Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating Default Mode and Sensorimotor Network Connectivity in Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative condition characterized by degeneration of upper motor neurons (UMN) arising from the motor cortex in the brain and lower motor neurons (LMN) in the brainstem and spinal cord. Cerebral changes create differences in brain activity captured by functional magnetic resonance imaging (fMRI), including the spontaneous and simultaneous activity occurring between regions known as the resting state networks (RSNs). Progressive neurodegeneration as observed in ALS may lead to a disruption of RSNs which could provide insights into the disease process. Previous studies have reported conflicting findings of increased, decreased, or unaltered RSN functional connectivity in ALS and do not report the contribution of UMN changes to RSN connectivity. We aimed to bridge this gap by exploring two networks, the default mode network (DMN) and the sensorimotor network (SMN), in 21 ALS patients and 40 age-matched healthy volunteers. An UMN score dichotomized patients into UMN+ and UMN- groups. Subjects underwent resting state fMRI scan on a high field MRI operating at 4.7 tesla. The DMN and SMN changes between subject groups were compared. Correlations between connectivity and clinical measures such as the ALS Functional Rating Scale—Revised (ALSFRS-R), disease progression rate, symptom duration, UMN score and finger tapping were assessed. Significant group differences in resting state networks between patients and controls were absent, as was the dependence on degree of UMN burden. However, DMN connectivity was increased in patients with greater disability and faster progression rate, and SMN connectivity was reduced in those with greater motor impairment. These patterns of association are in line with literature supporting loss of inhibitory interneurons.
A Polymorphism in the Cytidine Deaminase Promoter Predicts Severe Capecitabine-Induced Hand-Foot Syndrome

Purpose: Hand-foot syndrome (HFS) is one of the most relevant dose-limiting adverse effects of capecitabine, an oral prodrug of 5-fluorouracil used in the standard treatment of breast and colorectal cancer. We investigated the association between grade 3 HFS and genetic variations in genes involved in capecitabine metabolism. Experimental Design: We genotyped a total of 13 polymorphisms in the carboxylesterase 2 (CES2) gene, the cytidine deaminase (CDD) gene, the thymidine phosphorylase (TP) gene, the thymidylate synthase (TS) gene, and the dihydropyrimidine dehydrogenase (DPD) gene in 130 patients treated with capecitabine. We correlated these polymorphisms with susceptibility to HFS. Results: We found an association of HFS appearance with rs532545 located in the promoter region of CDD (OR = 2.02, 95% CI = 1.02–3.99, P = 0.039). Because we found no association between the rs532545 genotype and CDD mRNA expression in Epstein-Barr virus lymphoblastoid cells, we explored additional genetic variations across the CDD promoter. We found an insertion, rs3215400, in linkage disequilibrium with rs532545 (D′ = 0.92), which was more clearly associated with HFS (OR = 0.51, 95% CI = 0.27–0.95, P = 0.028) in patients and with total CDD gene expression (P = 0.004) in lymphoblastoid cells. In silico analysis suggested that this insertion might create a binding site for the transcriptional regulator E2F. Using a SNaPshot assay in lymphoblastoid cells, we observed a 5.7-fold increased allele-specific mRNA expression from the deleted allele. Conclusions: The deleted allele of rs3215400 shows an increased allele-specific expression and is significantly associated with an increased risk of capecitabine-induced HFS. Clin Cancer Res; 17(7); 2006–13. ©2011 AACR.
Using Textbook Illustration as Media for Developing Character Among Primary Students: Some Research-based Suggestion

Character building is usually being applied in everyday life at school and at home. It is expected that the character education is not only derived only from the teacher but also will be more attractive when it is included into the textbooks. In this literature study, the data were collected by analysing some research papers which relate to primary students’ visual knowledge and character building theory. The results show that character buildings could be included in the illustrations in elementary school textbooks using the students’ interest in illustrations. The illustration is drawn in the form of an overview of the positive values which touch children’s affective aspects. Hopefully, by cultivating the positive values, it will gradually form good character of the primary students.
Connecting Researchers to HPCS through Web Services

Researchers may find it difficult to run experiments on High Performance Computing Systems (HPCS) if they are unfamiliar with terminals and UNIX/Linux commands. Instead of using available HPCS resources, they may choose to run experiments on their personal computers, even if it takes them weeks to run small jobs. However, these researchers are familiar with using the Internet on a daily basis to check email or read the latest news. To make high performance computing more accessible and to help researchers use the HPCS available to them, the authors have developed a web based interface for running simulations from a web browser. This paper describes the design of this interface and its benefits.
PID Gain Tuning Using Genetic Algorithms and Fuzzy Logic for Robot Manipulator Control

