Miracle-dz/UniFAR-FTUs huggingface dataset:
Pf Filamentous Phage Requires UvrD for Replication in Pseudomonas aeruginosa

Biofilm development is a key component of the ability of Pseudomonas aeruginosa to evade host immune defenses and resist multiple drugs. Induction of the filamentous phage Pf, which usually is lysogenized in clinical and environmental isolates of P. aeruginosa, plays an important role in biofilm assembly, maturation, and dispersal. Despite the clinical relevance of Pf, the molecular biology of this phage is largely unknown. In this study, we found that rolling circle replication of Pf depends on UvrD, a DNA helicase normally involved in DNA repair. We also identified the initiator protein of Pf and found that it shares structural similarity with that of Vibrio cholerae phages CTXφ and VGJφ, which also use UvrD for replication. Our results reveal that, in addition to DNA repair, UvrD plays an essential role in rolling circle replication of filamentous phages among diverse bacteria genera, adding a new, previously unrecognized function of this accessory helicase. ABSTRACT Pf is a lysogenic filamentous phage that promotes biofilm development in Pseudomonas aeruginosa. Pf replicates by a rolling circle replication system which depends on a phage-encoded initiator protein and host factors usually involved in chromosome replication. Rep, an accessory replicative DNA helicase, is crucial for replication of filamentous phages in Escherichia coli. In contrast, here we show that, instead of depending on Rep, Pf replication depends on UvrD, an accessory helicase implicated in DNA repair. In this study, we also identified the initiator protein of Pf and found that it shares similarities with that of Vibrio phages CTXφ and VGJφ, which also depend on UvrD for replication. A structural comparative analysis of the initiator proteins of most known filamentous phages described thus far suggested that UvrD, known as a nonreplicative helicase, is involved in rolling circle replication of filamentous phages in diverse bacteria genera. This report consolidates knowledge on the new role of UvrD in filamentous phage replication, a function previously thought to be exclusive of Rep helicase. IMPORTANCE Biofilm development is a key component of the ability of Pseudomonas aeruginosa to evade host immune defenses and resist multiple drugs. Induction of the filamentous phage Pf, which usually is lysogenized in clinical and environmental isolates of P. aeruginosa, plays an important role in biofilm assembly, maturation, and dispersal. Despite the clinical relevance of Pf, the molecular biology of this phage is largely unknown. In this study, we found that rolling circle replication of Pf depends on UvrD, a DNA helicase normally involved in DNA repair. We also identified the initiator protein of Pf and found that it shares structural similarity with that of Vibrio cholerae phages CTXφ and VGJφ, which also use UvrD for replication. Our results reveal that, in addition to DNA repair, UvrD plays an essential role in rolling circle replication of filamentous phages among diverse bacteria genera, adding a new, previously unrecognized function of this accessory helicase.
Cultura no ensino de língua estrangeira

No ensino de lingua estrangeira * , o ensino de cultura ainda e um tema de debate acalorado. O que e cultura? Qual e a sua relacao com a lingua? Qual cultura deve ser ensinada? A cultura de quem? Qual o papel da cultura do aluno no processo de aquisicao de conhecimento da cultura-alvo? Como podemos evitar a essencializacao das culturas e o ensino de estereotipos culturais? Ainda, como podemos desenvolver, nos alunos, uma competencia intercultural em que a sua cultura e a cultura-alvo nao sejam tratadas de forma injusta, mas que sejam percebidas como mediadores culturais em um mundo globalizado? Este artigo explora essas questoes a partir da perspectiva obtida por meio de inumeras pesquisas desenvolvidas na Australia, na Europa e nos Estados Unidos nos ultimos 20 anos. Tambem relaciona o estudo da cultura com o estudo do discurso (KRAMSCH, 1993, 1998, 2004) e com o conceito de competencia transcultural e translingual proposto pela Modern Language Association (KRAMSCH, 2010). Uma atencao especial sera dada ao papel inigualavel que a antiga cultura persa pode ter como promotora dos mediadores culturais de amanha. * Esta e uma traducao do artigo Culture in Foreign Language Teaching, publicado no Iranian Journal of Language Teaching Research (http://www.urmia.ac.ir/ijltr), v. 1, n. 1, 2013. A publicacao da traducao foi autorizada pela autora, em email enviado no dia 12/04/2017, e pelo Editor-Chefe do periodico, o Dr. Karim Sadeghi, em email enviado no dia 23/06/2017. O link para o texto em ingles e http://www.urmia. ac.ir/ sites/www.urmia. ac.ir/files/Article%204_1. pdf
Effective Concept-Based Mining Model For Text Clustering

