Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotype-dependent Burst of Transposable Element Expression in Crowns of Hexaploid Wheat (Triticum aestivum L.) during Cold Acclimation

The expression of 1,613 transposable elements (TEs) represented in the Affymetrix Wheat Genome Chip was examined during cold treatment in crowns of four hexaploid wheat genotypes that vary in tolerance to cold and in flowering time. The TE expression profiles showed a constant level of expression throughout the experiment in three of the genotypes. In winter Norstar, the most cold-hardy of the four genotypes, a subset of the TEs showed a burst of expression after vernalization saturation was achieved. About 47% of the TEs were expressed, and both Class I (retrotransposons) and Class II (DNA transposons) types were well represented. Gypsy and Copia were the most represented among the retrotransposons while CACTA and Mariner were the most represented DNA transposons. The data suggests that the Vrn-A1 region plays a role in the stage-specific induction of TE expression in this genotype.
Optimality‐based modeling of planktonic organisms

On the basis of the assumption that natural selection should tend to produce organisms optimally adapted to their environments, we consider optimality as a guiding concept for abstracting the behavior of aquatic micro‐organisms (plankton) to develop models to study and predict the behavior of planktonic organisms and communities. This is closely related to trait‐based ecology, which considers that traits and functionality can be understood as the result of the optimization inherent in natural selection, subject to constraints imposed by fundamental processes necessary for life. This approach is particularly well suited to plankton because of their long evolutionary history and the ease with which they can be manipulated in experiments. We review recent quantitative modeling studies of planktonic organisms that have been based on the assumption that adaptation of species and acclimation of organisms maximize growth rate. Compared with mechanistic models not formulated in terms of optimality, this approach has in some cases yielded simpler models, and in others models of greater generality. The evolutionary success of any given species must depend on its interactions with both the physical environment and other organisms, which depend on the evolving traits of all organisms concerned. The concept of an evolutionarily stable strategy (ESS) can, at least in principle, constrain the choice of goal functions to be optimized in models. However, the major challenge remains of how to construct models at the level of organisms that can resolve short‐term dynamics, e.g., of phytoplankton blooms, in a way consistent with ESS theory, which is formulated in terms of a steady state.
THE HIGHEST RESOLUTION CHANDRA VIEW OF PHOTOIONIZATION AND JET–CLOUD INTERACTION IN THE NUCLEAR REGION OF NGC 4151

We report high resolution imaging of the nucleus of the Seyfert 1 galaxy NGC 4151 obtained with a 50 ks Chandra High Resolution Camera (HRC) observation. The HRC image resolves the emission on spatial scales of 0. ″5, ∼30 pc, showing an extended X-ray morphology overall consistent with the narrow-line region (NLR) seen in optical line emission. Removal of the bright point-like nuclear source and image deconvolution techniques both reveal X-ray enhancements that closely match the substructures seen in the Hubble Space Telescope [O iii] image and prominent knots in the radio jet. We find that most of the NLR clouds in NGC 4151 have [O iii]/soft X-ray ratio ∼10, despite the distance of the clouds from the nucleus. This ratio is consistent with the values observed in NLRs of some Seyfert 2 galaxies, which indicates a uniform ionization parameter even at large radii and a density decreasing as r−2 as expected for a nuclear wind scenario. The [O iii]/X-ray ratios at the location of radio knots show an excess of X-ray emission, suggesting shock heating in addition to photoionization. We examine various mechanisms for the X-ray emission and find that, in contrast to jet-related X-ray emission in more powerful active galactic nucleus, the observed jet parameters in NGC 4151 are inconsistent with synchrotron emission, synchrotron self-Compton, inverse Compton of cosmic microwave background photons or galaxy optical light. Instead, our results favor thermal emission from the interaction between radio outflow and NLR gas clouds as the origin for the X-ray emission associated with the jet. This supports previous claims that frequent jet–interstellar medium interaction may explain why jets in Seyfert galaxies appear small, slow, and thermally dominated, distinct from those kpc-scale jets in the radio galaxies.
Animal Models of Cardiac Disease and Stem Cell Therapy

Animal models that mimic cardiovascular diseases are indispensable tools for understanding the mechanisms underlying the diseases at the cellular and molecular level. This review focuses on various methods in preclinical research to create small animal models of cardiac diseases, such as myocardial infarction, dilated cardiomyopathy, heart failure, myocarditis and cardiac hypertrophy, and the related stem cell treatment for these diseases.
A Voronoi-Based Hybrid Meshing Method

