paper, we view health insurance as a combined hedge against the two consequences of falling ill: treatment expenditures and loss in income. We discuss how an individual’s ability when healthy affects her decision on whether to buy health insurance with treatment to full recovery if ill or with partial treatment combined with cash compensation for the resulting loss in income. We find that a highability individual demands full recovery and is fully insured, while a low-ability individual demands partial treatment and cash compensation and is only partly insured.
Resistive Oxygen Gas Sensors for Harsh Environments

Resistive oxygen sensors are an inexpensive alternative to the classical potentiometric zirconia oxygen sensor, especially for use in harsh environments and at temperatures of several hundred °C or even higher. This device-oriented paper gives a historical overview on the development of these sensor materials. It focuses especially on approaches to obtain a temperature independent behavior. It is shown that although in the past 40 years there have always been several research groups working concurrently with resistive oxygen sensors, novel ideas continue to emerge today with respect to improvements of the sensor response time, the temperature dependence, the long-term stability or the manufacture of the devices themselves using novel techniques for the sensitive films. Materials that are the focus of this review are metal oxides; especially titania, titanates, and ceria-based formulations.
A reliable multicast data distribution protocol based on software FEC techniques

Applications requiring the reliable distribution of data to groups of clients would be supported perfectly by reliable multicast protocols. In many cases, the problem of congestion control (a major research issue otherwise) does not exist because downlink bandwidth is "owned" or can be preallocated to a particular server by independent means, but the problems of insuring reliable data delivery to larcre groups, and adaptability to heterogeneous clients, still remain. These problems can be solved at once with the use of FEC techniques. In this paper we show the design of a Reliable Multicast data Distribution Protocol (RMDP) that we have built using these techniques, and discuss the implementation tradeoffs. Experimental results show that, albeit somewhat expensive, doing encoding/decoding in software is affordable for speeds in the Mbit/s range even on low-end PCs. Slower machines can still receive at high speed, thus optimizing network usage, by taking advantage of the fact that decoding needs not to be done in real time. Finally, our RMDP can work even without any feedback from the receivers, thus making it well suited to mobile/wireless systems.
Light Simulation with Participating Media

In this project we address the problem of light scattering in participating materials. We create a complete simulation of this phenomenon in a more general case than previous work. We analyse the directional part of light, in order to install a clear basis for future work. We derive two models from this analysis: the spherical Gaussians approximation and the double exponential approximation. These models are placed in the scope of the planned development of an improved method for scattering. We also code a custom ray tracer to have a complete pipeline of rendering and to understand the underneath concepts. The validation of our simulation is done by comparing against the results of Eugene d'Eon in his article of Quantized-diffusion.
Virtual lab: A concrete experience in building multi-purpose virtualized labs for Computer Science Education

The employment of virtualized infrastructures has increased significantly the resources and tools available to teachers to support the courses with practical exercises carried out with the aid of computers. In this paper, the design and the implementation of a virtual multiple lab is discussed along with the experiences and the issues raised by its deployment as a tool for teaching undergraduate courses in Computer Science. Particular emphasis is posed on infrastructure operation and maintenance highlighting its benefits, discussing its limitation and potential improvements.
Detection of Alzheimer’s disease based on automatic analysis of common objects descriptions

Many studies have been made on the lan- guage alterations that take place over the course of Alzheimer's disease (AD). As a consequence, it is now admitted that it is possible to discriminate between healthy and ailing patients solely based on the analysis of language production. Most of these studies, however, were made on very small samples—30 participants per study, on an average—, or involved a great deal of manual work in their analysis. In this paper, we present an automatic analysis of transcripts of elderly participants describ- ing six common objects. We used part- of-speech and lexical richness as linguistic features to train an SVM classifier to au- tomatically discriminate between healthy and AD patients in the early and moder- ate stages. The participants, in the corpus used for this study, were 63 Spanish adults over 55 years old (29 controls and 34 AD patients). With an accuracy of 88%, our experimental results compare favor- ably to those relying on the manual extrac- tion of attributes, providing evidence that the need for manual analysis can be over- come without sacrificing in performance.
Iterative Vector Diffusion for the Detection of Modularity in Large Networks

