Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconfiguring the Quorum-Sensing Regulator SdiA of Escherichia coli To Control Biofilm Formation via Indole and N-Acylhomoserine Lactones

ABSTRACT SdiA is a homolog of quorum-sensing regulators that detects N-acylhomoserine lactone (AHL) signals from other bacteria. Escherichia coli uses SdiA to reduce its biofilm formation in the presence of both AHLs and its own signal indole. Here we reconfigured SdiA (240 amino acids) to control biofilm formation using protein engineering. Four SdiA variants were obtained with altered biofilm formation, including truncation variants SdiA1E11 (F7L, F59L, Y70C, M94K, and K153X) and SdiA14C3 (W9R, P49T, N87T, frameshift at N96, and L123X), which reduced biofilm formation by 5- to 20-fold compared to wild-type SdiA in the presence of endogenous indole. Whole-transcriptome profiling revealed that wild-type SdiA reduced biofilm formation by repressing genes related to indole synthesis and curli synthesis compared to when no SdiA was expressed, while variant SdiA1E11 induced genes related to indole synthesis in comparison to wild-type SdiA. These results suggested altered indole metabolism, and corroborating the DNA microarray results in regard to indole synthesis, variant SdiA1E11 produced ninefold more indole, which led to reduced swimming motility and cell density. Also, wild-type SdiA decreased curli production and tnaA transcription, while SdiA1E11 increased tnaA transcription (tnaA encodes tryptophanase, which forms indole) compared to wild-type SdiA. Hence, wild-type SdiA decreased biofilm formation by reducing curli production and motility, and SdiA1E11 reduced biofilm formation via indole. Furthermore, an AHL-sensitive variant (SdiA2D10, having four mutations at E31G, Y42F, R116H, and L165Q) increased biofilm formation sevenfold in the presence of N-octanoyl-dl-homoserine lactone and N-(3-oxododecatanoyl)-l-homoserine lactone. Therefore, SdiA can be evolved to increase or decrease biofilm formation, and biofilm formation may be controlled by altering sensors rather than signals.
An unusual triad: Bilateral dilated odontoma, hypodontia and peg laterals

The dilated odontoma is an infrequent developmental alteration that appears in any area of the dental arches and can affect deciduous, permanent and supernumerary tooth. Dens invaginatus is a developmental anomaly resulting from invagination of a portion of crown forming within the enamel organ during odontogenesis. The most extreme form of dens invaginatus is known as dilated odontoma. The aim of this case report is to present a rare case of bilateral dilated odontoma affecting a microdontic permanent lateral incisor in a 30 year old female patient with hypodontia and peglateral teeth with its clinical, radiological and histological features, which has yet been not reported. Bilateral presence of dilated odontoma is not a common occurrence, although a single tooth involvement in each case has been reported in the literature.
Characterization of ENVISAT multipolarization SAR data with bidimensional statistics

This paper is about evaluating the interest between studying directs dual images statistical indices and the use of statistical indices build from two SAR multipolarization images. We show an original way of using this kind of images by using two dimensionned statistical calculation in a Markov random field classification. We present results of our segmentation on urban, forest and mangrove areas. Those results are computed from ENVISAT ASAR data in HH and VV polarizations in a tropical context, near Libreville.
Graph fibrations, graph isomorphism, and PageRank

PageRank is a ranking method that assigns scores to web pages using the limit distribution of a random walk on the web graph. A fibration of graphs is a morphism that is a local isomorphism of in- neighbourhoods, much in the same way a covering projection is a local isomorphism of neighbourhoods. We show that a deep connection re- lates fibrations and Markov chains with restart, a particular kind of Markov chains that include the PageRank one as a special case. This fact provides constraints on the values that PageRank can assume. Us- ing our results, we show that a recently defined class of graphs that admit a polynomial-time isomorphism algorithm based on the com- putation of PageRank is really a subclass of fibration-prime graphs, which possess simple, entirely discrete polynomial-time isomorphism algorithms based on classical techniques for graph isomorphism. We discuss efficiency issues in the implementation of such algorithms for the particular case of web graphs, in which O(n) space occupancy (where n is the number of nodes) may be acceptable, but O(m) is not (where m is the number of arcs).
On the Working De nition of Intelligence

