Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular analysis of enterotoxin plasmids of enterotoxigenic Escherichia coli of 14 different O serotypes

A total of 104 isolates of enterotoxigenic Escherichia coli derived from diarrheal patients from more than 10 countries were examined for serotype and toxigenicity. The transferability and molecular structure of the enterotoxin plasmids from each isolate were also examined. Enterotoxin plasmids from serotypes such as O6, O25, O27, O126, O128, and O159, which are frequently associated with E. coli diarrhea (classical strains) generally did not transfer by conjugation from clinical isolates, whereas those from serotypes such as O7, O17, O80, O98, O139, O150, and O153, which are rarely associated with diarrhea (rare strains) transferred almost always from the clinical isolates by conjugation. Analyses of enterotoxin plasmids by restriction endonucleases and DNA-DNA hybridization with the enterotoxin probes revealed that the strains with the same O serotype and toxigenicity carry closely related enterotoxin plasmids. These results suggest that classical strains resulted from the dissemination of ancestral clones which received enterotoxin plasmids long ago, while the rare strains acquired the enterotoxin plasmids recently by conjugation and have not yet been spread to the same degree as the ancestral clones.
Using Morphological Characters and Simple Sequence Repeat (SSR) Markers to Characterize Tunisian Fig (Ficus Carica L.) Cultivars

We used simple sequence repeat markers and 25 morphological characters to characterize 18 Tunisian fig (Ficus carica L.) cultivars. Morphological traits suggested a high level of variation in the germplasm. Principal component analysis (PCA) differentiated the studied cultivars. In the derived dendrogram the cultivars clustered independently of their geographical origin and sex of trees. Simple sequence repeat (SSR) markers were used to compare genetic polymorphism with the observed phenotypic variation. Using six microsatellite primers, 39 alleles and 59 genotypes were identified. The high values of polymorphism information content (PIC), ranging from 0.67 to 0.85, confirmed the effectiveness of microsatellite analysis for determining molecular polymorphism and characterizing the studied cultivars. Multilocus genotyping unambiguously distinguished all the cultivars. The ability of each type of feature to differentiate cultivars of this crop is discussed.
Title The Impacts of Albuminuria and Low eGFR on the Risk of Cardiovascular Death , All-Cause Mortality , and Renal Events in Diabetic Patients : Meta-Analysis

*KURAに登録されているコンテンツの利用については,著作権法に規定されている私的使用や引用などの範囲内で行ってください。 *著作権法に規定されている私的使用や引用などの範囲を超える利用を行う場合には,著作権者の許諾を得てください。 ただし,著作権者 から著作権等管理事業者(学術著作権協会,日本著作出版権管理システムなど)に権利委託されているコンテンツの利用手続については ,各著作権等管理事業者に確認してください。 Title The Impacts of Albuminuria and Low eGFR on the Risk of Cardiovascular Death, All-Cause Mortality, and Renal Events in Diabetic Patients: MetaAnalysis Author(s) Toyama, Tadashi; Furuichi, Kengo; Ninomiya, Toshiharu; Shimizu, Miho; Hara, Akinori; Iwata, Yasunori; Kaneko, Shuichi; Wada, Takashi Citation PLoS ONE, 8(8): e71810
Toward Using Matrix Visualizations for Graph Editing

Node-link and matrix representations are widely applied for graph exploration. However, when it comes to editing graphs, matrix representations are mostly neglected. In this work, we investigate the suitability of matrix representations especially for graph editing. Based on a review of the characteristics of matrices in terms of representation and interaction, we propose first techniques for edgebased editing tasks. We combine our matrix-based techniques with classic node-link solutions in an interactive prototype for touchenabled graph editing.
Zn-DTPA administered by slow-release implant.

