Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcription of AAT•ATT Triplet Repeats in Escherichia coli Is Silenced by H-NS and IS1E Transposition

Background The trinucleotide repeats AAT•ATT are simple DNA sequences that potentially form different types of non-B DNA secondary structures and cause genomic instabilities in vivo. Methodology and Principal Findings The molecular mechanism underlying the maintenance of a 24-triplet AAT•ATT repeat was examined in E.coli by cloning the repeats into the EcoRI site in plasmid pUC18 and into the attB site on the E.coli genome. Either the AAT or the ATT strand acted as lagging strand template in a replication fork. Propagations of the repeats in either orientation on plasmids did not affect colony morphology when triplet repeat transcription using the lacZ promoter was repressed either by supplementing LacIQ in trans or by adding glucose into the medium. In contrast, transparent colonies were formed by inducing transcription of the repeats, suggesting that transcription of AAT•ATT repeats was toxic to cell growth. Meanwhile, significant IS1E transposition events were observed both into the triplet repeats region proximal to the promoter side, the promoter region of the lacZ gene, and into the AAT•ATT region itself. Transposition reversed the transparent colony phenotype back into healthy, convex colonies. In contrast, transcription of an 8-triplet AAT•ATT repeat in either orientation on plasmids did not produce significant changes in cell morphology and did not promote IS1E transposition events. We further found that a role of IS1E transposition into plasmids was to inhibit transcription through the repeats, which was influenced by the presence of the H-NS protein, but not of its paralogue StpA. Conclusions and Significance Our findings thus suggest that the longer AAT•ATT triplet repeats in E.coli become vulnerable after transcription. H-NS and its facilitated IS1E transposition can silence long triplet repeats transcription and preserve cell growth and survival.
Ontology-based query expansion in the biomedicine domain

Ontologies conceptualize knowledge with concepts and the relevant relations among them. Domain-independent ontology represents common knowledge of natural language. Domain-specific ontology represents professional knowledge in a specific domain. Information retrieval system purposes to find the useful documents wanted by users. The major problem of information retrieval is ambiguity of language. There are several methods can be used to decrease the negative effect of ambiguity, including query expansion which add new terms into the original query terms. This project applies synonym and hyponym relations from domain-independent (WordNet) and domain-specific (UMLS) ontologies to expand the queries in biomedicine domain, and then evaluate their performance. In the result, WordNet doesn’t give obvious improvement on the retrieval performance, UMLS slightly improves the result on precision.
Removing node and edge overlapping in graph layouts by a modified EGENET solver

Graph layout problems, such as node and edge overlapping, occur widely in many industrial computer-aided design applications. Usually, these problems are handled in an ad-hoc manner by some specially designed algorithms. GENET and its extended model EGENET are local search models that are used to efficiently solve constraint satisfaction problems such as the car-sequencing problems. Both models use min-conflict heuristic-based artificial neural nets to update every finite-domain variable for finding local minima, and then apply heuristic learning rule(s) to escape those local minima not representing solutions. In the past, few researchers have ever considered to apply any local search method like the EGENET approach to solve graph layout problems. In this paper, we consider how to modify the original EGENET model for solving the graph layout problems formulated as continuous constrained optimization problems. An empirical evaluation of different approaches on the graph layout problems demonstrated some advantages of our modified EGENET approach, which requires further investigation. More importantly, this interesting proposal opens up numerous opportunities for exploring the other possible ways to modify the original EGENET model, or using the other local search methods to solve these graph layout problems.
Pregled metoda za raspoznavanje lica

Sažetak – Prepoznavanje lica jedno je o najuspješnijih primje na analize slike i kao takvo si je priskrbilo dosta pažnje i prou čavanja zadnjih godina. Razlog tome su razne komercijalne i policijske primjene kao i raspoloživ ost upotrebljivih tehnologija. Iako su današnji sustavi za prepoznavanje lica dosegli odre ñenu zrelost postoji još otvorenih problema. Prepoznavanje u nekontroliranim uvjetima, npr. razni izvori svjetlosti i nagib glave, još uvijek su neriješeni problemi. U ovom ra du dan je prikaz trenutnih metoda prepoznavanja i postoje ći problemi. Klju čne riječi – raspoznavanje lica, detekcija, video, osvjetljenje , poza
Dumpling: An Efficient Method Based on Clustering for Network Positioning

