Miracle-dz/UniFAR-FTUs huggingface dataset:
GAACO: Metaheuristic driven approach for routing in OppNet

Routing in delay tolerant network addresses the ability to transport or route bundles from a source to a destination, which is a primary responsibility that all communication networks must have. However, Opportunistic Networks (Opp-Nets) or Delay Tolerant Networks are characterized by the sparse connectivity resulting in a lack of instantaneous end-to-end path between source and destination. In such a challenging environment, popular ad hoc routing protocols such as AODV and DSR fail to establish routes. We introduce a new metaheuristic oriented routing protocol GAACO that utilizes the optimization techniques of Genetic Algorithm and Ant Colony Optimization to find the path between source and destination. GAACO has been simulated in Network Simulator (NS 2) and its performance has been compared with Epidemic routing Protocol on issues such as delay, number of hops traversed, energy consumed and throughput achieved.
A new robust Kalman filter algorithm under outliers and system uncertainties

This paper proposes a new robust Kalman filter algorithm under outliers and system uncertainties. The robust Kalman filter of Durovic and Kovacevic (1999) is extended to include unknown-but-bounded parameter uncertainties in the state or observation matrix. We first formulate the robust state estimation problem as an M-estimation problem, which leads to an unconstrained nonlinear optimization problem. This is then linearized and solved iteratively as a series of linear least-squares problems. These least-squares problems are subject to the bounded system uncertainties using the robust least squares method proposed by A. Ben-Tal and A. Nemirovski (2001). Simulation results show that the new algorithm leads to a better performance than the conventional algorithms under outliers as well as system uncertainties.
Numerical Simulation and Hydrodynamic Design Optimization of a Tesla-Type Valve for Micropumps

A numerical optimization methodology is applied to improve the design of a microchannel structure used in a valveless micropump. The flow simulation algorithm employs the control volume method for Cartesian grids, while advanced numerical techniques are implemented for automatic generation of unstructured, adaptively refined grids and for the representation of irregular boundaries. Several geometric properties of the microchannel are considered as free design variables, and an optimization software based on evolutionary algorithms is used to find the best performance design. The latter is characterized by the ratio of the pressure drop in reverse flow to that in forward flow through the channel, and represents the flow rectification efficiency of the valve, when it is used as a check valve in a reciprocating pump. The optimal design is obtained quite fast and its pressure drop ratio is 50% higher compared to a standard design. Effects of Reynolds number on the valve performance are also examined and presented. Finally, the dynamic behavior of the valve under periodic flow conditions encountered in a reciprocating micropump is simulated and discussed.
Extracting Family Relationship Networks from Novels

We present an approach to the extraction of family relations from literary narrative, which incorporates a technique for utterance attribution proposed recently by Elson and McKeown (2010). In our work this technique is used in combination with the detection of vocatives - the explicit forms of address used by the characters in a novel. We take advantage of the fact that certain vocatives indicate family relations between speakers. The extracted relations are then propagated using a set of rules. We report the results of the application of our method to Jane Austen's Pride and Prejudice.
A sialoglycoprotein complex linked to the microvillus cytoskeleton acts as a receptor for pilus (AF/R1) mediated adhesion of enteropathogenic Escherichia coli (RDEC-1) in rabbit small intestine

Escherichia coli strain RDEC-1 is an enteroadherent, diarrheagenic pathogen in rabbits that utilizes AF/R1 pili for initial (stage 1) adherence, but the host receptors for this adhesion are unknown. Here we demonstrate that RDEC-1 binds, via AF/R1 pili, to a specific rabbit ileal microvillus membrane glycoprotein receptor complex of subunits 130 and 140 kD. The binding involves sialic acid present on oligosaccharide moieties of the glycoprotein receptor. Furthermore, the microvillus membrane glycoprotein receptor complex appears to be associated with cytoskeletal components via brush border myosin 1. This newly described link between AF/R1 receptor and cytoskeletal components suggests that, in addition to this function in mucosal adherence, the pili may facilitate subsequent (second stage) close effacing attachment of RDEC-1 to the host epithelium by influencing cytoskeletal function.
Glycosyltransferases and Transpeptidases/Penicillin-Binding Proteins: Valuable Targets for New Antibacterials

