Miracle-dz/UniFAR-FTUs huggingface dataset:
GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms

Abstract Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei. edu.br/.
Multiple second order generalized integrators for harmonic synchronization of power converters

This paper presents a new frequency-adaptive synchronization method for grid-connected power converters which allows estimating not only the positive- and negativesequence components of the power signal at the fundamental frequency, but also other sequence components at multiple frequencies. The proposed system is called the MSOGI-FLL since it is based on a decoupled network consisting of multiple second order generalized integrators (MSOGI) which are frequency-adaptive by using a frequency-locked loop (FLL). In this paper, the MSOGI-FLL is analyzed and its performance is evaluated by both simulations and experiments.
Progress Report : Collaborative Filtering Using Bregman Co-clustering

Analytics are becoming increasingly important for business competition. Many of the top brands today employ analytics to improve efficiency and sales while at the same time maintaining increased customer satisfaction and loyalty. From a consumer’s point of view, these analytical systems are often manifested in the form of recommender systems, which use accrued user data to predict the items that would be of the most interest to the user. As larger selections are made available to users, often through the power of e-commerce, recommender systems are an increasingly important part of the user experience, and if they are executed well, such systems can increase sales and generate strong user loyalty.
Distinguishing Cartesian powers of graphs

The distinguishing number D(G) of a graph is the least integer d such that there is a d‐labeling of the vertices of G that is not preserved by any nontrivial automorphism of G. We show that the distinguishing number of the square and higher powers of a connected graph G ≠ K2, K3 with respect to the Cartesian product is 2. This result strengthens results of Albertson [Electron J Combin, 12 ( 2005 ), #N17] on powers of prime graphs, and results of Klavžar and Zhu [Eu J Combin, to appear]. More generally, we also prove that d(G □ H) = 2 if G and H are relatively prime and |H| ≤ |G| < 2|H| − |H|. Under additional conditions similar results hold for powers of graphs with respect to the strong and the direct product. © 2006 Wiley Periodicals, Inc. J Graph Theory 53: 250–260, 2006
Automated Synthesis of Generalized Reversible Cascades using Genetic Algorithms

We propose an automated synthesis of Reversible logic (RL) circuits using Darwinian and Lamarckian Genetic Algorithms (GA). Our designs are in a form of cascades of generalized gates which generalize factorized Exclusive-Or-Sum-of-Products (ESOP) circuits. GA can be used to explore the problem space of combinational functions and here it is used to evolve reversible logic circuits. We emphasize the role of problem encoding a well-designed encoding leads to improved results. Our method with well-encoded circuits is compared to standard method on classical benchmarks in GA, and shows good results for synthesis of both random functions and benchmark functions with practical meaning, such as adders.
What Is It Like to Have a Body?

Few issues in psychology are as fundamental or as elusive as the sense of one’s own body. Despite widespread recognition of the link between body and self, psychology has only recently developed methods for the scientific study of bodily awareness. Experimental manipulations of embodiment in healthy volunteers have allowed for important advances in knowledge. Synchronous multisensory inputs from different modalities play a fundamental role in producing body ownership: the feeling that my body is “mine. ” Indeed, appropriate multisensory stimulation can induce a sense of ownership over external objects, virtual avatars, and even other people’s bodies. We argue that bodily experience is not monolithic, but rather has measurable internal structure and components that can be identified psychometrically and psychophysically, which suggests that the apparent phenomenal unity of self-consciousness may be illusory. We further review evidence that the sense of one’s own body is highly plastic, with representations of body structure and size particularly sensitive to multisensory influences.
Hindered and accelerated coalescence of drops in Stokes flow

We analyze axisymmetric near-contact motion of two drops under the action of an external force or imposed flow. It is shown that the far-field stress generated in the near-contact region by the outer flow qualitatively affects drainage of the thin fluid film separating the drops. If this stress acts radially outward, exponential film drainage occurs. For a radially inward far-field stress, film drainage is arrested at long times. An asymptotic analysis of the stationary long-time film profile is developed for small deformation conditions, and the critical strength of van der Waals attraction for film rupture is calculated. Hindered and accelerated drop coalescence have not been predicted by previous theories, because the far-field stress was neglected.
Polymerase chain reaction based restriction fragment length polymorphism for the genotyping of cytomegalovirus (CMV) from patients with CMV disease in Chennai.

