Miracle-dz/UniFAR-FTUs huggingface dataset:
Potential long non-coding RNAs to be considered as biomarkers or therapeutic targets in gastric cancer

Long non-coding RNAs are attracting the attention of researchers in many fields. These RNAs are longer than 200 nucleotides and do not encode any protein. A subset of them is reported to be strongly correlated with poor patient prognosis, suggesting a potential role in cancer progression (Esteller, 2011). Gastric cancer is one of the most common malignant tumors worldwide. Therefore, there is an urgent need to find genes which are helpful in the diagnosis, prognosis, and understanding of the molecular pathways of this cancer (Hajjari et al., 2013a). Finding novel molecular biomarkers of malignancy has been always important for clinical management. Like proteins, mRNAs, and miRNAs, lncRNAs show potentials as novel biomarkers and therapeutic targets in different cancer types (Zhang et al., 2013). However, there are a few reports on studying the relationship between gastric cancer progression and lncRNAs. Some useful clues for further researches seem necessary for deciphering the potential role of lncRNAs in gastric cancer. In this report, we present and highlight some evidences about the potential role of lncRNAs in gastric cancer based on the data indicated in Microarray databases. The results may give novel perspectives for further researches on the role of lncRNAs in gastric carcinogenesis. We used different databases including Oncomine, Gene Expression Atlas, Gene Expression Omnibus (GEO), and Array Express Databases to analyze the expression level of most recent cited and noted lncRNAs in studies on cancer progression (Niland et al., 2012; Zhang et al., 2013). The selected lncRNAs have been regarded as the most potential biomarkers in the studies on different cancer types (Zhang et al., 2013). The RNAs include H19, MALAT-1, HOTAIR, ANRIL, CRNDE, and MEG3. Some descriptions of these lncRNAs are presented below. Oncomine cancer microarray database was used to mine the lncRNA expression profile data according to the established methodology (Rhodes et al., 2007). Four publicly available datasets [Chen Gastric (Chen et al., 2003), DErrico Gastric (D'Errico et al., 2009), Wang Gastric (Wang et al., 2012), and Cho Gastric (Cho et al., 2011)] were inquired for our analysis. By using Oncomine and other microarray expression data accessible from GEO, Gene expression Atlas, and Array Express database, we found some significant differences of expression level for the lncRNAs. The datasets and clinopathological data of each study are presented in Table ​Table11. Table 1 Different datasets and their clinicopathological data used in the current study. Student's t-test was used for the differential expression analyses. Those which have significant differences (Fold change > 1.5, P-value < 0.01) between gastric cancer and normal tissues are brought in Table ​Table22. Table 2 Significant difference (Fold change > 1.5, P-value < 0.01) of the expression level of lncRNAs between gastric cancer types and normal tissues.
Recognizing Unusual Behaviour for Intelligent Space

In these days when we go to public places like banks or post-offices, we always have to reckon with the risk of armed robbery, or terrorist attack. These places are protected by special security crew, but the increasing demand on improved security requires redundant and failsafe methods which eliminates the human factor. In this paper an Intelligent Space based project is introduced which can detect unusual human behaviour in the monitored environment using computer vision.
A Single Valine Residue Plays an Essential Role in Peripherin/rds Targeting to Photoreceptor Outer Segments

Peripherin/retinal degeneration slow (rds) is an integral membrane protein specifically localized to the light-sensing organelle of the photoreceptor cell, the outer segment. Within the outer segment, peripherin is found at the edges of photoreceptor discs, where it plays a critical role in disc morphogenesis and maintenance. Peripherin loss or mutations are often associated with severe forms of visual impairments. Like all other resident outer segment proteins, peripherin is synthesized in the photoreceptor cell body and subsequently transported to the outer segment. In an effort to further examine peripherin’s delivery to outer segments, we undertook a careful examination of its targeting sequence. Using a fluorescently labeled reporter expressed in the rods of transgenic tadpoles, we narrowed peripherin’s targeting sequence to ten amino acids within its C-terminal tail. This small stretch of amino acid residues is both necessary and sufficient for outer segment targeting. We also conducted alanine scanning of all residues within this sequence and found that only a single residue, valine at position 332, is essential for outer segment targeting. This valine is conserved in all species and its mutation is sufficient to completely abrogate the targeting of full-length peripherin in mouse rods.
Spectral Separation Coefficients for digital GNSS receivers

