Miracle-dz/UniFAR-FTUs huggingface dataset:
Pharmacogenomic Profiling of the PI 3 K / PTEN Pathway in Sporadic Breast Cancer

Background: Pharmacogenomics is the study of genetic variations among individuals to predict the probability that a patient will respond to single or multidrug chemotherapy. Breast cancer is one of the most common cancers among women worldwide. Treatment of breast cancer by application of biological rationales gives us the ability to match the correct pharmacology to individual tumour genetic profiles. The breast cancers exhibit multiple anomalies in phosphatidylinositol 3 kinase pathways, such as phosphatase and tensin homolog deleted on chromosome TEN loss that can be put in context of therapy with rapamycin analogues. Considering the high incidence of breast cancer in Iran, the potential role of tumor suppressor PTEN/MMAC1gene was investigated in Isfahanian breast cancer patients. Methods: In this study, PTEN was evaluated by means of polymerase chain reaction, single strand conformation polymorphism, Heteroduplex mobility assay and direct DNA sequencing in 72 breast cancer tumors for detection and characterization of mutations. Results: According to the results of this research, nucleotide substitutions were found in 5/72 (7%) of samples. The sporadic breast cancer patient was found to be heterozygote for the p.D92N, p.C105W, p.D107N, p.A121P and p.R130Q mutations. One novel mutation, p.D107N, was found in this study. Conclusion: Loss of PTEN function in breast cancer can occur either by mutation or reduction of PTEN expression in almost half of sporadic breast tumors. This rate of mutations is an important consideration for novel therapeutic in which biological efficacy is influenced by the activity of PTEN. Iran. Biomed. J. 13 (2):
Building a Fuzzy System for Opinion Classification Across Different Domains

Opinions are central in almost all human activities, because they are a relevant influence on peoples behavior. The internet and the web have created mechanisms that made possible for people to share their opinions and for other people and organizations to find out more about opinions and experiences from individuals and help in decision making. Still, opinions involve sentiments that are vague and inaccurate textual descriptions. Hence, due to data's nature, Fuzzy Logic can be a promising approach. This paper proposes a fuzzy system to perform opinion classification across different domains. Almost 70 features were extracted from documents and multiple feature selection algorithms were applied to select the most fitted features to classify documents. Over the selected features, the Wang-Mendel (WM) method was used to generate fuzzy rules and classify documents. The WM fuzzy system based achieved 71,25% of accuracy in a 10-fold cross-validation.
Sonic Hedgehog and Notch Signaling Can Cooperate to Regulate Neurogenic Divisions of Neocortical Progenitors

Background Hedgehog (Hh) signaling is crucial for the generation and maintenance of both embryonic and adult stem cells, thereby regulating development and tissue homeostasis. In the developing neocortex, Sonic Hedgehog (Shh) regulates neural progenitor cell proliferation. During neurogenesis, radial glial cells of the ventricular zone (VZ) are the predominant neocortical progenitors that generate neurons through both symmetric and asymmetric divisions. Despite its importance, relatively little is known of the molecular pathways that control the switch from symmetric proliferative to differentiative/neurogenic divisions in neural progenitors. Principal Findings Here, we report that conditional inactivation of Patched1, a negative regulator of the Shh pathway, in Nestin positive neural progenitors of the neocortex leads to lamination defects due to improper corticogenesis and an increase in the number of symmetric proliferative divisions of the radial glial cells. Hedgehog-activated VZ progenitor cells demonstrated a concomitant upregulation of Hes1 and Blbp, downstream targets of Notch signaling. The Notch signaling pathway plays a pivotal role in the maintenance of stem/progenitor cells and the regulation of glial versus neuronal identity. To study the effect of Notch signaling on Hh-activated neural progenitors, we inactivated both Patched1 and Rbpj, a transcriptional mediator of Notch signaling, in Nestin positive cells of the neocortex. Conclusions Our data indicate that by mid neurogenesis (embryonic day 14.5), attenuation of Notch signaling reverses the effect of Patched1 deletion on neurogenesis by restoring the balance between symmetric proliferative and neurogenic divisions. Hence, our results demonstrate that correct corticogenesis is an outcome of the interplay between the Hh and Notch signaling pathways.
Multi bounding volume hierarchies