The common techniques in text mining are based on the statistical analysis of a term, either word or phrase. Statistical analysis of a term frequency captures the importance of the term within a document only. Two terms can have the same frequency in their documents, but one term contributes more to the meaning of its sentences than the other term. Usually in text mining techniques the basic measures like term frequency of a term (word or phrase) is computed to compute the importance of the term in the document. But with statistical analysis, the original semantics of the term may not carry the exact meaning of the term. To overcome this problem, a new framework has been introduced which relies on concept based model and synonym based approach. The proposed model can efficiently find significant matching and related concepts between documents according to concept based and synonym based approaches. The relations between verbs and their arguments in the same sentence have the potential for analyzing terms within a sentence. The information about who is doing what to whom clarifies the contribution of each term in a sentence to the meaning of the main topic of that sentence. This work bridges the gap between natural language processing and text mining disciplines. A new concept-based mining model composed of four components, is proposed to improve the text clustering quality. By exploiting the semantic structure of the sentences in documents, a better text clustering result is achieved. A new concept-based mining model that analyzes terms on the sentence, document, and corpus levels is introduced. The concept-based mining model can effectively discriminate between nonimportant terms with respect to sentence semantics and terms which hold the concepts that represent the sentence meaning. The proposed mining model consists of sentence-based concept analysis, document- based concept analysis, corpus-based concept-analysis, and concept-based similarity measure. Experimental results demonstrate the substantial enhancement of the clustering quality using sentence based, document based, corpus based and combined approach concept analysis. A new similarity measure has been proposed to find the similarity between a document and the existing clusters, which can be used in classification of the document with existing clusters.
Object related reactive offset maneuver

This paper describes a method for an object related reactive offset maneuver increasing the number of action alternatives for an autonomous ground vehicle. The method improves a variety of time-critical maneuvers as for example merging into moving traffic, changing lanes, passing other traffic participants as well as emergency obstacle avoidance without having to replan a path using high-level planning methods. It is especially targeted at autonomous driving on country roads. As oncoming traffic increases the relative speed between participants, a quick reponse to changes of the traffic situation are critically important. Moreover the method does not require constant vehicle velocities throughout a lane change maneuver as most existing approaches do. Simulations show improvements of the behaviour capabilities of an autonomous vehicle using the presented lateral reactive offset maneuvers.
Automatic identification and restriction of the cointegration space

We automate the process of finding the cointegration relations in a cointegrated VAR. There is a rigorous separation between the theory part (search directions must be defined, a final model chosen) and the automated search. The decision rules are set in such a way that a theoretical upper limit can be given to the asymptotic size of recovering all overidentifying restrictions. A Monte Carlo study shows that the algorithm works well, but that the properties of the asymptotic tests are rather poor at times. The software (in Matlab) to execute the algorithm is available.
Biological Effects Induced by Specific Advanced Glycation End Products in the Reconstructed Skin Model of Aging