The prediction for network distance, as a function of network coordinate system, has already been proved by existing works. This paper, presents Dumpling, a decentralized network coordinate system for Internet distance prediction. It combines the mechanism of physical mass spring system and the clustering method in the internet which based on inter-host latencies. We have implemented the Dumpling algorithm and evaluated it through simulations. By performing experiment on the datasets collected from Planetlab, we show that Dumpling can predict network distances quickly and accurately, it also can protect the virtual network structure in the coordinate space and reduce the number of system oscillation.
High performance FPGA object detector: Hardware prototype

Summary form only given. In this demo, we introduce a novel architecture of an engine for high performance multi-scale detection of objects in videos based on WaldBoost training algorithm. The key properties of the architecture include processing of streamed data and low resource consumption. We implemented the engine in FPGA and we show that it can process 640 × 480 pixel video streams at over 160 FPS without the need of external memory.
ClimbTheWorld: real-time stairstep counting to increase physical activity

The increasing number of people that are overweight due to a sedentary life requires persuasive strategies to convince people to change their behaviors. In this paper, we present a machine learning based technique to recognize and count stairsteps when a person climbs or descends stairs. This technique has been used as part of ClimbTheWorld, a real-time smartphone application that aims at persuading people to use stairs instead of elevators or escalators, since an engaging activity has more chance to change people's life habits. We perform a fine-grained analysis by exploiting smartphone sensors to recognize single stairsteps. Data-dependent sliding windows are used facilitating the learning process and reducing the computational cost. Finally, energy consumption is widely investigated to optimize the trade-off between classification precision and battery usage, to avoid exhausting smartphone battery.
On the Acquisition of the Indefinite Article: A Cross-linguistic Study of French, Italian, Romanian and Spanish Child Speech

The present article argues that the idea of morphology-driven syntax carries over to first-language acquisition. Morphology encodes properties of functional categories, i.e. particular features and feature values that must be set according to the target (adult) language during the acquisition process. In agreement with previous findings concerning the acquisition of functional categories in the verbal domain, we discuss here some cross-linguistic data with respect to the nominal functional domain. In this respect, specificity can be said to develop stepwise, as the result of the valuation of the /number/ before the /person/ feature of noun phrases, which finds its reflection in the emergence of indefinite articles before definite articles.
A high-speed gearbox based on phase independent architecture for 100G Ethernet physical coding sublayer

This paper presents a phase independent 66:8 gearbox design for 100GE PCS TX system, compatible with IEEE P802.3ba standard. By using a kind of phase independent architecture, the gearbox can convert data width from 66-bit to 8-bit stably. In addition, architecture optimization and pipeline technique are also applied to increase the working speed of the gearbox circuit. The optimized PCS TX circuit including the 66:8 gearbox has been implemented and fabricated by using semicustom design method based on 0. 18μm CMOS standard cell library. Post simulation results show that the optimized circuit can work well at a frequency of 700 MHz, meeting the 100GE PCS design requirements.
Wave-equation inversion prestack Hessian

The angle-domain Hessian can be computed from the subsurface-offset domain Hessian by an offset-to-angle transformation. An understanding of how the seismic energy is distributed with reection angle can be gained by explicitly computing the angle-domain Hessian. The Hessian computation in a model with a single reector under a Gaussian velocity anomaly (creating uneven illumination) illustrates the theory.
Small World and Scale – Free Network Topologies in an Artificial Regulatory Network Model

Small world and scale–free network topologies commonly exist in natural and artificial systems. Many mechanisms for producing these topologies have been presented in the literature. We present an artificial regulatory network model generated by a duplication / divergence process on a randomly generated genetic string and show that networks with small world and scale–free topologies can be produced with some regularity.
Requirements engineering: The quest for the dependent variable

Requirements engineering is a vibrant and broad research area. It covers a range of activities with different objectives. By reviewing experiments previously included in systematic literature reviews, this paper provides an overview of the dependent variables used in experimental requirements engineering research. This paper also identifies the theoretical motivation for the use of these variables in the experiments. The results show that a wide range of different variables has been applied in experiments and operationalized through both subjective assessments (e.g., subjects' perceived utility of a technique) and objective measurements (e.g., the number of defects found in a requirements specification). The theoretical basis for these variables and operationalizations are unclear in most cases. Directions for theoretical work to identify suitable dependent variables are provided.
Efficient change control of XML documents

XML-based documents play a major role in modern information architectures and their corresponding workflows. In this context, the ability to identify and represent differences between two versions of a document is essential. Several approaches to finding the differences between XML documents have already been proposed. Typically, they are based on tree-to-tree correction, or sequence alignment. Most of these algorithms, however, are too slow and do not support the subsequent merging of changes. In this paper, we present a differencing algorithm tailored to ordered XML documents, called DocTreeDiff. It relies on our context-oriented XML versioning model which allows for document merging, presented in earlier work. An empiric evaluation demonstrates the efficiency of our approach as well as the high quality of the generated deltas.
A new digital report for disseminating meeting outcomes