Efficient tracing of single and incoherent rays is still a challenge in computer graphics. Coherent packet tracing has reached real-time performance, but ray packets bring about restrictions for the architecture of the renderer and their suitability for diverging secondary ray bundles is uncertain. The algorithm presented in this paper avoids these problems by not using ray packets at all. Instead, it uses triangle packets and bounding volume packets in a novel acceleration data structure called multi bounding volume hierarchy (MBVH). It is designed for SIMD single ray tracing. The hierarchy is built from a binary bounding volume hierarchy by collapsing subtrees of height two into SIMD nodes storing four bounding boxes. A modified cost function for construction guarantees that all but one of the leaf nodes contain exactly four triangles. The MBVH makes good use of data-level parallelism during traversal and triangle intersection, yielding speed-ups of up to 2.8times for random ray shooting. It consumes less memory than a regular bounding volume hierarchy and requires no modifications to the architecture of the rendering engine.
Two New Meal- and Web-Based Interactive Food Frequency Questionnaires: Validation of Energy and Macronutrient Intake

Background Meal-Q and its shorter version, MiniMeal-Q, are 2 new Web-based food frequency questionnaires. Their meal-based and interactive format was designed to promote ease of use and to minimize answering time, desirable improvements in large epidemiological studies. Objective We evaluated the validity of energy and macronutrient intake assessed with Meal-Q and MiniMeal-Q as well as the reproducibility of Meal-Q. Methods Healthy volunteers aged 20-63 years recruited from Stockholm County filled out the 174-item Meal-Q. The questionnaire was compared to 7-day weighed food records (WFR; n=163), for energy and macronutrient intake, and to doubly labeled water (DLW; n=39), for total energy expenditure. In addition, the 126-item MiniMeal-Q was evaluated in a simulated validation using truncated Meal-Q data. We also assessed the answering time and ease of use of both questionnaires. Results Bland-Altman plots showed a varying bias within the intake range for all validity comparisons. Cross-classification of quartiles placed 70%-86% in the same/adjacent quartile with WFR and 77% with DLW. Deattenuated and energy-adjusted Pearson correlation coefficients with the WFR ranged from r=0.33-0.74 for macronutrients and was r=0.18 for energy. Correlations with DLW were r=0.42 for Meal-Q and r=0.38 for MiniMeal-Q. Intraclass correlations for Meal-Q ranged from r=0.57-0.90. Median answering time was 17 minutes for Meal-Q and 7 minutes for MiniMeal-Q, and participants rated both questionnaires as easy to use. Conclusions Meal-Q and MiniMeal-Q are easy to use and have short answering times. The ranking agreement is good for most of the nutrients for both questionnaires and Meal-Q shows fair reproducibility.
Exploitation of an iron transporter for bacterial protein antibiotic import

