Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of topoisomerase II-alpha gene status by dual color chromogenic in situ hybridization in a set of Iraqi patients with invasive breast carcinoma

Background: The human epidermal growth factor receptor 2(HER2) proto-oncogene is overexpressed or amplified in approximately 15%–25% of invasive breast cancers. Approximately 35% of HER2-amplified breast cancers have coamplification of the topoisomerase II-alpha (TOP2A) gene encoding an enzyme that is a major target of anthracyclines. Hence, the determination of genetic alteration (amplification or deletion) of both genes is considered as an important predictive factor that determines the response of breast cancer patients to treatment. The aims of this study are to determinate TOP2A status gene amplification in a set of Iraqi patients with breast cancer that have had an equivocal (2+) and positive HER2/neu by immunohistochemistry (IHC) and to compare the results with estrogen receptor (ER) and progesterone receptor (PR) and HER2/neu status. Patients and Methods: A cross-sectional prospective study done on 53 patients with invasive breast carcinoma. Twenty-six out of total 53 cases were positive HER2/neu (3+), the remaining 27 equivocal HER2-IHC (2+) cases reanalyzed using dual-color chromogenic in situ hybridization (ZytoVision) probe kit for further identification of HER2/neu gene amplification. Using chromogenic in situ hybridization (CISH), TOP2A gene status determination was done for all cases. Results: There is a direct significant correlation between TOP2A gene amplification and HER2/neu positivity, P < 0.05 in that 15 (39.4%) out of 38 positive HER2/neu cases were associated with topoisomerase gene amplification. Regarding relation of topoisomerase gene to hormone receptor status (ER and PR), there was a significant negative relationship between the gene and ER receptor status. The higher level of gene amplification was noticed in ER and PR negative cases in about 13 (43.3%) and 14 (48.2%) for ER and PR, respectively. Conclusion: TOP2A gene status has a significantly positive correlation with HER2/neu status while it has a significantly negative correlation with hormone receptor status.
The Nuclear Pseudospin Symmetry Along an Isotopic Chain

We investigate the isospin dependence of pseudospin symmetry in the chain of tin isotopes (from 120 Sn until 170 Sn). Using a Woods-Saxon parametrization of the nuclear potential for these isotopes we study in detail the effect of the vector-isovector ‰ and Coulomb potentials in the energy splittings of neutron and proton pseudospin partners in the isotopic chain. We conclude that the realization of nuclear pseudospin symmetry does not change considerably with the mass number, and is always favored for neutrons. We also find that the ‰ potential accounts for essentially all the pseudospin isospin asymmetry observed and that the Coulomb potential plays a negligible role in this asymmetry. This can be explained by the dynamical nature of pseudospin symmetry in nuclei, namely the dependence of the pseudospin splittings on the shape of the nuclear mean-field potential.
REAL TIME COLOR OBJECT DETECTION AND TRACKING BY IMAGE PROCESSING

The goal of our research is efficient tracking of color objects from a sequence of live images for use in real-time applications including surveillance, video conferencing and robot navigation. Tracking can be defined as the problem of estimating the trajectory of an object in the image plane as it moves around a scene. The need for high power computers, the availability of high quality and inexpensive video cameras, and the increasing need for automated video analysis has generated a great deal of interest in object tracking algorithms. There are three key steps in video analysis, detection of interesting moving objects, tracking of such objects from frame to frame, and analysis of object tracks to recognize their behavior .
The HAL3‐PPZ1 dependent regulation of nonsense suppression efficiency in yeast and its influence on manifestation of the yeast prion‐like determinant [ISP+]

