Miracle-dz/UniFAR-FTUs huggingface dataset:
Probabilistic relational modelling of mammographic images

Computer-aided detection (CAD) is used in medical science as a means of supporting a doctor's observations and interpretations. While X-ray imaging techniques, such as mammography, yield a great deal of information, it is not always easy to evaluate detected mammographic regions as being suspicious for cancer, which results in a number of cancers to be misinterpreted or missed in an image. In this sense, CAD systems have as aim the increase of detection rates when analysing mammograms, by identifying features that are characteristic for breast cancer. In this research we aim at using the features extracted from mammographic images in order to analyse the development of suspicious lesions. Differently from other breast cancer models, the data modelling exploits object orientation. This allows not only for a natural description of domain entities and their intrinsic relations, but also the application of relational learning techniques, which handles our heterogeneous data instances both in terms of learning and inference.
The prognostic value of survivin expression in patients with colorectal carcinoma: a meta-analysis.

OBJECTIVE The prognostic role of survivin in colorectal carcinoma remains controversial. This meta-analysis aimed to explore the association between survivin expression and survival outcomes in patients with colorectal carcinoma. METHODS A comprehensive literature search for relevant studies published up to April 2013 was performed using PubMed, MEDLINE and ISI Web of Science. Only articles in which survivin was detected by immunohistochemical staining were included. This meta-analysis was done using STATA and Review Manager. RESULTS A total of 1784 patients from 14 studies were included in the analysis. Our results showed that survivin overexpression in patients with colorectal carcinoma was significantly associated with poor overall survival (hazard ratio, 1.505; 95% confidence interval, 1.197-1.893; P = 0.000) and disease-free survival (hazard ratio, 2.323; 95% confidence interval, 1.687-3.199; P = 0.000). The results indicated that a significant relationship between survivin expression and overall survival was also exhibited in studies with an Asian country (hazard ratio, 1.684; 95% confidence interval, 1.477-1.921), patient number >100 (hazard ratio, 1.604; 95% confidence interval, 1.371-1.877), the cut-off level <50% (hazard ratio, 1.449; 95% confidence interval, 1.045-2.010), the percentage of survivin overexpression >50% (hazard ratio, 1.528; 95% confidence interval, 1.056-2.211) and the hazard ratio estimated (hazard ratio, 1.643; 95% confidence interval, 1.262-2.139). Moreover, upregulation of survivin was associated with stages (III/IV vs. I/II: odds ratio, 1.08; 95% confidence interval, 0.80-1.46), the depth of invasion (T3/T4 vs. T1/T2: odds ratio, 1.79; 95% confidence interval 0.67-4.74), lymph node metastasis (positive vs. negative: odds ratio, 1.49; 95% confidence interval, 0.99-2.26), distant metastasis (positive vs. negative: odds ratio, 2.37; 95% confidence interval, 0.99-5.72) and grade of differentiation (well/moderate vs. poor: odds ratio, 1.02; 95% confidence interval, 0.43-2.41), but without significance. CONCLUSION The present meta-analysis indicated that upregulation of survivin was associated with poor prognosis in patients with colorectal carcinoma.
A Comparison of Techniques to Automatically Identify Complex Words.

Identifying complex words (CWs) is an important, yet often overlooked, task within lexical simplification (The process of automatically replacing CWs with simpler alternatives). If too many words are identified then substitutions may be made erroneously, leading to a loss of meaning. If too few words are identified then those which impede a user’s understanding may be missed, resulting in a complex final text. This paper addresses the task of evaluating different methods for CW identification. A corpus of sentences with annotated CWs is mined from Simple Wikipedia edit histories, which is then used as the basis for several experiments. Firstly, the corpus design is explained and the results of the validation experiments using human judges are reported. Experiments are carried out into the CW identification techniques of: simplifying everything, frequency thresholding and training a support vector machine. These are based upon previous approaches to the task and show that thresholding does not perform significantly differently to the more naive technique of simplifying everything. The support vector machine achieves a slight increase in precision over the other two methods, but at the cost of a dramatic trade off in recall.
VISUALIZING SOCIAL GROUPS