The extreme weakness of a GNSS (Global Navigation Satellite System) signal makes it vulnerable to almost every kind of interferences, that can be radically different in terms of time and frequency characteristics. For this reason the development of a consistent theory allowing comparative analysis was needed and the concepts of effective C/N0 and SSCs (Spectral Separation Coefficients) were introduced as reliable measures of the interfering degradations. However these parameters were defined only in the analog domain, not considering specific features due to digital synthesis. In this article an alternative derivation for the analog case and the extension to digital devices are provided. The analysis is particularly focused on the acquisition block, the first element of a GNSS receiver that provides a roughly estimated code delay and Doppler shift. The innovative approach presented in the paper is based on the fact that effective C/N0 and SCCs are interpreted in terms of ROCs (Receiver Operative Characteristics) showing how the system performance strictly depends on these parameters.
Mediation and Arbitration of Employment Disputes

Preface: Toward a Fair, Affordable, and Expeditions Procedure for Employment Conflict Resolution. The Authors. The Rise of Labor--Management Dispute Resolution. Labor--Management Arbitration as the Framework for Employment Law Dispute Resolution. The Emergence of Alternative Dispute Resolution. The Current State of Employment Law Arbitration. Employment Law Dispute Settlement Programs Developed by Private Business. Elements of Due Process Protection. Alternative Dispute Resolution in Government Agencies. A Case Study in System Design: The Massachusetts Comminsion Against Discrimination. The Future of Employment Law Dispute Resolution. Appendix A: List of Acronyms. Appendix B: The Protocol: Due Process Protocol for Mediation and Abitration of Statutory Disputes Arising Out of the Employment Relationship. Appendix C: Massachusetts Commision Against Discrimination Policy 96--1: Policy on Alternative Dispute Resolution. Notes. Index.
Programming language challenges in systems codes: why systems programmers still use C, and what to do about it

There have been major advances in programming languages over the last 20 years. Given this, it seems appropriate to ask why systems programmers continue to largely ignore these languages. What are the deficiencies in the eyes of the systems programmers? How have the efforts of the programming language community been misdirected (from their perspective)? What can/should the PL community do address this? As someone whose research straddles these areas, I was asked to give a talk at this year's PLOS workshop. What follows are my thoughts on this subject, which may or not represent those of other systems programmers.
Does size matter? Authorship attribution, small samples, big problem

The aim of this study is to find such a minimal size of text samples for authorship attribution that would provide stable results independent of random noise. A few controlled tests for different sample lengths, languages, and genres are discussed and compared. Depending on the corpus used, the minimal sample length varied from 2,500 words (Latin prose) to 5,000 or so words (in most cases, including English, German, Polish, and Hungarian novels). Another observation is connected with the method of sampling: contrary to common sense, randomly excerpted ‘bags of words’ turned out to be much more effective than the classical solution, i.e. using original sequences of words (‘passages’) of desired size. Although the tests have been performed using the Delta method ( Burrows, J.F . (2002). ‘Delta’: a measure of stylistic difference and a guide to likely authorship. Literary and Linguistic Computing , 17 (3): 267–87) applied to the most frequent words, some additional experiments have been conducted for support vector machines and k -NN applied to most frequent words, character 3-grams, character 4-grams, and parts-of-speech-tag 3-grams. Despite significant differences in overall attributive success rate between particular methods and/or style markers, the minimal amount of textual data needed for reliable authorship attribution turned out to be method-independent.
Modelling the relationships between emotional responses to, and musical content of, music therapy improvisations