The efficiency of stop codons read‐through in yeast is controlled by multiple interactions of genetic and epigenetic factors. In this study, we demonstrate the participation of the Hal3‐Ppz1 protein complex in regulation of read‐through efficiency and manifestation of non‐Mendelian anti‐suppressor determinant [ISP+]. Over‐expression of HAL3 in [ISP+] strain causes nonsense suppression, whereas its inactivation displays as anti‐suppression of sup35 mutation in [isp−] strain. [ISP+] strains carrying hal3Δ deletion cannot be cured from [ISP+] in the presence of GuHCl. Since Hal3p is a negative regulatory subunit of Ppz1 protein phosphatase, consequences of PPZ1 over‐expression and deletion are opposite to those of HAL3. The observed effects are mediated by the catalytic function of Ppz1 and are probably related to the participation of Ppz1 in regulation of eEF1Bα elongation factor activity. Importantly, [ISP+] status of yeast strains is determined by fluctuation in Hal3p level, since [ISP+] strains have less Hal3p than their [isp−] derivatives obtained by GuHCl treatment. A model considering epigenetic (possibly prion) regulation of Hal3p amount as a mechanism underlying [ISP+] status of yeast cell is suggested.
Learning through participatory simulations: network-based design for systems learning in classrooms

This project brings together two lines of researchothe study of complex dynamic systems and the use of participatory simulations as a powerful way into systems modelingoboth of which can be enabled and advanced through emerging network technologies. The study of dynamic systems stands as a new form of literacy for all. Participatory Simulations Activities can support new forms of classroom interaction and can serve to catalyze the engagement with dynamic systems modeling as a core feature of the education of all students. To accomplish these goals, we introduce a new architecture, HubNet. HubNet is an open client-server architecture, which enables many users at the "Nodes" (currently TI graphing calculators) to control the behavior of individual objects or agents and to view the aggregated results on a central computer known as the Hub. This network of nodes is integrated with a powerful suite of modeling, analysis and display tools that together give both the capacity to "fly" the system in intuitive mode, to reflect on the emergent result of their simulation and, also, to encode their strategies as rules which the system can then run independently. The HubNet system is being used in several middle and secondary classrooms. An illustrative example of classroom use is presented.
Prostorna nelinearna numerička analiza podzemnih čeličnih cjevovoda uslijed pomaka rasjeda ; A 3D nonlinear numerical analysis of buried steel pipes at strike-slip fault crossings

A 3D nonlinear soil-pipe interaction model is presented in this study to calculate the response of steel pipes subjected to strike-slip fault displacements. The generalpurpose finite element analysis program ABAQUS is used to determine the seismic response of high strength steel pipes, as well as for various surrounding soil conditions and diameter to thickness, D/t, ratios. Relatively low strength pipes X65, and high strength pipes X70 and X80, which correspond to European pipes L450, L485 and L555, respectively, have been studied for various pipe diameters and thicknesses.
Development of mammary tumors from hyperplastic alveolar nodules transplanted into gland-free mammary fat pads of female C3H mice.

The hyperp las t ic alveolar nodules, which norma l ly occur in the m a m m a r y glands of mice f rom susceptible s t ra ins infected wi th the m a m m a r y tumor virus, are general ly thought to be precancerous. This belief is suppor ted by considerable indirect evidence. Ear l ie r work on hyperp las t ic nodules in mouse m a m m a r y tumorigenesis has been reviewed extensively (2, 4-8, 10). The assumed precancerous na tu re of hyperplast ic alveolar nodules implies t h a t m a m m a r y tumors arise more f requent ly f rom nodules t h a n f rom normal m a m m a r y tissue. Di rec t evidence can be obta ined if exper imenta l condi t ions outl ined by F a u l k i n and D e O m e (4) can be met . This report presents three series of exper iments which fulfill the essential exper imenta l condit ions and which provide the desired direct evidence. I n addit ion, a new t r ansp lan ta t ion technic is described, which permi t s the t r ansp lan ta t ion of normal , nodular , and tumorous m a m m a r y tissues into host m a m m a r y fa t pads freed f rom host m a m m a r y tissue, and the subsequent deve lopment of character is t ic pa t te rns of outgrowth. I n each of the three exper imenta l series, nodules and samples of normal m a m m a r y tissue were transp lan ted into sites freed from host m a m m a r y tissue, and the n u m b e r of tumors derived f rom these t ransp lan ts was determined. Tissue samples were t r ansp lan ted e i ther into the dorsal subcutis , into gland-free (cleared) inguinal (#4) m a m m a r y fa t pads, or first into the subcutaneous sites and then re t ransp lan ted into the fa t pads. T h e three series of exper iments are presented under the following headings: (a) "Longt e rm t r ansp lan ta t ion into the dorsal subcu t i s" ; (b) "Longte rm t r ansp lan ta t ion into cleared m a m m a r y fa t p a d s " ; and (c) "Ret r ansp lan ta t ion of long-term subcutaneous transp lan ts into cleared m a m m a r y fa t pads . "
Streptococcus pneumoniae and Pseudomonas aeruginosa pneumonia induce distinct host responses