Because of the short biological retention half-time of injected Zn-DTPA and the desirability of a maintained blood level of the chelate, alternative modes for its administration were explored. Aqueous Zn-DTPA labeled with 65Zn was dried and ground to a fine powder and incorporated into implants of various combinations of cholesterol, polyethylene glycol 4000, beeswax, and peanut oil in order to produce a slow release of the chelation agent. Although the 65Zn tracer is known to be somewhat labile and exchanges with body stores of zinc and other metals, it was felt at the outset of the experiment that it would be an adequate tracer for Zn-DTPA in this study. Various types of implant pellets placed subcutaneously in the dorsal neck of young adult beagles produced a 24-hr excretion of 65Zn ranging from 3 to 83% of the implanted amount, increasing with the percentage of polyethylene glycol 4000 in the pellet. When 241Am citrate was injected intravenously into beagles pre-implanted with a DTPA pellet, the fraction of the injected 241Am excreted in the first 24 hr increased from 9% (control) to 38% ( = 2.9 pmole DTPA/kg/day) to 84% ( 70 pmole/kg/day).
Automatic Extraction of Linguistic Data from Digitized Documents

In lieu of an abstract, here is a brief excerpt: This paper presents a system for automatically extracting linguistic data from digitized linguistic documents using a combination of existing software packages and custom scripts. The system is designed to leverage existing resources in online digital libraries in order to bootstrap the creation of large, multi-lingual linguistic corpora, which can then be used to conduct data-driven experimental research into cross-linguistic or universal linguistic phenomena. The system identifies instances of foreign-language text accompanied by reference-language translations within the text of printed books that have been scanned into digital format, and extracts these to produce a parallel corpus of example sentences. While the system achieves a high precision on predicting foreign text, its accuracy overall is low, and directions for improvement and future work are identified.
The Twin Arginine Consensus Motif of Tat Signal Peptides Is Involved in Sec-independent Protein Targeting in Escherichia coli *

In Escherichia coli a subset of periplasmic proteins is exported through the Tat pathway to which substrates are directed by an NH2-terminal signal peptide containing a consensus SRRXFLK “twin arginine” motif. The importance of the individual amino acids of the consensus motif forin vivo Tat transport has been assessed by site-directed mutagenesis of the signal peptide of the Tat substrate pre-SufI. Although the invariant arginine residues are crucial for efficient export, we find that slow transport of SufI is still possible if a single arginine is conservatively substituted by a lysine residue. Thus, in at least one signal peptide context there is no absolute dependence of Tat transport on the arginine pair. The consensus phenylalanine residue was found to be a critical determinant for efficient export but could be functionally substituted by leucine, another amino acid with a highly hydrophobic side chain. Unexpectedly, the consensus lysine residue was found to retard Tat transport. These observations and others suggest that the sequence conservation of the Tat consensus motif is a reflection of the functional importance of the consensus residues. Tat signal peptides characteristically have positively charged carboxyl-terminal regions. However, changing the sign of this charge does not affect export of SufI.
Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis, Y. pseudotuberculosis, and Y. enterocolitica

ABSTRACT The genus Yersinia includes three human pathogens, of which Yersinia pestis is responsible for >2,000 illnesses each year. To aid in the development of detection assays and aid further phylogenetic elucidation, we sequenced and assembled the complete genomes of 32 strains (across 9 Yersinia species).
Automated heuristic growing of neural networks for nonlinear time series models

In this paper, we present a method for automatically selecting the optimal architecture of feedforward neural networks to build nonlinear time series models. A heuristic method is used to do an exhaustive search of all possible input/output combinations, while adjusting the lag times and the number of nodes in a fully connected single hidden layer network. Levenberg-Marquardt optimization is performed using the stop-search method of cross-validation. Statistics are maintained for all optimized structures which permits postprocessing based on performance criteria for final model selection. The methodology is applied to a case study for developing multi-variate autoregressive models for the day-ahead forecasting of electricity prices.
Spirometry in an unselected group of 6‐year‐old children: The DARC birth cohort study