This paper addresses an application that involves the control of robot manipulator joint. It presents a PID tuning method that uses a Genetic Algorithm (GA) as a main gain estimator and a fuzzy logic as a ranking basement for GA. The suggested approach is then used to tune the PID gains for different response specifications. Experimental results demonstrate that better performance can be achieved with this fuzzy based GA-PID tuning relative to 1) Ziegler-Nichols tuning and 2) trial and error tuning. This paper tries to explore the potential of using soft computing methodologies in control of plant (robot manipulator) with internal behavior of structure-unknown non-linear time variant dynamic systems. Industrial robot manipulator was used for the case study in this work. The manipulator is simulated with professional simulation software (consist of Solid work, Visual Nastran 4D and Matlab/Simulink).
Functional Implications of Local DNA Structures in Regulatory Motifs

The three-dimensional structure of DNA has been proposed to be a major determinant for functional transcription factors (TFs) and DNA interaction. Here, we use hydroxyl radical cleavage pattern as a measure of local DNA structure. We compared the conservation between DNA sequence and structure in terms of information content and attempted to assess the functional implications of DNA structures in regulatory motifs. We used statistical methods to evaluate the structural divergence of substituting a single position within a binding site and applied them to a collection of putative regulatory motifs. The following are our major observations: (i) we observed more information in structural alignment than in the corresponding sequence alignment for most of the transcriptional factors; (ii) for each TF, majority of positions have more information in the structural alignment as compared to the sequence alignment; (iii) we further defined a DNA structural divergence score (SD score) for each wild-type and mutant pair that is distinguished by single-base mutation. The SD score for benign mutations is significantly lower than that of switch mutations. This indicates structural conservation is also important for TFBS to be functional and DNA structures will provide previously unappreciated information for TF to realize the binding specificity.
Genetic diversity in Nothofagus alessandrii (Fagaceae), an endangered endemic tree species of the coastal maulino forest of Central Chile.

BACKGROUND AND AIMS The endemic tree Nothofagus alessandrii (Fagaceae) has been historically restricted to the coastal range of Region VII of central Chile, and its forests have been increasingly destroyed and fragmented since the end of the 19th century. In this study, the patterns of within- and among-population genetic diversity in seven fragments of this endangered narrowly endemic tree were examined. METHODS Allozyme electrophoresis of seven loci of N. alessandrii was used to estimate genetic diversity, genetic structure and gene flow. KEY RESULTS High levels of genetic diversity were found as shown by mean expected heterozygosity (H(e) = 0.182 +/- 0.034), percentage of polymorphic loci (P(p) = 61.2 %), mean number of alleles per locus (A = 1.8) and mean number of alleles per polymorphic locus (A(p) = 2.3). Genetic differentiation was also high (G(ST) = 0.257 and Nm = 0.7). These values are high compared with more widespread congeneric species. CONCLUSIONS Despite its endemic status and restricted geographical range N. alessandrii showed high levels of genetic diversity. The observed patterns of diversity are explained in part by historical processes and more recent human fragmentation.
Fine scale relationships between sex, life history, and dispersal of masu salmon

Identifying the patterns and processes driving dispersal is critical for understanding population structure and dynamics. In many organisms, sex-biased dispersal is related to the type of mating system. Considerably, less is known about the influence of life-history variability on dispersal. Here we investigated patterns of dispersal in masu salmon (Oncorhynchus masou) to evaluate influences of sex and life history on dispersal. As expected, assignment tests and isolation by distance analysis revealed that dispersal of marine-migratory masu salmon was male-biased. However, dispersal of resident and migratory males did not follow our expectation and marine-migratory individuals dispersed more than residents. This may be because direct competition between marine-migratory and resident males is weak or that the cost of dispersal is smaller for marine-migratory individuals. This study revealed that both sex and migratory life-history influence patterns of dispersal at a local scale in masu salmon.
Multiple Peer-to-Peer Communications Using a Network of Relays

We consider an ad hoc wireless network consisting of d source-destination pairs communicating, in a pairwise manner, via R relaying nodes. The relay nodes wish to cooperate, through a decentralized beamforming algorithm, in order to establish all the communication links from each source to its respective destination. Our communication strategy consists of two steps. In the first step, all sources transmit their signals simultaneously. As a result, each relay receives a noisy faded mixture of all source signals. In the second step, each relay transmits an amplitude- and phase-adjusted version of its received signal. That is each relay multiply its received signal by a complex coefficient and retransmits the so-obtained signal. Our goal is to obtain these complex coefficients (beamforming weights) through minimization of the total relay transmit power while the signal-to-interference-plus-noise ratio (SINR) at the destinations are guaranteed to be above certain predefined thresholds. Although such a power minimization problem is not convex, we use semidefinite relaxation to turn this problem into a semidefinite programming (SDP) problem. Therefore, we can efficiently solve the SDP problem using interior point methods. Our numerical examples reveal that for high network data rates, our space division multiplexing scheme requires significantly less total relay transmit power compared to other orthogonal multiplexing schemes, such as time-division multiple access schemes.
CoKey: fast token-based cooperative cryptography

