Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of Altered 3′- UTR miRNA-Binding Sites from RNA-Seq Data: The Swine Leukocyte Antigen Complex (SLA) as a Model Region

The SLA (swine leukocyte antigen, MHC: SLA) genes are the most important determinants of immune, infectious disease and vaccine response in pigs; several genetic associations with immunity and swine production traits have been reported. However, most of the current knowledge on SLA is limited to gene coding regions. MicroRNAs (miRNAs) are small molecules that post-transcriptionally regulate the expression of a large number of protein-coding genes in metazoans, and are suggested to play important roles in fine-tuning immune mechanisms and disease responses. Polymorphisms in either miRNAs or their gene targets may have a significant impact on gene expression by abolishing, weakening or creating miRNA target sites, possibly leading to phenotypic variation. We explored the impact of variants in the 3′-UTR miRNA target sites of genes within the whole SLA region. The combined predictions by TargetScan, PACMIT and TargetSpy, based on different biological parameters, empowered the identification of miRNA target sites and the discovery of polymorphic miRNA target sites (poly-miRTSs). Predictions for three SLA genes characterized by a different range of sequence variation provided proof of principle for the analysis of poly-miRTSs from a total of 144 M RNA-Seq reads collected from different porcine tissues. Twenty-four novel SNPs were predicted to affect miRNA-binding sites in 19 genes of the SLA region. Seven of these genes (SLA-1, SLA-6, SLA-DQA, SLA-DQB1, SLA-DOA, SLA-DOB and TAP1) are linked to antigen processing and presentation functions, which is reminiscent of associations with disease traits reported for altered miRNA binding to MHC genes in humans. An inverse correlation in expression levels was demonstrated between miRNAs and co-expressed SLA targets by exploiting a published dataset (RNA-Seq and small RNA-Seq) of three porcine tissues. Our results support the resource value of RNA-Seq collections to identify SNPs that may lead to altered miRNA regulation patterns.
A Guide to Formal Analysis of Join Processing in Massively Parallel Systems

Over the last decade, there has been an enormous increase in the volume of data that is being stored, processed and analyzed. In order to improve the performance of query processing on such amounts of data, many modern data management systems (e.g. Spark [23, 28], Hadoop [13, 9, 24], and others [19, 14]) have resorted to the power of parallelism to speed up computation. Parallelism enables the distribution of computation for data-intensive tasks into hundreds, or even thousands of machines, and thus significantly reduces the completion time for several crucial data processing tasks. In this paper, we present a survey on recent results [18, 4, 5, 17] that study the computational complexity of mulitway join processing in such massively parallel systems. Our goal is twofold. First, we introduce a simple theoretical model, called the MPC (Massively Parallel Computation) model, that allows us to rigorously analyze the computational complexity of various parallel algorithms for query processing. Second, using the MPC model as a theoretical tool, we show how we can design novel algorithms and techniques for multiway join processing, and how we can prove their optimality through tight lower bounds. Our analysis provides a deeper understanding of how much synchronization, communication and data load is required when we compute a multiway join query, and informs of what is possible to achieve under specific system constraints.
Frame synchronization at the sound of silence

A novel approach is introduced for the design of the unique word (UW) to be inserted into TDM/TDMA systems for frame synchronization purposes. In particular, the UW is composed by all zero symbols that are distributed along the frame in order to improve the autocorrelation properties. The resulting UW is identified as silent-UW (S-UW). We show in this paper that S-UW leads to an optimum detector with very limited complexity, and with performance that can be significantly better than the classic UW in the presence of frequency offsets or at moderate to high signal-to-noise ratios. A fully analytical performance characterization is presented reporting also comparisons with state-of-the-art alternatives.
Visualization of Flow Behavior in Earth Mantle Convection