Peptidoglycan (PG) is an essential macromolecular sacculus surrounding most bacteria. It is assembled by the glycosyltransferase (GT) and transpeptidase (TP) activities of multimodular penicillin-binding proteins (PBPs) within multiprotein complex machineries. Both activities are essential for the synthesis of a functional stress-bearing PG shell. Although good progress has been made in terms of the functional and structural understanding of GT, finding a clinically useful antibiotic against them has been challenging until now. In contrast, the TP/PBP module has been successfully targeted by β-lactam derivatives, but the extensive use of these antibiotics has selected resistant bacterial strains that employ a wide variety of mechanisms to escape the lethal action of these antibiotics. In addition to traditional β-lactams, other classes of molecules (non-β-lactams) that inhibit PBPs are now emerging, opening new perspectives for tackling the resistance problem while taking advantage of these valuable targets, for which a wealth of structural and functional knowledge has been accumulated. The overall evidence shows that PBPs are part of multiprotein machineries whose activities are modulated by cofactors. Perturbation of these systems could lead to lethal effects. Developing screening strategies to take advantage of these mechanisms could lead to new inhibitors of PG assembly. In this paper, we present a general background on the GTs and TPs/PBPs, a survey of recent issues of bacterial resistance and a review of recent works describing new inhibitors of these enzymes.
Transmission Time-Based Mechanism to Detect Wormhole Attacks

Important applications of Wireless Ad Hoc Networks make them very attractive to attackers, therefore more research is required to guarantee the security for Wireless Ad Hoc Networks. In this paper, we proposed a transmission time based mechanism (TTM) to detect wormhole attacks - one of the most popular & serious attacks in Wireless Ad Hoc Networks. TTM detects wormhole attacks during route setup procedure by computing transmission time between every two successive nodes along the established path. Wormhole is identified base on the fact that transmission time between two fake neighbors created by wormhole is considerably higher than that between two real neighbors which are within radio range of each other. TTM has good performance, little overhead and no special hardware is required.
A rapid real-time quantitative PCR assay to determine the minimal inhibitory extracellular concentration of antibiotics against an intracellular Francisella tularensis Live Vaccine Strain

Francisella tularensis is a highly virulent facultative intracellular bacterium. The lack of a safe and efficient vaccine makes antibiotics the preferred treatment. F. tularensis antibiotic susceptibility tests are based on the in vitro standard CLSI-approved microdilution method for determining the MIC. However, limited data are available regarding the minimal inhibitory extracellular concentration (MIEC) needed to eradicate intracellular bacteria. Here, we evaluated the MIEC values of various WHO-recommended antibiotics and compared the MIEC values to the established MICs. We describe a rapid 3-h quantitative PCR (qPCR) intracellular antibiogram assay, which yields comparable MIEC values to those obtained by the classical 72-h cfu assay. This rapid qPCR assay is highly advantageous in light of the slow growth rates of F. tularensis. Our results showed that the MIECs obtained for doxycycline, chloramphenicol and ciprofloxacin were indicative of intracellular activity. Gentamicin was not effective against intracellular bacteria for at least 32 h post treatment, raising the question of whether slow-penetrating gentamicin should be used for certain stages of the disease. We suggest that the qPCR intracellular antibiogram assay may be used to screen for potentially active antibiotics against intracellular F. tularensis as well as to detect strains with acquired resistance to recommended antibiotics.
Simple striate neurons in the cat. I. Comparison of responses to moving and stationary stimuli.

