Miracle-dz/UniFAR-FTUs huggingface dataset:
Text Mining in Biomedical Domain with Emphasis on Document Clustering

Objectives With the exponential increase in the number of articles published every year in the biomedical domain, there is a need to build automated systems to extract unknown information from the articles published. Text mining techniques enable the extraction of unknown knowledge from unstructured documents. Methods This paper reviews text mining processes in detail and the software tools available to carry out text mining. It also reviews the roles and applications of text mining in the biomedical domain. Results Text mining processes, such as search and retrieval of documents, pre-processing of documents, natural language processing, methods for text clustering, and methods for text classification are described in detail. Conclusions Text mining techniques can facilitate the mining of vast amounts of knowledge on a given topic from published biomedical research articles and draw meaningful conclusions that are not possible otherwise.
A Comparison of Two Classes of Methods for Estimating False Discovery Rates in Microarray Studies

The goal of many microarray studies is to identify genes that are differentially expressed between two classes or populations. Many data analysts choose to estimate the false discovery rate (FDR) associated with the list of genes declared differentially expressed. Estimating an FDR largely reduces to estimating π 1, the proportion of differentially expressed genes among all analyzed genes. Estimating π 1 is usually done through P-values, but computing P-values can be viewed as a nuisance and potentially problematic step. We evaluated methods for estimating π 1 directly from test statistics, circumventing the need to compute P-values. We adapted existing methodology for estimating π 1 from t- and z-statistics so that π 1 could be estimated from other statistics. We compared the quality of these estimates to estimates generated by two established methods for estimating π 1 from P-values. Overall, methods varied widely in bias and variability. The least biased and least variable estimates of π 1, the proportion of differentially expressed genes, were produced by applying the “convest” mixture model method to P-values computed from a pooled permutation null distribution. Estimates computed directly from test statistics rather than P-values did not reliably perform well.
Psychology, the psychological, and critical praxis: A phenomenologist reads Frantz Fanon

This article situates the role of psychological investigations in analyses of social problems like colonialism and racism, via a phenomenological reading of the writings of Frantz Fanon. Emerging scholarship on Fanon’s use of psychology is beginning to elucidate how his style of analysis enables an interweaving of psychological insights with sociopolitical ones. The present paper builds on this research by explicating the essential moments of Fanon’s approach. Fanonian investigations are shown to be characterized by a focus on: experience, concrete examples, evidence, meaning, unprejudiced seeing from multiple perspectives, delineation of essential structure, and critical and liberating praxis. Fanon is then compared to other theorists operating at the nexus of psychology and society in order to delineate an overall structure of psychopolitical investigations. Overall, the paper attempts to sketch ways in which psychology can be advanced as a science and praxis of human liberation.
Syntactic Annotation in the Columbia Arabic Treebank

Abstract The Columbia Arabic Treebank (CATiB) is a database of syntactic analyses of Arabic sentences. CATiB contrasts with previous approaches to Arabic treebanking in its emphasis on faster production with some constraints on linguistic richness. Two basic ideas inspire the CATiB approach. First, CATiB avoids the annotation of redundant linguistic information that is determinable automatically from syntax and morphological analysis, e.g., nominal case. And secondly, CATiB uses linguistic representation and terminology inspired by the long tradition of Arabic syntactic studies. This makes it easier to train annotators and not be restricted to hire annotators who have degrees in linguistics. This paper describes CATiB’s representation and compares it to other Arabic treebanking efforts.
Performance Evaluation of Key IMS Operations over IPv6-Capable 3G UMTS Networks

Due to the rapid development of high bit-rate IP-based mobile networking architectures, the increasing number of end-user terminals, and the emerging convergence of different communication services with the IP world, the IPv6 protocol and the IP Multimedia Subsystem (IMS) are considered to be the key technologies towards the realization of next generation mobile and wireless telecommunications. Both IPv6 and IMS are widely covered in the literature as self-possessed researches and studies. However, the challenge of provisioning IPv6-based IMS services over 3rd Generation (3G) Universal Mobile Telecommunication System (UMTS) networks as well as related problems and performance issues were not considered so far. In this work, we try to fill this gap and raise attention on some potentially significant aspects of the integration of 3G UMTS, IMS and IPv6. Our research in this context mainly concerns the questions and challenges of the transition from IPv4 to IPv6 in all-IP 3G and beyond multimedia systems and their impacts on the performance of IMS services and applications. Different methods providing IPv6 support in existing mobile telecommunication architectures and the co-existence of IPv4/v6 during the first phases of the integration of the new Internet Protocol have substantial impact on the network and service/application performance. In order to quantify these effects, we designed and implemented a 3G UMTS testbed (including the IMS core) and compared the performance characteristics of three selected transition techniques with native IPv4 and IPv6 scenarios. Our results expose the main benefits and drawbacks of the five technologies and their actually available implementations.
Association between ANKK1 (rs1800497) and LTA (rs909253) Genetic Variants and Risk of Schizophrenia

