Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantification of the alteration in the Resting State Networks for measuring brain pathologies and diseases

1. Computational Neuroimaging Lab. Biocruces Health Research Institute. Cruces University Hospital, Barakaldo, Spain 2. Quantitative Biomedicine Unit. Biocruces Health Research Institute. Cruces University Hospital, Barakaldo, Spain 3. Dipartimento di Fisica, Universit degli Studi di Bari and INFN, Bari, Italy 4. Ikerbasque, The Basque Foundation for Science. Bilbao, Spain *Correspondence to jesus.cortesdiaz@osakidetza.net
Association between Polymorphisms of the IL-23R Gene and Allergic Rhinitis in a Chinese Han Population

Objective Polymorphism of the interleukin-23 receptor gene corresponds with susceptibility to several immune-related diseases. For the terminal differentiation of IL-17-producing effector T-helper cells in vivo, the interleukin-23 receptor gene is of vital importance. As shown recently, Th17 cells probably have a great influence on the pathogenesis of allergic airway diseases. Our intention was to establish an association between polymorphisms in the IL-23R gene and allergic rhinitis (AR) in the Chinese Han population. Methods We included 358 AR patients and 407 control Chinese subjects in a case-control comparison. The study involved obtaining blood samples for DNA extraction genotyping and determination of 4 selected single-nucleotide polymorphisms in IL-23R by performing PCR restriction fragment length polymorphism analysis (PCR-RFLP). Results A substantially growing prevalence of the homozygous rs7517847 GG genotype and G allele appeared in the AR patients unlike that observed in the control individuals (P<0.001). In addition, substantially high frequencies of the GGCA and GGCG haplotypes were observed in the AR patients, unlike that observed in the control individuals (P<0.05). The results suggest that the AGTG haplotype may provide protection against AR (P<0.001). Conclusions To the best of our knowledge, this is the first study to demonstrate an important association between polymorphisms in IL-23R and AR in the Chinese Han population. A strong association between rs7517847 in a SNP of IL-23R, and AR was identified.
Scalasca support for MPI+OpenMP parallel applications on large-scale HPC systems based on Intel Xeon Phi

Intel Xeon Phi coprocessors based on the Many Integrated Core (MIC) architecture are starting to appear in HPC systems, with Stampede being a prominent example available within the XSEDE cyber-infrastructure. Porting MPI and OpenMP applications to such systems is often no more than simple recompilation, however, execution performance needs to be carefully analyzed and tuned to effectively exploit their unique capabilities. For performance measurement and analysis tools, the variety of execution modes need to be supported in a consistent and convenient manner, and especially execution configurations involving large numbers of compute nodes each with several multicore host processors and many-core coprocessors. Early experience using the open-source Scalasca toolset for runtime summarization and automatic trace analysis with the NPB BT-MZ MPI+OpenMP parallel application on Stampede is reported, along with discussion of on-going and future work.
Scale-based clustering using the radial basis function network

Adaptive learning dynamics of the radial basis function network (RBFN) are compared with a scale-based clustering technique and a relationship between the two is pointed out. Using this link, it is shown how scale-based clustering can be done using the RBFN, with the radial basis function (RBF) width as the scale parameter. The technique suggests the "right" scale at which the given data set must be clustered and obviates the need for knowing the number of clusters beforehand. We show how this method solves the problem of determining the number of RBF units and the widths required to get a good network solution. <<ETX>>
Release of normal bases from intact DNA by a native DNA repair enzyme

Base excision repair is initiated by DNA glycosylases removing inappropriate bases from DNA. One group of these enzymes, comprising 3‐methyladenine DNA glycosylase II (AlkA) from Escherichia coli and related enzymes from other organisms, has been found to have an unusual broad specificity towards quite different base structures. We tested whether such enzymes might also be capable of removing normal base residues from DNA. The native enzymes from E.coli, Saccharomyces cerevisiae and human cells promoted release of intact guanines with significant frequencies, and further analysis of AlkA showed that all the normal bases can be removed. Transformation of E.coli with plasmids expressing different levels of AlkA produced an increased spontaneous mutation frequency correlated with the expression levels, indicating that excision of normal bases occurs at biologically significant rates. We propose that the broad specificity 3‐methyladenine DNA glycosylases represent a general type of repair enzyme ‘pulling’ bases in DNA largely at random, without much preference for a specific structure. The specificity for release of damaged bases occurs because base structure alterations cause instability of the base–sugar bonds. Damaged bases are therefore released more readily than normal bases once the bond activation energy is reduced further by the enzyme. Qualitatively, the model correlates quite well with the relative rate of excision observed for most, if not all, of the substrates described for AlkA and analogues.
Research of cooperative product design based on a rapid inducing solid model