: 1. Peristimulus time (PST) histograms of simple striate responses to static presentations of narrow bright and dark bars in an array of receptive-field (RF) positions have demonstrated one to four response regions with distinct response properties. 2. There is a high degree of correlation of these responses with PST histograms of responses to the same stimuli moving smoothly ("dynamic" stimuli) in a direction perpendicular to the long axis of the RF. 3. Trailing responses to smoothly moving bar stimuli usually occur as the stimulus leaves an apparently inhibitory (for that stimulus) RF region. 4. Spatially leading responses to smoothly moving stimuli occur just as a bar stimulus enters an excitatory RF region, and may be based on certain gradient-detecting properties of neurons. 5. Close agreement in peak firing rates and in positions of responses for statically and dynamically elicited responses in units that are not strongly directionally selective suggests the possibility that in most respects smooth movement responses may be the sequential linear superposition of static responses. A quantitative superposition of static responses from two units supports this conclusion. 6. The dependence on a steady background for sustained responses to static presentation of dark bars illustrates the significance of steady illumination in the RF and raises questions about the efficacy of using edge stimuli as elemental visual probes.
Lessons for managing IS in small firms

i Interested in guest editing a special theme issue of IRMJ? Contact the editor at irmj@idea-group.com Small and medium-sized firms (SMEs) are a vibrant part of all economies. Although the definition of an SME varies, for most economies, the focus is on firms with less than than 250 employees. The changes engendered by large corporations that focus on their core compe-tencies have fostered a resurgence for SMEs. Entrepreneurs identify new markets to support, which leads to a rise in specialist firms in many industries. However, the SME sector is unforgiving , with 50% of all SMEs failing within their first three years (Burns, 2001). Failure often is not due to poor business ideas but is caused more by a lack of understanding of the management issues required in order to be successful (Storey, 1994). Management means different things at different times in the life of an SME as power is delegated to managers and the SME moves from a Web-based structure that centers on the owner to a more matrix-or hierarchy-based structure that is required of larger organizations. As management structures become more formalized, SMEs require better information. Information systems (IS) are integral to the management development process. Management IS in SMEs is typically simple in the early stages of a firm. Spreadsheets are used to manage accounts, although growing firms usually adopt simple accounting packages. As firms grow, managing customers effectively becomes important, and databases begin to be used. Many SMEs have local area networks and use external e-mail. Internal e-mail is used in larger SMEs in order to improve communication. Many SMEs have developed brochureware Web sites. However, there is little evidence of successful e-business in SMEs (Brown & Lockett, 2004). SMEs tend to be followers when adopting management IS. While the SME sector is lauded for its flexible response to customers, there is little evidence of flexibility in its management IS. Replacement of management IS often occurs as a response to a crisis rather than a recognition that the business has outgrown the system's ability to deliver. Most SMEs focus on survival rather than competitive advantage, which limits the agility of response to investment in IS. This is due primarily to limited resources, particularly finance, in small firms. There is also nervousness about whether the purchased system will satisfy business requirements. Since most SME IS development is outsourced, there also are concerns about adequate technical support. These …
Learning Morphology of Romance, Germanic and Slavic Languages with the Tool Linguistica

In this paper we present preliminary work conducted on semi-automatic induction of inflectional paradigms from non annotated corpora using the open-source tool Linguistica (Goldsmith 2001) that can be utilized without any prior knowledge of the language. The aim is to induce morphology information from corpora such as to compare languages and foresee the difficulty to develop morphosyntactic lexica. We report on a series of corpus-based experiments run with Linguistica in Romance languages (Catalan, French, Italian, Portuguese, and Spanish), Germanic languages (Dutch, English and German), and Slavic language Polish. For each language we obtained interesting clusters of stems sharing the same suffixes. They can be seen as mini inflectional paradigms that include productive derivative suffixes. We ranked results depending on the size of the paradigms (maximum number of suffixes per stem) per language. Results show that it is useful to get a first idea of the role and complexity of inflection and derivation in a language, to compare results with other languages, and that it could be useful to build lexicographic resources from scratch. Still, special post-processing is needed to face the two principal drawbacks of the tool: no clear distinction between inflection and derivation, and not taking allomorphy into account.
Location-Based Crowdsourcing for Vehicular Communication in Hybrid Networks

