Miracle-dz/UniFAR-FTUs huggingface dataset:
Implementation of Equity in Resource Allocation for Regional Earthquake Risk Mitigation Using Two‐Stage Stochastic Programming

This article presents a new methodology to implement the concept of equity in regional earthquake risk mitigation programs using an optimization framework. It presents a framework that could be used by decisionmakers (government and authorities) to structure budget allocation strategy toward different seismic risk mitigation measures, i.e., structural retrofitting for different building structural types in different locations and planning horizons. A two‐stage stochastic model is developed here to seek optimal mitigation measures based on minimizing mitigation expenditures, reconstruction expenditures, and especially large losses in highly seismically active countries. To consider fairness in the distribution of financial resources among different groups of people, the equity concept is incorporated using constraints in model formulation. These constraints limit inequity to the user‐defined level to achieve the equity‐efficiency tradeoff in the decision‐making process. To present practical application of the proposed model, it is applied to a pilot area in Tehran, the capital city of Iran. Building stocks, structural vulnerability functions, and regional seismic hazard characteristics are incorporated to compile a probabilistic seismic risk model for the pilot area. Results illustrate the variation of mitigation expenditures by location and structural type for buildings. These expenditures are sensitive to the amount of available budget and equity consideration for the constant risk aversion. Most significantly, equity is more easily achieved if the budget is unlimited. Conversely, increasing equity where the budget is limited decreases the efficiency. The risk‐return tradeoff, equity‐reconstruction expenditures tradeoff, and variation of per‐capita expected earthquake loss in different income classes are also presented.
Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains

Xylella fastidiosa (Xf) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative analysis of the complete genome of Xf pv citrus and the partial genomes of two recently sequenced strains of this species: Xf pv almond and Xf pv oleander, which cause leaf scorch in almond and oleander plants, respectively. We report a reanalysis of the previously sequenced Xf 9a5c (CVC, citrus) strain and the two “gapped” Xf genomes revealing ORFs encoding critical functions in pathogenicity and conjugative transfer. Second, a detailed whole-genome functional comparison was based on the three sequenced Xf strains, identifying the unique genes present in each strain, in addition to those shared between strains. Third, an “in silico” cellular reconstruction of these organisms was made, based on a comparison of their core functional subsystems that led to a characterization of their conjugative transfer machinery, identification of potential differences in their adhesion mechanisms, and highlighting of the absence of a classical quorum-sensing mechanism. This study demonstrates the effectiveness of comparative analysis strategies in the interpretation of genomes that are closely related.
Financial Volatility, Dynamic Correlations, and Macroeconomic Fundamentals

This dissertation consists of four research articles that deal with different aspects of the modeling of financial volatility and dynamic correlations. They all focus on the U.S. stock market and its link to macroeconomic fundamentals by applying MIDAS techniques. The contributions of the articles are of theoretical, methodological, and empirical nature. Each chapter is self-contained and can be read independently. Chapter 1 and 2 consider GARCH-MIDAS component models and the relationship between long-term financial volatility, the variance risk premium, and the stance of the macroeconomy. Chapter 3 presents a new GARCH model that links time-varying volatility persistence to explanatory variables. Finally, Chapter 4 applies the multivariate DCC-MIDAS model to returns on the stock and the oil market and analyzes their relation to macroeconomic fundamentals.
Bacterial Pathogens as Biological Weapons and Agents of Bioterrorism

&NA; Bacterial pathogens have been identified as agents that have been, or could be, used as weapons of biological warfare and/or biological terrorism. These agents are relatively easily obtained, prepared, and dispersed, either as weapons of mass destruction or for more limited terrorist attacks. Although phylogenetically diverse, these agents all have the potential for aerosol dissemination. Physicians in the United States and most of the developed world have never encountered most of these agents and the diseases they produce. Public health programs must be prepared, and individual primary care providers must be able to recognize, diagnose, treat, and prevent infection with these agents.
THE ROLE OF SELF-EFFICACY IN PREDICTING USE OF DISTANCE EDUCATION TOOLS AND LEARNING MANAGEMENT SYSTEMS