This article reports a study in which listeners were asked to provide continuous ratings of perceived emotional content of clinical music therapy improvisations. Participants were presented with 20 short excerpts of music therapy improvisations, and had to rate perceived activity, pleasantness and strength using a computer-based slider interface. A total of nine musical features relating to various aspects of the music (timing, register, dynamics, tonality, pulse clarity and sensory dissonance) were extracted from the excerpts, and relationships between these features and participants' emotion ratings were investigated. The data were analysed in three stages. First, inter-dimension correlations revealed that ratings of activity and pleasantness were moderately negatively correlated, activity and strength were strongly positively correlated, and strength and pleasantness were moderately negatively correlated. Second, a series of cross-correlation analyses revealed that the temporal lag between musical features and listeners' dimension ratings differed across both variables and dimensions. Finally, a series of linear regression analyses produced significant feature prediction models for each of the three dimensions, accounting for 80 percent (activity), 57 percent (pleasantness ) and 84 percent (strength) of the variance in participants' ratings. Activity was best predicted by high note density and high pulse clarity, pleasantness by low note density and high tonal clarity, and strength by high mean velocity and low note density. The results are discussed in terms of their fit with other work reported in the music psychology literature, and their relevance to clinical music therapy research and practice.
Cell Models to Study Regulation of Cell Transformation in Pathologies of Retinal Pigment Epithelium

The retinal pigment epithelium (RPE) plays a key role in the development of many eye diseases leading to visual impairment and even blindness. Cell culture models of pathological changes in the RPE make it possible to study factors responsible for these changes and signaling pathways coordinating cellular and molecular mechanisms of cell interactions under pathological conditions. Moreover, they give an opportunity to reveal target cells and develop effective specific treatment for degenerative and dystrophic diseases of the retina. In this review, data are presented on RPE cell sources for culture models, approaches to RPE cell culturing, phenotypic changes of RPE cells in vitro, the role of signal pathways, and possibilities for their regulation in pathological processes.
A Demand System Analysis of Organic and Conventional Fresh Milk in Germany Segmented by Consumer Groups

* The article was written in the framework of a research project which is funded by the German Federal Ministry of Education and Research (BMAS). The project funding reference number is 2808OE148. The author takes full responsibility for the contents of this paper. Special thanks go to the staff members of the Department of Agricultural and Food Marketing at the University of Kassel under the direction of Prof. Dr. Ulrich Hamm. They prepared the data for this research project and provided them to the Institute of Agricultural Policies and Market Research at the University of Giessen for further research.
Novel Representation of Multidimensional Datasets: The Framework n D-EVM/Kohonen

- In this paper we are going to describe the steps that conform a novel approach for representation of multidimensional datasets through the proposed Framework n D-EVM/Kohonen. In this sense two phases are going to be taken in account: 1) the application of 1-Dimensional Kohonen Self-Organizing Maps (1D-KSOMs) in order to achieve ( n -1)D hypervoxelizations' segmentations, n ≥ 2, taking in account their geometrical and topological properties to characterize the information contained in the datasets. 2) The segmented multidimensional datasets are specified as Orthogonal Polytopes whose n -th Dimension is associated to a 1D-KSOM classification. Subsequently, the n D representation is concisely expressed via the Extreme Vertices Model in the n -Dimensional Space ( n D-EVM). There is presented a comparative analysis based on the use of False Color Maps in order to understand they way our considered 1D-KSOMs distribute appropriately their weights vectors along the classification space, even better than classifications based exclusively on color intensity. Additionally, we present some arguments to sustain that a 1D-KSOM is an adequate option in terms of temporal complexity and, on the other hand, that our representation is concise in terms of spatial complexity because of the n D-EVM properties.
Alk3/Alk3b and Smad5 Mediate BMP Signaling during Lymphatic Development in Zebrafish

