Miracle-dz/UniFAR-FTUs huggingface dataset:
ARCS-Motif: discovering correlated motifs from unaligned biological sequences

MOTIVATION The goal of motif discovery is to detect novel, unknown, and important signals from biology sequences. In most models, the importance of a motif is equal to the sum of the similarity of every single position. In 2006, Song et al. introduced Aggregated Related Column Score (ARCS) measure which includes correlation information to the evaluation of motif importance. The paper showed that the ARCS measure is superior to other measures. Due to the complicated nature of the ARCS motif model, we cannot directly apply existing sequential motif discovery methods to find motifs with high ARCS values. RESULTS This article presents a novel mining algorithm, ARCS-Motif, to discover related sequential motifs in biological sequences. ARCS-Motif is applied to 400 PROSITE datasets and compared with five alternative methods (CONSENSUS, Gibbs sampler, MEME, SPLASH and DIALIGN-TX). ARCS-Motif outperforms all the methods in accuracy, and most of the methods in efficiency. Although SPLASH has better efficiency than ARCS-Motif, ARCS-Motif has much better accuracy than SPLASH. On average, ARCS-Motif is able to produce the motifs which are at least 10% better than the best of the alternative methods. Among the 400 PROSITE datasets, ARCS-Motif produces the best motifs for more than 200 families. Other than SPLASH, the execution time of ARCS-Motif is less than a third of that of the fastest alternative method and its execution time grows at the slowest rate with respect to the number of sequences and the average sequence among all methods.
The Compute-and-Forward Protocol: Implementation and Practical Aspects

In a recent work, Nazer and Gastpar proposed the Compute-and-Forward strategy as a physical-layer network coding scheme. They described a code structure based on nested lattices whose algebraic structure makes the scheme reliable and efficient. In this work, we consider the implementation of their scheme for real Gaussian channels and one dimensional lattices. We relate the maximization of the transmission rate to the lattice shortest vector problem. We explicit, in this case, the maximum likelihood criterion and show that it can be implemented by using an Inhomogeneous Diophantine Approximation algorithm.
From Color Quantization to Image Segmentation

A new technique is presented for color image segmentation. Five processes are accomplished that are respectively dealing with color image quantization, noisy regions removal, removal of thin regions, color-based region merging, and area-based region merging. Some parameters involved in the method are automatically computed, others are fixed depending on the specific application. Thus, the method is characterized by some flexibility that makes it useful for different applications. The method has been checked on color images from publicly available repositories. The performance of the method has been evaluated in terms of Precision, Recall and F-measure. The obtained results are satisfactory from both a qualitative and a quantitative point of view.
GaAs and InAs Nanowires for Ballistic Transport

Tailoring of GaAs and InAs nanowires (NWs) to be suited for measurements of ballistic transport is discussed in this paper. Methods used to avoid imperfections most harmful for the transport properties are described. We consider the imperfections, which frequently occur in III-V NWs: occasional stacking faults, unintentional impurities (like gold atoms originating from the catalyst in the vapor-liquid-solid growth method) and imperfections associated with the NW side facets. Foremost important is obtaining GaAs and InAs NWs, in which either a pure wurtzite or pure zinc-blende structure is enforced, i.e., overcoming the inherent tendency of the two structures to intermix in III-V NWs. Next follows elimination, or at least minimization of the number of incorporated impurities. In InAs NWs, this has been achieved by using low-growth temperature combined with a low-growth rate. Finally, embedding the NWs in an in situ grown shell has provided a robust way for passivation of the surface states and keeping the electrons away from any impurities adhered to the surface.
The Theory of ‘Belonging’: Defining concepts used within Belonging, Being and Becoming—The Australian Early Years Learning Framework

Abstract The implementation in 2009–10 of the Early Years Learning Framework (EYLF) spearheaded the efforts of the Australian Commonwealth government to institute a national curriculum. The theme of the new early childhood framework follows three guiding concepts: Belonging, Being and Becoming. In this article, we discuss these three concepts in order to provide a theoretical context to the Early Years Learning Framework and to enrich the debate surrounding its writing and implementation. In particular, we address the significance of posing Belonging in contiguity with the concepts of Being and Becoming. The authors suggest a strategy to cultivate a deeper appreciation of the dialectical relationships between sameness and difference, belonging and nothingness. Our premise is that ‘belonging’ refers essentially to different beings, and implicitly to the prospect of a ‘together-ness’ or identity according to which different beings are located, understood and associated, in order that Becoming can take effect. We offer these commentaries as a means of deepening conversation about the importance of scholarly approaches to philosophy for early childhood research, and especially with respect to curriculum and pedagogy.
BIUTEE: A Modular Open-Source System for Recognizing Textual Entailment