BACKGROUND & OBJECTIVES Since cytomegalovirus (CMV) is heterogenous and exhibits genomic polymorphism, polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) was applied to identify the glycoprotein B subtypes in patients diagnosed to have CMV disease. METHODS CMV standard strain (AD 169) and 55 clinical specimens from 50 patients (35 males; 15 females) positive for CMV by PCR coding for the morphological transforming region II gene were subjected to PCR coding for gp 55 region of CMV gB gene. PCR amplified products were subjected to RFLP using Hinf I. RESULTS Of 50 patients, 26 (52.0%) (20 males; 6 females) were positive by PCR (gB gene). Upon RFLP, AD 169 and CMV strains of 14 (53.8%) patients (14 males) were typed as subtype II, and 12 (46.1%) (6 males; 6 females) as subtype III. Of 11 paediatric patients, 7 (63.6%) were infected with CMV subtype II and 4 (36.4%) with subtype III. CMV strains of the dual specimens from 3 PCR positive patients belonged to the same subtype. INTERPRETATION & CONCLUSION In this study on CMV genotypes, CMV gB subtypes II and III were found in 53.8 and 46.1 per cent patients studied respectively, while I and IV were not present.
A fixed-point blind source extraction algorithm and its application to ECG data analysis

Generalized autocorrelations and complexity pursuit are two recently developed methods for extracting interesting component from time series. They are the extensions of projection pursuit to time series data. In this paper, a fixed-point blind source extraction (BSE) algorithm for generalized autocorrelations and complexity pursuit of the desired signals is presented. The fixed-point algorithm inherits the advantages of the well-known FastICA algorithm of ICA, which is very simple, converges fast, and does not need to choose any learning step sizes. Numerical experiments on electrocardiogram (ECG) data indicate its better performance.
Fostering Science Teachers' Design for Inquiry-Based Learning by Using a Serious Game

There is wide consensus internationally amongst scientific communities that Inquiry-Based Learning can be employed to foster acquisition of clearly defined, 'certain' knowledge such as the conceptual foundations of a scientific discipline. Alternatively, it can be used to engage students with uncertainty, multiple perspectives and contestation through exploration of scientific problems. In order to enact inquiry-based learning effectively, science teachers need to be aware of how to design inquiry-based learning activities and the most effective ways of facilitating inquiry-based learning in the classroom. This paper, presents Sim AULA, a serious game for helping science teachers to create engaging activities for involving students in inquiry-based quests. The paper proposes a cyclical model comprising seven inquiry steps or phases and translates these steps into practical inquiry-based activities performed in the serious game. Sim AULA's overarching architecture is presented in the context of the in-game inquiry-based learning activities, which will be implemented and evaluated in a number of schools across Europe.
Algorithms for flow time scheduling

We study scheduling algorithms for problems arising in client-server systems. In the client-server setting, there are multiple clients that submit requests for service to the server(s) over time. Typical examples of such systems include operating systems, web-servers and database query servers. As there could be multiple clients requesting a service, the goal of a scheduling algorithm is to provide service to the clients in some reasonable way. A natural measure of the quality of service received by a client is its flow time, defined as the time since the client submits a request until it is completed. In this thesis, we study some fundamental problems related to minimizing flow time and its variants. These include ep norms of flow time, weighted flow time, stretch (flow time divided by its service requirement) and completion time. We consider these problems in various settings, such as online, offline, scheduling when the processing requirements are unknown and scheduling when jobs can be rejected at some cost.
Social Isolation and Loneliness: Prospective Associations With Functional Status in Older Adults

Objective: The present analysis aimed to examine the associations of isolation and loneliness, individually as well as simultaneously, with 2 measures of functional status (gait speed and difficulties in activities of daily living) in older adults over a 6-year period using data from the English Longitudinal Study of Ageing, and to assess if these associations differ by SES. Method: Loneliness was measured using the short form of the Revised UCLA scale, and an index of social isolation was computed incorporating marital status; frequency of contact with friends, family, and children; and participation in social activities. Measures of functional status were assessed identically at baseline and 6 years later for 3070 participants (mean age 69 years). Wealth was used as an indicator of SES. Results: In fully and mutually adjusted models, social isolation and loneliness were found to be associated with a decrease in gait speed at follow-up, with stronger effects among more disadvantaged individuals. Loneliness was associated with an increase in difficulties with activities of daily living. Conclusions: Isolation and loneliness were adversely associated with different aspects of functional status. Interventions to reduce isolation and loneliness may be particularly beneficial for individuals in disadvantaged groups.
Using Shallow Syntax Information to Improve Word Alignment and Reordering for SMT