This study presents reference equations for spirometric parameters in 6‐year‐old children and evaluates the ability of spirometry to discriminate healthy children from children with asthma. Baseline spirometry and respiratory symptoms were assessed in 404 children participating in a longitudinal birth cohort study. Children with known asthma, possible asthma and a control group also performed bronchodilator measurements. At least two acceptable flow‐volume curves at baseline were obtained by 368/404 children (91%). The two best values for FEV1 and FVC were within 5% of each other in 88% and 83% of children, respectively. Linear regression analyses for 242 children included in the reference population demonstrated height to be the main predictor of all spirometric indices except FEV1/FVC. FEV1, FEV75, and FVC correlated reasonably to anthropometric data in contrast to flow parameters. Gender differences were found for FEV1, FVC, and FEV75, but not for flow parameters. Asthma was diagnosed in 25/404 children. Baseline lung function in healthy children and children with asthma overlapped, although asthmatic children could be discriminated to some extent. Bronchodilator tests showed a difference in ΔFEV1(mean) between healthy children and children with asthma (3.1% vs. 6.1%, P < 0.05). At a cut‐off point of ΔFEV1 = 7.8%, bronchodilator tests had a sensitivity of 46% and a specificity of 92% for current asthma. Spirometry including bronchodilator measurements was demonstrated to be feasible in 6‐year‐old children and reference values were determined. Spirometry aids the diagnosis of asthma in young children, but knowledge on sensitivity and specificity of these measurements is a prerequisite. Pediatr Pulmonol. 2008; 43:806–814. © 2008 Wiley‐Liss, Inc.
Explorer Chase Termination for Guarded Existential Rules

The chase procedure is considered as one of the most fundamental algorithmic tools in database theory. It has been successfully applied to different database problems such as data exchange, and query answering and containment under constraints, to name a few. One of the central problems regarding the chase procedure is all-instance termination, that is, given a set of tuple-generating dependencies (TGDs) (a.k.a. existential rules), decide whether the chase under that set terminates, for every input database. It is well-known that this problem is undecidable, no matter which version of the chase we consider. The crucial question that comes up is whether existing restricted classes of TGDs, proposed in different contexts such as ontological reasoning, make the above problem decidable. In this work, we focus our attention on the oblivious and the semi-oblivious versions of the chase procedure, and we give a positive answer for classes of TGDs that are based on the notion of guardedness.
Alouatta seniculus: Density, Home Range and Group Structure in a Bamboo Forest Fragment in the Colombian Andes

We evaluated population density, group structure and home range of red howler monkeys in a bamboo forest fragment in the Cordillera Central mountain range of Colombia. We estimated a density of 377.7 individuals/km2, which is a higher density than normally reported for this species. The average home range size was 3.6 ± 1.1 ha. We found large groups (15.1 ± 4.0 individuals) with subgrouping behavior (daily divisions in foraging subgroups), and a high number of adult and subadult individuals of both sexes per group (mean of 5 males and 7 females per group). The small home range and large group size observed may be related to the high density of howler monkeys in this fragment, which we suggest could be the result of limited dispersal opportunities for these monkeys. The results illustrate the great plasticity of the genus Alouatta, which enables the monkeys to live in a wide range of conditions.
Low-voltage low-power current-mode amplitude shift keying (ASK) demodulator

A low-voltage low-power amplitude shift keying (ASK) demodulator using UMC 0.13 μm CMOS technology for wireless sensor network is presented. The circuit is developed based on a current-mode precision full wave rectifier, envelop detector, phase inverter and Schmitt trigger using dynamic threshold voltage MOS (DTMOS) transistor, quasi floating gate and self-cascode techniques. The circuit can operate at 0.5 V supply voltage at 2 Mbps with the power dissipation of 55 μW.
Pharmacokinetic and pharmacodynamic evaluation of tigecycline