This paper introduces BiuTee, an open-source system for recognizing textual entailment. Its main advantages are its ability to utilize various types of knowledge resources, and its extensibility by which new knowledge resources and inference components can be easily integrated. These abilities make BiuTee an appealing RTE system for two research communities: (1) researchers of end applications, that can benefit from generic textual inference, and (2) RTE researchers, who can integrate their novel algorithms and knowledge resources into our system, saving the time and effort of developing a complete RTE system from scratch. Notable assistance for these researchers is provided by a visual tracing tool, by which researchers can refine and "debug" their knowledge resources and inference components.
Parceria escola-empresa no Estado de São Paulo: mapeamento e caracterização

This paper presents a survey and characterization of partnerships between state schools in Sao Paulo and enterprises, in 1996 and 1997. After showing Government initiatives to increase this partnership at state level, are presented statements of school principals and representatives of partner enterprises that show the wideness, nature and prospects of actions in development. It is evident that at the same time we see an increasing governmental involvement to develop partnerships, in last years, there is not a correspondent raise of this practice at state level.
Accelerating Crowdsourcing Based Indoor Localization Using CSI

Indoor localization is of importance for many applications. Crowdsourcing individual users' measurements can provide accurate localization without costly site-survey. However, crowdsourcing based approaches suffer from the cold start problem, in which at the beginning of system deployment, there are insufficient users to contribute their measurements, resulting in inaccurate and time-inefficient localization. In this paper, we propose a hybrid indoor localization method to solve such problem, called ACIL. We first employ the inertial navigation technique to localize some core positions or paths. To tackle the inaccuracy problem, we propose an effective method that utilizes the channel state information (CSI) of wireless signals for accurate distance estimation. This method is based on a new observation: there is a ripple-like fading pattern in wireless signals upon moving objects. Leveraging this observation, our system is capable of calculating the distance of human's movement and his/her direction. We also propose a graph-matching algorithm to setup the correlation between the trajectory and floor map. With those extra obtained location information, the impact of cold start issue will be significantly mitigated, while the LBS can be guaranteed with high localization accuracy. Extensive experiments show that the effectiveness in the human localization and movement detection. Extensive experiments validate the great performance of our protocol in case of various human locations and diverse channel conditions.
Resistance, acquiescence or incorporation? An introduction to land grabbing and political reactions ‘from below’

Political reactions ‘from below’ to global land grabbing have been vastly more varied and complex than is usually assumed. This essay introduces a collection of ground-breaking studies that discuss responses that range from various types of organized and everyday resistance to demands for incorporation or for better terms of incorporation into land deals. Initiatives ‘from below’ in response to land deals have involved local and transnational alliances and the use of legal and extra-legal methods, and have brought victories and defeats. The relevance of political reactions to land grabbing is discussed in light of theories of social movements and critical agrarian studies. Future research on reactions ‘from below’ to land grabbing must include greater attention to gender and generational differences in both impacts and political agency.
Transitional processes culminating in extreme violence

Purpose – This paper seeks to review transitional processes that foster transitions from non‐aggression to extreme aggression. Most studies on aggression focus either on traits within violent individuals or social contexts that generate violence, less attention has been paid to transitional mechanisms.Design/methodology/approach – The paper reviews “long‐term”, i.e. societal transitions that occur prior to and during genocides; mid‐term transitions such as induction into a military or paramilitary societies; and short‐term (situational) transitions that occur in situ. It reviews alterations in emotion, cognition, and behaviour that occur in these transitions and concludes with a description of the generated output behaviours of an extreme and often sadistic nature.Findings – The paper concludes with a review of Nell's “Pain‐Blood‐Death” complex as a hypothetical inherited disposition that may be triggered by any or all of these transitional processes leading to cruel aggression.Originality/value – The pap.
Modeling Transit Trip Time using Archived Bus Dispatch System Data

Transit travel time and operating speed influence service attractiveness, operating cost, and system efficiency. The objective of this paper is to estimate the values of parameters that affect the total travel time for a particular bus route in Portland, Oregon. The Metropolitan Transportation District of Oregon (TriMet) provides transit service in the three-county Portland metropolitan area. TriMet has implemented a Bus Dispatch System (BDS) as a part of its overall service control and management system. This BDS provides a rich array of archived data that were used in this study to develop the trip time model for the route under study. This trip time model provides heightened understanding of the factors that affect the trip time on the route. The value of the model was revealed when sensitivity analyses were performed using data from the studied route. This analysis concluded that improvements can be readily achieved after understanding the factors that affect total trip time. Finally, some conclusions and recommendations are presented and suggestions for additional research are provided.
Comparative Analysis of Acidobacterial Genomic Fragments from Terrestrial and Aquatic Metagenomic Libraries, with Emphasis on Acidobacteria Subdivision 6