This study aims to investigate the role of self-efficacy in predicting students’ use of distance education tools and learning management systems (LMSs). A total of 124 undergraduate students who enrolled in a course on Distance Education and selected using convenience sampling willingly participated in the study. The participants had little prior knowledge about distance education tools and LMSs. Therefore, they received instructions from the researcher over the course of a semester. The study proposed a research model based on the Technology Acceptance Model that has been widely used to predict user acceptance and use. Structural equation modelling was used to test the research model against the data collected through questionnaire surveys. Pretest-posttest results suggested that the students had significant learning by participating in the instruction. The results of the main analysis also suggested that self-efficacy positively affects perceived ease of use, while usefulness and ease of use perceptions positively affect attitudes toward using distance education tools and systems. Implications are provided along with limitations of the study discussed.
Does abortion reduce the mental health risks of unwanted or unintended pregnancy? A re-appraisal of the evidence

Objective: There have been debates about the linkages between abortion and mental health. Few reviews have considered the extent to which abortion has therapeutic benefits that mitigate the mental health risks of abortion. The aim of this review was to conduct a re-appraisal of the evidence to examine the research hypothesis that abortion reduces rates of mental health problems in women having unwanted or unintended pregnancy. Methods: Analysis of recent reviews (Coleman, 2011; National Collaborating Centre for Mental Health, 2011) identified eight publications reporting 14 adjusted odds ratios (AORs) spanning five outcome domains: anxiety; depression; alcohol misuse; illicit drug use/misuse; and suicidal behaviour. For each outcome, pooled AORs were estimated using a random-effects model. Results: There was consistent evidence to show that abortion was not associated with a reduction in rates of mental health problems (p>0.75). Abortion was associated with small to moderate increases in risks of anxiety (AOR 1.28, 95% CI 0.97−1.70; p<0.08), alcohol misuse (AOR 2.34, 95% CI 1.05−5.21; p<0.05), illicit drug use/misuse (AOR 3.91, 95% CI 1.13−13.55; p<0.05), and suicidal behaviour (AOR 1.69, 95% CI 1.12−2.54; p<0.01). Conclusions: There is no available evidence to suggest that abortion has therapeutic effects in reducing the mental health risks of unwanted or unintended pregnancy. There is suggestive evidence that abortion may be associated with small to moderate increases in risks of some mental health problems.
Frequency scaling algorithm for One-Stationary Spotlight Bistatic SAR imaging

The frequency scaling algorithm (FSA) is proposed to process One-Stationary Spotlight Bistatic SAR (BiSAR) data acquired via the dechirp-on-receive approach. By using series reversion, we can derives the two-dimensional point target spectrum for this BiSAR configuration. This algorithm leads to a very precise and efficient processing since it performs the focusing in the frequency domain and no interpolation is required in the whole processing chain. This algorithm is verified with a point target simulation.
Optimal motion planning of juggling by 3-DOF manipulators using adaptive PSO algorithm

SUMMARY Three-DOF manipulators were employed for juggling of polygonal objects in order to have full control over object's configuration. Dynamic grasp condition is obtained for the instances that the manipulators carry the object on their palms. Manipulation problem is modeled as a nonlinear optimal control problem. In this optimal control problem, time of free flight is used as a free parameter to determine throw and catch times. Cost function is selected to get maximum covered horizontal distance using minimum energy. By selecting third-order polynomials for joint motions, the problem is changed to a constrained parameter selection problem. Adaptive particle swarm optimization method is consequently employed to solve the optimization problem. Effectiveness of the optimization algorithm is verified by a set of simulations in MSC. ADAMS.
Detection of Aspergillus fumigatus and a Mutation That Confers Reduced Susceptibility to Itraconazole and Posaconazole by Real-Time PCR and Pyrosequencing