Objective:Pathogens that cause pneumonia may be treated in a targeted fashion by antibiotics, but if this therapy fails, then treatment involves only nonspecific supportive measures, independent of the inciting infection. The purpose of this study was to determine whether host response is similar after disparate infections with similar mortalities. Design:Prospective, randomized controlled study. Setting:Animal laboratory in a university medical center. Interventions:Pneumonia was induced in FVB/N mice by either Streptococcus pneumoniae or two different concentrations of Pseudomonas aeruginosa. Plasma and bronchoalveolar lavage fluid from septic animals was assayed by a microarray immunoassay measuring 18 inflammatory mediators at multiple time points. Measurements and Main Results:The host response was dependent on the causative organism as well as kinetics of mortality, but the pro-inflammatory and anti-inflammatory responses were independent of inoculum concentration or degree of bacteremia. Pneumonia caused by different concentrations of the same bacteria, Pseudomonas aeruginosa, also yielded distinct inflammatory responses; however, inflammatory mediator expression did not directly track the severity of infection. For all infections, the host response was compartmentalized, with markedly different concentrations of inflammatory mediators in the systemic circulation and the lungs. Hierarchical clustering analysis resulted in the identification of five distinct clusters of the host response to bacterial infection. Principal components analysis correlated pulmonary macrophage inflammatory peptide-2 and interleukin-10 with progression of infection, whereas elevated plasma tumor necrosis factor sr2 and macrophage chemotactic peptide-1 were indicative of fulminant disease with >90% mortality within 48 hrs. Conclusions:Septic mice have distinct local and systemic responses to Streptococcus pneumoniae and Pseudomonas aeruginosa pneumonia. Targeting specific host inflammatory responses induced by distinct bacterial infections could represent a potential therapeutic approach in the treatment of sepsis.
Distinct Tissue Site-Specific Requirements of Mast Cells and Complement Components C3/C5a Receptor in IgG Immune Complex-Induced Injury of Skin and Lung1

We induced the passive reverse Arthus reaction to IgG immune complexes (IC) at different tissue sites in mice lacking C3 treated or not with a C5aR-specific antagonist, or in mice lacking mast cells (KitW/KitW-v mice), and compared the inflammatory responses with those in the corresponding wild-type mice. We confirmed that IC inflammation of skin can be mediated largely by mast cells expressing C5aR and FcγRIII. In addition, we provided evidence for C3-independent C5aR triggering, which may explain why the cutaneous Arthus reaction develops normally in C3−/− mice. Furthermore, some, but not all, of the acute changes associated with the Arthus response in the lung were significantly more intense in normal mice than in C3−/− or KitW/KitW-v mice, indicating for C3- and mast cell-dependent and -independent components. Finally, we demonstrated that C3 contributed to the elicitation of neutrophils to alveoli, which corresponded to an increased synthesis of TNF-α, macrophage-inflammatory protein-2, and cytokine-induced neutrophil chemoattractant. While mast cells similarly influenced alveolar polymorphonuclear leukocyte influx, the levels of these cytokines remained largely unaffected in mast cell deficiency. Together, the phenotypes of C3−/− mice and KitW/KitW-v mice suggest that complement and mast cells have distinct tissue site-specific requirements acting by apparently distinct mechanisms in the initiation of IC inflammation.
Mixing Music as Linked Data: SPARQL-based MIDI Mashups