We describe two methods to improve SMT accuracy using shallow syntax information. First, we use chunks to refine the set of word alignments typically used as a starting point in SMT systems. Second, we extend an N-gram-based SMT system with chunk tags to better account for long-distance reorderings. Experiments are reported on an Arabic-English task showing significant improvements. A human error analysis indicates that long-distance reorderings are captured effectively.
Empirical investigation of the role of privacy and data protection in the implementation of electronic government in Ghana

This study investigates the role of privacy and data protection in the implementation of e-government in developing countries. It examines the privacy and data protection issues which arise when e-government is introduced in Ghana. E-government is a way that governments liaise with their various departments and agencies through the use of information and communication technologies (ICTs). Through e-government, governments are able to provide better, effective and efficient services to their citizens. This new form of governments’ delivering services electronically to their citizens, businesses and various departments potentially offers benefits (for example, economic development, low costs and improved services) to society. However the implementation of e-government carries potential risks to users. The potential for online identity theft and fraud raises privacy concerns. From a theoretical foundation, fieldwork in Ghana, through interviews and focus groups, is used to investigate the issue of privacy and data protection in e-government implementation in an empirical setting. Interviewees included senior civil servants, political leaders, members of the Select Committee on Communication, academics, university students as well as stakeholders from private and public organisations. The research borrowed from the Straussian grounded theory approach as a technique to analyse the fieldwork data. The results of the study indicate that privacy and data protection does not currently play a significant role in e-government implementation in a developing country such as Ghana. Other factors such as access to information and communication technologies (Internet accessibility) and e-skills were found to be challenges which significantly impact individuals’ use of e-government. The study found that there is a low privacy concern among Ghanaian citizens. This was found to be significantly related to a lack of awareness of privacy issues; and also the national cultural dimensions of Ghanaian society.
A framework for dynamic sensory substitution

In this paper we present a framework for dynamic substitution of different sensory modalities with existing physical sensors. Our system is capable of finding the most optimal set of mathematical and physical transformations between two modalities of physical and virtual sensors. It allows a creation of new virtual sensors from given set of physical sensors. The virtual sensing may extend to new sensing modalities for which no direct physical sensors exist. The framework optimizes for a minimal error and optimal observation in the resulting fusion. It is processing the chain for a given spatial measurement and measurement range. The framework is capable of increasing the reliability of acquired data in multi-sensor systems by being able to asses the amount of accumulated errors. We give two examples of real-world applications of this framework in robotic environments.
Characteristics of the m2000 Automated Sample Preparation and Multiplex Real-Time PCR System for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae

ABSTRACT We evaluated a new real-time PCR-based prototype assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae developed by Abbott Molecular Inc. This assay is designed to be performed on an Abbott m2000 real-time instrument system, which consists of an m2000sp instrument for sample preparation and an m2000rt instrument for real-time PCR amplification and detection. The limit of detection of this prototype assay was determined to be 20 copies of target DNA for both C. trachomatis and N. gonorrhoeae, using serially diluted linearized plasmids. No cross-reactivity could be detected when 55 nongonococcal Neisseria isolates and 3 non-C. trachomatis Chlamydia isolates were tested at 1 million genome equivalents per reaction. Concordance with the Roche Amplicor, BDProbeTec ET, and Gen-Probe APTIMA Combo 2 tests was assessed using unlinked/deidentified surplus clinical specimens previously analyzed with these tests. For C. trachomatis, concordance for positive results ranged from 93.7% to 100%, while concordance for negative results ranged from 98.2% to 100%. For N. gonorrhoeae, concordance for positive and negative results ranged from 91.4% to 100% and 99.3% to 100%, respectively. A workflow analysis of the prototype assay was conducted to obtain information on throughput under laboratory conditions. At 48 samples/run, the time to first result for both C. trachomatis and N. gonorrhoeae was 4.5 h. A total of 135 patient specimens could be analyzed in 8.9 h, with 75 min of hands-on time. This study demonstrated the technical and clinical feasibility of the new Abbott real-time PCR C. trachomatis/N. gonorrhoeae assay.
Circular partitions with applications to visualization and embeddings