ABSTRACT A real-time PCR and pyrosequencing method was developed to detect Aspergillus fumigatus in whole blood by amplifying the cyp51A gene and sequencing the codon for glycine 54. Mutations in this codon can result in amino acid substitutions that confer reduced susceptibility to itraconazole and posaconazole.
Molecular dynamics of a far positioned SOD1 mutant V14M reveals pathogenic misfolding behavior

Human superoxide dismutase (Cu/Zn SOD1) is a homodimeric enzyme. Mutations in Cu/Zn SOD1 causes a familial form of amyotrophic lateral sclerosis (fALS), and aggregation of mutant SOD1 has been proposed to play a role in neurodegeneration. Though a majority of the mutations are point substitutions, there are a few changes that result in amino acid deletions or truncations of the polypeptide. These pathogenic mutations are scattered throughout the three-dimensional structure of the dimeric enzyme, which creates a puzzling pattern to investigate the molecular determinants of fALS. The most common hypothesis proposed that the misfolding of SOD1 mutants are primarily triggered by decreased affinity for metal ions. However, this hypothesis is challenging, as a significant number of disease-causing mutations are located far away from the metal-binding site and dimer interface. So in the present study, we have investigated the influence of such a far positioned pathogenic mutation, V14M, in altering the stability and folding of the Cu/Zn SOD1. Though the location of Val14 is far positioned, it has a vital role in the stability of SOD1 by preserving its hydrophobic cluster at one end of the β barrel domain. We have performed MD simulations of the V14M mutant for 80 ns timescale. The results reveal the fact that irrespective of its location, V14M mutation triggers a conformational change that is more similar to that of the metal-deficient holo form and could resemble an intermediate state in the folding reaction which results in protein misfolding and aggregation.
From mice to elephants: overturning the 'one size fits all' paradigm in marine plankton food chains.

It is widely believed that consumer control is a weak regulator of marine phytoplankton communities. It remains unclear, however, why this should be the case when marine consumers routinely regulate their prey at higher trophic levels. One possibility is that the weak consumer control of phytoplankton communities results from the inability of field researchers to effectively account for consumer-prey trophic relationships operating at the scale of the plankton. We explored this issue by reviewing studies of trophic control in marine plankton. Experimental studies indicate that size is a critical determinant of feeding relationships among plankton. In sharp contrast, of the 51 field studies reviewed, 78% did not distinguish among the sizes or species of phytoplankton and their consumers, but instead assumed a general bulk phytoplankton-zooplankton trophic connection. Such an approach neglects the possibility that several trophic connections may separate the smallest phytoplankton (0.2 μm) from the larger zooplankton (~ 1000 μm), a remarkable size differential exceeding that between a mouse (~10 cm) and an elephant (~2500 cm). The size-based approach we propose integrates theory, experiments and field observations and has the potential to greatly enhance our understanding of the causes and consequences of recently documented restructuring of plankton communities.
The Created Environment for Physical Assessment by Case Managers

Goals of gerontological nursing include maximizing health and confronting functional impairments. The health of older adults is often fragile because of age-related change, complicated by chronic illnesses. Identification of changes in health status permits responsive care and consultation but requires proficiency in physical assessment. In 1995, research was conducted in Alberta, Canada, on registered nurse case managers’ reported use of assessment skills. Nineteen continuing-care facilities in 1 of 17 provincial health regions participated (N = 189). After expert review and pilot testing, questionnaires were distributed to two independent groups: nurse administrators/staff development coordinators and case managers (response rate = 73%). Qualitative data were subjected to descriptive, interpretive, and pattern coding. Reported are factors constraining or facilitating physical assessment in continuing care. Neuman’s concept of the created environment provided a factor-organizing framework. A holistic view of environment and data source triangulation increased confidence in the comprehensiveness and credibility of results.
Reliability of Hoechst 33342 Staining under Wide-Field Microscopy for Evaluation of the Nuclear Status of Living Dog Oocytes