This paper is about the philosophical and methodological foundation of arti cial intelligence (AI). After discussing what is a good \working de nition", \intelligence" is de ned as \the ability for an information processing system to adapt to its environment with insu cient knowledge and resources". Applying the de nition to a reasoning system, we get the major components of Non-Axiomatic Reasoning System (NARS), which is a symbolic logic implemented in a computer system, and has many interesting properties that are closely related to intelligence. The de nition also clari es the di erence and relationship between AI and other disciplines, such as computer science. Finally, the de nition is compared with other popular de nitions of intelligence, and its advantages are argued. 1 To De ne Intelligence
U-DBSCAN : A density-based clustering algorithm for uncertain objects

In recent years, uncertain data have gained increasing research interests due to its natural presence in many applications such as location based services and sensor services. In this paper, we study the problem of clustering uncertain objects. We propose a new deviation function that approximates the underlying uncertain model of objects and a new density-based clustering algorithm, U-DBSCAN, that utilizes the proposed deviation. Since, there is no cluster quality measurement of density-based clustering at present. Thus, we also propose a metric which specifically measures the density quality of clustering solution. Finally, we perform a set of experiments to evaluate the quality effectiveness of our algorithm using our metric. The results reveal that U-DBSCAN gives better clustering quality while having comparable running time compared to a traditional approach of using representative points of objects with DBSCAN.
The Personal Name Problem and a Data Mining Solution

Almost every person has a life-long personal name which is officially recognised and has only one correct version in their language. Each personal name typically has two components/parts: a first name (also known as given, fore, or Christian name) and a last name (also known as family name or surname). Both these name components are strongly influenced by cultural, economic, historical, political, and social backgrounds. In most cases, each of these two components can have more than a single word and the first name is usually gender-specific. (see Figure 1). There are three important practical considerations for personal name analysis: • Balance between manual checking and analytical computing. Intuitively, a small proportion of names should be manually reviewed, the result has to be reasonably accurate, and each personal name should not take too long to be processed. • Reliability of the verification data has to be examined. By keeping the name verification database’s updating process separate from incoming names, it can prevent possible data manipulation/corruption over time. However, the incompatibility of names in databases can also be caused by genuine reasons as such as cultural and historical traditions, translation and transliteration, reporting and recording variations, and typographical and phonetic errors (Borgman and Siegfried, 1992).
Building Slovene WordNet

A WordNet is a lexical database in which nouns, verbs, adjectives and adverbs are organized in a conceptual hierarchy, linking semantically and lexically related concepts. Such semantic lexicons have become oneof the most valuable resources for a wide range of NLP research and applications, such as semantic tagging, automatic word-sense disambiguation, information retrieval and document summarisation. Following the WordNet design for the English languagedeveloped at Princeton, WordNets for a number of other languages havebeen developed in the past decade, taking the idea into the domain ofmultilingual processing. This paper reports on the prototype SloveneWordNet which currently contains about 5,000 top-level concepts. Theresource has been automatically translated from the Serbian WordNet, with the help of a bilingual dictionary, synset literals ranked according to the frequency of corpus occurrence, and results manually corrected. The paper presents the results obtained, discusses some problems encountered along the way and points out some possibilitiesof automated acquisition and refinement of synsets in the future.
Pregnant women's beliefs and influences regarding exercise during pregnancy.