A fundamental characteristic of fluid flow is that it causes mixing: introduce a dye into a flow, and it will disperse. Mixing can be used as a method to visualize and characterize flow. Because mixing is a process that occurs over time, it is a 4D problem that presents a challenge for computation, visualization, and analysis. Motivated by a mixing problem in geophysics, we introduce a combination of methods to analyze, transform, and finally visualize mixing in simulations of convection in a self-gravitating 3D spherical shell representing convection in the Earth's mantle. Geophysicists use tools such as the finite element model CitcomS to simulate convection, and introduce massless, passive tracers to model mixing. The output of geophysical flow simulation is hard to analyze for domain experts because of overall data size and complexity. In addition, information overload and occlusion are problems when visualizing a whole-earth model. To address the large size of the data, we rearrange the simulation data using intelligent indexing for fast file access and efficient caching. To address information overload and interpret mixing, we compute tracer concentration statistics, which are used to characterize mixing in mantle convection models. Our visualization uses a specially tailored version of Direct Volume Rendering. The most important adjustment is the use of constant opacity. Because of this special area of application, i. e. the rendering of a spherical shell, many computations for volume rendering can be optimized. These optimizations are essential to a smooth animation of the time-dependent simulation data. Our results show how our system can be used to quickly assess the simulation output and test hypotheses regarding Earth's mantle convection. The integrated processing pipeline helps geoscientists to focus on their main task of analyzing mantle homogenization.
Particle attraction localisation

In this paper, we present an original method for Bayesian localisation based on particle approximation. Our method overcomes a majority of problems inherent in previous Kalman filter and Bayesian approaches, including the recent Monte Carlo localisation methods. The algorithm converges quickly to any desired precision. It does not over-converge in the case of highly accurate sensor data and thus does not require a mixture-based approach. Also, the algorithm recovers well from random repositioning. These benefits are not hindered by computation which can be performed in real time on low powered processors. Further, the algorithm is intuitive and easy to implement. This algorithm is evaluated in simulation and has been applied to our entrant in the Sony four legged league of RoboCup, where it has been tested over many hours of international competition.
Mutations in -Tubulin Map to Domains Involved in Regulation of Microtubule Stability in Epothilone- resistant Cell Lines

The epothilones (Epos) are a group of natural products isolated from the myxobacterium, Sorangium cellulosum. They have a mechanism of action similar to that of Taxol, i.e., they stabilize microtubules and induce the formation of microtubule bundles in cells. Because they are simpler in structure than Taxol and preserve their activity in P-glycoprotein-expressing cells, they are being studied as potential antitumor drugs. In this work, a series of Epo-resistant A549 and HeLa cell lines have been selected and analyzed. Class I -tubulin, the major isotype of -tubulin in these Eporesistant cell lines, has been sequenced in a search for mutations. In the Epo B-resistant A549 cells, there is a mutation at 292 from Gln to Glu, in the Epo Aresistant HeLa cell line there is a mutation at 173 from Pro to Ala, and in the Epo B-resistant HeLa cell line there is a heterozygous mutation at 422 from Tyr to a mixture of Tyr and Cys. These mutations are close to the M-loop, the nucleotide-binding site, and the microtubule-associated protein binding sites, respectively. It is likely that these mutations in tubulin provide cells with a mechanism of resistance to the Epos and taxanes. Among these resistant cell lines, A549.EpoB40 is hypersensitive to microtubuledestabilizing drugs, such as vinblastine and colchicine, and HeLa.EpoB1. 8 is dependent on the Epos or taxanes for growth. Our studies provide evidence that the M-loop, the GTP binding site, and the microtubuleassociated protein binding sites at the COOH terminus in -tubulin are critical for the regulation of microtubule stability.
The role of local school quality in rural employment and population growth.