Significance The outer membrane (OM) excludes antibiotics such as vancomycin that kill gram-positive bacteria, and so is a major contributor to multidrug resistance in gram-negative bacteria. Yet, the OM is readily bypassed by protein bacteriocins, which are toxins released by bacteria to kill their neighbors during competition for resources. Discovered over 60 y ago, it has been a mystery how these proteins cross the OM to deliver their toxic payload. We have discovered how the bacteriocin pyocin S2 (pyoS2), which degrades DNA, enters Pseudomonas aeruginosa cells. PyoS2 tricks the iron transporter FpvAI into transporting it across the OM by a process that is remarkably similar to that used by its endogenous ligand, the siderophore ferripyoverdine. Unlike their descendants, mitochondria and plastids, bacteria do not have dedicated protein import systems. However, paradoxically, import of protein bacteriocins, the mechanisms of which are poorly understood, underpins competition among pathogenic and commensal bacteria alike. Here, using X-ray crystallography, isothermal titration calorimetry, confocal fluorescence microscopy, and in vivo photoactivatable cross-linking of stalled translocation intermediates, we demonstrate how the iron transporter FpvAI in the opportunistic pathogen Pseudomonas aeruginosa is hijacked to translocate the bacteriocin pyocin S2 (pyoS2) across the outer membrane (OM). FpvAI is a TonB-dependent transporter (TBDT) that actively imports the small siderophore ferripyoverdine (Fe-Pvd) by coupling to the proton motive force (PMF) via the inner membrane (IM) protein TonB1. The crystal structure of the N-terminal domain of pyoS2 (pyoS2NTD) bound to FpvAI (Kd = 240 pM) reveals that the pyocin mimics Fe-Pvd, inducing the same conformational changes in the receptor. Mimicry leads to fluorescently labeled pyoS2NTD being imported into FpvAI-expressing P. aeruginosa cells by a process analogous to that used by bona fide TBDT ligands. PyoS2NTD induces unfolding by TonB1 of a force-labile portion of the plug domain that normally occludes the central channel of FpvAI. The pyocin is then dragged through this narrow channel following delivery of its own TonB1-binding epitope to the periplasm. Hence, energized nutrient transporters in bacteria also serve as rudimentary protein import systems, which, in the case of FpvAI, results in a protein antibiotic 60-fold bigger than the transporter’s natural substrate being translocated across the OM.
The evolution of the French collaborative network of innovation: towards clustering?

Since the beginning of 2005, the French government supports collaborative innovative projects involving actors of public and private research through the competitiveness cluster policy (poles de competitivite). By these projects we aim to offer an original approach of the impact of the cluster policy on the organization and the intensity of innovation network (on the overall French territory). Concretely, the present paper analyses the evolution (from 2005 to 2010) of the French collaborative network of innovation, by scanning collaborative projects funded by the FUI. Our main research interest lies in testing whether the network progressively gets connected, concentrated, clustered around some (specific? ) competitiveness clusters or if, on the contrary, it extends on the French territory, actors building collaborations with intra but also extracompetitiveness clusters? members and becoming more loosely-coupled to one another. We are also interested in analyzing the existence/creation/disappearance of innovative cohesive groups within the overall network. We privilege a social network analysis for our empirical study. It enables us to calculate and follow the evolution of indicators depicting at the same time the structure and spread of the network, and the respective positions of nodes within the network. An its allow us to characterize the impact (if any) of the competitiveness cluster policy on the organization and the intensity of innovation on the French territory.
Quality Assessment for Fingerprints Collected by Smartphone Cameras

We propose an approach to assess the quality of fingerprint samples captured by smartphone cameras under real-life scenarios. Our approach extracts a set of quality features for image blocks. Without needing segmentation, the approach determines a sample's quality by checking all image blocks divided from the sample and for each block a trained support vector machine gives a binary indication - "high-quality" or "non-high-quality" (including the low quality case and the background block case). A quality score is then generated for the whole sample. Experiments show this approach performs well in identifying the high quality blocks - the Spearman correlation coefficient between the proposed quality scores and samples' normalized comparison scores (ground truth) reaches 0.53 while the rate of false detection (background blocks judged as high-quality ones) is still low as 4.63 percent over a challenging dataset collected under various real-life scenarios.
Services and the Web of Data: An Unexploited Symbiosis

The Web of Data is certainly a great success for data publication but the state of the art of the applications processing linked data is however not that outstanding. In this paper we highlight an unexploited symbiosis between Semantic Web Services and the Web of Data that could give birth to new families of highly advanced Web applications.
Best practices in new product development : the Zyray wireless case study