OBJECTIVE To sample women's exercise habits and beliefs regarding exercise during pregnancy and to determine patient awareness and physician communication of ACOG's 2002 guidelines for exercise during pregnancy. METHODS A 28-item questionnaire was completed by 211 patients at a private obstetric and gynecology (Ob/Gyn) group practice during a 4-week study period. RESULTS Ninety-five percent of the women believed that participating in prenatal exercise was helpful. There was a significant correlation (P<0.000) between a woman's beliefs regarding the benefits of prenatal exercise and whether or not she chose to exercise during pregnancy. Forty-one percent of women surveyed and 41.6% of women who exercised indicated that their doctor had the most influence on their beliefs regarding exercise. Approximately 92% of the women who discussed exercise with their physicians were encouraged by them to exercise. In addition, women who were encouraged to exercise by their physician were more likely (P=0.005) to exercise than those who were not. Only 9.8% of the 133 women who talked to their physician reported that their physician helped them develop an exercise program. Over 69% of women were advised by their physician to place limitations on their exercise habits according to ACOG's 1985 guidelines rather than the current guidelines. A significant relationship was found between BMI and whether or not women exercised (P=0.001). Despite the previously known correlation between BMI and gestational diabetes, we failed to find a significant relationship between BMI and whether or not their physician encouraged them to exercise (P=0.531). CONCLUSION A majority of women studied believed that exercise will have a positive impact on their pregnancy, are deciding to exercise during their pregnancy, and indicated that their doctor had the most influence on their beliefs about exercise during pregnancy. Because women's behaviors are influenced by their physician's instructions, physicians should be prepared to counsel their healthy ante-partum patients on the benefits of prenatal exercise and be informed of ACOG's current guidelines.
2. Morphology and dynamics of the Pinatubo aerosol layer in the northern hemisphere as detected from a ship-borne lidar

Scattering ratios of the Pinatubo aerosol layer obtained by the ship-borne lidar of the Roscomhydromet of Russia on-board PROFESSOR ZUBOV are presented. During a campaign primarily in the low-latitude (8°N–43°N) Atlantic Ocean, 48 days of data were obtained within the 73 day period spanning 11-July and 21-September of 1991 [Avdyushin et al., 1992]. These data show the aerosol cloud to be primarily in the 16–27 km altitude region, with a high degree of variability in the vertical structure and in the longitudinal structure, and to a lesser degree, in the latitudinal structure. Scattering ratios of up to 50 were recorded in the multi-layered structure which was often observed. These are the first lidar observations showing a high degree of zonal variability of the vertical structure of the aerosol layer. We show the latitudinal range of the Pinatubo aerosol cloud in the northern hemisphere over a 2 month period and estimate the latitudinal dispersion rate for the months of the measurements to be approximately 5° latitude per month. A clear periodic variability was observed in the altitude structure during the entire data-set primarily within 8°N–22°N latitude and within the altitude region of the layer, from which a mean zonal wind profile was produced by a spectral analysis of the aerosol profiles.
Discovering Search Engine Related Queries Using Association Rules

This work presents a method for online generation of query related suggestions for a Web search engine. The method uses association rules to extract related queries from the log of sbumitted queries to the search engine. Experimental results were performed on a real log containing more than 2.3 million queries submitted to a commercial search engine. For the top 5 related terms our method presented correct suggestions in 90.5% of the time. Using queries randomly selected from a log we obtained 93.45% of correct suggestions. A study of the user behavior showed that in 92.23% of the clicks on suggestions, users found useful information. The same approach can be used to provide terms to the classic problem of query expansion. For instance, the average precision of the answers of the Google search engine was improved by 23.16% using our aproach as a query expansion method.
Adverse Effects of Second-Generation Antipsychotics in Children and Adolescents: A Bayesian Meta-Analysis

