Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitation of promoter methylation of multiple genes in urine DNA and bladder cancer detection.

BACKGROUND The noninvasive identification of bladder tumors may improve disease control and prevent disease progression. Aberrant promoter methylation (i.e., hypermethylation) is a major mechanism for silencing tumor suppressor genes and other cancer-associated genes in many human cancers, including bladder cancer. METHODS A quantitative fluorogenic real-time polymerase chain reaction (PCR) assay was used to examine primary tumor DNA and urine sediment DNA from 15 patients with bladder cancer and 25 control subjects for promoter hypermethylation of nine genes (APC, ARF, CDH1, GSTP1, MGMT, CDKN2A, RARbeta2, RASSF1A, and TIMP3) to identify potential biomarkers for bladder cancer. We then used these markers to examine urine sediment DNA samples from an additional 160 patients with bladder cancers of various stages and grades and from an additional 69 age-matched control subjects. Data were analyzed on the basis of a prediction model and were internally validated using a jacknife procedure. All statistical tests were two-sided. RESULTS For all 15 patients with paired DNA samples, the promoter methylation pattern in urine matched that in the primary tumors. Four genes displayed 100% specificity. Of the 175 bladder cancer patients, 121 (69%, 95% confidence interval [CI] = 62% to 76%) displayed promoter methylation in at least one of these genes (CDKN2A, ARF, MGMT, and GSTP1), whereas all control subjects were negative for such methylation (100% specificity, 95% CI = 96% to 100%). A logistic prediction model using the methylation levels of all remaining five genes was developed and internally validated for subjects who were negative on the four-gene panel. This combined, two-stage predictor produced an internally validated ROC curve with an overall sensitivity of 82% (95% CI = 75 % to 87%) and specificity of 96% (95% CI = 90% to 99%). CONCLUSION Testing a small panel of genes with the quantitative methylation-specific PCR assay in urine sediment DNA is a powerful noninvasive approach for the detection of bladder cancer. Larger independent confirmatory cohorts with longitudinal follow-up will be required in future studies to define the impact of this technology on early detection, prognosis, and disease monitoring before clinical application.
Building A Security-Aware Query Answering System Based On Hierarchical Data Masking

Knowledge based query answering system takes advantage of data mining techniques to provide answers to user queries that involve incomplete or foreign attribute values. However, such process may cause a security issue when the system contains confidential data required to be protected. The confidential data as well as other values can be treated as missing or incomplete, and vulnerable to improper disclosure of their true values. To minimize such vulnerability, data transformation techniques are often utilized. In this paper, we present a method that exploits hierarchical structure of attributes to minimize the changes from the original information system while accommodating a given security requirement. In particular, our method replaces the existing data with more generalized ones in such a way that the value replacement cannot be used to predict the confidential data.
Business Process Management : a Bird ' sEye View and Research Agenda

Recently, Business Process Management (BPM) has gained a lot of attention both from the academic world and the industrial world. The similarities between workflow management and business process management can make one wonder whether it's all old wine in new bottles. But although there are many similarities and many results from workflow research still apply, recent technological developments have changed the domain in a substantial way, resulting in new opportunities and interesting research questions. The convergence of workflow management and Enterprise Application Integration yields prospects for integrating the organisational view and the engineering or automation view of an information system. Internet technologies such as XML and SOAP offer the potential of massive scalability and interconnectivity. In this paper, we first provide a broad overview of the domain of BPM and identify challenges from a modelling quality perspective. Thereafter, we zoom into the use of web services technology for business processes enactment. Furthermore, we review some obvious and less obvious application domains of business process management and business process enactment. Finally, we suggest a research agenda for BPM, by proposing some open issues. Monique Snoeck KULeuven, Department of Applied
Self-organized criticality and mass extinction in evolutionary algorithms

The gaps in the fossil record gave rise to the hypothesis that evolution proceeded in long periods of stasis, which alternated with occasional, rapid changes that yielded evolutionary progress. One mechanism that could cause these punctuated bursts is the recolonization of changing and deserted niches after mass extinction events. Furthermore, paleontological studies have shown that there is a power law relationship between the frequency of species extinction events and the size of the extinction impact. Power law relationships of this kind are typical for complex systems, which operate at a critical state between chaos and order, known as self-organized criticality (SOC). Based on this background, we used SOC to control the size of spatial extinction zones in a diffusion model. The SOC selection process was easy to implement and implied only negligible computational costs. Our results show that the SOC spatial extinction model clearly outperforms simple evolutionary algorithms (EAs) and the diffusion model (CGA). Further, our results support the biological hypothesis that mass extinctions might play an important role in evolution. However, the success of simple EAs indicates that evolution would already be a powerful optimization process without mass extinction, though probably slower and with less perfect adaptations.
Native malware detection in smartphones with android OS using static analysis, feature selection and ensemble classifiers