We introduce a method to build volumetric hybrid meshes suitable for finite element computations. The generated mesh is conformal to a set of input surfaces; thin sections are meshed with prisms, pyramids, and tetrahedra, while the remaining of the domain is meshed with Delaunay tetrahedra.
Desigualdades sociais no estado nutricional e consumo alimentar de escolares brasileiros

Introduction: Evidence shows that individuals with low socioeconomic status are prone to malnutrition, which contributes to health inequalities and increases the prevalence of nutritional disorders in childhood. In addition, there are no studies in Brazil assessing the social inequality in adolescents’ nutritional status and food consumption. Objective: To assess social inequalities regarding the nutritional status and food consumption of Brazilian students. Materials and Methods: We used the data from the 2015 National Adolescent School-based Health Survey (PeNSE – Pesquisa Nacional de Saúde do Escolar), which was a research with students aged 13 to 17 years of public and private schools in urban and rural areas in Brazil. The variables of interest were the demographic characteristics, sex, nutritional status and food consumption of fruits, vegetables, soft drinks, treats and fast food. We created a wealth score based on answers about the ownership of goods and access to services by means of the principal component analysis (PCA), later divided into quintiles. We calculated the Slope index of inequalities and the Concentration index, along with simple inequality measures based on differences and ratios. The t-test identified statistically significant differences in sex inequality. Results: Male students were more prone to obesity in the wealthiest quintile. The SII of +7.79 and CIX of +15.23 showed that inequality favored the richest students. Regarding consumption, the inequality indices had similar positive values for all foods analyzed, showing that inequality favored the richest individuals. Conclusion: Social inequality among adolescents fostered unequal consumption and nutritional deviations. The richest ones were more affected by obesity and by a higher consumption of healthy and unhealthy foods.
Inattention And Hyperactivity Among Preschool Age Children Born Prematurely

INATTENTION AND HYPERACTIVITY AMONG PRESCHOOL AGE CHILDREN BORN PREMATURELY by ANDREW HEITZER December 2014 Advisor: Dr. Sarah Raz Major: Psychology (clinical) Degree: Master of Arts A large body of literature shows that compared to children born at term, pretermchildren are at increased risk for difficulties with inattention and hyperactivity. Less consistency exists, however, in the limited body of research exploring the contribution of early biological risk to behavioral disinhibition within the population of children born prematurely. Therefore, our goal was to examine perinatal variables that may influence activity level and hyperactivity among preterm preschoolers. One-hundred (23.4 33.9 weeks gestation) preschoolers (3-4 years) participated in the study. Direct measures of inattention and hyperactivity as well as parental ratings were used to evaluate behavior. We used simultaneous linear regression analyses with gestational age, perinatal complications, and growth rate z-score (birth weight standardized by gestational age) as predictors of interest. Socioeconomic status, sex, multiple gestation, and age at testing were our
THE EFFECTS OF PERCEIVED BARRIERS AND PERCEIVED ENJOYMENT ON USERS’ INTENTION TO USE 3D PRINTER TECHNOLOGY

The main purpose of this study is to investigate the intention of consumers to use desktop 3D printers with taking into account the dimensions of perceived barriers and enjoyment. This study contributes to the early understanding of Turkish consumers’ intention to use desktop 3D printers. According to the results of the research; the effect of the perceived enjoyment on intention to use of 3D Printer was positive and the effect of the perceived barrier on intention to use was negative. When the results are anticipated in terms of 3D Printer ownership; the perceived enjoyment in user group who have 3D Printer was lower than the group who do not have, whereas risk perceptions stems from barriers was higher for this group.
Molecular Determinants and Evolutionary Dynamics of Wobble Splicing