Introduction: As the spread of multidrug-resistant (MDR) and extensive drug-resistant (XDR) organisms constitutes a real threat for patients, new antimicrobials are needed. Tigecycline, the first-in-class glycylcycline, possesses an extended spectrum of antimicrobial activity including MDR and XDR organisms, which holds promise as a treatment option beyond currently approved indications and deserves expanded evaluation of its pharmacokinetics/pharmacodynamics (PK/PD). Areas covered: This review highlights the areas where our knowledge on PK/PD of tigecycline has been both strengthened and questioned during the recent years. New information has become available on the PK of tigecycline in patients with complicated skin and skin structure infections, complicated intra-abdominal infection, community- and nosocomial-acquired pneumonia. Human PD data from clinical trials linking tigecycline drug exposure to clinical, microbiological and toxicological outcomes are also of great interest. Expert opinion: Tigecycline remains one of our last resorts against MDR pathogens; its clear role has to be re-defined through intense PK/PD applications; dose escalation and exploration of combinations with other antibiotics seem to be the first step towards an expansion of its currently approved indications. The lung remains the most controversial and challenging site regarding the PK/PD standpoint due to the predominance of Acinetobacter baumannii and carbapenemase-producing Klebsiella pneumoniae among ventilator-associated pneumonia infections, for which tigecycline is mostly used off-label.
Field observations of wave-driven circulation over spur and groove formations on a coral reef

Spur and groove (SAG) formations are found on the forereefs of many coral reefs worldwide. Modeling results have shown that SAG formations together with shoaling waves induce a nearshore Lagrangian circulation pattern of counter-rotating circulation cells, but these have never been observed in the field. We present results from two separate field studies of SAG formations on Palmyra Atoll which show their effect on waves to be small, but reveal a persistent order 1 cm/s depth-averaged Lagrangian offshore flow over the spur and onshore flow over the grooves. This circulation was stronger for larger, directly incident waves and low alongshore flow conditions, consistent with predictions from modeling. Favorable forcing conditions must be maintained on the order of 1 h to accelerate and develop the SAG circulation cells. The primary cross and alongshore depth-averaged momentum balances were between the pressure gradient, radiation stress gradient, and nonlinear convective terms, and the bottom drag was similar to values found on other reefs. The vertical structure of these circulation cells was previously unknown and the results show a complex horizontal offshore Lagrangian flow over the spurs near the surface driven by alongshore variability in radiation stress gradients. Vertical flow was downward over the spur and upward over the groove, likely driven by alongshore differences in bottom stress and not by vortex forcing.
Effectiveness of SiGe Buffer Layers in Reducing Dark Currents of Ge-on-Si Photodetectors

The effectiveness of thin SiGe buffer layers in terminating threading dislocations and reducing photodiode dark current for Ge epitaxially grown on Si (001) has been investigated. The structural morphology of the films was studied by atomic force microscopy and transmission electron microscopy. The dark current of Ge on Si photodiodes can be reduced by over an order of magnitude by incorporating two different composition SiGe buffer layers. The origin of dark current and the effectiveness of thermal annealing the SiGe layers were also studied
Development and validation of a new Prescription Quality Index.

AIMS The aims were to develop and validate a new Prescription Quality Index (PQI) for the measurement of prescription quality in chronic diseases. METHODS The PQI were developed and validated based on three separate surveys and one pilot study. Criteria were developed based on literature search, discussions and brainstorming sessions. Validity of the criteria was examined using modified Delphi method. Pre-testing was performed on 30 patients suffering from chronic diseases. The modified version was then subjected to reviews by pharmacists and clinicians in two separate surveys. The rater-based PQI with 22 criteria was then piloted in 120 patients with chronic illnesses. Results were analysed using SPSS version 12.0. 1 RESULTS Exploratory principal components analysis revealed multiple factors contributing to prescription quality. Cronbach's α for the entire 22 criteria was 0.60. The average intra-rater and inter-rater reliability showed good to moderate stability (intraclass correlation coefficient 0.76 and 0.52, respectively). The PQI was significantly and negatively correlated with age (correlation coefficient -0.34, P<0.001), number of drugs in prescriptions (correlation coefficient -0.51, P<0.001) and number of chronic diseases/conditions (correlation coefficient -0.35, P<0.001). CONCLUSIONS The PQI is a promising new instrument for measuring prescription quality. It has been shown that the PQI is a valid, reliable and responsive tool to measure quality of prescription in chronic diseases.
Seasonal Population Dynamics and Interactions of Competing Bacteriophages and Their Host in the Rhizosphere