"This study investigates the influence of school quality (measured at the high school level) on 1980 to 1990 population and employment change for nonmetropolitan fringe and hinterland census tracts in South Carolina. A Boarnet variation of the Carlino-Mills model is used to examine the interdependence of population and employment change. Results.indicate that fringe tracts' population growth was positively related to student test scores, and hinterland tracts population and employment growth were negatively related to student-teacher ratios. Empirical results suggest that local school quality provided a positive influence on rural growth, primarily in terms of residential growth. The role of school quality for employment growth was less clear. "
Finding Themes in Medline Documents: Probabilistic Similarity Search

Large on-line document databases, such as Medline, pose a major challenge of retrieving the few documents most releva nt to the user’s needs, while minimizing the return rate of nonrelevant documents. Retrieval of documents similar to a use rprovided example document is a promising query paradigm towards meeting this goal. We present a new theme-based probabilistic approach for find ing documents relevant to a given query document, and summarizi ng their contents. Preliminary experiments conducted over a s ubset of Medline documents related to AIDS demonstrate the effectiveness of our approach.
Yif1B Is Involved in the Anterograde Traffic Pathway and the Golgi Architecture

Yif1B is an intracellular membrane‐bound protein belonging to the Yip family, shown previously to control serotonin 5‐HT1A receptor targeting to dendrites. Because some Yip proteins are involved in the intracellular traffic between the ER and the Golgi, here we investigated the precise localization of Yif1B in HeLa cells. We found that Yif1B is not resident into the Golgi, but rather belongs to the IC compartment. After analyzing the role of Yif1B in protein transport, we showed that the traffic of the VSVG protein marker was accelerated in Yif1B depleted HeLa cells, as well as in hippocampal neurons from Yif1B KO mice. Conversely, Yif1B depletion in HeLa cells did not change the retrograde traffic of ShTx. Interestingly, in long term depletion of Yif1B as in Yif1B KO mice, we observed a disorganized Golgi architecture in CA1 pyramidal hippocampal neurons, which was confirmed by electron microscopy. However, because short term depletion of Yif1B did not change Golgi structure, it is likely that the implication of Yif1B in anterograde traffic does not rely on its role in structural organization of the Golgi apparatus, but rather on its shuttling between the ER, the IC and the Golgi compartments.
Clustering based leaders' selection in multi-objective evolutionary algorithms

Clustering-based Leaders Selection (CLS) is a novel leaders selection technique in multi-objective evolutionary algorithms. Clustering is applied on both the objective and solution spaces whereby each individual is assigned to two clusters; one in the objective space and the other in the solution space. Mapping between clusters in both spaces is then applied to recognize regions with potentially better solutions. A leaders archive is used where a representative of each cluster in the objective and solution spaces is stored. The results of applying CLS integrated with NSGAII on seven standard multi-objective problems, show that clustering based leaders selection NSGAII (NSGAII/C) is highly competitive comparing with the original algorithm.
Overexpression of cation-dependent mannose 6-phosphate receptor prevents cell death induced by serum deprivation in PC12 cells.

PC12 cells express well cation-independent mannose 6-phosphate receptors (CI-MPR), but not cation-dependent (CD)-MPR as much. To examine CD-MPR dependency of transport of cathepsins B and D to lysosomes in PC12 cells, we prepared the cells overexpressing CD-MPR. Immunoreactivity for cathepsin B became more distinct and larger in size in the transfected cells than in wild-type cells. No difference in the distribution of cathepsin D was seen between these two cells. The viability of the cells following serum deprivation was significantly higher in the transfected cells than in wild-type cells. This increased viability of the transfected cells was blocked by CA074, a specific inhibitor of cathepsin B, while pepstatin A suppressed the action of CA074. The results suggest that CD-MPR preferentially transport cathepsin B in PC12 cells, and cathepsins B and D participate in the regulation of PC12 cell apoptosis.
The impact of tangled code changes

When interacting with version control systems, developers often commit unrelated or loosely related code changes in a single transaction. When analyzing the version history, such tangled changes will make all changes to all modules appear related, possibly compromising the resulting analyses through noise and bias. In an investigation of five open-source Java projects, we found up to 15% of all bug fixes to consist of multiple tangled changes. Using a multi-predictor approach to untangle changes, we show that on average at least 16.6% of all source files are incorrectly associated with bug reports. We recommend better change organization to limit the impact of tangled changes.
Online trajectory generation for omnidirectional biped walking