Abstract Advanced glycation end products (AGEs) accumulate in the aging skin. To understand the biological effects of individual AGEs, skin reconstructed with collagen selectively enriched with Nɛ-(carboxymethyl)-lysine (CML), Nɛ-(carboxyethyl)-lysine (CEL), methylglyoxal hydroimidazolone (MG-H1), or pentosidine was studied. Immunohistochemistry revealed increased expression of α6 integrin at the dermal epidermal junction by CEL and CML (p<0.01). Laminin 5 was diminished by CEL and MG-H1 (p<0.05). Both CML and CEL induced a robust increase (p<0.01) in procollagen I. In the culture medium, IL-6, VEGF, and MMP1 secretion were significantly decreased (p<0.05) by MG-H1. While both CEL and CML decreased MMP3, only CEL decreased IL-6 and TIMP1, while CML stimulated TIMP1 synthesis significantly (p<0.05). mRNA expression studies using qPCR in the epidermis layer showed that CEL increased type 7 collagen (COL7A1), β1, and α6 integrin, while CML increased only COL7A1 (p<0.05). MG-H1-modified collagen had no effect. Importantly, in the dermis layer, MMP3 mRNA expression was increased by both CML and MG-H1. CML also significantly increased the mRNAs of MMP1, TIMP1, keratinocyte growth factor (KGF), IL-6, and monocyte chemoattractant protein 1 (MCP1) (p<0.05). Mixed effects were present in CEL-rich matrix. Minimally glycoxidized pentosidine-rich collagen suppressed most mRNAs of the genes studied (p<0.05) and decreased VEGF and increased MCP1 protein expression. Taken together, this model of the aging skin suggests that a combination of AGEs tends to counterbalance and thus minimizes the detrimental biological effects of individual AGEs.
Automatic detection of English words in Benglish text: A statistical approach

Code-mixing and code-switching create challenges in the field of natural language processing applications like Machine Translation and Speech-to-Speech Translation. Detection of foreign words is very much essential for smooth processing of natural language. A statistical language independent approach for automatic detection of foreign words in mixed language has been introduced in this paper. Initially, the proposed approach has been applied on Benglish text which is combination of Bangla text contains English words. The methodology can be easily adopted for other languages where such code mixing exists. The proposed approach yields an accuracy of 71.82% when tested on sentences collected from Bangla blogs and social networking websites.
Study of Grape Polyphenols by Liquid Chromatography-High-Resolution Mass Spectrometry (UHPLC/QTOF) and Suspect Screening Analysis

Suspect screening analysis is a targeted metabolomics method in which the identification of compounds relies on specific available information, such as their molecular formula and isotopic pattern. This method, coupled to liquid chromatography-high-resolution mass spectrometry, is effective in the study of grape metabolomics, in particular for characterization of flavonols, stilbene derivatives, and anthocyanins. For identification of compounds expected in the samples, a new database of putative compounds was expressly constructed by using the molecular information on potential metabolites of grape and wine from the literature and other electronic databases. Currently, this database contains around 1,100 compounds. The method allows identification of several hundred grape metabolites with two analyses (positive and negative ionization modes), and performing of data reprocessing using “untargeted” algorithms also provided the identification of some flavonols and resveratrol trimers and tetramers in grape for the first time. This approach can be potentially used in the study of metabolomics of varieties of other plant species.
A Retrievability Analysis: Exploring the Relationship Between Retrieval Bias and Retrieval Performance

Retrievability provides an alternative way to assess an Information Retrieval (IR) system by measuring how easily documents can be retrieved. Retrievability can also be used to determine the level of retrieval bias a system exerts upon a collection of documents. It has been hypothesised that reducing the retrieval bias will lead to improved performance. To date, it has been shown that this hypothesis does not appear to hold on standard retrieval performance measures (MAP and P@10) when exploring the parameter space of a given retrieval model. However, the evidence is limited and confined to only a few models, collections and measures. In this paper, we perform a comprehensive empirical evaluation analysing the relationship between retrieval bias and retrieval performance using several well known retrieval models, five large TREC test collections and ten performance measures (including the recently proposed PRES, Time Biased Gain (TBG) and U-Measure). For traditional relevance based measures (MAP, P@10, MRR, Recall, etc) the correlation between retrieval bias and performance is moderate. However, for TBG and U-Measure, we find that there is strong and significant negative correlations between retrieval bias and performance (i.e as bias drops, performance increases). These findings suggest that for these more sophisticated, user oriented measures the retrievability bias hypothesis tends to hold. The implication is that for these measures, systems can then be tuned using retrieval bias, without recourse to relevance judgements.
ASAP-II: From the Alignment of Phrases to Textual Similarity