It is a challenge to design efficient routing protocols for vehicular ad hoc networks (VANETs) because of their highly dynamic properties. We address the vehicular communication problem in urban hybrid networks and present a hybrid routing scheme for data dissemination in VANETs. Location-based crowdsourcing of nearby roadside units (RSUs) has been applied to the infrastructural support of inter-vehicle, vehicle-to-roadside, and inter-roadside communications in hybrid VANETs. The combination of RSU resources and ad hoc networks involves an online probabilistic RSU retrieval algorithm that uses coarse- and fine-grained localization to estimate the number and location of available RSUs; a network coding based multicast routing for dense VANETs using maximum distance separation (MDS) code and local topology information from the forwarding set to achieve robust communication and max-flow min-cut data dissemination; an application of opportunistic routing, using a carry-and-forward scheme to solve the forwarding disconnection problem in sparse VANETs; and a routing switch mechanism to guarantee quality of service (QoS) under various network connectivity and deployment configurations. The performance of our hybrid routing scheme is evaluated using both simulations and real testbed experiments.
3D reconstruction and virtual forming in rotationally symmetric space

For reconstructing 3D objects and for generating arbitrary views of the scene, accurate calibration of multiple cameras is very important. We introduce rotationally symmetric space, and show that in rotationally symmetric space, cameras can be calibrated and 3D points can be reconstructed just from a single basis line reliably. The proposed method is applied for deforming virtual clay in rotationally symmetric space and for generating augmented reality images of virtual pottery.
CYP3A5 variant allele frequencies in Dutch Caucasians.

BACKGROUND Enzymes of the cytochrome P450 3A (CYP3A) family are responsible for the metabolism of >50% of currently prescribed drugs. CYP3A5 is expressed in a limited number of individuals. The absence of CYP3A5 expression in approximately 70% of Caucasians was recently correlated to a genetic polymorphism (CYP3A5*3). Because CYP3A5 may represent up to 50% of total CYP3A protein in individuals polymorphically expressing CYP3A5, it may have a major role in variation of CYP3A-mediated drug metabolism. Using sequencing, have been identified (Hustert et al. Pharmacogenetics 2001;11:773-9; Kuehl et al. Nat Genet 2001;27:383-91) variant alleles *2 through *7 for CYP3A5. Detection of CYP3A5 variant alleles, and knowledge about their allelic frequency in specific ethnic groups, is important to establish the clinical relevance of screening for these polymorphisms to optimize pharmacotherapy. METHODS In a group of 500 healthy Dutch Caucasian blood donors, we determined the allelic frequency of the CYP3A5*2, *3, *4, *5, *6, and *7 alleles by use of newly developed PCR-restriction fragment length polymorphism assays. RESULTS The frequency of the defective CYP3A5*3 allele in the Dutch Caucasian population was 91%, followed by the CYP3A5*2 (1%) and CYP3A5*6 (0.1%) alleles. The CYP3A5*4, *5, and *7 alleles were not detected. CONCLUSIONS On the basis of its allelic frequency, screening for the CYP3A5*3 allele in the Caucasian population is extremely relevant. In addition, screening for the CYP3A5*2 allele may be taken into consideration in individuals heterozygous for the CYP3A5*3 allele. The CYP3A5*4, *5, *6, and *7 alleles have low allelic frequencies that do not support initial screening.
The Application of Information Visualization in Business Site of China

Various techniques have been researched after the information visualization conception was proposed at 90th 20 century. These techniques come from different fields and have many styles. There are many kinds of information in E-Commerce systems. The application Information visualization in E-Commerce is certain. This paper analyzed the kinds of information in E-Commerce systems, chose the information that is appropriate for visualization, gave some examples and discussed the statues of information visualization application in E-Commerce.
Difficult Instances of the Counting Problem for 2-quantum-SAT are Very Atypical