Systems biology is an emerging discipline which attempts to understand complex biological systems as coherent systems, rather than as collections of components. Complex biological systems can often be viewed as networks for this purpose, with the nodes of the network representing entities such as genes, proteins, or individual organisms, and the edges between nodes representing interactions between those entities. Many of the biological systems which have been recast as networks have proven to be scale free and/or small world networks (Watts & Strogatz, 1998; Wagner & Fell, 2000; Jeong et al., 2000; Wagner, 2001), a finding which leads to the hypothesis that such an organization may be more or less ubiquitous in natural systems.
Altered A-to-I RNA Editing in Human Embryogenesis

Post-transcriptional events play an important role in human development. The question arises as to whether Adenosine to Inosine RNA editing, catalyzed by the ADAR (Adenosine Deaminase acting on RNA) enzymes, differs in human embryogenesis and in adulthood. We tested the editing of various target genes in coding (FLNA, BLCAP, CYFIP2) and non-coding sequences at their Alu elements (BRCA1, CARD11, RBBP9, MDM4, FNACC), as well as the transcriptional levels of the ADAR1 enzymes. This analysis was performed on five fetal and adult human tissues: brain, heart, liver, kidney, and spleen, as well as on human embryonic stem cells (hESCs), which represent the blastocyst stage in early human development. Our results show substantially greater editing activity for most adult tissue samples relative to fetal ones, in six of the eight genes tested. To test the effect of reduced A-to-I RNA editing activity in early human development we used human embryonic stem cells (hESCs) as a model and tried to generate hESC clones that overexpress the ADAR1–p110 isoform. We were unable to achieve overexpression of ADAR1–p110 by either transfection or lentiviral infection, though we easily generated hESC clones that expressed the GFP transgene and overexpressed ADAR1-p110 in 293T cells and in primary human foreskin fibroblast (HFF) cells. Moreover, in contrast to the expected overexpression of ADAR1-p110 protein following its introduction into hESCs, the expression levels of this protein decreased dramatically 24–48 hr post infection. Similar results were obtained when we tried to overexpress ADAR1-p110 in pluripotent embryonal carcinoma cells. This suggests that ADAR1 protein is substantially regulated in undifferentiated pluripotent hESCs. Overall, our data suggest that A-to-I RNA editing plays a critical role during early human development.
Interactive elastic motion editing through space–time position constraints

We present an intuitive and interactive approach for motion editing through space–time constraints on positions. Given an input motion of an elastic body, our approach enables the user to interactively edit node positions in order to alter and fine‐tune the motion. We formulate our motion editing as an optimization problem with dynamics constraints to enforce a physically plausible result. Through linearization of the editing around the input trajectory, we simplify this constrained optimal control problem into an unconstrained quadratic optimization. The optimal motion thus becomes the solution of a dense linear system, which we solve efficiently by applying the adjoint method in each iteration of a conjugate gradient solver. We demonstrate the efficiency and quality of our motion editing technique on a series of examples. Copyright © 2013 John Wiley & Sons, Ltd.
Suppression of IκBα increases the expression of matrix metalloproteinase-2 in human ciliary muscle cells