ThisThis work is licensed under a Creative Commons Attribution 4.0 International Licence. Page numbers and proceedings footer are added by the organisers. Licence details: http://creativecommons.org/licenses/by/4.0/ paper describes the second version of the ASAP system 1 and its participation in the SemEval-2015, task 2a on Semantic Textual Similarity (STS). Our approach is based on computing the WordNet semantic relatedness and similarity of phrases from distinct sentences. We also apply topic modeling to get topic distributions over a set of sentences as well as some linguistic heuristics. In a special addition for this task, we retrieve named entities and compound nouns from DBPedia. All these features are used to feed a regression algorithm that learns the STS function.
All Your Bulbs Are Belong to Us: Investigating the Current State of Security in Connected Lighting Systems

ZigBee Light Link (ZLL) is the low-power mesh network standard used by connected lighting systems, such as Philips Hue, Osram Lightify, and GE Link. These lighting systems are intended for residential use but also deployed in hotels, restaurants, and industrial buildings. In this paper, we investigate the current state of security in ZLL-based connected lighting systems. We extend the scope of known attacks by describing novel attack procedures to show that the ZLL standard is insecure by design. Using our penetration testing framework, we are able to take full control over all three systems mentioned above. Besides novel attack procedures, we also extend the intended wireless range of max. 2 meters for configuring a ZLL device to over 30 meters, thus making ZLL-based systems susceptible to war driving. We conclude with a discussion about the security needs of connected lighting systems and derive several lessons for Internet of Things security that can be learned from the insecure design of ZLL-based connected lighting systems.
Call Admission for Prerecorded Sources with Packet Loss

We develop call admission policies for statistically multiplexing prerecorded sources over a bufferless transmission link. Our model is appropriate for video on demand, as well as other on-demand multimedia applications. In particular, we allow users to specify when the sources begin transmission; we also allow the user to invoke VCR actions such as pause and temporal jumps. We suppose that the quality of service (QoS) requirement allows for a small amount of packet loss. We develop a stochastic model which captures the random phases of the sources. We then apply large deviation theory to our model to develop global admission rules. The accuracy of the large deviation approximation is verified with simulation experiments employing importance sampling techniques. We also propose a refined admission rule which combines the global test and a myopic test. Numerical results are presented for the Star Wars trace; we find that the statistical multiplexing gain is potentially high and often insensitive to the QoS parameter. Finally, we develop efficient schemes for the real-time implementation of our global test. In particular, we demonstrate that the Taylor series expansion of the logarithmic moment generating function of the frame size distribution allows for fast and accurate admission decisions.
Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA

Emerging DNA sequencing technologies open up exciting new opportunities for genome sequencing by generating read data with a massive throughput. However, produced reads are significantly shorter and more error-prone compared to the traditional Sanger shotgun sequencing method. This poses challenges for de-novo DNA fragment assembly algorithms in terms of both accuracy (to deal with short, error-prone reads) and scalability (to deal with very large input data sets). In this paper we present a scalable parallel algorithm for correcting sequencing errors in high-throughput short-read data. It is based on spectral alignment and uses the CUDA programming model. Our computational experiments on a GTX 280 GPU show runtime savings between 10 and 19 times (for different error-rates using simulated datasets as well as real Solexa/Illumina datasets).
Are lawyers neurotic?