We introduce a hierarchical partitioning scheme of the Euclidean plane, called circular partitions. Such a partition consists of a hierarchy of convex polygons, each having small aspect ratio, and satisfying specified volume constraints. We apply these partitions to obtain a natural extension of the popular Treemap visualization method. Our proposed algorithm is not constrained in using only rectangles, and can achieve provably better guarantees on the aspect ratio of the constructed polygons. Under relaxed conditions, we can also construct circular partitions in higher-dimensional spaces. We use these relaxed partitions to obtain improved approximation algorithms for embedding ultrametrics into d-dimensional Euclidean space. In particular, we give a polylog(Delta)-approximation algorithm for embedding n-point ultrametrics into R^d with minimum distortion (Delta denotes the spread of the metric). The previously best-known approximation ratio for this problem was polynomial in n [Badoiu et al. SoCG 2006]. This is the first algorithm for embedding a non-trivial family of weighted graph metrics into a space of constant dimension that achieves polylogarithmic approximation ratio.
The Influence of Specific Foods and Oral Hygiene on the Microflora of Fissures and Smooth Surfaces of Molar Teeth: A 5–Day Study

A group of 20 students, harbouring >104 mutans streptococci per millilitre of saliva, was enrolled into the study. Models for sampling, reproducibly, the dental plaque present in specific sites (fissure and smooth surface) on the dentition were developed and validated. Withdrawal of normal oral hygiene procedures for only 1 day resulted in approximately 10–fold increases in the number of micro–organisms recovered from both sites. The effect of supplementing the subjects’ diets with particular food items given 5 times per day [lemonade (5.8% w/v sugars, 250 ml), biscuits (digestive biscuits, 67.6% w/w carbohydrate of which 22% w/w was sugars and 45.6% w/w was starch), caramel toffees and sugar lumps] on the number of micro–organisms recovered and on the composition of the flora at both sites was determined. Dental plaque samples were taken after 5 days and it was found that supplementation of the diet with toffee and sugar lumps resulted in significantly more micro–organisms at both sampling sites. The supplementation of the diets with lemonade or biscuits did not significantly alter the numbers of micro–organisms recovered from either site. The percentage composition of the plaque samples from both dental sites remained relatively unaffected by oral hygiene although there were lower levels of mutans streptococci which might be related to the use of an antimicrobial toothpaste containing fluoride, triclosan and zinc citrate. This study suggests that the cariogenicity of certain sucrose–containing foods may, in part, be due to the enhancement of plaque accumulation in addition to other effects on the percentage composition of the plaque which may become manifest on prolonged usage of these dietary foodstuffs. These observations are consistent with dietary survey findings which often find consumption of confectionery related to caries experience or incidence.
Semi-automatic antenna design via sampling and visualization

Optimization-based approaches to antenna design have enjoyed limited success. The task is often computationally intractable. Moreover, it is also often difficult to capture all relevant design issues and tradeoffs in a single mathematical objective function. Therefore, human experts typically specify and refine antenna designs "by hand," using computers only to evaluate their candidate designs by simulation. In this paper we propose a middle ground between this traditional approach and fully automatic optimization. We use computation to sample a space of possible antenna designs, and we rely on human judgment to select good designs from the samples returned by the computer. The key elements of our computer system are a parallel algorithm for intelligently sampling a space of possible antenna designs and a graphical user interface for visualizing and exploring candidate designs and managing the sampling process.
Protective Effects of Tumor Necrosis Factor in Experimental Legionella pneumophila Infections of Mice via Activation of PMN Function

Tumor necrosis factor (TNF) was found in the lung lavage fluids of Legionella pneumophila‐infected mice within 24 hr of intratracheal (i.t.) inoculation. Since this cytokine has been reported to activate polymorphonuclear leukocyte (PMN) function, the effect of TNF on the in vitro bactericidal capacity of PMN‐enriched cultures was determined. Murine thioglycollate‐elicited PMN which were treated with recombinant human TNF demonstrated augmented killing of L. pneumophila bacteria in vitro. Furthermore, treatment of PMN suspensions with cytokine‐containing lung lavage fluid was found to enhance the bactericidal activity of PMN. The addition of anti‐cachectin/TNF antibodies partially abrogated the stimulatory effects of the lavage fluid, suggesting that in vivo activation of PMN during the course of infection was likely, and that TNF was partially responsible for the enhanced bactericidal activity. In vivo treatment of animals with TNF resulted in significant protection of the animals from mortality. Furthermore, the rate of clearance of bacteria from the lung tissues of infected mice was increased in those animals treated with TNF, and correlated with the ability of this cytokine to protect the animals. These data suggest that the induction of TNF by Legionella bacteria during infection are involved in the non‐specific host defense mechanisms, and that PMN activated by the TNF may be instrumental in clearing the organism from infected lung tissues, thereby protecting the animal.