A large number of datasets about music are available today in the Linked Open Data cloud, but most of them only describe music metadata. Datasets representing music notation (i.e. fine-grained musical transcriptions) are scarce, and hence musicians do not have the possibility to exploit Web technologies to their full potential. In particular, this situation hampers the musician’s process of creating mashups, new musical compositions produced by remixing existing tracks. Recently, the MIDI Linked Data cloud has interlinked and published more than 300K MIDI songs as Linked Data. In this paper, we investigate the use of Semantic Web technology to produce musical mashups, and we present a framework to generate them systematically. We evaluate our approach with SPARQL-DJ, a prototype implementation that can be used to find, match, select and synchronize existing MIDI Linked Data, mix them, and create new musical content.
Improving the performance of evolutionary algorithms by soft-constraining their sampling capabilities

In this paper we argue that to produce good optimization performances, the exploration of the solution space does not need to be carried out in the unorderly fashion most evolutionary algorithms use. Other strategies that seek to minimize the cost involved in successive evaluation processes should be explored. This does not imply a fundamental change on how evolutionary algorithms work, but rather, it brings some structure onto how solution spaces are explored by contemplating decoding cost as one of the elements to be minimized when sampling. The traditional implementations of most evolutionary algorithms assume that any point in the solution space can be evaluated any time and at no cost. However, this is not always the case and often each step of the process only part of the solution space is available for evaluation giving rise to a class of problems we have called Constrained Sampling optimization problems over which evolutionary algorithms are quite inefficient. To address these problems we have proposed a modification of the general strategy of evolutionary algorithms to address these constraints efficiently. Here, we study the effects of this approach when applied to problems that are not constrained, thus modifying the way the solution space is explored. This study is carried out to determine how these modification impact the performance of a set of popular evolutionary algorithms over a representative set of benchmark functions corresponding to fitness landscapes with a variety of characteristics. We show that by restricting the sampling capabilities of most algorithms, the cost of the optimization procedure is reduced for most types of fitness landscapes without affecting their results.
Mom, Dad, Help Please: The Home Environment’s Influences on a Child’s Math Ability

Recently, there has been a big surge of research and public interest in increasing the math capabilities and skills of American children. This paper serves as a literature review examining how the home environment, specifically parents, can help with that. This meta-analysis delves into the factors of maternal math talk, a parent’s own math anxiety, and the relationship between a parent and child in the context of a parent’s gender stereotypes and a parent’s perception on his or her child’s math abilities. Interventions, suggestions, and future implications are also discussed. This paper will hopefully bring needed awareness to parents about their roles in their child’s math development, abilities, and achievement.
The development of 'drama' in YouTube discourse

This thesis presents a systematic discourse analysis of sustained antagonistic debate—called 'drama'—on the video-sharing website, YouTube. Following a two-year observation of a YouTube community of practice discussing Christianity and atheism, 20 video 'pages' (including talk from videos and text comments) from a drama event were identified and transcribed, producing a 86,859 word corpus comprising 136 minutes of video talk and 1,738 comments. Using metaphor-led discourse analysis (Cameron & Maslen, 2010b) of the total corpus, metaphor vehicles were identified, coded, and grouped by semantic and narrative relationships to identify systematic use and trace the development of discourse activity. Close discourse analysis of a subset of the corpus was then employed to investigate membership categorisation (Housley & Fitzgerald, 2002), impoliteness (Culpeper, 2011), and positioning (Harre & van Langenhove, 1998), providing a systematic description of different factors contributing to the emergence of 'drama'. Analysis shows that 'drama' developed when negative views of one user's impolite words exposed the different expectations of other users about acceptable YouTube interaction. Hyperbolic, metaphorical language derived from the Bible and narratives about tragic historical events often exaggerated, escalated, and extended negative evaluations of others. Categories like 'Christian' were used dynamically to connect impolite words and actions of individuals to social groups, thereby also extending negative evaluations. With implications for understanding 'flaming' and transgression of social norms in web 2.0 environments, this thesis concludes that inflammatory language led to 'drama' because: (1) users had diverse expectations about social interaction and organisation, (2) users drew upon the Bible's moral authority to support opposing actions, and (3) the online platform's technical features afforded immediate reactions to non-present others. The 'drama' then developed when users' responses to one another created both additional topics for antagonistic debate and more disagreement about which words and actions were acceptable.
The use of artificial intelligent in power system stability