Keys for symmetric cryptography are usually stored in RAM and therefore susceptible to various attacks, ranging from simple buffer overflows to leaks via cold boot, DMA or side channels. A common approach to mitigate such attacks is to move the keys to an external cryptographic token. For low-throughput applications like asymmetric signature generation, the performance of these tokens is sufficient. For symmetric, data-intensive use cases, like disk encryption on behalf of the host, the connecting interface to the token often is a serious bottleneck. In order to overcome this problem, we present CoKey, a novel concept for partially moving symmetric cryptography out of the host into a trusted detachable token. CoKey combines keys from both entities and securely encrypts initialization vectors on the token which are then used in the cryptographic operations on the host. This forces host and token to cooperate during the whole encryption and decryption process. Our concept strongly and efficiently binds encrypted data on the host to the specific token used for their encryption, while still allowing for fast operation. We implemented the concept using Linux hosts and the USB armory, a USB thumb drive sized ARM computer, as detachable crypto token. Our detailed performance evaluation shows that our prototype is easily fast enough even for data-intensive and performance-critical use cases like full disk encryption, thus effectively improving security for symmetric cryptography in a usable way.
Local affinity-based color propagation of images

Scribble-based colorization algorithms have become greatly popular due to the ease of user interaction. The key of propagating the user scribbles to the entire image is to define a similarity measure between pixels. We propose here a new affinity function with several computation times of similarity weights for each pair of adjacent pixels, while the traditional methods only with one such computation. It is proved that our method can better capture the local intrinsic structure of pixels. Furthermore, we apply a superpixel representation of the target image to reduce the computation cost. Experiments show that the new method can yields better colorization results and remarkably speed up the colorization process.
Incidence of Symptomatic and Asymptomatic Leishmania donovani Infections in High-Endemic Foci in India and Nepal: A Prospective Study

Incidence of Leishmania donovani infection and Visceral Leishmaniasis (VL) was assessed in a prospective study in Indian and Nepalese high-endemic villages. DAT-seroconversion was used as marker of incident infection in 3 yearly surveys. The study population was followed up to month 30 to identify incident clinical cases. In a cohort of 9034 DAT-negative individuals with neither active signs nor history of VL at baseline, 42 VL cases and 375 asymptomatic seroconversions were recorded in the first year, giving an infection∶disease ratio of 8.9 to 1. In the 18 months' follow-up, 7 extra cases of VL were observed in the seroconverters group (N = 375), against 14 VL cases among the individuals who had not seroconverted in the first year (N = 8570) (RR = 11.5(4.5<RR<28.3)). Incident asymptomatic L. donovani infection in VL high-endemic foci in India and Nepal is nine times more frequent than incident VL disease. About 1 in 50 of these new but latent infections led to VL within the next 18 months.
A Maximum-Flow-Based Complex Network Approach for Power System Vulnerability Analysis

This paper proposes a maximum-flow-based complex network approach for the analysis of the vulnerability of power systems. A new centrality index is proposed, taking into consideration the maximum flow from the source (generator) nodes to the sink (load) nodes, for assessing the network. The Max-Flow Min-Cut Theorem, also known as Ford-Fulkerson Theorem, is used for evaluating the capacity of links. The proposed methodology is then used to identify vulnerable lines of the IEEE 118 bus system and its effectiveness is demonstrated through simulation studies.
Confidential Data Identification Using Data Mining Techniques in Data Leakage Prevention System

Data leakage means sending confidential data to an unauthorized person. Nowadays, identifying confidential data is a big challenge for the organizations. We developed a system by using data mining techniques, which identifies confidential data of an organization. First, we create clusters for the training data set. Next, identify confidential terms and context terms for each cluster. Finally, based on the confidential terms and context terms, the confidentiality level of the detected document calculated in terms of score. If the score of the detected document beyond a predefined threshold, then the document is blocked and marked as a confidential.
The Class of Constraint Satisfaction Problems over a Knot