ABSTRACT The bacterial phylum Acidobacteria has a widespread distribution and is one of the most common and diverse phyla in soil habitats. However, members of this phylum have often been recalcitrant to cultivation methods, hampering the study of this presumably important bacterial group. In this study, we used a cultivation-independent metagenomic approach to recover genomic information from soilborne members of this phylum. A soil metagenomic fosmid library was screened by PCR targeting acidobacterial 16S rRNA genes, facilitating the recovery of 17 positive clones. Recovered inserts appeared to originate from a range of Acidobacteria subdivisions, with dominance of subdivision 6 (10 clones). Upon full-length insert sequencing, gene annotation identified a total of 350 open reading frames (ORFs), representing a broad range of functions. Remarkably, six inserts from subdivision 6 contained a region of gene synteny, containing genes involved in purine de novo biosynthesis and encoding tRNA synthetase and conserved hypothetical proteins. Similar genomic regions had previously been observed in several environmental clones recovered from soil and marine sediments, facilitating comparisons with respect to gene organization and evolution. Comparative analyses revealed a general dichotomy between marine and terrestrial genes in both phylogeny and G+C content. Although the significance of this homologous gene cluster across subdivision 6 members is not known, it appears to be a common feature within a large percentage of all acidobacterial genomic fragments recovered from both of these environments.
Efficient Characteristic Set Algorithms for Equation Solving in Finite Fields and Application in Analysis of Stream Ciphers

Efficient characteristic set methods for computing solutions of a polynomial equation system in a finite field are proposed. We introduce the concept of proper triangular sets and prove that proper triangular sets are square-free and have solutions. We present an improved algorithm which can be used to reduce the zero set of an equation system in general form to the union of zero sets of proper triangular sets. Bitsize complexity for the algorithm is given in the case of Boolean polynomials. We also give a characteristic set method for Boolean polynomials, where the size of the polynomials are effectively controlled. The methods are implemented and extensive experiments show that they are quite efficient for solving equations raised in analyzing certain classes of stream ciphers.
A comparison of the clinical, demographic and psychiatric profiles among patients with erosive and non-erosive reflux disease in a multi-ethnic Asian country.

AIM To examine the clinical spectrum of gastroesophageal reflux disease (GERD) and compare erosive (ERD) with non-erosive (NERD) in terms of clinical, demographic and psychiatric profiles. METHODS Patients with reflux symptoms were enrolled and stratified to NERD and ERD after endoscopy (LA classification). Patients with ERD presenting with dyspepsia were included. Patients on proton pump inhibitors (PPI) or H2 receptor antagonists before endoscopy were excluded. Demographic data, Helicobacter pylori (H pylori) status and presence of minor psychiatric morbidity (based on General Health Questionnaire-28) were analyzed. RESULTS Among 690 patients screened, 533 were eligible for analysis (male to female ratio: 3:2; Chinese: 75.4%; Malay: 9.8%; Indian: 14.8%). Clinical spectrum of GERD: N: 40.5%; A: 46%; B: 9.2%; C: 2.1%; D: 0.6%; Barrett's esophagus: 1.7%. Compared to patients with NERD, patients with ERD were significantly older (45 vs 39.4 years), more likely to be male (64.4% vs 53.7%), tended to smoke (19.6% vs 9.7%), less likely to have minor psychiatric morbidity (26.4 vs 46.7%) and were more likely to respond to PPI (79.7 vs 66.8%). There was also a trend towards a higher BMI (24.5 vs 23.5). Race, alcohol consumption and H pylori status were not significant. On multivariate analysis, age and presence of minor psychiatric morbidity remained with significant differences. CONCLUSION The majority of patients who have typical symptoms of GERD have NERD or mild erosive reflux disease. Compared to patients with erosive reflux disease, patients with NERD were younger and had a higher prevalence of minor psychiatric morbidity.
New Concepts of Asynchronous Circuits Worst-Case Delay and Yield Estimation