Limited research has assessed associations between schizophrenia and genetic variants of the ankyrin repeat and kinase domain containing 1 (ANKK1) and lymphotoxin-alpha (LTA) genes among individuals of Middle Eastern ancestry. Here we present the first association study investigating the ANKK1 rs1800497 (T>C) and LTA rs909253 (A>G) single-nucleotide polymorphisms in an Egyptian population. Among 120 patients with DSM-IV and PANSS (Positive and Negative Syndrome Scale) assessments of schizophrenia and 100 healthy controls, we determined the genotypes for the polymorphisms using endonuclease digestion of amplified genomic DNA. Results confirmed previous findings from different ethnic populations, in that the rs1800497 and rs909253 polymorphisms were both associated with risk of schizophrenia. Differences between the genotypes of cases and controls were strongly significant (P = 0.0005 for rs1800497 and P = 0.001 for rs909253). The relative risk to schizophrenia was 1.2 (P = 0.01) for the C allele and 0.8 (P = 0.04) for the G allele. The CC, GG, and combined CC/AA genotypes were all more frequent in cases than in controls. These results support an association between ANKK1 and LTA genetic markers and vulnerability to schizophrenia and show the potential influence of just one copy of the mutant C or G allele in the Egyptian population.
Acceleration of transistor-level evolution using Xilinx Zynq Platform

The aim of this paper is to introduce a new accelerator developed to address the problem of evolutionary synthesis of digital circuits at transistor level. The proposed accelerator, based on recently introduced Xilinx Zynq platform, consists of a discrete simulator implemented in programmable logic and an evolutionary algorithm running on a tightly coupled embedded ARM processor. The discrete simulator was introduced in order to achieve a good trade-off between the precision and performance of the simulation of transistor-level circuits. The simulator is implemented using the concept of virtual reconfigurable circuit and operates on multiple logic levels which enables to evaluate the behavior of candidate transistor-level circuits at a reasonable level of detail. In this work, the concept of virtual reconfigurable circuit was extended to enable bidirectional data flow which represents the basic feature of transistor level circuits. According to the experimental evaluation, the proposed architecture speeds up the evolution in one order of magnitude compared to an optimized software implementation. The developed accelerator is utilized in the evolution of basic logic circuits having up to 5 inputs. It is shown that solutions competitive to the circuits obtained by conventional design methods can be discovered.
Acute myocardial infarction activates progenitor cells and increases Wnt signalling in the bone marrow.

AIMS We aimed to characterize the influence of acute myocardial infarction (AMI) on the metabolic activity of the bone marrow (BM) and on the composition and functional activity of BM-derived mononuclear cells (BMC). Acute ischaemia or other stressors induce the mobilization of progenitor cells from the BM stem cell niche. The effect of AMI on the numbers and functional activity of cells within the BM is unknown. METHODS AND RESULTS In patients of the REPAIR-AMI trial as well as in mice, the number and functionality of BMC was compared with respect to the time interval from AMI. Activation of Wnt signalling was assessed after AMI induction in TOP-GAL transgenic reporter mice, carrying a β-galactosidase gene driven by an LEF/TCF/β-catenin responsive promoter. The metabolic activity of the BM, as determined by F-18-fluorodeoxyglucose-positron emission tomography, was significantly higher in patients with AMI compared with patients with chronic post-ischaemic heart failure. Moreover, the number of haematopoietic CD34(+) (P < 0.05) and CD133(+) (P < 0.05) cells in the BM aspirates was significantly increased in patients within 7 days after AMI. In order to confirm these clinical data, we induced AMI in mice, which time-dependently increased the number of c-kit + Sca-1 + lin- cells and colony-forming units in the BM. Activation of the BM by AMI induced a significant increase in Wnt signalling, which is known to induce proliferation of haematopoietic stem cells, and demonstrated increased levels of the Wnt target Axin-2 in BM-derived cells on Day 7 (P < 0.01 vs. control). CONCLUSION Acute myocardial infarction is associated with an increased metabolic activity and increased levels of progenitor cells within days after AMI. These findings document an activation of the stem cell niche within the BM following AMI, which may have important implications for the optimal timing of cell aspirations used for therapeutic application in patients with AMI.
Spontaneous Membrane-Translocating Peptide Adsorption at Silica Surfaces: A Molecular Dynamics Study