Abstract In adults, second-generation antipsychotics (SGAs) have a low frequency of extrapyramidal syndrome (EPS) and a moderate frequency of metabolic adverse effects. Here we aimed to assess short-term adverse effects of SGAs in children and adolescents. We searched for relevant studies in MEDLINE and EMBASE (1996–2010), Food and Drug Administration and European Medicines Agency clinical trial registries, and reference lists of review articles. We found 41 were short-term (3–12 weeks) controlled studies that evaluated SGA adverse effects in youths. Using Bayesian meta-analysis, we analyzed odds ratios (ORs) or mean average effects. Numbers of arms (subjects) in the 41 trials were aripiprazole, 10 (n = 671); olanzapine, 14 (n = 413); quetiapine, 10 (n = 446); risperidone, 25 (n = 1040); ziprasidone, 4 (n = 228); clozapine, 5 (n = 79); and placebo/untreated, 23 (n = 1138), totaling 93 arms (4015 patients). Clozapine was assessed only for weight gain and somnolence. Compared with placebo, significant treatment-related increases were observed for weight gain with olanzapine (mean ± SD = 3.99 ± 0.42 kg; 95% credible interval, 3.17–4.84 kg), clozapine (2.38 ± 1.13 kg; 95% credible interval, 0.19–4.62 kg), risperidone (2.02 ± 0.32 kg; 95% credible interval, 1.39–2.66 kg), quetiapine (1.74 ± 0.38 kg; 95% credible interval, 0.99–2.5 kg), and aripiprazole (0.89 ± 0.32 kg; 95% credible interval, 0.26–1.51 kg); glucose levels with risperidone (3.7 ± 1.36 mg/dL; 95% credible interval, 1.08–6.42 mg/dL) and olanzapine (2.09 ± 1.08 mg/dL; 95% credible interval, 0.13–4.32 mg/dL); cholesterol levels with quetiapine (10.77 ± 2.14 mg/dL; 95% credible interval, 6.6–14.95 mg/dL) and olanzapine (4.46 ± 1.65 mg/dL; 95% credible interval, 1.24–7.73 mg/dL); triglyceride levels with olanzapine (20.18 ± 5.26 mg/dL; 95% credible interval, 9.85–30.53 mg/dL) and quetiapine (19.5 ± 3.92 mg/dL; 95% credible interval, 11.84–27.17 mg/dL); hyperprolactinemia with risperidone (OR, 38.63; 95% credible interval, 8.62–125.6), olanzapine (OR, 15.6; 95% credible interval, 4.39–41.1), and ziprasidone (OR, 9.35; 95% credible interval, 1.24–37.03); and EPS with ziprasidone (OR, 20.56; 95% credible interval, 3.53–68.94), olanzapine (OR, 6.36; 95% credible interval, 2.43–13.84), aripiprazole (OR, 3.79; 95% credible interval, 2.17–6.17), and risperidone (OR, 3.71; 95% credible interval, 2.18–6.02). All SGAs increased the risk of somnolence/sedation. We conclude that short-term metabolic effects and EPS are frequent in children treated with SGAs. Second-generation antipsychotics have distinct profiles of secondary effects, which should be considered in making treatment decisions.
An upper-mantle S-wave velocity model for Northern Europe from Love and Rayleigh group velocities

SUMMARY A model of upper-mantle S-wave velocity and transverse anisotropy beneath northwestern Europe is presented, based on regional surface wave observations. Group velocities for both Love and Rayleigh surface waves are measured on waveform data from international and regional data archives (including temporary deployments) and then inverted for group velocity maps, using a method accounting for Fresnel zone sensitivity. The group velocity variations are larger than in global reference maps, and we are able to resolve unprecedented details. We then apply a linear inversion scheme to invert for local 1-D shear wave velocity profiles which are consequently assembled to a 3-D model. By choosing conservative regularization parameters in the 2-D inversion, we ensure the smoothness of the group velocity maps and hence of the resulting 3-D shear wave speed model. To account for the different tectonic regimes in the study region and investigate the sensitivity of the 1-D inversions to inaccuracies in crustal parameters, we analyse inversions with different reference models of increasing complexity (pure 1-D, 3-D crust/1-D mantle and pure 3-D). We find that all inverted models are very consistent at depths below 70 km. At shallower depths, the constraints put by the reference models, primarily Moho depth which we do not invert for, remain the main cause for uncertainty in our inversion. The final 3-D model shows large variations in S-wave velocity of up to ±12 per cent. We image an intriguing low-velocity anomaly in the depth range 70–150 km that extends from the Iceland plume beneath the North Atlantic and in a more than 400 km wide channel under Southern Scandinavia. Beneath Southern Norway, the negative perturbations are around 10 per cent with respect to ak135, and a shallowing of the anomaly is indicated which could be related to the sustained uplift of Southern Scandinavia in Neogene times. Furthermore, our upper-mantle model reveals good alignment to ancient plate boundaries and first-order crustal fronts around the triple junction of the Baltica-Avalonia–Laurentia collision in the North Sea.
Hybrid Position-Based 3D Routing Algorithms with Partial Flooding

Position-based routing algorithms use the location information to reduce routing overhead in mobile ad-hoc networks. In this paper we propose two position-based routing algorithms which combine progress-based routing with restricted directional flooding-based routing algorithms for routing in 3 dimensional environments (3D). The first algorithm 3D_ABLAR(m) chooses m neighbors according to a space-partition heuristic and forwards the message to all these nodes. The second algorithm (C, G)-3D_ABLAR(m)-(C, G) uses progress-based routing until a local minimum is reached. The algorithm then switches to the first algorithm for one step and then progress-based routing is resumed. We evaluate our algorithm and compare it with current routing algorithms. The simulation results show a significant improvement in delivery rate (99% compared to 63%) and reduction in traffic (up to 50%)
Software defect prediction in large space systems through hybrid feature selection and classification