The problem 2-QUANTUM-SATISFIABILITY (QSAT[2]) is the generalisation of the 2-CNF-SAT problem to quantum bits, and is equivalent to determining whether or not a spin-1/2 Hamiltonian with two-body terms is frustration-free. imilarly to the classical problem #SAT[2], the counting problem #QSAT[2] of determining the size (i.e. the dimension) of the set of satisfying states is #P-complete. However, if we consider random instances of QSAT[2] in which constraints are sampled from the Haar measure, intractible instances have measure zero. An apparent reason for this is that almost all two-qubit constraints are entangled, which more readily give rise to long-range constraints. We investigate under which conditions product constraints also give rise to efficiently solvable families of #QSAT[2] instances. We consider #QSAT[2] involving only discrete distributions over tensor product operators, which interpolates between classical #SAT[2] and #QSAT[2] involving arbitrary product constraints. We find that such instances of #QSAT[2], defined on Erdos-Renyi graphs or bond-percolated lattices, are asymptotically almost surely efficiently solvable except to the extent that they are biased to resemble monotone instances of #SAT[2].
A Model for Carbohydrate Metabolism in the Diatom Phaeodactylum tricornutum Deduced from Comparative Whole Genome Analysis

Background Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids. Methodology/Principal Findings The whole genome sequence of the diatom Phaeodactylum tricornutum has recently been completed. We identified and annotated genes for enzymes involved in carbohydrate pathways based on extensive EST support and comparison to the whole genome sequence of a second diatom, Thalassiosira pseudonana. Protein localization to mitochondria was predicted based on identified similarities to mitochondrial localization motifs in other eukaryotes, whereas protein localization to plastids was based on the presence of signal peptide motifs in combination with plastid localization motifs previously shown to be required in diatoms. We identified genes potentially involved in a C4-like photosynthesis in P. tricornutum and, on the basis of sequence-based putative localization of relevant proteins, discuss possible differences in carbon concentrating mechanisms and CO2 fixation between the two diatoms. We also identified genes encoding enzymes involved in photorespiration with one interesting exception: glycerate kinase was not found in either P. tricornutum or T. pseudonana. Various Calvin cycle enzymes were found in up to five different isoforms, distributed between plastids, mitochondria and the cytosol. Diatoms store energy either as lipids or as chrysolaminaran (a β-1,3-glucan) outside of the plastids. We identified various β-glucanases and large membrane-bound glucan synthases. Interestingly most of the glucanases appear to contain C-terminal anchor domains that may attach the enzymes to membranes. Conclusions/Significance Here we present a detailed synthesis of carbohydrate metabolism in diatoms based on the genome sequences of Thalassiosira pseudonana and Phaeodactylum tricornutum. This model provides novel insights into acquisition of dissolved inorganic carbon and primary metabolic pathways of carbon in two different diatoms, which is of significance for an improved understanding of global carbon cycles.
Document Similarity using Feed Forward Neural Networks CS 224 D Final Project Writeup

Throughout this course we have learnt a lot about similarity and differences between words and phrases. However, for many natural language processing tasks this is not informative enough, often it is more useful and important to find similarities and differences between entire documents. Thus, for our final project, we decided that we wanted to use deep learning to compare documents and decide whether they were related to one another or not. When deciding how to approach this task, it quickly became clear that the difference between two documents is more than the sum of differences between their word vector representations. Having learnt about Siamese Neural Networks during the midterm, and having done more research into their usefulness, we decided our best option would be to use existing neural network architecture to build our own Siamese Network. We would then run through different types of document vectors, in order to see whether we could learn anything meaningful. After a lot of trial and error, our final idea was, given two documents, we could compare them using what our network had learnt, and the two documents would be classified as related or unrelated. Having tried a number of combinations of similarity metrics and document vector representations, we strayed from the siamese model. Instead, we moved a step back to a normal feed forward network, trying out different combinations of non-linear layers. We have come to the conclusion, that neural networks are in fact very good at distinguishing similar documents, and are able to learn the difference between related and unrelated ones they easily contend with non-deep learning methods.