Abstract: This paper explores the "digitalization" of a particular genre of written documents, the ones produced by meeting processes, especially supported by Electronic Meeting Systems. Although it is now common to find meeting reports in a digital format, it was found that they are simply replicas of the paper versions. As long as a purpose of a meeting report is to disseminate meeting outcomes it is important understanding what kind of new digital document must be produced to improve this process. In this paper it is proposed a solution based on the notions of meeting genre and meeting genre system, but extends the last concept to incorporate the context notion. In order to implement the proposed solution, it was analyzed the actual digital meeting reports produced. Then, it was set up an experiment with a small sample of users to understand the impact of the additional characteristics in the dissemination process.
The layout of iso-orientation domains in area 18 of cat visual cortex: optical imaging reveals a pinwheel-like organization

In this study we used optical imaging based on activity-dependent intrinsic signals to determine the distribution of cells responding to gratings of various orientations moving in different directions in area 18 of cat visual cortex. To test directional-selective clustering of neurons, we compared cortical activity maps obtained by stimulation with two gratings of identical orientation but moving in opposite directions. We found those maps to be almost identical, suggesting that neurons are not notably clustered into directionality columns. We also compared activity maps obtained with gratings of different orientations. Each of the orientation maps was similar to the 2- deoxyglucose maps previously reported. Having compiled the information obtained from the different orientations into one “orientation preference map,” we found, in contrast to earlier reports, that iso- orientation domains are not elongated parallel bands but are small patches organized in “pinwheels” around points that we refer to as “orientation centers. ” We furthermore show that the only locations at which orientation preference changes rapidly are these orientation centers and not lines or loops. In addition, this report clarifies that our observations on the functional architecture of cat area 18, although at first sight at variance with earlier observations, are actually fully consistent with them. We therefore propose that in cat visual cortex pinwheel-like patterns of orientation preference form an irregular mosaic of modular units with an average density of 1.2 pinwheels per square millimeter.
Comparing Curves Using Additive Models

Advances in technology have increased dramatically the amount of data measured in industrial processes. Thousands of measurements are often available in operations where previously only a single measurement, at a given point in time or space, was taken. These measurements allow the reconstruction of the whole profile or “signature” of the operation over time or space. Examples are the tonnage applied in a stamping press during a stroke and the density profile of particleboard. Many of these signatures have complicated forms that are not well modeled with parametric models. In this paper, a relatively new class of models called additive models is used to assess the sources of variation active on these signatures. The models used contain a nonparametric or smooth portion to model the form of the signature, and a parametric portion to incorporate other sources of variation. A table is developed to assess the magnitude of the sources of variation. These techniques are illustrated using density profiles of engineered wood boards. Instructions on the implementation of these techniques in S-Plus and SAS are given.
Gabor-Based Kernel Independent Component Analysis for Face Recognition

In this paper, a new Gabor-based Kernel Independent Component Analysis (GKICA) method for face recognition is presented. This method first derives a Gabor feature vector from a set of down-sampled Gabor wavelet representations of face images, then reduces the dimensionality of the vector by means of kernel principal component analysis, and finally defines the independent Gabor kernel features based on the Independent Component Analysis (ICA). Experiments are performed to test the proposed algorithm on ORL dataset and Yale dataset. Results show that our new algorithm achieves higher recognition rates than ICA and Kernel Independent Component Analysis (KICA), and costs less time than Gable-based ICA (GICA).
Silicon synapses self-correct for both mismatch and design inhomogeneities

A neuromorphic chip with an array of neurons has connections (`synapses`) which implement a biological learning mechanism known as spike-timing-dependent plasticity. STDP is a homeostatic mechanism which regulates the firing rate of neurons. In this reported work, this mechanism is shown to reduce variation in performance between neurons, due to both mismatch in fabrication and inhomogeneities in the electronic design.
IMPROVING SEARCH ENGINE PERFORMANCE WITH CONTEXT EXTRACTION USING LUCENE, DBPEDIA-SPOTLIGHT, AND WORDNET