Abstract Due to the marked cytoplasmic opacity of canine oocytes, the diagnosis of their nuclear status is difficult. The objective of the present study was to evaluate the accuracy of Hoechst staining observed under epifluorescence wide-field microscopy [living oocyte observation (LivOO)] by comparison to a reference technique [DNA staining with ethidium homodimer-2 under confocal microscopy; fixed oocyte observation (FixOO)]. Four Hoechst 33342 concentrations (200 ng, 500 ng, 1 μg, 2 μg/mL) were tested and 1 μg/mL was the lowest one with the lowest proportion of oocytes in which DNA was missed. At this concentration, LivOO procedure did not affect the degeneration rate. On 379 oocytes observed individually with the two techniques successively, diagnosis of meiosis resumption by LivOO was exact in 87.3% of the cases, but the meiosis resumption rate was underestimated (23.5% versus 34.3% with FixOO; p < 0.001). Diagnosis for metaphase II was exact in 80% of the cases, but LivOO detected only 72.7% of the metaphase II oocytes present. Metaphase rates did not differ between LivOO and FixOO. This study contributes to a better interpretation of in vitro maturation results. The developmental potential of metaphase II canine oocytes sorted after Hoechst staining is to be evaluated.
Classification of keyphrases from scientific publications using WordNet and word embeddings

The ScienceIE task at SemEval-2017 introduced an epistemological classification of keyphrases in scientific publications, suggesting that research activities revolve around the key concepts of process (methods and systems), material (data and physical resources) and task. In this paper we present a method for the classification of keyphrases according to the ScienceIE classification, using WordNet and word embeddings derived features. The method outperforms the best system at SemEval-2017, although our experiments highlighted some issues with the collection. RÉSUMÉ. Dans le contexte du challenge ScienceIE à SemEval-2017, ses organisateurs ont introduit une classification des phrases clés dans les publications scientifiques. Selon leur hypothèse, les activités de recherche tournent autour des concepts clés de “process" (methodes, systèmes), “material" (ressources matériellles, données, produits) et “task" (problèmes, activités à poursuivre). Dans cet article, nous présentons une méthode pour la classification des phrases clés selon la classification donné par ScienceIE, en utilisant des caractéristiques dérivées à partir de WordNet et de “word embeddings". La méthode proposée dépasse le meilleur système au SemEval-2017; toutefois, nos expériences ont mis en évidence certains problèmes d’annotation avec la collection.
Fused pose estimation using geometric and texture information

This paper addresses the problem of estimating the alignment pose between two models by using structure-specific local descriptors which are generated by combining 2D image data and 3D contextual shape data. The 2D texture information is represented by a robust SIFT descriptor, and the geometric information is represented by a histogram supported by the orders of curvature and angles between normal vectors. The proposed pose estimation method combines the homography relation and epipolar geometry (fundamental matrix) with the EPnP algorithm. We present experiments both in controlled and real-life scenarios to validate the approach. The quantitative evaluations show that the proposed fused pose estimation provides lower mean square registration error compared to EPnP algorithm.
Genetic diversity and molecular characterization of several Heliconia species in Colombia.

Researchers have classified the Heliconia genus as a group of highly variable and diverse plants. Species and cultivars are visually differentiated primarily on the basis of the color and size of inflorescence bracts. At taxonomic level, flower type (parabolic, sigmoid, or erect) and size are taken into account. The vast morphological diversity of heliconias at intra-specific, intra-population, and varietal levels in central-west Colombia prompted the present study. We characterized the genetic variability of 67 genotypes of cultivated heliconias belonging to Heliconia caribaea Lamarck, H. bihai (L.) L. , H. orthotricha L. Andersson, H. stricta Huber, H. wagneriana Petersen, and H. psittacorum L. f. , as well as that of several interspecific hybrids such as H. psittacorum L. f. x H. spathocircinata Aristeguieta and H. caribaea Lamarck x H. bihai (L.) L. We also created an approximation to their phylogenetic analysis. Molecular analysis using amplified fragment length polymorphism (AFLP) markers revealed a total of 170 bands. Two large, well-defined groups resulted: the first grouped cultivars of the very closely related H. caribaea and H. bihai species with those of H. orthotricha and H. psittacorum, and the second grouped H. stricta and H. wagneriana cultivars. The lowest percentage of polymorphism was found in H. psittacorum (17.65%) and the highest was in H. stricta (55.88%). Using AFLP, phylogenetic analysis of the species studied revealed the monophyletic origin of the Heliconiaceae family, and identified the Heliconia subgenus as monophyletic while providing evidence of the polyphyletic origin of several representatives of the Stenochlamys subgenus.
Finding Fluorescent Needles in the Cardiac Haystack: Tracking Human Mesenchymal Stem Cells Labeled with Quantum Dots for Quantitative In Vivo Three‐Dimensional Fluorescence Analysis