Although they might not agree with the precise terms of Moreno’s statement, most contemporary structural analysts would still subscribe to the view that visual images continue to play a key role in both exploring and presenting the patterns displayed by structural data. Among the many kinds of structural patterns that have been explored and presented visually, one stands out. Structural analysts have devoted an enormous amount of attention to the problem of uncovering social groups. This attention to the group concept makes sense, since groups have been a concern of sociologists from the beginning (see Durkheim [4], Tönnies [27], Simmel, [25] and Cooley [3]). All of these early sociologists saw groups in structural terms—as a patterning of interaction. Freeman and Webster [10] described this view:
ASH1 mRNP-core factors form stable complexes in absence of cargo RNA at physiological conditions

Asymmetric ASH1 mRNA transport during mitosis of budding yeast constitutes one of the best-studied examples of mRNA localization. Recently, 2 studies used in vitro motility assays to prove that motile ASH1 mRNA-transport complexes can be reconstituted entirely from recombinant factors. Both studies, however, differed in their conclusions on whether cargo RNA itself is required for particle assembly and thus activation of directional transport. Here we provide direct evidence that stable complexes do assemble in absence of RNA at physiologic conditions and even at ionic strengths above cellular levels. These results directly confirm the previous notion that the ASH1 transport machinery is not activated by the cargo RNA itself, but rather through protein-protein interactions.
Advances in Predictive Model Generation for Data Mining

Predictive models have been widely used long before the development of the new eld that we call data mining. Expanding application demand for data mining of ever increasing data warehouses, and the need for understandability of predictive models with increased accuracy of prediction, all have fueled recent advances in automated predictive methods. We rst examine a few successful application areas and technical challenges they present. We discuss some theoretical developments in PAC learning and statistical learning theory leading to the emergence of support vector machines. We then examine some technical advances made in enhancing the performance of the models both in accuracy (boosting, bagging, stacking) and scalability of modeling through distributed model generation. Relatively new techniques for selecting good feature variables, feature discretization, generating probabilistic models, and the use of practical measures for performance will also be discussed.
LZTS2 and PTEN collaboratively regulate ß-catenin in prostatic tumorigenesis

The leucine zipper tumor suppressor 2 (LZTS2) was identified as a tumor susceptibility gene within the 10q24.3 chromosomal region, and is approximately 15Mb from the PTEN locus. This region containing the both loci is frequently deleted in a variety of human malignancies, including prostate cancer. LZTS2 is a ß-catenin-binding protein and a negative regulator of Wnt signaling. Overexpression of PTEN in prostate cancer cell lines reduces ß-catenin-mediated transcriptional activity. In this study, we examined the collaborative effect of PTEN and LZTS2 using multiple in vitro and in vivo approaches. Co-expression of PTEN and LZTS2 in prostate cancer cells shows stronger repressive effect on ß-catenin mediated transcription. Using a newly generated mouse model, we further assessed the effect of simultaneous deletion of Pten and Lzts2 in the murine prostate. We observed that mice with both Lzts2 and Pten deletion have an earlier onset of prostate carcinomas as well as an accelerated tumor progression compared to mice with Pten or Lzts2 deletion alone. Immunohistochemical analyses show that atypical and tumor cells from compound mice with both Pten and Lzts2 deletion are mainly composed of prostate luminal epithelial cells and possess higher levels of cytoplasmic and nuclear β-catenin. These cells also exhibit a higher proliferative capacity than cells isolated from single deletion mice. These data demonstrate the significance of simultaneous Pten and Lzts2 deletion in oncogenic transformation in prostate cells and implicates a new mechanism for the dysregulation of Wnt/β-catenin signaling in prostate tumorigenesis.
Analysis and design of RNA sequencing experiments for identifying mRNA isoform regulation