Lymphatic vessels are essential to regulate interstitial fluid homeostasis and diverse immune responses. A number of crucial factors, such as VEGFC, SOX18, PROX1, FOX2C, and GJC2, have been implicated in differentiation and/or maintenance of lymphatic endothelial cells (LECs). In humans, dysregulation of these genes is known to cause lymphedema, a debilitating condition which adversely impacts the quality of life of affected individuals. However, there are no currently available pharmacological treatments for lymphedema, necessitating identification of additional factors modulating lymphatic development and function which can be targeted for therapy. In this report, we investigate the function of genes associated with Bone Morphogenetic Protein (BMP) signaling in lymphatic development using zebrafish embryos. The knock-down of BMP type II receptors, Bmpr2a and Bmpr2b, and type I receptors, Alk3 and Alk3b, as well as SMAD5, an essential cellular mediator of BMP signaling, led to distinct lymphatic defects in developing zebrafish. Therefore, it appears that each constituent of the BMP signaling pathway may have a unique function during lymphatic development. Taken together, our data demonstrate that BMP signaling is essential for normal lymphatic vessel development in zebrafish.
Experiments with SMS Translation and Stochastic Gradient Descent in Spanish Text Author Profiling Notebook for PAN at CLEF 2013

Inspired by our ongoing work in the project WENDY, which addresses age detection in social networks by linguistic processing (among other methods), we have built a system that makes use of a number of linguistic resources (a Spanish dictionary, and a SMS-language dictionary) and algorithms (custom text utterances tokenization, SMS to standard Spanish translation, and a number of normalization rules) in order to apply a learning-based approach using a custom Stochastic Gradient Descent algorithm adapted to text, to the Spanish Author Profiling task at PAN’2013. We believe the results obtained in internal testing on a validation set extracted from training dataset do validate our approach in WENDY, while the results obtained in the PAN task are not as good as expected.
A New Image Segmentation Method Based on Grey Graph Cut

To improve the performance of image segmentation, the paper suggests a new image segmentation method based on grey graph cut, which integrates grey theory and graph cut theory. In the method, the image is taken as a weighted undirected graph first. And then, after the relationships of grey-levels and positions in local regions are discussed via grey relational analysis, a grey weight matrix is established, based on which a grey partition function is constructed. Next, the image is binarized with the gray-level that corresponds to the minimum value of the grey partition function. Experimental results on visible light image and SAR image indicate that the proposed method, being superior to some existing methods like Otsu and Normalized Cut etc., not only can segment the images with obvious difference between targets and backgrounds, but also suppress image noise effectively.
Local and Central Wage Bargaining

The literature on wage bargaining usually considers either central or local wage bargaining; an exception is Holmlund (1986). Throughout most of the unionized part of the private sector in Norway, wage bargaining takes place on two levels, first centrally and then locally. In the economic policy debate, it has been argued that this system leads to higher wages and lower employment than bargaining on only one level, regardless of whether it is central or local; see e.g. Skatnland (1983). In this paper, I present a model with wage bargaining on two levels and show that, in this system, the above argument is proved false. We focus on an industry with n identical firms which produce one homogeneous product. For simplicity, the output price and input prices other than wages are considered given. On the central level, there is a utility-maximizing labor union with a quasi-concave utility function increasing in the arguments employment (L) and total wage ( VV). There is a local labor union in each firm. We analyze the system during one period, say a year. Wage setting in this period consists of three stages. In the first stage the central labor union sets the tariff wage q unilaterally. This follows the monopoly model of e.g. Dunlop (1944) and Oswald (1985). In the second stage the firms determine the employment L which prevails until the next period. In the third and final stage the local union negotiates with the management of the firm about local wage drift. The total wage is W= q + wage drift. The assumption that the firms determine employment prior to wage bargaining is used by e.g. Moene (1987) and Horn & Wolinsky (1985). Both the central labor union and the firms know how local wage bargaining functions and can therefore perfectly anticipate what the result-
Computational Modelling of Membrane Biosensors Acting in Stirred and Non-stirred Solutions