This paper describes the online generation of trajectories for omnidirectional walking on two legs. The gait can be parameterized using walking direction, walking speed, and rotational speed. Our approach has a low computational complexity and can be implemented on small onboard computers. We tested the proposed approach using our humanoid robot Jupp. The competitions in the RoboCup soccer domain showed that omnidirectional walking has advantages when acting in dynamic environments
Predicting Financial Crashes Using Discrete Scale Invariance

We present a synthesis of all the available empirical evidence in the light of recent theoretical developments for the existence of characteristic log-periodic signatures of growing bubbles in a variety of markets including 8 unrelated crashes from 1929 to 1998 on stock markets as diverse as the US, Hong-Kong or the Russian market and on currencies. To our knowledge, no major financial crash preceded by an extended bubble has occurred in the past 2 decades without exhibiting such log-periodic signatures.
The Sixth Metaheuristics International Conference ? ?-1 Particle Swarm Optimization and Sequential Sampling in Noisy Environments

In many real-world optimization problems, function values can only be estimated but not determined exactly. Falsely calibrated measurement instruments, inexact scales, scale reading errors, etc. are typical sources for measurement errors. If the function of interest is the output from stochastic simulations, then the measurements may be exact, but some of the model output variables are random variables. The term “noise” will be used in the remainder of this article to subsume these phenomena.
Magnetic Nanowires as Materials for Cancer Cell Destruction

Magnetic Nanowires as Materials for Cancer Cell Destruction Maŕıa Fernanda Contreras Gerenas Current cancer therapies are highly cytotoxic and their delivery to exclusively the a↵ected site is poorly controlled, resulting in unavoidable and often severe side e↵ects. In an e↵ort to overcome such issues, magnetic nanoparticles have been recently gaining relevance in the areas of biomedical applications and therapeutics, opening pathways to alternative methods. This led to the concept of magnetic particle hyperthermia in which magnetic nano beads are heated by a high power magnetic field. The increase in temperature kills the cancer cells, which are more susceptible to heat in comparison to healthy cells. In this dissertation, the possibility to kill cancer cells with magnetic nanowires is evaluated. The idea is to exploit a magnetomechanical e↵ect, where nanowires cause cancer cell death through vibrating in a low power magnetic field. Specifically, the magnetic nanowires e↵ects to cells in culture and their ability to induce cancer cell death, when combined with an alternating magnetic field, was investigated. Nickel and iron nanowires of 35 nm diameter and 1 to 5 μm long were synthesized by electrodeposition into nanoporous alumina templates, which were prepared using a two-step anodization process on highly pure aluminum substrates. For the cytotoxicity studies, the nanowires were added to cancer cells in culture, varying the incubation time and the concentration. The cell-nanowire interaction was thoroughly studied at the cellular level (mitochondrial metabolic activity, cell membrane integrity and, apoptosis/necrosis assay), and optical level (transmission electron and confocal microscopy). Furthermore, to investigate their therapeutic potential, an alternating magnetic field was applied varying its intensity and frequency. After the magnetic field application, cells health was measured at the mitochondrial activity level.
A Survey on Device-Free Passive Localization and Gesture Recognition via Body Wave Reflections

Localization of RF signals has been well understood and realized in a multitude of wireless sensor networks. Recently, there has been a surge in research interest surrounding wireless human tracking via RF. This broadly defined domain encompasses areas of research as diverse and expansive as RF Communication Networks, DSP, HCI, and Computer Vision. Traditionally, human tracking is achieved either using a wireless device attached to the subject or utilizing line-of-sight communication. Many existing systems employ wearable wireless tracking devices such as passive tags or active tags that may be monitoring GPS, ultrasonic, or accelerometer data. Obvious drawbacks to wearable tracking devices are the practicalities of users remembering to wear the device, device cost, and power management in active tags. Line-of-sight communication systems usually work in the visible and IR light spectrum and offers relief from these problems, but offer little flexibility around the obvious and inherent line-of-sight constraint. Hence, existing human localization techniques leave much to be desired within the domain of practical home applications. In this article, we explore systems that are able to localize a human in 3D space without a wearable RF device or line-of-sight constraints by measuring body reflections in the non-visible spectrum. Furthermore, we explore how RF-based and near-visible device-free localization can be used for pose estimation, for example in fall detection.
Some geometric critical exponents for percolation and the random-cluster model.

