Miracle-dz/UniFAR-FTUs huggingface dataset:
Absolute Bioavailability and Absorption Characteristics of Aerosolized Tobramycin in Adults with Cystic Fibrosis

Administration of antibiotics by the inhalational route has become part of standard protocols for treatment of and prophylaxis for Pseudomonal pneumonias in patients with cystic fibrosis. For tobramycin, however, limited data are available on the aerosol absorption patterns, and no absolute bioavailability data for tobramycin exist. The purpose of this study was to measure the absolute bioavailability and systemic absorption characteristics of tobramycin when administered in high doses by a nebulizer. Multiple serum concentrations of tobramycin were measured after administration of an intravenous dose (mean, 2.9 mg/kg every 6 hours) and after an inhalational dose (5.6 mg/kg over 1 hour). Inhalational doses were superimposed over the “tail” of a steady‐state intravenous dose to improve the sensitivity of the assay procedure (Abbott‐TDX). Absolute bioavailability (F) was determined from AUC ratios normalized for dose. Model‐independent pharmacokinetic parameters (volume of distribution [Vss] and total clearance [CLt]) were determined for each subject. Absorption characteristics (absorption rate constant [Ka] and mean absorption time [MAT]) were assessed after calculation of the cumulative fraction of drug absorbed, amount of bioavailable drug, and percent remaining to be absorbed per unit time using the Loo‐Riegelman method. Three men and three women completed the study, and all received concurrent doses of ceftazidime. Mean absolute bioavailability (± standard deviation) was 9.13% (± 3.82), and the rate of absorption into the systemic circulation was consistent with a zero‐order model profile for all subjects. Mean absorption time values reflected a wide degree of subject variability and ranged from approximately 15 to 150 minutes. The authors conclude that there is limited uptake of tobramycin into the systemic circulation when administered by nebulizer aerosol into the lungs even in high doses. Absorption of tobramycin from the alveolar space into the pulmonary vasculature appears to be rate limited, but this may be characteristic for adults with cystic fibrosis. The authors also conclude that high doses of tobramycin administered by aerosolized nebulizer in these patients would contribute little to the risk of toxicity because of the poor systemic uptake of this drug.
The Redux 0 Server

Redux 0 is a subset of the full REDUX modell7]. The latter performs problem solving. In contrast Redux 0 does not and acts only as a decision maintenance server. It takes objects of types deened in an ontology of decision components and maintains dependencies between them. Redux 0 is domain-independent. The dependency relationships are maintained on the basis of proposition type and not content, except for some string matching. Redux 0 servers are proposed as a mechanism for federating heterogeneous design agents by encapsulating their design decisions within a simple model and providing coordination services, especially for design revision. This proposal is described within the context of the SHADE and PACT projects.
Transformation mapping of the regulatory elements of the ecdysone-inducible P1 gene of Drosophila melanogaster

The transcription of the P1 gene is induced by 20-hydroxyecdysone in fat bodies of third-instar larvae. Germ line transformation showed that sequences between -138 to +276 contain elements required for a qualitatively correct developmental and hormonal regulation of P1 transcription. Sequences from -138 to -68 are essential for this expression.
Step-Based Experiment Design and System Identification for Aeroelastic Dynamic Modeling

This paper gives an overview of the main ideas behind a new estimation technique that is able to deliver a consistent estimate of (poorly-damped) structural resonance modes induced by aeroservoelastic interaction without user intervention. Instead of using broadband sinusoidal or sine-sweep excitation signals, the new estimation method proposed in this paper uses simple step-based excitation signals that can be applied to any of the control surfaces to formulate a model of the aerodynamically-induced structural vibration modes. Simple step-based excitation signals address the issue of broadband excitation while allowing a reasonable (short-time) excitation signal on the control surfaces. The proposed estimation method has been tailored to find consistent model estimates on the basis of step-based input signals. The estimation method uses a modified version of the well-known realization algorithm that is extended to arbitrary input signals to formulate a discrete-time model directly on the basis of step-based experiments. Since the numerical implementation only requires a singular value decomposition and a standard least-squares estimation, robust numerical algorithms can be put in place to formulate a dynamical model with little or no user intervention. The procedure is illustrated on time-domain data obtained from a high fidelity model of an F/A-18 to find a low-order model that captures the structural parameters, such as damping and location of the first main resonance modes.
Isolation of the pericellular matrix of human fibroblast cultures