ABSTRACT We describe two prolonged bacteriophage blooms within sugar beet rhizospheres ensuing from an artificial increase in numbers of an indigenous soil bacterium. Further, we provide evidence of in situ competition between these phages. This is the first in situ demonstration of such microbial interactions in soil. To achieve this, sugar beet seeds were inoculated with Serratia liquefaciensCP6RS or its lysogen, CP6RS-ly-Φ1. These were sown, along with uninoculated seeds, in 36 field plots arranged in a randomized Latin square. The plots were then sampled regularly over 194 days, and the plants were assayed for the released bacteria and any infectious phages. Both the lysogen and nonlysogen forms of CP6RS survived equally well in situ, contradicting earlier work suggesting lysogens have a competitive disadvantage in nature. A Podoviridae phage, identified as ΦCP6-4, flourished on the nonlysogen-inoculated plants in contrast to those plants inoculated with the lysogen. Conversely, the Siphoviridae phage ΦCP6-1 (used to construct the released lysogen) was isolated abundantly from the lysogen-treated plants but almost never on the nonlysogen-inoculated plants. The uninoculated plants also harbored some ΦCP6-1 phage up to day 137, yet hardly any ΦCP6-4 phages were found, and this was consistent with previous years. We show that the different temporal and spatial distributions of these two physiologically distinct phages can be explained by application of optimal foraging theory to phage ecology. This is the first time that such in situ evidence has been provided in support of this theoretical model.
Walk on City Maps - Mathematical and Physical phenomenology of the City, a Geometrical approach. (Promenade dans les cartes de villes - Phénoménologie mathématique et physique de la ville - une approche géométrique)

We are interested in the phenomenology of cities by restricting them to the geometry of their street network. This study aims at being synthetic, functional and interdisciplinary. It follows the large work that has been performed from the early XXth century by townplanners, social scientists, geographers, statisticians, physicists. We try to demonstrate that the street - as a coherent alignment of street segments - can be considered as an essential elementary structure of the city. How much information is encoded in the street network? To what extent does it constraint the city use? How are the current urban layout and its evolution determined jointly by traffic axis and structuring elements? We present a mathematical and computational framework allowing to consider the map of a city as a geometric continuum associated to the topology of a planar graph. To this graph we juxtapose a hypergraph structure using the street geometry to obtain easily the notion of axis and a multi-scale representation of the city. In spite of an apparent shape diversity, we show that the street network of a city is subjected to general laws that leave hallmarks on a city map. We propose several morphogenesis models of the city, implementing the idea that the city's growth follows a structured extension / division of space logic and able to reproduce hallmarks observed on actual maps. The understanding of regulation mechanism of the city allows us to propose functional algorithms whose computational efficiencies are very interesting. We present an algorithm recovering streets from a collection of street segments; the notion of simplest centrality whose calculus on a map allows a hierarchical analysis of it, revealing for instance main traffic axis and ill-deserved area; a fast approximate algorithm to nd the shortest path between two random points; and a Spectral Clustering based algorithm to produce morphological segmentations of maps. We also work on the identi cation of random tessellation models to be substituted to an actual road network and to solve large optimization problems using statistical equivalence.
Optical mapping design for murine atrial electrophysiology

Abstract Optical mapping is an important tool for assessment of cardiac electrophysiology. We demonstrate a system for quantification and automatic measurement of electrophysiological parameters in isolated cardiac tissue. The system makes use of voltage sensitive fluorescent dyes. These shift in wavelength in response to millivolt changes in potential across cell membranes located on the left atrium. Automated analysis of the pixel-wise measurements yields information on action potential durations and isochronal maps allowing for high throughput of data analysis. The algorithms that we propose reliably describe activation sequences and allow for quantification of conduction velocities.