Purpose: An increase of matrix metalloproteinase-2 (MMP-2) has been found to improve outflow through the uveoscleral pathway. This experiment was designed to test whether reduction of inhibitor of nuclear factor kappa B alpha (IκBα) levels could enhance MMP-2 expression in human ciliary muscle (HCM) cells in vitro. Methods: The small interfering RNA (siRNA) targeting inhibitor of nuclear factor kappa B (IκBα) was transfected into HCM cells. The mRNA and protein levels of IκBα, nuclear factor-kappa B (NF-κB)p65, MMP-2, tissue inhibitor of metalloproteinase-2 (TIMP-2), and membrane-type 1 matrix metalloproteinase (MT1-MMP) in HCM cells were examined 24 h, 48 h, and 72 h after IκBα siRNA transfection by real-time reverse transcription polymerase chain reaction (RT–PCR) and western blot. The activation of NF-κBp65 was determined through the translocation of NF-κBp65 by fluorescence microscope. Gelatin zymography was used to detect the secretion and activity of MMP-2. Results: Real-time RT–PCR and western blot showed that transfection of IκBα siRNA led to gradual downregulation of IκBα and TIMP-2 both at the mRNA and protein level after 24 h, 48 h and 72 h. The IκBα and TIMP-2 mRNA levels decreased 92.7%±1.6% and 70.3%±13.1%, respectively, and the protein levels were reduced 87.3%±2.0% and 62.9% ±0.8% (p<0.01), respectively, when compared to the control 72 h after siRNA transfection. Conversely, the MMP-2 and MT1-MMP mRNA and protein levels increased in the time-dependent manner after IκBα siRNA transfection. The MMP-2 and MT1-MMP mRNA levels increased 178%±4.6% and 165%±8.2%, respectively, while protein levels were raised to 162%±3.7% and 157.6%±5.7% (p<0.01), respectively, when compared to the control 72 h after IκBα siRNA transfection. Although no obvious changes were seen in either mRNA or protein levels of total NF-κBp65 (p>0.05), the protein level of NF-κBp65 increased dramatically in the nucleus as revealed by western blot and fluorescence staining 24 h, 48 h, and 72 h after IκBα siRNA transfection. Moreover, gelatin zymography indicated that the secretion and activity of MMP-2 in treated cells were higher than those in the control cells. The maximum increases of pro-MMP-2 and active-MMP-2 were 172%±15% and 151%±14% (p<0.01), respectively, when compared to the control at the experiment’s conclusion 72 h after siRNA transfection. Conclusions: Expression and activity of MMP-2 was enhanced by the IκBα siRNA in HCM cells through the activation of the NF-κB signaling pathway. Our results suggested that IκBα may therefore be a potential target for controlling the uveoscleral outflow pathway in glaucoma.
Multi Media e-Learning Software TRIANGLE Case-Study: Experimental Results and Lessons Learned

This paper reports on results of experiments carried out with TRIANGLE. The software has been designed and developed since 2001 in several modifications as an experimental prototype for an interactive multimedia learning object. During the design, it was essential to provide a user interface with good usability in order to support the teachers with only a minimum knowledge of computers. It was also necessary to provide a simple data structure and open architecture including runtime evaluation. The basic idea was to provide a quiz show game in order to uphold as strong a level of motivation as possible. The purpose of this prototype was to test the efficiency of three main psychological concepts in terms of learning: motivation, incidental learning, and something we call the Tamagotchi effect, which refers to the concept of personal responsibility. A pre-test/post-test control group design was chosen. The experiments were carried out in real-life classroom settings including N=44 K8 students. Mathematics was chosen as the subject. Three hypotheses were tested: 1) This game based learning software provides a level of motivation high enough to make learning fun, even with less popular subjects; 2) Chunks of knowledge mixed into informational text, within a hypertext structure, are efficient enough to facilitate student learning; 3) An additional virtual partner (avatar), to which a student feels personal responsibility, further increases motivation. Based on the results of our studies, hypotheses 1 and 2 could be proven, however, not hypothesis 3. Consequently, TRIANGLE can stimulate learning by making unpopular subjects fun; incidental learning can increase the process of integrating new knowledge; however, no positive effect could be measured of the personal responsibility for the avatar, possibly due to the low occurrence of personalization within the experimental settings.
Wolbachia Bacteria Reside in Host Golgi-Related Vesicles Whose Position Is Regulated by Polarity Proteins

Wolbachia pipientis are intracellular symbiotic bacteria extremely common in various organisms including Drosophila melanogaster, and are known for their ability to induce changes in host reproduction. These bacteria are present in astral microtubule-associated vesicular structures in host cytoplasm, but little is known about the identity of these vesicles. We report here that Wolbachia are restricted only to a group of Golgi-related vesicles concentrated near the site of membrane biogenesis and minus-ends of microtubules. The Wolbachia vesicles were significantly mislocalized in mutant embryos defective in cell/planar polarity genes suggesting that cell/tissue polarity genes are required for apical localization of these Golgi-related vesicles. Furthermore, two of the polarity proteins, Van Gogh/Strabismus and Scribble, appeared to be present in these Golgi-related vesicles. Thus, establishment of polarity may be closely linked to the precise insertion of Golgi vesicles into the new membrane addition site.