The pericellular matrix of human fibroblast cultures was isolated, using sequential extraction with sodium deoxycholate and hypotonic buffer in the presence of protease inhibitor. The matrix attached to the growth substratum had a "sackcloth-like" structure as seen by phase contrast, immunofluorescence, and scanning electron microscopy, and it had a vaguely filamentous ultrastructure similar to that seen in intact cell layers. The matrix consisted of hyaluronic acid and heparan sulfate as the major glycosaminoglycan components and fibronectin and procollagen as major polypeptides as shown by metabolic labeling, gel electrophoresis, immunofluorescence, and collagenase digestion. This pericellular matrix can be regarded as an in vitro equivalent of the loose connective tissue matrix.
Draft Genome Sequence of Bacillus amyloliquefaciens XK-4-1, a Plant Growth-Promoting Endophyte with Antifungal Activity

ABSTRACT Here, we report the draft genome sequence of a bacterial plant-growth-promoting endophyte, Bacillus amyloliquefaciens XK-4-1, which consists of one circular chromosome of 3,941,805 bp with 3,702 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with its plant-beneficial characteristics.
Logmap Results for Oaei 2011 1 Presentation of the System 1.1 Motivation and Problem Statement

We present the preliminary results obtained by the ontology matching system LogMap within the OAEI 2011 campaign. This is the first participation of LogMap in the campaign, and the results have so far been quite promising. The LogMap project started in January 2011 with the objective of developing a scalable and logic-based ontology matching system. Such system should be able to deal efficiently with large-scale ontologies; furthermore , it should exploit logic-based reasoning and diagnosis techniques to compute output mappings that do not lead to logical inconsistencies when integrated with the input ontologies [7]. Although the development of LogMap is relatively recent, the authors' experience in the field of ontology integration dates back to 2008 [9, 11]. Despite the impressive state of the art, large-scale biomedical ontologies still pose serious challenges to existing ontology matching tools [14, 6]. Insufficient scalability. Although existing matching tools can efficiently deal with moderately sized ontologies (e.g. those in the OAEI Anatomy track), large-scale on-tologies such as FMA, SNOMED CT and NCI are still beyond their reach. Logical inconsistencies. OWL ontologies have well-defined semantics based on first-order logic, and mappings are commonly represented as OWL class axioms. Many existing tools, however, disregard the semantics of the input ontologies; thus, they are unable to detect and repair inconsistencies that logically follow from the union of the input ontologies and the computed mappings. Although there is a growing interesting in applying reasoning techniques to ontology matching, reasoning is known to severely aggravate the scalability problem. LogMap is a highly scalable ontology matching system with 'built-in' reasoning and diagnosis capabilities, which aims at addressing the aforementioned challenges. We next present a brief overview of LogMap and refer the reader to [7] for a comprehensive description. The main steps performed by LogMap are schematically represented in Figure 1.
Identification of the cyclic-nucleotide-binding domain as a conserved determinant of ion-channel cell-surface localization