This paper presents mathematical models of potentiometric as well as amperometric biosensors, based on an electrode covered with an enzyme membrane. The models involve three regions: the enzyme layer where enzyme reaction as well as mass transport by diffusion takes place, a diffusion limiting region where only the diffusion takes place, and a convective region, where the analyte concentration is maintained constant. Using computer simulation the influence of the thickness of both the enzyme and the diffusion layers on the biosensor response was investigated. The effect of the diffusion layer on the biosensor response was evaluated for different conditions of the enzymatic reaction and types of mixers. This paper deals also with the conditions when the mass transport in the exterior diffusion region may be neglected to simulate the biosensor response assuming the buffer solution is well-stirred and in powerful motion. The digital simulation was carried out using the finite difference technique.
MTBF Bounds for Multistage Synchronizers

Synchronizers are used to mitigate the effects of metastability in multiple clock domain System-on-Chip devices. In order to enable reliable synchronization, the synchronizer MTBF (Mean Time Between Failures) should be much longer than the product lifetime. To achieve such high margins, multistage synchronizers are used. Several simulation methods have been developed to determine their probability of failure and the number of stages to use. While simulation methods have improved in recent years, accurate analytical models for failure calculations are scant. Some previously published models do not reflect estimations of MTBF but only loose lower bounds that give rise to a high number of synchronizer stages reducing the overall system performance. Others provide improved accuracy but are difficult to operate and simulation for each stage is required. In this paper, we review published analytical models for MTBF calculations of multistage synchronizers. We show that existing models often underestimate MTBF, and in some cases they even overestimate it. A new model that calculates a MTBF lower bound with significantly smaller margins is introduced. These estimates are shown to be consistent with state of the art simulations and measurements. A method for calculating these estimates for a variety of applications is presented based on a limited number of intrinsic synchronizer parameters determined by simulation.
A New Concept in Ubiquitous Network Management: Guest Node Monitoring--Applications of the MobileIPv6-MIB--

To keep pace with the recent growth of mobile and ubiquitous networking environment, new technologies in network management need to be explored. MobileIPv6-MIB has been proposed at the IETF as a core technology for effective management of mobile and ubiquitous networks based on MobileIPv6 technology. In this paper we explain the functionalities of MobileIPv6-MIB, and discuss a new concept in ubiquitous network management viz. "guest node monitoring" that significantly expands the scope and reach of network management. We focus on the problem of monitoring guest nodes attached to a management domain. It is difficult for the local network manager to monitor such nodes directly. We propose a novel model for guest node monitoring based on MobileIPv6-MIB. We have implemented the prototype system of our model, and conducted experiments on how the system works
Epidemiology of Inflammatory Bowel Diseases in Iran and Asia; A Mini Review

The prevalence of inflammatory bowel diseases (IBDs) is set to stabilize in Western Europe and North America, as opposed to its increasing trend in developing countries in Asia. The epidemiology of IBDs in areas where the incidence and prevalence are relatively low provides an opportunity for researchers to determine the unknown aspects of them. In this review article, the PubMed and MEDLINE databases were searched from 1970 to 2012 and the epidemiological aspects assessed in Iranian articles were compared with identical subjects in other Asian countries. During this period, there were 21 documented articles on IBD epidemiology in Iran and 52 in Asia. According to the present review, CTLA-gene polymorphism and male/female ratio in ulcerative colitis (UC), incidence of extra-intestinal manifestations, extent of intestinal involvement, and family history in both UC and Crohn’s disease (CD) seemed to be different between Asia and Iran. In contrast, the incidence of primary sclerosing cholangitis in IBD patients and association between NO2/CARD15 mutation and CD as C3435-T allele and UC were nearly the same. The rate of IBD has increased significantly in Iran, as has that of other Asian countries during the last decade. A thorough, well-designed, population-based, multi-regional epidemiologic study seems mandatory due to the substantial demographic and characteristic variability in IBD patients in our region.