ABSTRACT This paper reports on an ethnographic exploration of the lawyer–client relationship focusing on the attitudes held by legally aided lawyers to their criminal clients. The study combines formal interviews with participant observation in a mixed methodology approach designed to give voice to the lawyers taking part as well as allow the researcher to provide their own perspective. The research produced two quite contradictory viewpoints as lawyers claimed to hold positive attitudes of their clients in interview while presenting negative attitudes under observation. To reconcile this difference, the author suggests considering psychoanalytic literature on self-image, which can be applied to show that the lawyers may have been displaying signs of Freudian defence mechanisms and, ultimately, presented as neurotic in their practise.
Generating flexible proper name references in text: Data, models and evaluation

This study introduces a statistical model able to generate variations of a proper name by taking into account the person to be mentioned, the discourse context and variation. The model relies on the REGnames corpus, a dataset with 53,102 proper name references to 1,000 people in different discourse contexts. We evaluate the versions of our model from the perspective of how human writers produce proper names, and also how human readers process them. The corpus and the model are publicly available.
Architecting mobile enterprise app: a modeling approach to adapt enterprise applications to the mobile

Mobile business applications have become the trend of the day. However, studies suggest that most of the mobile business appli-cations so far are lightweight, consisting of a few thousand lines of code. Indeed, most of these mobile business apps are nothing more than specialized information query engines relying on the backend server to process the queries. However, we now see a trend toward making enterprise-size apps mobile . But if the "design while coding" approach may have worked for limited size applications, this is clearly not enough for enterprise-size apps. Indeed, such applications will encounter the same maintenance problems as traditional applications. In this paper we propose an agile architecting approach to adapt the enterprise apps to the mobile. This approach promotes the code understandability Quality Attribute to lower the future maintenance cost of the application.
Toric geometry and local Calabi-Yau varieties: An introduction to toric geometry (for physicists)

These lecture notes are an introduction to toric geometry. Particular focus is put on the description of toric local Calabi-Yau varieties, such as needed in applications to the AdS/CFT correspondence in string theory. The point of view taken in these lectures is mostly algebro-geometric but no prior knowledge of algebraic geometry is assumed. After introducing the necessary mathematical definitions, we discuss the construction of toric varieties as holomorphic quotients. We discuss the resolution and deformation of toric Calabi-Yau singularities. We also explain the gauged linear sigma-model (GLSM) Kahler quotient construction.
Strain uses gap junctions to reverse stimulation of osteoblast proliferation by osteocytes

Identifying mechanisms by which cells of the osteoblastic lineage communicate in vivo is complicated by the mineralised matrix that encases osteocytes, and thus, vital mechanoadaptive processes used to achieve load‐bearing integrity remain unresolved. We have used the coculture of immunomagnetically purified osteocytes and primary osteoblasts from both embryonic chick long bone and calvariae to examine these mechanisms. We exploited the fact that purified osteocytes are postmitotic to examine both their effect on proliferation of primary osteoblasts and the role of gap junctions in such communication. We found that chick long bone osteocytes significantly increased basal proliferation of primary osteoblasts derived from an identical source (tibiotarsi). Using a gap junction inhibitor, 18β‐glycyrrhetinic acid, we also demonstrated that this osteocyte‐related increase in osteoblast proliferation was not reliant on functional gap junctions. In contrast, osteocytes purified from calvarial bone failed to modify basal proliferation of primary osteoblast, but long bone osteocytes preserved their proproliferative action upon calvarial‐derived primary osteoblasts.
Parallax and Companion: Set-based Browsing for the Data Web

The arrival of the Data Web will bring an abundance of explicit semantics either complementary to or embedded within traditional web content. This body of semantics both demands and enables new interaction techniques to be introduced into the web experience. In this position paper, we proposes that the current web browsing paradigm of “one web page at a time” needs to be updated because the typical unit of web information to interact with will no longer be a whole and single web page but can be smaller and numerous bits of data. We introduce the set-based browsing paradigm that lets the user traverse graph-based data that will be found on the Data Web in an efficient manner, moving from a set of things to a related set of things rather than from one single thing to one single other thing. We demonstrate this paradigm as a standalone application on a web-like database and as a browser extension on existing web pages.