Mutations of a putative cyclic-nucleotide-binding domain (CNBD) can disrupt the function of the hyperpolarization-activated cyclic-nucleotide-gated channel (HCN2) and the human ether-a-go-go-related gene potassium channel (HERG). Loss of function caused by C-terminal truncation, which includes all or part of the CNBD in HCN and HERG, has been related to abnormal channel trafficking. Similar defects have been reported for several of the missense mutations of HERG associated with long QT syndrome type 2 (LQT2). Thus, we postulate that normal processing of these channels depends upon the presence of the CNBD. Here, we show that removal of the entire CNBD prevents Golgi transit, surface localization and function of HERG channel tetramers. This is also true when any of the structural motifs of the CNBD is deleted, suggesting that deletion of any highly conserved region along the entire length of the CNBD can disrupt channel trafficking. Furthermore, we demonstrate that defective trafficking is a consequence of all LQT2 mutations in the CNBD, including two mutations not previously assessed and two others for which there are conflicting results in the literature. The trafficking sensitivity of the CNBD might be of general significance for other ion channels because complete deletion of the CNBD or mutations at highly conserved residues within the CNBD of the related ERG3 channel and HCN2 also prevent Golgi transit. These results broadly implicate the CNBD in ion-channel trafficking that accounts for the commonly observed loss of function associated with CNBD mutants and provides a rationale for distinct genetic disorders.
Canonical Wnt signaling regulates Slug activity and links epithelial–mesenchymal transition with epigenetic Breast Cancer 1, Early Onset (BRCA1) repression

Slug (Snail2) plays critical roles in regulating the epithelial–mesenchymal transition (EMT) programs operative during development and disease. However, the means by which Slug activity is controlled remain unclear. Herein we identify an unrecognized canonical Wnt/GSK3β/β-Trcp1 axis that controls Slug activity. In the absence of Wnt signaling, Slug is phosphorylated by GSK3β and subsequently undergoes β-Trcp1–dependent ubiquitination and proteosomal degradation. Alternatively, in the presence of canonical Wnt ligands, GSK3β kinase activity is inhibited, nuclear Slug levels increase, and EMT programs are initiated. Consistent with recent studies describing correlative associations in basal-like breast cancers between Wnt signaling, increased Slug levels, and reduced expression of the tumor suppressor Breast Cancer 1, Early Onset (BRCA1), further studies demonstrate that Slug—as well as Snail—directly represses BRCA1 expression by recruiting the chromatin-demethylase, LSD1, and binding to a series of E-boxes located within the BRCA1 promoter. Consonant with these findings, nuclear Slug and Snail expression are increased in association with BRCA1 repression in a cohort of triple-negative breast cancer patients. Together, these findings establish unique functional links between canonical Wnt signaling, Slug expression, EMT, and BRCA1 regulation.
An Intraday Analysis of the Effectiveness of Foreign Exchange Intervention

This paper assesses the effectiveness of Canada's official foreign exchange intervention in moderating intraday volatility of the Can$/US$ exchange rate, using a 2-1/2-year sample of 10-minute exchange rate data. The use of high frequency data (higher than daily frequency) should help in assessing the impact of intervention since the foreign exchange market is efficient and reacts rapidly to new information. The estimated equations explain volatility in terms of four major factors: intraday seasonal pattern; daily volatility persistence; macroeconomic news announcements; and the impact of central bank intervention. Rule-based (or expected) intervention apparently had no direct impact on the reduction of foreign exchange volatility, although the existence of a non-intervention band seemed to provide a small stabilizing influence. This result is interpreted to mean that the stabilizing effect of expected intervention came into play as the Canadian dollar approached the upper or lower limits of the band. When the dollar exceeded the band, actual intervention did not have any direct impact because it was expected. Moreover, the results show that discretionary (or unexpected) intervention might have been effective in stabilizing the Canadian dollar, although the impact of an intervention sequence diminished as it increased beyond a few days.
Development of a Measure to Assess the Complexity of Information Systems Development Projects

Information systems development (ISD) projects are becoming increasingly complex. ISD project complexity makes it difficult for project managers to deliver effective systems within time and budget constraints. As a result, the success of ISD projects is increasingly dependent on an organization’s ability to effectively assess and manage complexity. The purpose of this paper is to develop a measure for assessing ISD project complexity. A two-dimensional conceptual framework is proposed to define four distinct types of software project complexity: structural organizational complexity, structural IT complexity, dynamic organizational complexity, and dynamic IT complexity. Based on field interviews, focus group discussions, and a large-scale survey of ISD project managers, a measure of ISD project complexity with 17 indicators was developed. The results of an exploratory data analysis provide strong evidence that the final measure has satisfactory measurement properties. The contributions of this research to both theory development and practice are discussed.
Treatment of Traumatized Victims of War and Torture: A Randomized Controlled Comparison of Narrative Exposure Therapy and Stress Inoculation Training