Successful high-tech start-up companies are rare. This case study investigates the New Product Development (NPD) process of Zyray Wireless, a very successful startup 3G technology company that originated in South Africa but relocated to California in the USA. The research looked into the differences between generally accepted NPD best practices and those implemented by this start-up company. Zyray Wireless scored above the industry average in the following categories: customer involvement, project selection, product strategy, technological leadership, and product goal. The best practices for metrics, human resource development, documentation, and change control implemented by Zyray Wireless scored at or below the industry average. The best practice results showed that this very successful start-up company focused more on strategy and engineering and less on process control than average. OPSOMMING Suksesvolle nuwe hoe-tegnologie maatskappye is skaars. Hierdie gevallestudie het die Nuwe Produk Ontwikkelingproses (NPO) ondersoek van Zyray Wireless, ŉ baie suksesvolle nuwe maatskappy wat in Suid-Afrika ontstaan het maar na Kalifornie in die VSA verskuif is. Die navorsing het na die verskille gekyk tussen algemeen aanvaarde NPO beste praktyke en die wat deur hierdie maatskappy geimplementeer is. Zyray Wireless het bo die industriegemiddelde gepresteer in die volgende kategoriee: klientbetrokkenheid, projekkeuse, produkstrategie, tegnologiese leierskap, en produkdoelwitte. Die beste praktyke vir maatstawwe, menslike hulpbronontwikkeling, dokumentasie, en veranderingsbeheer wat deur Zyray Wireless geimplementeer is, het onder die industriegemiddeldes gepresteer. Die beste praktykresultate het getoon dat hierdie baie suksesvolle nuwe maatskappy meer gefokus het op strategie en ingenieurswese en minder op prosesbeheer as die gemiddelde.
Optimal placement of passive sensors for robot localisation

We consider the problem of self-localisation for a mobile robot in an environment with a requested level of accuracy. The robot moves in a known environment following typical trajectories, which can be characterised in statistical terms. One of the main drivers of this paper is its application to assistive robots guiding senior or impaired users in shopping centres or in other public spaces. To localise itself the robot uses onboard sensors such as encoders and inertial platforms. The level of noise in these sensors and the lack of absolute measurements determines a steady growth of the uncertainty on its position. To alleviate the problem, we assume the presence of a number of visual markers deployed in the environment. Whenever the robot comes across one of these sensors, the uncertainty on its position is reset. In the paper, we show a methodology to minimise the number of these sensors and to select their position so that the uncertainty is never worse than a given target threshold with an assigned probability.
The supersymmetric Camassa–Holm equation and geodesic flow on the superconformal group

We study a family of fermionic extensions of the Camassa–Holm equation. Within this family we identify three interesting classes: (a) equations, which are inherently Hamiltonian, describing geodesic flow with respect to an H1 metric on the group of superconformal transformations in two dimensions, (b) equations which are Hamiltonian with respect to a different Hamiltonian structure and (c) supersymmetric equations. Classes (a) and (b) have no intersection, but the intersection of classes (a) and (c) gives a system with interesting integrability properties. We demonstrate the Painleve property for some simple but nontrivial reductions of this system, and also discuss peakon-type solutions.
Designing, developing and verifying interactive components iteratively with djnn

Introducing iterative user interface design methods into the development processes of safety-critical software creates technical and methodological challenges. This article describes a new programming paradigm aimed at addressing some of these challenges: interaction-oriented programming. In this paradigm any piece of software consists of a hierarchical collection of components that can interact among themselves and with their environment, and its execution consists in propagating activation through interactions between components. We first describe the principles of interaction-oriented programming, and illustrate them by describing the basic components provided by the djnn programming framework to create interactive software. We then show how interactive programming provides a basis for formulating and checking properties that capture requirements on interactive components. The rest of the article is dedicated to example design and development scenarios that illustrate how development environments could leverage interactive programming in the future so as to jointly address the requirements of modern user interface design and safety-critical software development .
A Multi-Tag Emulator for the UHF RFID System