Stem cells show promise for repair of damaged cardiac tissue. Little is known with certainty, however, about the distribution of these cells once introduced in vivo. Previous attempts at tracking delivered stem cells have been hampered by the autofluorescence of host tissue and limitations of existing labeling techniques. We have developed a novel loading approach to stably label human mesenchymal stem cells with quantum dot (QD) nanoparticles. We report the optimization and validation of this long‐term tracking technique and highlight several important biological applications by delivering labeled cells to the mammalian heart. The bright QD crystals illuminate exogenous stem cells in histologic sections for at least 8 weeks following delivery and permit, for the first time, the complete three‐dimensional reconstruction of the locations of all stem cells following injection into the heart.
Is it sensible to "deform" dose? 3D experimental validation of dose-warping.

PURPOSE Strategies for dose accumulation in deforming anatomy are of interest in radiotherapy. Algorithms exist for the deformation of dose based on patient image sets, though these are sometimes contentious because not all such image calculations are constrained by physical laws. While tumor and organ motion has been a key area of study for a considerable amount of time, deformation is of increasing interest. In this work, we demonstrate a full 3D experimental validation of results from a range of dose deformation algorithms available in the public domain. METHODS We recently developed the first tissue-equivalent, full 3D deformable dosimetric phantom-"DEFGEL. " To assess the accuracy of dose-warping based on deformable image registration (DIR), we have measured doses in undeformed and deformed states of the DEFGEL dosimeter and compared these to planned doses and warped doses. In this way we have directly evaluated the accuracy of dose-warping calculations for 11 different algorithms. We have done this for a range of stereotactic irradiation schemes and types and magnitudes of deformation. RESULTS The original Horn and Schunck algorithm is shown to be the best performing of the 11 algorithms trialled. Comparing measured and dose-warped calculations for this method, it is found that for a 10 × 10 mm(2) square field, γ(3%∕3mm) = 99.9%; for a 20 × 20 mm(2) cross-shaped field, γ(3%∕3mm) = 99.1%; and for a multiple dynamic arc (0.413 cm(3) PTV) treatment adapted from a patient treatment plan, γ(3%∕3mm) = 95%. In each case, the agreement is comparable to-but consistently ∼1% less than-comparison between measured and calculated (planned) dose distributions in the absence of deformation. The magnitude of the deformation, as measured by the largest displacement experienced by any voxel in the volume, has the greatest influence on the accuracy of the warped dose distribution. Considering the square field case, the smallest deformation (∼9 mm) yields agreement of γ(3%∕3mm) = 99.9%, while the most significant deformation (∼20 mm) yields agreement of γ(3%∕3mm) = 96.7%. CONCLUSIONS We have confirmed that, for a range of mass and density conserving deformations representative of those observable in anatomical targets, DIR-based dose-warping can yield accurate predictions of the dose distribution. Substantial differences can be seen between the results of different algorithms indicating that DIR performance should be scrutinized before application todose-warping. We have demonstrated that the DEFGEL deformable dosimeter can be used to evaluate DIR performance and the accuracy of dose-warping results by direct measurement.