Background: The aim of the present randomized controlled trial was to compare the outcome of 2 active treatments for posttraumatic stress disorder (PTSD) as a consequence of war and torture: narrative exposure therapy (NET) and stress inoculation training (SIT). Methods: Twenty-eight PTSD patients who had experienced war and torture, most of them asylum seekers, received 10 treatment sessions of either NET or SIT at the Outpatient Clinic for Refugees, University of Konstanz, Germany. Posttests were carried out 4 weeks after treatment, and follow-up tests were performed 6 months and 1 year after treatment. The main outcome measure was the PTSD severity score according to the Clinician-Administered PTSD Scale (CAPS) at each time point. Results: A significant reduction in PTSD severity was found for NET, but not for SIT. A symptom reduction in the NET group occurred between pretest and the 6-month follow-up examination, the effect size being d = 1.42 (for SIT: d = 0.12), and between pretest and the 1-year follow-up, the effect size being d = 1.59 (for SIT: d = 0.19). The rates and scores of major depression and other comorbid disorders did not decrease significantly over time in either of the 2 treatment groups. Conclusions: The results indicate that exposure treatments like NET lead to a significant PTSD symptom reduction even in severely traumatized refugees and asylum seekers.
A metamaterial-based symmetrical periodic antenna with efficiency enhancement

A metamaterial-based microstrip patch antenna with a symmetrical periodic structure is proposed in this paper. Additionally, the efficiency enhancement method of the proposed symmetrical periodic antenna (SPA) is also presented using triangular slots embedded on the ground plane. The proposed antenna has a monopole-like omni-directional radiation occurred by the characteristic of composite right/left handed (CRLH) transmission line (TL). The proposed antenna resonates at 3.325 GHz in the zeroth-order frequency and 5.165 GHz in the right-handed (RH) frequency due to the symmetrical periodicity, respectively. The measured efficiency of the proposed antenna is increased about 13% at the zeroth-order resonant mode by increasing the triangular slot length (L) from 0 mm to 5.5 mm.
A semantic analysis of the annotations of the human genome

The correct interpretation of any biological experiment depends in an essential way on the accuracy and consistency of the existing annotation databases. Such databases are ubiquitous and used by all life scientists in most experiments. However, it is well known that such databases are incomplete and many annotations may also be incorrect. In this paper we describe a technique that can be used to analyze the semantic content of such annotation databases. Our approach is able to extract implicit semantic relationships between genes and functions. This ability allows us to discover novel functions for known genes. This approach is able to identify missing and inaccurate annotations in existing annotation databases, and thus help improve their accuracy. We used our technique to analyze the current annotations of the human genome. From this body of annotations, we were able to predict 212 additional gene-function assignments. A subsequent literature search found that 138 of these gene-functions assignments are supported by existing peer-reviewed papers. An additional 23 assignments have been confirmed in the meantime by the addition of the respective annotations in later releases of the Gene Ontology database. Overall, the 161 confirmed assignments represent 75.95% of the proposed gene-function assignments. Only one of our predictions (0.4%) was contradicted by the existing literature. We could not find any relevant articles for 50 of our predictions (23.58%). The method is independent of the organism and can be used to analyze and improve the quality of the data of any public or private annotation database.
Respiratory infectious phenotypes in acute exacerbation of COPD: an aid to length of stay and COPD Assessment Test