Radio-frequency identification technology has been booming over the past few years, and the corresponding product varieties and standards are becoming more and more widely available. It is important to test the products and standards before putting them on the market, but it is inconvenient to simulate the real environment to test the efficiency of a reader, because different tag distributions in varying applications will lead to different electromagnetic field intensity distributions. In this paper, based on the analysis of the responses of multiple tags and quantification of the response times, a multitag emulator is proposed that is capable of emulating the responses of multiple passive ISO/IEC 18000-6C tags. A verification system is set up, and the measurement results show that, based on the pipeline structure at the frequency of 40 MHz, the system can emulate 50 tags with a link data rate of 40 kb/s. This multitag emulator can be applied not only to verify the inventory and anti-collision algorithm but also to debug a reader. Compared to the conventional reading efficiency test method, the proposed method is capable of achieving the same goal and saving time and resources.
A stress integration algorithm for phase transforming steels

A new stress integration algorithm for the constitutive models of materials that undergo strain-induced phase transformation is presented. The most common materials that fall into this category are metastable austenitic stainless (TRIP) steels. These materials can be classi¯ed as metal-matrix composites which comprise a soft and a hard metallic phase. A homogenization algorithm is presented that can estimate the evolution of state variables in each phase for a given strain increment. The elastic-plastic behavior of the phases are calculated individually using large deformation theory and the calculated algorithmic tangent moduli are used in different homogenization schemes. Furthermore, the phase transformation process in austenitic stainless steels involves a volumetric expansion and an inelastic shape change collinear with the deviatoric stress. This transformation plasticity is approximated by a phenomenological model and incorporated in the stress update algorithm.
The curriculum in the Palestinian Territories: drama processes in theatre making and self-liberation

ABSTRACT The Israeli occupation and its strategies employed for controlling the Palestinian Territories have reflected negatively on all aspects of Palestinians’ lives. The occupation has also created a closed environment where people have little room to act and react freely. This article highlights the importance of drama and theatre making for Palestinians who are still facing all sorts of challenges in their daily life. In addition, it offers a clear picture of the educational sector in the Palestinian Territories, particularly the Palestinian curriculum and the position of drama and theatre making in curriculum design and development. Finally, based on research studies and personal experiences, the article sheds light on the effective role of drama and theatre making on Palestinian learners from different levels.
The Effect of Propofol Concentration on Dispersion of Myocardial Repolarization in Children

BACKGROUND:QT interval prolongation on the electrocardiogram (ECG) may be drug-induced and is traditionally associated with torsades des pointes. A better predictor of torsades des pointes is the time interval between the peak and the end of the T-wave (Tp-e). Older studies of propofol’s effect on the corrected interval (QTc) are conflicting and confounded by polypharmacy. It was recently shown that target-controlled infusion of propofol at 3 &mgr;g/mL has no effect on QTc or Tp-e. This plasma concentration of propofol is at the extreme lower end of the range for surgical anesthesia. In this randomized, double-blind, clinical study, we investigated the dose–response relationship between propofol, QTc, and Tp-e in a range of doses clinically relevant for surgical anesthesia. METHODS:Sixty healthy unpremedicated children, aged 3–10 yr, were recruited. Subjects were randomized to receive target-controlled infusions of propofol, to achieve 1 of 3 plasma concentrations: 3, 4.5, and 6 &mgr;g/mL. A preoperative 12 lead ECG was performed and repeated 5 min after induction. Two investigators, blinded to group allocation and to the timing of the ECG traces, independently measured QTc and Tp-e within and between each group. Paired t-tests were used to compare QTc and Tp-e within groups. One-way analysis of variance was used for intergroup analysis. The primary outcome measure was a change of >25 ms in Tp-e both within and between groups. RESULTS:ECG recordings were obtained in 51 children. There were no demographic or ECG differences at baseline, at which time QTc and Tp-e values were within normal limits. There were no differences in QTc or Tp-e after induction within or between the three different groups. DISCUSSION:Propofol has no effect on myocardial repolarization in healthy children at clinically relevant doses. This suggests that propofol would be a rational choice for children with a preexisting repolarization abnormality.