Web-based interactive design always brings out mass of data transferring and makes it difficult to display real-time model. In order to decrease transferring data, a model called RISM (rapid inducing solid model) is provided to build the shape representation and operation structure. Based on the structure, an operation history tree is built by extending traditional CSG model. Then traditional product CAD model is divided into two parts in RISM, one is displaying model contained surface attributes for product design and run in client, the other is represented model contained geometry attributes for transforming to CAM model and running in server. According to the idea, RISM structure is built to construct CSG-based operations history tree. Then based on RISM common operations set and RISM message mechanism, a CSCD framework is proposed. Therefore, displaying model and representation model could work individually and integrate in one united body. At last, a cooperative design system based on ACIS is implemented for testing. It is shown that the RISM enhance design system effectively by decreasing transferring data largely, and the model provides a new framework to realize distributed Web application.
Benzoquinone from Fusarium pigment inhibits the proliferation of estrogen receptor-positive MCF-7 cells through the NF-κB pathway via estrogen receptor signaling

Natural pigments are known for possessing a wide range of pharmacological and health-promoting properties. The pigments, produced by a new strain Fusarium (Fusarium sp. JN158) previously identified in our laboratory, were found to have 6 peaks (representing 6 compounds) by high-performance liquid chromatography with a diode-array detector (HPLC-DAD) separation. The 6th peak compound (compound VI) is a benzoquinone compound. In this study, we examined the effects of compound VI on the proliferation of breast cancer cells and aimed to elucidate the underlying mechamisms. Compound VI exerted anti-proliferative effects on MCF-7 estrogen receptor (ER)+ cells in a dose-dependent manner (IC25, 7 µM; IC50, 11 µM), whereas it had no effect on MDA-MB-231 ER− cells and normal cells. The cell index (CI) began to decrease at 24 h following treatment with benzoquinone. Mechanistically, the results from molecular analysis revealed that compound VI inhibited the expression of ERα, progesterone receptor (PR), vascular endothelial growth factor (VEGF), Bcl-2, cyclin D1 and nuclear factor-κB (NF-κB) p65, while it increased the expression of cleaved caspase-3 and Bax in the MCF-7 cells. Taken together, our findings indicate that compound VI exerts anti-proliferative effects on MCF-7 cells through the NF-κB pathway via the regulation of ER signaling. Our data may indicate that benzoquinone from Fusarium pigment may have potential for use as an anti-proliferative agent in the treatment of breast cancer.
Performance Analysis of Traffic Load and Node Density in Ad hoc Networks

In ad hoc mobile networks nodes typically communicate over wireless channels and are capable of movement. Wireless nodes also have the unique capability of transmission at different power levels. As the transmission power is varied, a tradeoff exists between the number of hops and the overall bandwidth available to individual nodes. Nodes in mobile ad hoc networks are typically battery operated. Because both the battery lifetime and the channel bandwidth are limited resources, it is important to determine the effect different transmission power levels have on the overall performance of the network. This paper explores the effect different traffic loads have on the network performance when the transmission power is varied. It is shown that in order to find an optimum node density, both the traffic load and the rate of mobility have to be taken into account. It is also shown that for sparser networks there exists a threshold after which the delivery ratio starts to decline. When the traffic load is below the point where network saturation occurs, denser networks achieve a higher delivery ratio, but at a higher cost.
A generalized cost optimal decision model for record matching

Record (or entity) matching or linkage is the process of identifying records in one or more data sources, that refer to the same real world entity or object. In record linkage, the ultimate goal of a decision model is to provide the decision maker with a tool for making decisions upon the actual matching status of a pair of records (i.e., documents, events, persons, cases, etc.). Existing models of record linkage rely on decision rules that minimize the probability of subjecting a case to clerical review, conditional on the probabilities of erroneous matches and erroneous non-matches. In practice though, (a) the value of an erroneous match is, in many applications, quite different from the value of an erroneous non-match, and (b) the cost and the probability of a misclassification, which is associated with the clerical review, is ignored in this way. In this paper, we present a decision model which is optimal, based on the cost of the record linkage operation, and general enough to accommodate multi-class or multi-decision case studies. We also present an example along with the results from applying the proposed model to large comparison spaces.
An Overview of the Programatica Toolset

Industry and academia have attacked this problem in many different ways, demonstrating concretely that the use of techniques such as systematic design processes, rigorous testing, or formal methods can each contribute significantly to increased reliability, security, and trustworthiness. There are obviously some significant differences between these techniques, but there is also a unifying feature: each one results in some tangible form of evidence that provides a basis for trust. Examples of such evidence include a record of the meeting where a code review was conducted, the set of test cases to which an application was subjected, or a formal proof that establishes the validity of a critical property.
Benefits of Opportunistic Routing, Implicit Acknowledgments, and Network Coding on a Linear Broadcast Network