In this project the use of Artificial Intelligence in Power System Stability Enhancement is studied. The focus of the project is on low frequency oscillation in power systems. These oscillations known as electromechanical modes of oscillation were observed in power systems in the early 1960’s. They are the result of kinetic energy exchange between synchronous generators in a power system. Power System Stabilizers has been used to dampen these oscillations. Conventional Power System Stabilizers (CPSS) have been used for decades in power systems. They consist of a washout filter and two lead lag blocks to compensate the phase lag of the system. Tuning of CPSS is of paramount importance for proper response and function. In this project, a Genetic Algorithm (GA) optimization process is introduced in order to tune the parameters of a CPSS in a Single Machine Infinite Bus system. The power system is modelled in PowerFactory and GA optimization uses the MATLAB Optimization Toolbox. An effective data exchange is engineered between PowerFactory and MATLAB to facilitate the tuning process. The optimization is performed using the position of the eigenvalues of the power system which are found by running Modal Analysis in PowerFactory. The main goal of optimization is to tune the parameters of CPSS to maximize the dampening ratio of all oscillatory modes. In the next section of the project an Artificial Neural Network (ANN) based power stabilizer is introduced. Two neural networks are designed. First is a Neural Identifier to model the dynamics of the system and to predict the future output of the system. Second is a Neural Controller to provide proper stabilizing signals to dampen the oscillation by comparing the output of Neural Identifier with the desired value. A data interface between PowerFactory and MATLAB is established in order to enable the training and simulation of the proposed control structure.
Computer Simulations of Particle Deposition in the Developing Human Lung

ABSTRACT An age-dependent theoretical model has been developed to predict PM dosimetry in children's lungs. Computer codes have been written that describe the dimensions of individual airways and the geometry of branching airway networks within developing lungs. Breathing parameters have also been formulated as functions of subject age. Our computer simulations suggest that particle size, age, and activity level markedly affect deposition patterns of inhaled air pollutants. For example, the predicted lung deposition fraction is 38% in an adult but is nearly twice as high (73%) in a 7-month-old for 2-um particles inhaled during heavy breathing. Tracheobronchial (TB) and pulmonary (or alveolated airways, P) deposition patterns may also be calculated using the model. Due to different clearance processes in the TB and P airways (i.e., mucociliary transport and macrophage action, respectively), the determination of compartmental dose is important for PM risk assessment analyses. Furthermore, the results of such simulations may aid in the setting of regulatory standards for air pollutants, as the data provide a scientific basis for estimating dose delivered to a designated sensitive subpopulation (children).
Novice and Expert Performance of KeyScretch: A Gesture-Based Text Entry Method for Touch-Screens

KeyScretch is a text entry method for devices equipped with touch-screens, based on a menu-augmented soft keyboard. In these keyboards, a menu containing a small number of frequent characters is shown, while a key is pressed, allowing further character entry by menu selection. KeyScretch improves the previously studied menu-based methods by enabling the interpretation of compound strokes, which allow the input of text chunks longer than two characters. The performance of the method is analyzed on different kinds of touch-screens: First, we present a 25-session user study on a stylus-based device, showing that an instance of the method optimized for Italian can be learned in a reasonable time by the users and significantly outperforms the traditional method based on the tapping interaction. Then, we define and validate a model for predicting expert text entry rates on finger-based devices. The predicted rates for instances of KeyScretch optimized for different Western languages vary from about 44-50 words/min on the Qwerty layout, enabling improvements in the range of 30-49% as compared with the traditional method.