The use of Smartphones (SPs)with Android Operating System (AOS) has reached unprecedented popularity. This is due to the many features that these devices offer as Internet connection, storage of information as well as the ability to perform diverse online transactions. As a result, these devices have become the main target of malware attacks that try to exploit the security vulnerabilities of AOS.Therefore, in order to mitigate these attacks, methods for malware analysis and detection are needed.In this work a method for analysis and detection of malware, which can run natively in the device, is proposed. The approach can analyze applications already installed on the device, monitor new apps installations or updates. Static analysis is used to determine the permissions, hardware and software features requested by applications. An application being analyzed is classified as malware or benign using a model based on ensemble machine learning classifiers and feature selection algorithms. To validate the proposed method, 1377 malware samples and 1377 benign samples, collected from different sources, were used.Results show that the proposed approach detects malware with 96.26%of accuracy. Additional tests were conducted in three different SPs devices to validate malware detection performance in a real environment andto obtain an average execution time. Results of these tests show that the proposed method detects malware with 94.48% of accuracy, getting the analysis results of an application in 35milliseconds.
GENERAL PARADIGMS FOR IMPLEMENTING ADAPTIVE LEARNING SYSTEMS

In this paper, we consider adaptive learning system in the framework of context-aware computing. We i ntroduce general paradigms for implementing real adaptivity. The par adigms consider inferring the contexts (user and us e situation), selecting the action in the given context, social f iltering approach when context is not known, and ut ilizing information about system dynamics in the form of hidden Markov models.
CyanoBase: a large-scale update on its 20th anniversary

The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes. We have also optimized the user interface for large genomic data to include the use of semantic web technologies and JBrowse and have extended community-based reannotation resources through the re-annotation of Synechocystis sp. PCC 6803 by the cyanobacterial research community. These updates have markedly improved CyanoBase, providing cyanobacterial genome annotations as references for cyanobacterial research.
A Survey on Mining Software Repositories

This paper presents fundamental concepts, overall process and recent research issues of Mining Software Repositories. The data sources such as source control systems, bug tracking systems or archived communications, data types and techniques used for general MSR problems are also presented. Finally, evaluation approaches, opportunities and challenge issues are given. key words: mining, software, repository, extraction, change, evolution, analysis
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV

Endonuclease IV belongs to a class of important apurinic/apyrimidinic endonucleases involved in DNA repair. Although a structure-based mechanistic hypothesis has been put forth for this enzyme, the detailed catalytic mechanism has remained unknown. Using thermodynamic integration in the context of ab initio quantum mechanics/molecular mechanics molecular dynamics, we examined certain aspects of the phosphodiester cleavage step in the mechanism. We found the reaction proceeded through a synchronous bimolecular (ANDN) mechanism with reaction free energy and barrier of −3.5 and 20.6 kcal/mol, in agreement with experimental estimates. In the course of the reaction the trinuclear active site of endonuclease IV underwent dramatic local conformational changes: shifts in the mode of coordination of both substrate and first-shell ligands. This qualitative finding supports the notion that structural rearrangements in the active sites of multinuclear enzymes are integral to biological function.
Straight Line Extraction for Stereoimage Feature Matching

Linear feature can provide more information than point feature and can be extracted and described conveniently compared with the planar structure in the aerial images, a new straight line extraction method for steroimage feature matching is proposed, mainly for the man-made objects. The fusion and the filtering strategies are designed for the linear features extracted from the aerial images, and then feature grouping is implemented among the linear features, and each feature group contains its associated matching relationships. The experimental results show that the proposed algorithm is not only more efficient and robust but also can get richer and more accurate straight line information, especially for the buildings.
One rhinophore probably provides sufficient sensory input for odour-based navigation by the nudibranch mollusc Tritonia diomedea