Supplementary Figure 1 Annotated isoforms in human and mouse genomes. Supplementary Figure 2 Estimates of  using single‐end reads. Supplementary Figure 3 Steps of MISO statistical inference procedure Supplementary Figure 4 Evidence for exon size‐dependent qRT‐PCR bias. Supplementary Figure 5 MISO estimation for 52 alternative exons in breast cancer tissue. Supplementary Figure 6 mRNA‐Seq data for hnRNPAB in breast cancer tissue. Supplementary Figure 7 Comparison of MISO and qRT-PCR values for hnRNP H knockdown dataset 
Model-Based Design of Tree WSNs for Decentralized Detection

The classical decentralized detection problem of finding the optimal decision rules at the sensor and fusion center, as well as variants that introduce physical channel impairments have been studied extensively in the literature. The deployment of WSNs in decentralized detection applications brings new challenges to the field. Protocols for different communication layers have to be co-designed to optimize the detection performance. In this paper, we consider the communication network design problem for a tree WSN. We pursue a system-level approach where a complete model for the system is developed that captures the interactions between different layers, as well as different sensor quality measures. For network optimization, we propose a hierarchical optimization algorithm that lends itself to the tree structure, requiring only local network information. The proposed design approach shows superior performance over several contentionless and contention-based network design approaches.
A robust sparse representation based face recognition system for smartphones

Many research works have been done in face recognition during the last years that indicates the importance of face recognition systems in many applications including identity authentication. In this paper we propose an approach for face recognition which is suitable for unconstrained image acquisition and has a low computational cost. Since in practical applications such as in smartphones, imaging conditions are not limited to existing images in the database, robustness of the recognition algorithm is very important. Here a sparse representation framework is proposed which achieves some degree of robustness. Using double sparse representation the high computational cost of sparsity-based classifications is resolved. The experimental result indicates that the proposed method outperforms other well-known algorithms in terms of robustness and it is still fast enough for real-time applications in smartphones.
Corporate Communications: An International Journal Impression management and self-presentation dissimulation in Portuguese chairman's statements

Purpose – Drawn on social psychology theory of impression management, the present study tries to assess the way Portuguese managers build their narratives in Chairman’s Statement to manage stakeholders’ perceptions on corporate image, in a period of time of scarce resources. Design/methodology/approach – The paper’s theoretical framework draws on elements of social psychology theory of impression management developed by Leary and Kowalski (1990). Through the use of the two-component model of impression management (impression motivation and impression construction) the 45 Chairmen’s Statements of Portuguese non-finance companies were content analysed to understand how managers build their voluntary communication strategies. Findings – Results indicate that organizational outcome does not influence the adoption of impression management strategies. But public visibility and consumer proximity are crucial factors in explaining them. Larger companies with high consumer proximity present themselves in a favourable way, but consistent with an overall reading of the annual report. These companies show a higher level of verbosity, consistent to the argument of retrospective rationality. Originality – The present study goes beyond Merkl-Davies et al. (2011) work and obtains insightful knowledge on the influence of goal-relevance of impression in three different perspectives: company’s public visibility, company’s dependency from debtholders, and consumer proximity. Moreover, the analysis uses a period of scarce resources and a European Latin country, with no tradition in publishing Chairmen’s Statements, but that recently has changed its financial reporting practices from an institutional code-law logic to an institutional common-law logic. A research setting like this has not been studied hitherto.
FreeMMG: A Scalable and Cheat-Resistant Distribution Model for Internet Games