Search engines are common tools which retrieve information from considerable amount of data according to the user needs. The data size that needs to be handled and retrieving relevant information, are the main problems of every search engine. Additionally, in order to improve the performance of a search engine, there are various approaches and methods are applied. On the other hand, using context information besides words in the document is a quite new area. Including “Context Information” into the game is a promising field of work. In this research, we use context information extracted from the documents in the collection to improve the performance of the search engine. In first step, we extract context using Lucene, DBPedia-Spotlight, and Wordnet. As the second step, we build a graph using extracted context information. In the third step, in order to group similar contexts, we cluster context graph. In the fourth step, we rescore results using context-clusters and context-information of documents, as well as queries. In the fifth step, we implement a data collection tool to collect gold-standard data. In the sixth and final step, we compare the results of our algorithm with gold-standard data set. According to experimental results, using context information may improve the search engine performance but the collection should be relatively big.
Encoding of images based on a lapped orthogonal transform

Traditional block transform image coding systems generate artifacts near block boundaries which degrade low bit rate coded images. To reduce these artifacts, a class of unitary transformations, called lapped orthogonal transforms (LOT), is investigated. The basis function on which the signal is projected are overlapped for adjacent blocks. An example of an LOT optimized in terms of energy compaction is numerically derived, using an augmented Lagrangian optimization algorithm. Using this LOT, intraframe coding experiments for 256*240 pixel images were performed at bit rates between 0.1 and 0.35 bits/pixel. The LOT improved the coded image subjective quality over other transforms. The LOT was also used in interframe full-motion video coding experiments for head and shoulder sequences at 28 and 56 kb/s. Significant improvement resulted at low data rates and if no motion compensation were used. However, the improvement was no longer significant at 56 kb/s with full motion compensation. >
Analysis of aarchitectural features for enhancing the performance of a database machine

RAP (Relational Associative Processor) is a “back-end” database processor that is intended to take over much of the effort of database management in a computer system. In order to enhance RAP's performance its design includes mechanisms for permitting features analogous to multiprogramming and virtual memory as in general purpose computer systems. It is the purpose of this paper to present the detailed design of these mechanisms, along with some analysis that supports their value. Specifically, (1) the response time provided by RAP under several scheduling disciplines involving priority by class is analyzed, (2) the cost effectiveness of the additional hardware in RAP necessary to support multiprogramming is assessed, and (3) a detailed design of the RAP virtual memory system and its monitor is presented.
Object Connectivity in a Concurrent Calculus of Classes — Extended

The concurrent ν-calculus has been investigated as a core calculus for imperative, object-oriented languages with multithreading and heap-allocated objects. From an abstract point of view, the combination of this form of concurrency with objects corresponds to features known from the popular language Java. One distinctive feature, however, of the concurrent object calculus is that it is object-based, whereas the mainstream of object-oriented languages is class-based. This work extends the concurrent ν-calculus by introducing classes and exploring some of the semantical consequences. The external behavior of a component, given as a set of threads and objects, can be described in a linear-time setting as the set of traces of interactions with the environment. Considering classes as part of the component makes instantiation a possible interaction between component and environment. A striking consequence of this new interaction is that we need to take into account connectivity information, i.e., the way objects may have knowledge of each other, in order to get a precise characterization of possible traces. We formulate an operational semantics that incoporates the connectivity information into the scoping mechanism of the ν-calculus. Since instantiation itself is to be considered as non-observable, we formulate a semantics where objects are instantiated only when they are accessed for the first time (“lazy instantiation”).
Design for a real-time high-quality volume rendering workstation

A design is presented for a workstation capable of rendering arbitrary mixtures of analytically defined geometry and sampled scalar fields of three spatial dimensions in realtime or near real-time. The design is based on volumetric compositing, a relatively new approach to visualizing scalar fields by computing 2D projections of a colored semi-transparent volume. Geometric primitives are added by filtering and 3D scan-converting them into the dataset prior to rendering. Speedups totaling four orders of magnitude over published volumetric compositing techniques are obtained through a combination of algorithmic improvements and hardware implementation on Pixelplanes 5, a massively parallel raster display engine incorporating custom logic-enhanced memory chips. A preliminary design is also presented for a two-handed volumeof-interest data exploration tool.
Merging the adaptive random walks planner with the randomized potential field planner

In this paper we investigate whether it is advantageous to merge some ideas formerly found in the randomized potential field planner with our recently introduced adaptive random walks planner. These aspects are biasing the generation of samples, an attractor for the samples generator, and the possibility to backtrack when the planner gets stuck while exploring the configuration space. We illustrate the numerical results of different experiments using these strategies one at the time, or combined together. It turns out that benefits of different amplitude can be obtained using them, but it is in general hard to incorporate these components in a general way independent from the problem instance to be solved.