Tritonia diomedea (synonymous with Tritonia tetraquetra) navigates in turbulent odour plumes, crawling upstream towards prey and downstream to avoid predators. This is probably accomplished by odour-gated rheotaxis, but other possibilities have not been excluded. Our goal was to test whether T. diomedea uses odour-gated rheotaxis and to simultaneously determine which of the cephalic sensory organs (rhinophores and oral veil) are required for navigation. In a first experiment, slugs showed no coherent responses to streams of odour directed at single rhinophores. In a second experiment, navigation in prey and predator odour plumes was compared between animals with unilateral rhinophore lesions, denervated oral veils, or combined unilateral rhinophore lesions and denervated oral veils. In all treatments, animals navigated in a similar manner to that of control and sham-operated animals, indicating that a single rhinophore provides sufficient sensory input for navigation (assuming that a distributed flow measurement system would also be affected by the denervations). Amongst various potential navigational strategies, only odour-gated positive rheotaxis can produce the navigation tracks we observed in prey plumes while receiving input from a single sensor. Thus, we provide strong evidence that T. diomedea uses odour-gated rheotaxis in attractive odour plumes, with odours and flow detected by the rhinophores. In predator plumes, slugs turned downstream to varying degrees rather than orienting directly downstream for crawling, resulting in greater dispersion for negative rheotaxis in aversive plumes. These conclusions are the first explicit confirmation of odour-gated rheotaxis as a navigational strategy in gastropods and are also a foundation for exploring the neural circuits that mediate odour-gated rheotaxis.
Weighted Information Retrieval Algorithms for Onsite Object Service

Designing proper algorithm is necessary for applications that query and analyze mass-information for high efficiency in various information services. In this paper, we discuss weighted information retrieval algorithms for an newly service, onsite object service. Four retrieval algorithms with one-dimension weight and one retrieval algorithm with multi-dimension weight are proposed to address the requirements of OOS. Detailed performance analysis and comparison about the advantage and disadvantage of these 5 different algorithms are presented later. And at last a conclusion is drawn about the recommendation for these algorithms in different scenarios.
Relative effectiveness of score normalization methods in speaker identification fusing acoustic and prosodic information

In this paper, an investigation on the fusion of acoustic and prosodic information for GMM-UBM based text-independent speaker identification is presented. When acoustic and prosodic based systems are established, it is advantageous to normalize the dynamic ranges of the score dimensions, that is, likelihood scores from different quality of acoustic- and prosodic-based models. Score normalization methods, linear scaling to unit range and linear scaling to unit variance, are applied to transform the output scores using the background instances so as to obtain meaningful comparison between speaker models. In this fusion system based on linear score weighting approach, the performance of speaker identification is further improved when incorporating prosodic level of information. Experimental results on part of the NIST 1999 SRE corpus are reported.
A taxonomy of visual feedback for interactive systems

In an interactive system, the term of visual feedback is applied to any graphic form of communication directed from the application towards the users. The visual feedback is predominant in current interactive systems, but it is difficult for a designer to identify the pertinent visual feedback for this type of system. This paper addresses these issues with a taxonomy of visual feedback which is described on detail with meaningful examples. The goal is to offer a designer a high level description of visual responses of an interactive system independent of any graphical environment. Key-Words: Interactive system, visual feedback, taxonomy, interaction styles and architectural models
On scheduling algorithm for device-to-device communication in 60 GHz networks

The world is witnessing a tremendous increase in data demands which is subject to the new emerging technologies, applications and services. 60 GHz communication network is one of such technology, claiming data rate in multi-gigabits. In this paper, we propose a scheduling algorithm for device-to-device 60 GHz network having directional antennas. The proposed algorithm utilizes the vertex coloring scheme and is optimized to improve system throughput. A threshold minimum distance between conflicting flows is used to keep the accumulative interference limited. Also, when there are conflicts among different flows, those with better data rate prospects will be scheduled priorly. Simulation results show that our scheme has brought significant improvement to system throughput almost by 19% and average flow number per slot is improved by 12%, as compared to other scheduling algorithms.
“I am Done with Toys!” — The Benefits, Joys and Risks of Creativity and Innovation in Graduate Writing Support

Writing is a necessary part of the graduate student’s journey; it can also be a stressful and frustrating one that leaves students feeling “stuck” and disheartened. In this article we discuss four playful and alternative strategies that aim to free-up and inspire our graduate writers: our use of shape cards, LEGO®, walking tutorials, and yoga and meditation for writing. Through a combination of reflection on experience, initial primary research, and engagement with wider discussions, we demonstrate the benefits and joys of our creative and innovative writing support work. However, we also acknowledge that such techniques involve risks and challenges, and they certainly will not suit every graduate writer: as one of our students put it, “I am done with toys! ” Nevertheless, as this article demonstrates, such practices have a real potential to support, empower, and deepen graduate student writing.
The Chromatin Landscape of Kaposi’s Sarcoma-Associated Herpesvirus