This work studies the benefits of using opportunistic routing, implicit acknowledgments, and network coding on a linear broadcast packet network. Nodes are arranged in a line, and the first node wishes to communicate with the end node. When node i transmits, it is received at node j with a probability P(i,j). Several communication protocols are proposed and their performance studied using the mean and variance of the completion time as metrics. The protocols studied use end-to-end coding and link-by-link retransmission with network coding both with and without opportunistic routing. Simulation and analytical results are presented. The link-by-link protocols significantly outperform end-to-end coding using both metrics, especially when the packet loss probability is high. Opportunistic routing shows a mixed benefit over link-by-link protocols without it. When using opportunistic routing, the variance of the completion time is higher, and the mean is either similar or lower, depending on the channel conditions. When the loss probabilities are higher, opportunistic routing shows little benefit, whereas with a lower probability of packet loss, opportunistic routing shows a significant reduction in mean completion time.
Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA.

We have been unable to "force" double-stranded RNA to fold into nucleosome-like structures using several different histone-RNA "reconstitution" procedures. Even if the histones are first stabilized in octameric form by dimethylsuberimidate cross-linking they are still unable to form specific complexes with the RNA. Moreover double-stranded RNA is unable to induce histones to assemble into octamers although we confirm that the non-nucleic acid homopolymer, polyglutamic acid, has this ability. We have also determined, using pyrimidine tract analysis, that nucleosomes will not form over a sufficiently long segment of poly(dA). poly(dT) in a recombinant DNA molecule. Thus nucleosomes cannot fold DNA containing an 80 base pair poly(dA). poly(dT) segment but a 20 base pair segment can be accommodated in nucleosomes fairly well. Segments of intermediate length can be accommodated but are clearly selected against. Poly(dA). poly(dT) differs only slightly from natural DNA in helix structure. Therefore either this homopolymer resists folding, or nucleosomes are very exacting in the nucleic acid steroid parameters they will tolerate. Such constraints may be relevant to nucleosome positioning in chromatin.
A real-time finite line detection system based on FPGA

Image processing and analysis are active research topics. An intelligent vehicle and a service robot require these techniques. In particular, there is a big demand for line detection because it has a wide range of applications. The line features in an image are used for object identification, robot navigation, and intelligent vehicle control. To detect the lines, a Hough transform is generally used. The Hough transform has good detection results and it is robust to noise, but it takes a long time to execute and it requires a great deal of memory to store the parameter space. This paper proposes a dedicated line detection hardware system. To increase the processing speed, it has a parallel Hough transform unit, and it partitions the parameter space to decrease the memory requirements. It can detect not only the line parameters, but also the exact start and end points of each line, and it sorts these lines by length. It can display the detected line on a monitor via the DVI interface. This system is designed with VHDL and implemented on an XC4VLX200 FPGA. The device usage is about 15% and the maximum clock frequency is 67 MHz. It can detect up to 256 lines in one image frame and it can process up to 149 frames per second. The simulation and real experimental results are given to verify the system performance.
Cosmological models discrimination with Weak Lensing

Weak gravitational lensing provides a unique method to map directly the dark matter in the Universe. The majority of lensing analyses uses the two-point statistics of the cosmic shear field to constrain the cosmological model yielding degeneracies, such as that between �8 and m, respectively the r.m.s. of the mass fluctuations at a scale of 8Mpc/h and the matter density parameter both at z = 0. However, the two-point statistics only measure the Gaussian properties of the field and the weak lensing field is non-Gaussian. It has been shown that the estimation of non-Gaussian statistics on weak lensing data can improve the constraints on cosmological parameters. In this paper, we systematically compare a wide range of non-Gaussian estimators in order to determine which one provides tighter constraints on the cosmological parameters. These statistical methods include skewness, kurtosis and the Higher Criticism test in several sparse representations such as wavelet and curvelet; as well as the bispectrum, peak counting and a new introduced statistic called Wavelet Peak Counting (WPC). Comparisons based on sparse representations show that the wavelet transform is the most sensitive to non-Gaussian cosmological structures. It appears also that the best statistic for non-Gaussian characterization in weak lensing mass maps is the WPC. Finally, we show that the �8-m degeneracy could be even better broken if the WPC estimation is performed on weak lensing mass maps filtered by the wavelet method, MRLens.
Tolerant and Adaptive Information Retrieval with Neural Networks