State-of-the-art Massively Multiplayer Games such as EverQuest and Ultima Online are currently implemented as client-server systems. Although this approach allows the development of commercially viable MMG services, the costs associated with running a scalable client-server MMG service are often too high for small companies or research projects. This paper proposes FreeMMG, a mixed peer-to-peer and client-server approach to the distribution aspect ofMMGs. It is argued that the FreeMMG model supports scalable, cheat-resistant, massively multiplayer realtime strategy (RTS) games using a lightweight server that delegates the bulk of the game simulation to the clients. A working prototype game called FreeMMG Wizards is presented, together with some preliminary scalability test results featuring up to 300 simulated game clients connected to a FreeMMG server. The results show that the measured server traffic can be considered very low if compared with more centralized alternatives.
A Radial Basis Function Approach to Credit Barrier Model

Albanese and et. al. (2003) and Avellaneda and Zhu (2001) develop the framework of Credit Barrier Model. They provide special solutions to the model in case of simple stochastic structure. The technical aspect of the model remains wide open for general stochastic structure that is crucial when the model is required to calibrate with aggregate amount of empirical data. This paper provides a technical solution to this problem with the use of radial basis function (RBF). This paper discusses the numerical implementation of the credit barrier model using the RBF method. It also demonstrates that the RBF method is numerically tractable in this problem and allows in the model richer stochastic structure capable of capturing relevant market information.
Data Parallel Three-Dimensional Cahn-Hilliard Field Equation Simulation on GPUs with CUDA

Computational scientific simulations have long used parallel computers to increase their performance. Recently graphics cards have been utilised to provide this functionality. GPGPU APIs such as NVidia’s CUDA can be used to harness the power of GPUs for purposes other than computer graphics. GPUs are designed for processing twodimensional data. In previous work we have presented several two-dimensional Cahn-Hilliard simulations that each utilise different CUDA memory types and compared their results. In this paper we extend these ideas to three dimensions. As GPUs are not intended for processing threedimensional data arrays, the performance of the memory optimisations is expected to change. Here we present several three-dimensional Cahn-Hilliard simulations to explore the challenges and the performance of the different memory types in three-dimensions. The results show that the simulation design with the best performance in threedimensions uses a different memory type to the optimal two-dimensional simulation.
Semliki Forest virus mRNA capping enzyme requires association with anionic membrane phospholipids for activity

The replication complexes of all positive strand RNA viruses of eukaryotes are associated with membranes. In the case of Semliki Forest virus (SFV), the main determinant of membrane attachment seems to be the virus‐encoded non‐structural protein NSP1, the capping enzyme of the viral mRNAs, which has guanine‐7‐methyltransferase and guanylyltransferase activities. We show here that both enzymatic activities of SFV NSP1 are inactivated by detergents and reactivated by anionic phospholipids, especially phosphatidylserine. The region of NSP1 responsible for binding to membranes as well as to liposomes was mapped to a short segment, which is conserved in the large alphavirus‐like superfamily of viruses. A synthetic peptide of 20 amino acids from the putative binding site competed with in vitro synthesized NSP1 for binding to liposomes containing phosphatidylserine. These findings suggest a molecular mechanism by which RNA virus replicases attach to intracellular membranes and why they depend on the membranous environment.
Individual Differences in Middle School and College Students’ Texting

The present study surveyed a sample of middle school students on their technology habits, with a primary focus on texting behaviors. A secondary sample of college students was surveyed as a comparison group to examine individual differences in texting behaviors. Results indicate that college students text more frequently than middle schoolers; however, college students’ texting behaviors decrease in frequency as they get older, whereas middle schoolers’ texting behaviors increase in frequency. Females also generally reported texting more frequently than males. Extraversion was found to be predictive of texting in the middle school sample, but both Extraversion and Neuroticism were found to be predictive of texting in the college sample. Results are discussed in the context of previous research and with respect to human factors and developmental psychology, such that the study of technology use could offer insight into the social development of adolescents and young adults.
Selective localization of the polytopic membrane protein prominin in microvilli of epithelial cells - a combination of apical sorting and retention in plasma membrane protrusions.