We introduce several infinite families of critical exponents for the random-cluster model and present scaling arguments relating them to the k -arm exponents. We then present Monte Carlo simulations confirming these predictions. These exponents provide a convenient way to determine k -arm exponents from Monte Carlo simulations. An understanding of these exponents also leads to a radically improved implementation of the Sweeny Monte Carlo algorithm. In addition, our Monte Carlo data allow us to conjecture an exact expression for the shortest-path fractal dimension d(min) in two dimensions: d(min)=[over ? ](g+2)(g+18)/(32 g) , where g is the Coulomb-gas coupling, related to the cluster fugacity q via q=2+2 cos(gpi/2) with 2< or =g< or =4 .
Exploiting Synonyms to Improve Question and Answering Systems

Community Question and Answering (CQA) systems are a popular way for Internet users to get answers to complex and common everyday questions. One of the challenges with CQA is that some of the asked questions are not answered [8]. This paper addresses this challenge by using a synonym-based approach that expands each unanswered question into several related questions. This paper argues that the number of unanswered questions can be reduced by searching the data set for the most similar resolved question(s) (questions that have been satisfactorily answered) to either the unanswered question and / or any of its expanded questions. If this search returns more than one resolved question, we rank the returned questions and choose the highest ranking resolved question as the most similar to the unanswered question. General Terms Information Extraction
SMAWL: A SMAll Workflow Language Based on CCS

This paper provides a overview of SMAWL, a SMAll Workflow Lan- guage based on CCS (Calculus of Communicating Systems). There has been a prolonged debate in the workflow community about the relative suitability of Petri nets versus …-calculus as a formal foundation for workflow languages. Here we demonstrate how to build a workflow language based on CCS (a predecessor of …-calculus). To facilitate comparison with other approaches SMAWL is de- signed to be able to express the same 20 patterns that originally led to the design of the Petri net-based workflow language YAWL by van der Aalst and ter Hofst- ede. After an initial example of a SMAWL program, some design considerata are discussed, and the constructs of the language are presented along with excerpts of the compositional source-level translation to CCS.
A Polymer-Based Microfluidic Resistive Sensor for Detecting Distributed Loads

This paper reports on a polymer-based microfluidic resistive sensor for detecting distributed loads. The sensor is comprised of a polymer rectangular microstructure with an embedded electrolyte-filled microchannel and an array of electrodes aligned along the microchannel length. Electrolyte solution in the microchannel serves as impedance transduction. Distributed loads acting on the polymer microstructure give rise to different deflection along the microstructure length, which is recorded as the resistance change in electrolyte solution. This sensor can detect distributed loads by monitoring the resistance change at each pair of electrodes. A sensor with an in-plane dimension of ∼20mm×10mm and five pairs of electrodes is fabricated using a CNC machine. 1M KCl solution is used as the electrolyte. Using a custom built electronic circuit on breadboard and a custom LabVIEW program, the static and dynamic performance of the sensor is characterized, demonstrating the feasibility of employing this sensor to detect distributed loads.Copyright © 2012 by ASME
How to Read a Visualization Research Paper: Extracting the Essentials

When pursuing an unfamiliar research direction, a researcher, possibly a PhD student, must undertake a literature search. This search aims to discover what research has already been carried out in a given field (solved problems) and what research hasn't (unsolved problems). However, in visualization and computer graphics, reading a refereed conference or journal paper can be challenging owing to its high level of specialization, complexity, and detail. Such papers often present a detailed mathematical framework accompanied by algorithms and data structures to carry them out and are usually written by (or with the aid of) experts in the field with many years' experience. This complex ity comes as no great surprise because a single paper is often the result of many (combined) person-years of work.