This work presents a method for associating a class of constraint satisfaction problems to a three-dimensional knot. Given a knot, one can build a knot quandle, which is a generally an infinite, free algebra. The desired collection of problems is derived from the finite quotients of the knot quandle by applying theory that relates finite algebras to constraint languages. Along the way, notions of tractable and NP-complete quandles and knots are developed. Finally, a partial, computational classification of Rolfsen’s Knot Table [26] is undertaken where it is shown that all tricolorable knots in this collection are NP-complete.
Branching diffusion in inhomogeneous media

We investigate the long-time evolution of branching diffusion processes (starting with a finite number of particles) in inhomogeneous media. The qualitative behavior of the processes depends on the intensity of the branching. In the super-critical regime, we describe the asymptotics of the number of particles in a given domain. In the sub-critical and critical regimes, we show that the limiting number of particles is finite and describe its distribution.
Numerical recipes in C++: the art of scientific computing, 2nd Edition (C++ ed., print. is corrected to software version 2.10)

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Space-time interpolation and automatic mapping of TEC using TNPGN-active

Turkish National Permanent GPS Network (TNPGN) is the Reference Station Network of 146 continuously-operating GNSS stations o which are distributed uniformly across Turkey and North Cyprus Turkish Republic since May 2009. IONOLAB group, formed by researchers and students in Hacettepe University, Bilkent University and General Command of Mapping is currently investigating new techniques for space-time interpolation, and automatic mapping of TEC through a TUBITAK research grant. This study presents the developments in monitoring of space weather, and correction of geodetic positioning errors due to ionosphere using TNPGN.
An NoC Simulator That Supports Deflection Routing, GPU/CPU Integration, and Co-Simulation

We present deflection routing network on chip simulator (DNOC), a network-on-chip simulator. DNOC is primarily a deflection routing simulator, it simulates custom network topologies with detailed deflection router models, and a basic virtual channel router. DNOC can generate various statistics, such as network latency and power. We evaluate the simulator in three typical use cases. In stand-alone simulation, synthetic traffic generators are used to offer load to the network. In synchronous co-simulation, the simulator is integrated as a module within a larger system simulator with synchronization every simulated cycle. In the faster model-based co-simulation mode, a latency model is built, and retuned periodically at longer time intervals. We demonstrate co-simulation by running applications from the Rodinia and SPLASH-2 benchmark sets on mesh variants. DNOC is also able to run on multicore processors, speeding up the simulation of large networks.
A Slightly-modified GI-based Author-verifier with Lots of Features (ASGALF)

This paper presents the performance evaluation of an authorship verification technique that is based on a modified version of General Impostors (GI) [2]. The novelties of this implementation are: 1. a modified way of combining the min-max similarity measure and, 2. a relatively large set of diverse features that spans letter-level, word-level, function word-level, word shape-level, and word tag-level features. The technique ranked high in overall in the author identification task of PAN 2014.
The Price of Isolation : an Integrated Study of System Inefficiencies

We present in this paper an integrated study on the selfish behavior of the players participating in the system (modeled by a noncooperative game) and the myopic attitudes of the players (modeled by the ‘rolling-horizon’ type of strategies in the dynamic decision-making process), and introduce a solution termed myopic Nash equilibrium to characterize the equilibrium state when all the players are selfish and myopic. To characterize the loss of system efficiencies caused by such behaviors, we use a (worst possible) ratio between the total social value at the worst myopic Nash equilibrium and the optimal total social value, which is termed the Price of Isolation (PoI) in this paper. We consider some specific game models to bound this ratio. We first consider an extension of the static transportation game, with K players competing on a given set of routes to get their jobs done at minimum cost, over T stages. If the unit cost on each route in different stages are all affine linear in the total demand and the unit cost of the previous stage, then it is shown that the PoI of this game is precisely 4 as T → ∞. We then turn to dynamic profit maximization games, including generalized settings of the Cournot and/or Bertrand competition games, with K producers competing to sell their products in the market over T stages. We prove that the PoI is in the order of 1 KT if the commodities are substitute in the Cournot game, and are complementary in the Bertrand game, when the unit costs of the resources used to manufacture the products and the selling prices of the finished products are assumed to be affine linear functions. Interpretations of these results are also discussed.
Statistical fraud detection: A review

Fraud is increasing dramatically with the expansion of modem technology and the global superhighways of communication, resulting in the loss of billions of dollars worldwide each year. Although prevention technologies are the best way to reduce fraud, fraudsters are adaptive and, given time, will usually find ways to circumvent such measures. Methodologies for the detection of fraud are essential if we are to catch fraudsters once fraud prevention has failed. Statistics and machine learning provide effective technologies for fraud detection and have been applied successfully to detect activities such as money laundering, e-commerce credit card fraud, telecommunications fraud and computer intrusion, to name but a few. We describe the tools available for statistical fraud detection and the areas in which fraud detection technologies are most used.