Although the benefits of asynchronous design style are undeniable, this style is still a road that designers rather avoid. There are, however, serious advantages of this digital design concept that are making it favourable for many applications. Asynchronous circuits need no clock generation and distribution (Sparso, 2006; Martin & Nystrom 2006), which leaves the problems related to clock skew behind and saves a lot of chip area. Asynchronous circuits are characterized with much easier technology migration and good modularity. Very low EMI occurs during operation, while achieving high noise immunity (Lewis & Brackenbury 2001). Power is consumed only when useful work is done. The absence of the clock itself reduces the power consumption. These issues are very important while designing portable systems where battery size and lifetime are important. Synchronous circuit design styles have enormous commercial practice and very significant pedigree, and those are the major reasons for the lack of motivation to apply asynchronous circuit techniques (Davis & Nowick, 1997). Nevertheless, the motivation to pursue the study of asynchronous circuits is based on the simple fact that all high-performance ‘‘synchronous” design styles are ‘‘asynchronous in the small” (Cortadella et al. 1999) Because of that, some techniques for desynchronization of synchronous circuits have appeared lately (Cortadella et al. 2006; Andrikos 2007). Beside their benefits, some problems related to asynchronous circuit design are still waiting to be solved. One of the most important is the estimation of asynchronous circuit performances. That is, determining the delays of the paths in a particular asynchronous circuit. Early evaluation of the path delays in the circuit helps avoiding early timing problems as well as circuit performance characterization (Sokolovic, Litovski & Zwolinski 2009). Precise paths delays, of course, can be estimated only in the final steps of the design process. That is because the delay is extracted from the circuit after layout synthesis. If the delays do not satisfy the required speed of the circuit, the circuit has to be redesigned. The same conclusion stands when timing problems occur. This strongly suggests that new methods are to be offered enabling delay estimation to be performed during the early phases of digital system design. Our aim here is to establish the application of a standard logic simulator in asynchronous circuit path delay analysis and parametric yield estimation. The simplest way to determine the circuit delay is simulation. At the transistor level complex circuits’ simulation becomes inefficient. To verify the logic function and the timing
Predictability and Immediate Memory for Consonant Sequences

Two measures which have been shown to predict the ease of learning trigrams, namely log letter frequency and sequential predictability, were applied to data from an experiment on short term memory. This involved the immediate recall of 120 six-letter consonant sequences which were presented visually one letter at a time. A significant correlation was found between the probability that a given sequence would be recalled correctly and both its mean log letter frequency (r = 0.308, p < 0.001), and its mean predictability (r = 0.393, p < 0.001). Partial correlation showed only a marginally significant effect of log letter frequency when predictability was partialled out (r = 0.161, 0.05 < p < 0.1). With log letter frequency partialled out, however, a reliable correlation between predictability and recall score remained (r = 0.300, p < 0.001).
Using Social Media Presence for Alleviating Cold Start Problems in Privacy Protection

Recommender systems play an important role in most modern e-commerce applications. They have allowed users to become aware of the myriad choices available to them. The ease of information and the abundance of options have helped users make educated decisions. A recommender system studies a user's preferences and continues learning the user's changing interests, so as to suggest items that incline with the user's interests. In cases where a user is new to the application, or the user prefers not to discourse preferences, the recommender system is unable to gather the user's preference on any item. This is called the cold start problem; wherein the system can make valid recommendations only once the user starts informing the system about his/her choices. In this paper, we discuss the challenges faced by the cold start problem and how this problem may be alleviated using social media. We suggest an approach where we collect public information from users' social media accounts and analyze this information to understand their preferences. In particular, we gather the new user's information using their Twitter profile; i.e., the user's interest and preferences are extracted from his/her Twitter profile by analyzing his/her tweets. These interests will help the system understand what kind of movies the user will be most interested in. We compare these preferences with the metadata about the individual items. Using this approach, we develop a movie recommendation system wherein we produce top-N movie recommendations for a user. We used the MovieTweetings dataset to model the application. Two sets of results have been produced. In the first, smaller set of 770 users, 72.67% of users have received 100% accurate movie recommendations while nearly 80% of users got more than 75% accuracy. For the second, larger set of more than 3,500 users, 53 % of users have received 100% accurate recommendations while 72% of users got more than 75% accuracy. These encouraging results have demonstrated that the approach is effectively in alleviating cold start problems in recommendation systems, and may be applicable to many other e-commerce applications.
Underwater human-robot interaction via biological motion identification

We present an algorithm for underwater robots to visually detect and track human motion. Our objective is to enable human-robot interaction by allowing a robot to follow behind a human moving in (up to) six degrees of freedom. In particular, we have developed a system to allow a robot to detect, track and follow a scuba diver by using frequencydomain detection of biological motion patterns. The motion of biological entities is characterized by combinations of periodic motions which are inherently distinctive. This is especially true of human swimmers. By using the frequency-space response of spatial signals over a number of video frames, we attempt to identify signatures pertaining to biological motion. This technique is applied to track scuba divers in underwater domains, typically with the robot swimming behind the diver. The algorithm is able to detect a range of motions, which includes motion directly away from or towards the camera. The motion of the diver relative to the vehicle is then tracked using an Unscented Kalman Filter (UKF), an approach for non-linear estimation. The efficiency of our approach makes it attractive for real-time applications onboard our underwater vehicle, and in future applications we intend to track scuba divers in real-time with the robot. The paper presents an algorithmic overview of our approach, together with experimental evaluation based on underwater video footage. Fig. 1. An underwater robot servoing off a colored target carried by a diver.