Spontaneous membrane-translocating peptides (SMTPs) have recently been shown to directly penetrate cell membranes. Adsorption of a SMTP, and some engineered extensions, at model silica surfaces is studied herein using fully atomistic molecular dynamics simulations in order to assess their potential to construct novel drug delivery systems. The simulations are designed to reproduce the electric fields above single, siloxide-rich charged surfaces, and the trajectories indicate that the main driving force for adsorption is electrostatic. An increase in the salt concentration slows down but does not prevent adsorption of the SMTP to the surface; it also does not result in peptide desorption, suggesting additional binding via hydrophobic forces. The results are used to design extensions to the peptide sequence which we find enhance adsorption but do not affect the adsorbed conformation. We also investigate the effect of surface hydroxylation on the peptide adsorption. In all cases, the final adsorbed conformations are with the peptide flattened to the surface with arginine residues, which are key to the peptide’s function, anchoring it to the surface so that they are not exposed to solution. This conformation could impact their role in membrane translocation and thus has important implications for the design of future drug delivery vehicles.
Wireless Communication and Power Supply Strategy for Sensor Applications Within Closed Metal Walls

Passive or semiactive wireless sensors, i.e., sensors that require neither wires nor external power supply/batteries, are attractive for many measurement problems. Standard approaches based on Radio Frequency Identification technology usually have difficulties when a fairly conductive matter such as steel or a large amount of water is in the vicinity of the devices. This paper investigates methods for power and data transmission, even through the metal walls, e.g., of a tank or a pipe using super low frequency carrier signals. The feasibility is demonstrated by means of finite-element analysis and laboratory experiments and validated with a prototype setup for both a steel pipe and a tin container. Experimental results for capacitive fill-level measurement inside a metallic container are reported.
Research on Optimizing Region-based Clustering for LEACH RoutingProtocol of WSN

This paper intends to improve the current LEACH Hierarchical Routing Protocol of WSN, in order to solve the problems of uneven distribution of cluster heads and the imbalanced energy consumption caused by randomly selecting the cluster heads. This paper proposes an algorithm of optimizing the number of the cluster heads, which divides the clus- ter regions evenly according to the minimum distance of the cluster heads which are determined by the optimal number of cluster heads. Furthermore, our novel approach restricts the cluster heads rotation within the cluster region, with our opti- mized algorithm, so it can guarantee an optimal balanced point for each interval of the cluster rotations, which saves the network energy consumption, and prolongs the generation period of the network, and improves the load balance of the network as well. Therefore, our approach improves the network performance of WSN significantly.
A Roadmap for caGrid, an Enterprise Grid Architecture for Biomedical Research

caGrid is a middleware system which combines the Grid computing, the service oriented architecture, and the model driven architecture paradigms to support development of interoperable data and analytical resources and federation of such resources in a Grid environment. The functionality provided by caGrid is an essential and integral component of the cancer Biomedical Informatics Grid (caBIG) program. This program is established by the National Cancer Institute as a nationwide effort to develop enabling informatics technologies for collaborative, multi-institutional biomedical research with the overarching goal of accelerating translational cancer research. Although the main application domain for caGrid is cancer research, the infrastructure provides a generic framework that can be employed in other biomedical research and healthcare domains. The development of caGrid is an ongoing effort, adding new functionality and improvements based on feedback and use cases from the community. This paper provides an overview of potential future architecture and tooling directions and areas of improvement for caGrid and caGrid-like systems. This summary is based on discussions at a roadmap workshop held in February with participants from biomedical research, Grid computing, and high performance computing communities.
Automatic hair color de-identification

A process of de-identification used for privacy protection in multimedia content should be applied not only for primary biometric traits (face, voice) but for soft biometric traits as well. This paper deals with a proposal of the automatic hair color de-identification method working with video records. The method involves image hair area segmentation, basic hair color recognition, and modification of hair color for real-looking de-identified images.
Coordinated expression of galectin‐3 and caveolin‐1 in thyroid cancer