Prominin is a recently identified polytopic membrane protein expressed in various epithelial cells, where it is selectively associated with microvilli. When expressed in non-epithelial cells, prominin is enriched in plasma membrane protrusions. This raises the question of whether the selective association of prominin with microvilli in epithelial cells is solely due to its preference for, and stabilization in, plasma membrane protrusions, or is due to both sorting to the apical plasma membrane domain and subsequent enrichment in plasma membrane protrusions. To investigate this question, we have generated stably transfected MDCK cells expressing either full-length or C-terminally truncated forms of mouse prominin. Confocal immunofluorescence and domain-selective cell surface biotinylation experiments on transfected MDCK cells grown on permeable supports demonstrated the virtually exclusive apical localization of prominin at steady state. Pulse-chase experiments in combination with domain-selective cell surface biotinylation showed that newly synthesized prominin was directly targeted to the apical plasma membrane domain. Immunoelectron microscopy revealed that prominin was confined to microvilli rather than the planar region of the apical plasma membrane. Truncation of the cytoplasmic C-terminal tail of prominin impaired neither its apical cell surface expression nor its selective retention in microvilli. Both the apical-specific localization of prominin and its selective retention in microvilli were maintained when MDCK cells were cultured in low-calcium medium, i.e. in the absence of tight junctions. Taken together, our results show that: (i) prominin contains dual targeting information, for direct delivery to the apical plasma membrane domain and for the enrichment in the microvillar subdomain; and (ii) this dual targeting does not require the cytoplasmic C-terminal tail of prominin and still occurs in the absence of tight junctions. The latter observation suggests that entry into, and retention in, plasma membrane protrusions may play an important role in the establishment and maintenance of the apical-basal polarity of epithelial cells.
Architectural, histochemical, and contractile characteristics of a unique biarticular muscle: the cat semitendinosus.

I. The semitendinosus (ST) muscle of the cat consists of two anatomically distinct sets of fibers connected in series by a dense connective tissue band that divides the “muscle” into a proximal and distal compartment, each having separate innervation. 2. Isometric and isotonic contractile properties of the ST were studied for three stimulation conditions: 1) proximal activated (STp), 2) distal-activated (STd), 3) whole muscle activated (ST). In addition, the architectural and histochemical profiles of each compartment were determined. 3. The fiber type composition was similar in the STp and STd, with the majority of the fibers staining darkly for alkaline myofibrillar adenosine triphosphatase ( ATPase). The muscle fibers of the STd were twice as long as the fibers of the STp. The cross-sectional areas of the two compartments were similar. 4. The in situ maximum isometric tension (P,) was identical for all three stimulation conditions. However, the maximum twitch tension (P,) was greatest when ST was activated and least when only the STp was activated. The time to peak tension (TPT) and half relaxation times (95 RT) were the same for all three conditions. The absolute maximal shortening velocity (V,,,) revealed an orderly progression of speeds in relation to the fiber length. When the V,,, of the STd (424 t 26 mm/s) and STp (224 t 23 mm/s) were added, the sum was approximately the same as the V,,, obtained for the ST (624 t 30 mm/s). The intrinsic speed of shortening (millimeters per second per 1,000 sarcomeres) recorded at the common tendon of insertion was the same for all three conditions. 5. The identical nature of the P, values demonstrated the significance of the architectural design, specifically, the physiological cross-sectional area, in determining the potential force production of a muscle. In contrast, the P, values were significantly different for each stimulation condition. These differences were probably influenced in part by the “stiffness-compliance” properties of the muscle-connective tissue unit, which varied with different activation states of the ST muscle. 6. The similarity in TPT and 1/2 RT values for all three conditions illustrated the independence of the isometric speed-related parameters from the architecture of the muscle. The differences in the absolute V,,, data, however, revealed a positive relationship between the maximum speed of shortening and the fiber length. 7. These data demonstrate the necessity of the neuromotor command being matched with the architectural as well as the biochemical properties of each sarcomere (e.g., myosin ATPase and sarcoplasmic reticulum) of the muscles in the control of forces and velocities in vivo.