Purpose To investigate the respiratory infectious phenotypes and their impact on length of stay (LOS) and the COPD Assessment Test (CAT) Scale in acute exacerbation of COPD (AECOPD). Patients and methods We categorized 81 eligible patients into bacterial infection, viral infection, coinfection, and non-infectious groups. The respiratory virus examination was determined by a liquid bead array xTAG Respiratory Virus Panel in pharyngeal swabs, while bacterial infection was studied by conventional sputum culture. LOS and CAT as well as demographic information were recorded. Results Viruses were detected in 38 subjects, bacteria in 17, and of these, seven had both. Influenza virus was the most frequently isolated virus, followed by enterovirus/rhinovirus, coronavirus, bocavirus, metapneumovirus, parainfluenza virus types 1, 2, 3, and 4, and respiratory syncytial virus. Bacteriologic analyses of sputum showed that Pseudomonas aeruginosa was the most common bacteria, followed by Acinetobacter baumannii, Klebsiella, Escherichia coli, and Streptococcus pneumoniae. The longest LOS and the highest CAT score were detected in coinfection group. CAT score was positively correlated with LOS. Conclusion Respiratory infection is a common causative agent of exacerbations in COPD. Respiratory coinfection is likely to be a determinant of more severe acute exacerbations with longer LOS. CAT score may be a predictor of longer LOS in AECOPD.
Interleukin-18 promoter polymorphism is associated with lung cancer: A case-control study

Background. Interleukin-18 (IL-18) is a multifunctional cytokine that augments IFN-γ production and affects tumor immune response. In the present case-control study, we tested whether IL-18 promoter polymorphism contributes to lung cancer susceptibility in Iranian patients. Material and methods. The study groups were 73 patients with lung cancer, including 53 with squamous carcinoma (SC) and 20 with small cell lung carcinoma (SCLC), and 97 healthy regional aged-matched individuals. The frequency of IL-18 promoter single nucleotide polymorphisms (SNPs) at positions -656 (G/T), -607 (C/A), and -137 (G/C) was determined by polymerase chain reaction analyses. Results. There were significant differences in the IL-18 -607 allele and genotype distributions between the 73 lung cancer patients and controls. A significantly higher A allele frequency at position -607, which is associated with lower IL-18 production, was observed in lung cancer patients (48.6% vs. 35%; OR = 1.75; 95% CI 1.13–2.72). Also, patients with the -607 CA and the AA genotypes had a 2.60-fold (95% CI 1.26–5.36) and 3.15-fold (95% CI 1.16–8.55) increase in risk of lung cancer. Subdivision of the patients according to histological type revealed that SC was significantly associated with IL-18 -607 SNPs. Although the percentages of -607 alleles and genotypes in SCLC patients were similar to the results in SC patients, the differences compared to control individuals did not reach statistical significance. Analysis with Arlequin software identified eight haplotypes from three SNPs analyzed here. The distributions of IL-18 gene haplotypes were not significantly different between patients and controls after Bonferroni correction. Discussion. This is the first report to investigate the association between IL-18 polymorphism and lung cancer. Our results suggest that IL-18 polymorphism contributes to the lung cancer risk, particularly among SC patients. Further studies with larger numbers of patients are required to determine the possible association between IL-18 polymorphisms and different histological types of lung cancer.
A resilient architecture for automated fault tolerance in virtualized data centers

Virtualization is a key enabler to autonomic management of hosted services in data centers. We show that it can be used to manage reliability of these virtual entities with virtual backups. An architecture is proposed to autonomously manage and allocate the physical resources, ensure reliability guarantees, and manage the pools of virtual backups for failure recovery and resource conservation. It is fault tolerant by design so that component failures do not bring down the entire data center.
3D Architectural Modeling: Efficient RANSAC for n-gonal Primitive Fitting

We present a modeling approach to automatically ﬁt 3D primitives to point clouds in order to generate a CAD like model. For detailed modeling we propose a new n-gonal 3D primitive and a novel RANSAC based ﬁtting approach. Non-planar surfaces are modeled through surface of revolution with B-spline proﬁles. We ﬁrst reduce the dimension by projecting the 3D data onto a 2D plane. Primitive ﬁtting algorithm is then applied in this 2D space. Our approach compares favorably both with manually and automatically generated models. Not only is it much more time efﬁcient than manual modeling, but it also gives signiﬁcantly better output than state-of-the-art automatic methods. Since the focal technique of our approach is the ﬁtting of detailed primitives, our results are ideal in the domain of architecture and preservation of heritage.