Galectin‐3 (Gal3) is the single most accurate marker for the diagnosis of differentiated thyroid cancer (DTC). Gal3 overrides the tumour suppressor activity of caveolin‐1 (Cav1) and functions in concert with Cav1 to promote focal adhesion turnover and tumour cell migration and invasion. To study their coordinated role in progression of a human cancer, we investigated the expression of Gal3 and Cav1 in specimens of human benign thyroid lesions, DTC and anaplastic thyroid cancer (ATC). Gal3 and Cav1 expression is significantly associated with DTC and ATC, but not benign nodules. Essentially all Cav1‐positive DTC cancers express Gal3, supporting the synergistic activity of these two proteins in DTC progression. Similarly, coordinated elevated Gal3/Cav1 expression was observed in three DTC‐derived cell lines (papillary TCP1 and KTC1 and follicular FTC133) but only one (ACT1) of five ATC‐derived cell lines. Using siRNA knockdown, Gal3 and Cav1 were shown to be required for RhoA GTPase activation, stabilization of focal adhesion kinase (FAK; a measure of focal adhesion signalling and turnover) and increased migration of the DTC cell lines studied, but not the ATC cell lines, including ACT1, which expresses elevated levels of Gal3 and Cav1. Co‐expression of Gal3 and Cav1 in the T238 anaplastic cell line stabilized FAK‐GFP in focal adhesions. Gal3 and Cav1 therefore function synergistically to promote focal adhesion signalling, migration and progression of DTC. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Cache-based Document-level Statistical Machine Translation

Statistical machine translation systems are usually trained on a large amount of bilingual sentence pairs and translate one sentence at a time, ignoring document-level information. In this paper, we propose a cache-based approach to document-level translation. Since caches mainly depend on relevant data to supervise subsequent decisions, it is critical to fill the caches with highly-relevant data of a reasonable size. In this paper, we present three kinds of caches to store relevant document-level information: 1) a dynamic cache, which stores bilingual phrase pairs from the best translation hypotheses of previous sentences in the test document; 2) a static cache, which stores relevant bilingual phrase pairs extracted from similar bilingual document pairs (i.e. source documents similar to the test document and their corresponding target documents) in the training parallel corpus; 3) a topic cache, which stores the target-side topic words related with the test document in the source-side. In particular, three new features are designed to explore various kinds of document-level information in above three kinds of caches. Evaluation shows the effectiveness of our cache-based approach to document-level translation with the performance improvement of 0.81 in BLUE score over Moses. Especially, detailed analysis and discussion are presented to give new insights to document-level translation.
Analyzing the Spanish strip cipher by combining combinatorial and statistical methods

ABSTRACT According to historical reports, many telegrams that date from the Spanish Civil War (1936–1939) still remain undisclosed. It is believed that these telegrams were encrypted with a cryptosystem called the “Spanish Strip Cipher” (SSC). During this civil war, SSC was the most used cryptographic algorithm. This method corresponds to a homophonic substitution cipher in which a plaintext letter can map to between three and five ciphertext symbols. By means of cryptanalysis, the authors detect a weakness in the encryption process of the SSC. In this article, they describe how this vulnerability is exploited to efficiently reconstruct a plaintext from a relatively short ciphertext. The attack is based on combinatorial and statistical methods, and it is divided into three phases: homophones-table analysis, letter-frequency analysis, and dictionary search. The attack was implemented in Java and tested on a laptop with an i7 processor and 4 GB of RAM. The tests were carried out with several real telegrams from the Spanish Civil War. In this article, the authors provide the results of one test that was successfully performed only using the first 201 ciphertext symbols of a Spanish telegram.
A new nonlinear HEMT model for AlGaN/GaN switch applications

We present here a new set of equations for modeling the I-V characteristics of FETs, particularly optimized for AlGaN/GaN HEMTs. These equations describe the whole characteristics from negative to positive breakdown loci, and reproduce the current saturation at high level. Using this model allow reducing the modeling procedure duration when a same transistor topology is used for several applications in a T/R module. It can even be used for switches design, witch is the most demanding application in terms of I-V swing. Moreover, a particular care was taken to model accurately the first third orders of the current derivatives, which is important for multitone applications. There are 18 parameters for the main current source (and 6 for both diodes Igs and Igd). This can be compared to the Tajima's equations based Model [1] (13 parameters) or to the Angelov Model (14 parameters) [2], which only fit the I-V characteristics for positive values of Vds. We will detail here the model formulation, and show some measurements/modeling comparisons on both I-V and [S]-parameters obtained for a 8×75 µm GaN HEMT.
Individual preferences towards knowledge creation and knowledge sharing: First empirical results

This working paper presents findings from research project on individual preferences towards participation in knowledge creation and knowledge sharing processes. Contemporary literature usually views knowledge creation and knowledge sharing as either independent or positively related processes. However, analyzing various conditions for efficient course of these processes, we have proposed that in some cases these conditions (and, respectively, the processes themselves) may contradict each other. Translating this idea into individual level of analysis of organizational knowledge-related processes, we hypothesized that there were two distinct non-overlapping groups of individuals â€“ those more disposed towards knowledge creation, and those more disposed towards knowledge sharing. Data analysis proved our hypothesis and revealed some factors that may influence affiliation of an individual with one of these groups.