: Data mining and machine learning techniques have been used in several scientific applications including software fault predictions in large space systems. State-of the-art research revealed that existing space systems succumb to enigmatic software faults leading to critical loss of life and capital. This article presents a novel approach to solve this issue of overlooking software faults by utilizing both features selection and classification techniques to accurately predict software defects in aerospace systems. The main objective was to identify the preeminent feature selection and prediction technique that enhanced the software fault prediction accuracy with the optimal set of features. The investigations affirmed that a novel hybrid feature selection method revealed the most optimal set of predictive features although no particular predictive technique was suitable to predict faults in all space system datasets. Besides, the exploration of data mining techniques in fault prediction on the NASA Lunar space system software data clearly portrayed the improved fault prediction accuracy (~82% to ~98%) with the feature set selected by the proposed Hybrid Feature Selection method. Also, the random sub sampling method revealed an improved mean Matthew’s Correlation Coefficient (MCC) and accuracy ranging from ~0.7 to ~0.9 and ~86% to ~98% respectively. This we believe generates further scope for future investigations on the most contributing space system features for fault prediction thus enabling design of aerospace systems with minimal faults and enhanced performance.
Mutations of human cationic trypsinogen (PRSS1) and chronic pancreatitis

Ten years ago, the groundwork for the discovery of the genetic basis of chronic pancreatitis was laid by linkage analyses of large kindreds with autosomal dominant hereditary chronic pancreatitis. Subsequent candidate gene sequencing of the 7q35 chromosome region revealed a strong association of the c.365G>A (p.R122 H) mutation of the PRSS1 gene encoding cationic trypsinogen with hereditary pancreatitis. In the following years, further mutations of this gene were discovered in patients with hereditary or idiopathic chronic pancreatitis. In vitro the mutations increase autocatalytic conversion of trypsinogen to active trypsin and thus probably cause premature, intrapancreatic trypsinogen activation in vivo. The clinical presentation is highly variable, but most affected mutation carriers have relatively mild disease. In this review, we summarize the current knowledge on trypsinogen mutations and their role in pancreatic diseases. Hum Mutat 27(8), 721–730, 2006. © 2006 Wiley‐Liss, Inc.
Biosynthesis of UDP-GlcNAc, UndPP-GlcNAc and UDP-GlcNAcA Involves Three Easily Distinguished 4-Epimerase Enzymes, Gne, Gnu and GnaB

We have undertaken an extensive survey of a group of epimerases originally named Gne, that were thought to be responsible for inter-conversion of UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-N-acetylgalactosamine (UDP-GalNAc). The analysis builds on recent work clarifying the specificity of some of these epimerases. We find three well defined clades responsible for inter-conversion of the gluco- and galacto-configuration at C4 of different N-acetylhexosamines. Their major biological roles are the formation of UDP-GalNAc, UDP-N-acetylgalactosaminuronic acid (UDP-GalNAcA) and undecaprenyl pyrophosphate-N-acetylgalactosamine (UndPP-GalNAc) from the corresponding glucose forms. We propose that the clade of UDP-GlcNAcA epimerase genes be named gnaB and the clade of UndPP-GlcNAc epimerase genes be named gnu, while the UDP-GlcNAc epimerase genes retain the name gne. The Gne epimerases, as now defined after exclusion of those to be named GnaB or Gnu, are in the same clade as the GalE 4-epimerases for inter-conversion of UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal). This work brings clarity to an area that had become quite confusing. The identification of distinct enzymes for epimerisation of UDP-GlcNAc, UDP-GlcNAcA and UndPP-GlcNAc will greatly facilitate allocation of gene function in polysaccharide gene clusters, including those found in bacterial genome sequences. A table of the accession numbers for the 295 proteins used in the analysis is provided to enable the major tree to be regenerated with the inclusion of additional proteins of interest. This and other suggestions for annotation of 4-epimerase genes will facilitate annotation.