The COSIMIR (Cognitive Similarity Learning in Information Retrieval) model applies the powerful backpropagation algorithm to Information Retrieval, integrating human centered, soft and tolerant computing to the core of the retrieval processes. An overview of neural networks in Information Retrieval shows that current systems do not fully exploit the potential of neural networks. An empirical evaluation of COSIMIR has led to positive and promising results.
Children’s and Adolescents’ Peer Relationships as Contexts for Forgiveness and Nonforgiveness

This study investigated how children and adolescents describe forgiveness and nonforgiveness experiences within the context of their relationships with peers. Specifically, we examined (1) the types of relationships youth described in their narrative accounts of forgiveness and nonforgiveness, (2) how youth described changes in the nature of their relationships following forgiveness and nonforgiveness, and (3) the circumstances in which youth ultimately described forgiving or not forgiving their close friends for transgressions. A total of 100 children and adolescents (7-, 11- and 16-years-old) described two experiences in which they forgave or did not forgive a peer who had hurt them. At all ages, youth described friends more frequently in forgiveness narratives, and disliked peers more frequently in nonforgiveness narratives. Further, adolescents differentiated more between friends and good friends than 7-year-olds. Youth overall described more positive consequences in their relationships following forgiveness than nonforgiveness, but these effects were qualified by the manner in which youth described their experience of forgiveness. In particular, negative consequences for relationships were more often described following a lack of intrapersonal forgiveness (i.e., describing unresolved emotions persisting into the present). Last, a qualitative analysis of youths’ forgiveness and nonforgiveness experiences with good friends suggested that the type of harm, intentionality, and offender’s response following the harm influenced youths’ willingness to forgive a best friend. These findings provide new insight into the ways in which youth describe relationships as contexts for forgiveness and nonforgiveness experiences and changes in their peer relationships following experiences.
Socialización, trayectorias y poscarrera de ministros en Chile, 1990-2010

Se analizan las carreras politicas de los ministros en los gabinetes chilenos entre 1990 y 2010, con datos de una encuesta de 386 miembros de la elite que fueron parte del campo politico. De la muestra, solo 108 casos fueron ministros, lo que representa mas de 60 por ciento de los nombramientos del periodo. Se describe al grupo y se presenta un analisis comparado cualitativo (qca por sus siglas en ingles) de carreras politicas con trayectorias de larga duracion. Ademas, se presenta un analisis de trayectorias y carreras posministeriales, en el que se aprecian patrones de circulacion comunes. Se evidencia un grupo con circulos sociales compartidos, y trayectorias y capitales especificos.
A Source-Code Based Extraction Way for Micro Processes Influencing Software Complexity

We propose a way of extracting micro processes that influence software complexity. Purposes of extracting the micro processes are (1) clarifying what micro processes influence software complexity, and (2) preventing software complexity from increasing by the micro processes. In the extraction way, at first, modules in which micro processes occurred are detected by interviews to developers of ¿known projects¿. Because relationships between complexity and occurrences of micro processes are analyzed, micro processes influencing complexity are clarified in ¿known projects¿. After that, we evaluate whether the micro processes similarly influence complexity of modules of the other ¿known¿ projects. As a result, three micro processes influencing complexity have been detected. After constructing difference models based on the relationships, the difference models have been adapted to ¿unknown¿ projects such as open source projects. Modules in which the micro processes might occur have been detected. In addition, we developed a programming editor including a function of automatic detection of occurrence of the micro processes. Using the editor, we tried to prevent source code complexity from increasing.
A Metabonomic Study of the Effect of Methanol Extract of Ginger on Raji Cells Using 1HNMR Spectroscopy

Cancer is currently a major international health problem. The development of resistance to chemotherapy has resulted in the search for herbal drugs. Ginger is a medicinal plant with several clinical applications. Metabolomics is a simultaneous detection of all the metabolites by use of 1HNMR or mass spectroscopy and interpretation by modeling software. The purpose of this study was to detect the altered metabolites of Raji cells in the presence of ginger extract in vitro. Cells were cultured in the presence and absence of methanolic ginger extract in RPMI medium. IC50 determined by MTT and lipophilic and hydrophilic extracts were prepared from control and treated groups which were analyzed by 1HNMR. The IC50 was 1000 μg/mL. Modeling of spectra was carried out on the two groups using OSC-PLS with MATLAB software and the main metabolites detected. Further analysis was carried out using MetaboAnalyst database. The main metabolic pathways affected by the ginger extract were detected. Ginger extract was seen to effect the protein biosynthesis, amino acid, and carbohydrate metabolism and had a strong cytotoxic effect on Raji cells in vitro.