Kaposi’s sarcoma-associated herpesvirus is an oncogenic γ-herpesvirus that causes latent infection in humans. In cells, the viral genome adopts a highly organized chromatin structure, which is controlled by a wide variety of cellular and viral chromatin regulatory factors. In the past few years, interrogation of the chromatinized KSHV genome by whole genome-analyzing tools revealed that the complex chromatin landscape spanning the viral genome in infected cells has important regulatory roles during the viral life cycle. This review summarizes the most recent findings regarding the role of histone modifications, histone modifying enzymes, DNA methylation, microRNAs, non-coding RNAs and the nuclear organization of the KSHV epigenome in the regulation of latent and lytic viral gene expression programs as well as their connection to KSHV-associated pathogenesis.
Adaptive Markov Chain Monte Carlo through Regeneration

Abstract Markov chain Monte Carlo (MCMC) is used for evaluating expectations of functions of interest under a target distribution π. This is done by calculating averages over the sample path of a Markov chain having π as its stationary distribution. For computational efficiency, the Markov chain should be rapidly mixing. This sometimes can be achieved only by careful design of the transition kernel of the chain, on the basis of a detailed preliminary exploratory analysis of π. An alternative approach might be to allow the transition kernel to adapt whenever new features of π are encountered during the MCMC run. However, if such adaptation occurs infinitely often, then the stationary distribution of the chain may be disturbed. We describe a framework, based on the concept of Markov chain regeneration, which allows adaptation to occur infinitely often but does not disturb the stationary distribution of the chain or the consistency of sample path averages.
The Effects of Noise and Sampling on the Spectral Correlation Function

The effects of noise and sampling on the spectral correlation function (SCF) introduced by Rosolowsky and coworkers are studied using observational data, numerical simulations of magnetohydrodynamic turbulence, and simple models of Gaussian spectral line profiles. The most significant innovations of this paper are (1) the normalization of the SCF based on an analytic model for the effect of noise and (2) the computation of the SCF as a function of the spatial lag between spectra within a map. A new definition of the "quality" of a spectrum, Q, is introduced, which is correlated with the usual definition of signal-to-noise ratio. The prenormalization value of the SCF is a function of Q. We derive analytically the effect of noise on the SCF, and then normalize the SCF to its analytic approximation. By computing the dependence of the SCF on the spatial lag, S0(Δr), we have been able to conclude the following: (1) S0(Δr) is a power law, with slope α, in the range of scales ℓi < ℓ < ℓo. (2) The correlation outer scale, ℓo, is determined by the size of the map, and no evidence for a true departure from self-similarity on large scales has been found. (3) The correlation inner scale, ℓi, is a true estimate of the smallest self-similar scale in a map. (4) The spectral slope, α, in a given region, is independent of velocity resolution (above a minimum resolution threshold), spatial resolution, and average spectrum quality. (5) Molecular transitions that trace higher gas density yield larger values of α (steeper slopes) than transitions tracing lower gas density. (6) Nyquist sampling, bad pixels in detector arrays, and reference-sharing data acquisition need to be taken into account for a correct determination of the SCF at Δr = 1. The value of α, however, can be computed correctly without a detailed knowledge of observational procedures.
Emergence and Frustration of Magnetism with Variable-Range Interactions in a Quantum Simulator

Magnetic Frustration The study of magnetic frustration has a long history in solid-state physics, but cold-atom systems now offer the possibility of simulating the problem with exquisite control. Islam et al. (p. 583) study a system of 16 trapped ions, using the Coulomb interactions between the ions to simulate exchange interactions present in magnetic systems. The measured spin correlations provide a window into the behavior of the system, as the effective magnetic field and the range of the interactions are tuned. Coulomb interactions in a system of 16 trapped ions are used to simulate magnetism with varying degrees of frustration. Frustration, or the competition between interacting components of a network, is often responsible for the emergent complexity of many-body systems. For instance, frustrated magnetism is a hallmark of poorly understood systems such as quantum spin liquids, spin glasses, and spin ices, whose ground states can be massively degenerate and carry high degrees of quantum entanglement. Here, we engineer frustrated antiferromagnetic interactions between spins stored in a crystal of up to 16 trapped 171Yb+ atoms. We control the amount of frustration by continuously tuning the range of interaction and directly measure spin correlation functions and their coherent dynamics. This prototypical quantum simulation points the way toward a new probe of frustrated quantum magnetism and perhaps the design of new quantum materials.