Alternative splicing at tandem splice sites (wobble splicing) is widespread in many species, but the mechanisms specifying the tandem sites remain poorly understood. Here, we used synaptotagmin I as a model to analyze the phylogeny of wobble splicing spanning more than 300 My of insect evolution. Phylogenetic analysis indicated that the occurrence of species-specific wobble splicing was related to synonymous variation at tandem splice sites. Further mutagenesis experiments demonstrated that wobble splicing could be lost by artificially induced synonymous point mutations due to destruction of splice acceptor sites. In contrast, wobble splicing could not be correctly restored through mimicking an ancestral tandem acceptor by artificial synonymous mutation in in vivo splicing assays, which suggests that artificial tandem splice sites might be incompatible with normal wobble splicing. Moreover, combining comparative genomics with hybrid minigene analysis revealed that alternative splicing has evolved from the 3′ tandem donor to the 5′ tandem acceptor in Culex pipiens, as a result of an evolutionary shift of cis element sequences from 3′ to 5′ splice sites. These data collectively suggest that the selection of tandem splice sites might not simply be an accident of history but rather in large part the result of coevolution between splice site and cis element sequences as a basis for wobble splicing. An evolutionary model of wobble splicing is proposed.
LiteLab : Towards Efficient Large-scale Network Experiment

Large-scale network experiments is a challenging problem. Simulations, emulations, and real-world testbeds all have their advantages and disadvantages. In this paper we present LiteLab, a light-weight platform specialized for largescale networking experiments. We cover in detail its design, key features, and architecture. We also perform an extensive evaluation of LiteLab’s performance and accuracy and show that it is able to both simulate network parameters with high accuracy, and also able to scale up to very large networks. LiteLab is flexible, easy to deploy, and allows researchers to perform large-scale network experiments with a short development cycle. We have used LiteLab for many different kinds of network experiments and are planning to make it available for others to use as well.
Automatic alignment of 3D reconstructions using a Digital Surface Model

We present a novel technique for the automatic alignment of Structure from Motion (SfM) models, acquired at ground level or by micro aerial vehicles, to an overhead Digital Surface Model (DSM) using GPS information. An additional refinement step based on the correlation of the DSM height map with the model height map corrects for the GPS localization uncertainties and results in precisely aligned models. Our approach successfully handles cases where previous methods had problems, including objects on the ground, unoccupied space, and models covering a small area. We conclude our work by presenting several applications of our approach, namely the fusion of detailed SfM model information into the original DSM, season-invariant matching using aligned models, and alignment for providing context in visualization.
Localization of AUVs using depth information of underwater structures from a monocular camera

In this paper, we propose a method of AUV localization and mapping using visual measurement of underwater structures. Since the inertial navigation system (INS) of AUV suffers from drift, observing fixed objects can enhance the localization performance. Depth map estimation of underwater structures and tracking of an AUV are complementarily handled in a framework of pose graph optimization. Estimation of absolute scale is resolved by exploiting incremental measurements of inertial sensors. The proposed method is validated by experiments performed in a structured basin environment.
A deep XMM-Newton observation of the ultraluminous X-ray source HoII X-1 : the case against a 1000 solar mass black hole

We present results from a 112 ks long look by XMM-Newton at the ultraluminous X-ray source (ULX) Holmberg II X-1, long thought to be the one of best candidates for the missing class of intermediate mass black holes (IMBHs). Our data comprises the first high quality XMM-Newton/RGS spectrum of an ULX, and an XMM-Newton/EPIC spectrum with unprecedented signal-to-noise. A detailed timing analysis shows that any variability on time-scales of minutes to hours is very weak (< few per cent fractional rms), though larger amplitude variations on much shorter time-scales could be hidden by photon counting statistics. This result suggests that if Ho II X-1 harbours an IMBH, then we are observing this source in a highly unusual and atypical state when compared with the known variability behaviour of other accreting systems of large mass. Moreover unlike Galactic X-ray binaries, our spectral analysis indicates the possible presence of an optically-thick low temperature corona. Taken together our timing and spectral analysis suggests that the compact companion is most-likely a high luminosity analogue of black hole binary systems similar to GRS 1915+105, the Galactic microquasar, harbouring a compact object of mass no greater than 100 solar masses.
Crystal Structure of the Mycobacterium fortuitum Class A β-Lactamase: Structural Basis for Broad Substrate Specificity

ABSTRACT β-Lactamases are the main cause of bacterial resistance to penicillins and cephalosporins. Class A β-lactamases, the largest group of β-lactamases, have been found in many bacterial strains, including mycobacteria, for which no β-lactamase structure has been previously reported. The crystal structure of the class A β-lactamase from Mycobacterium fortuitum (MFO) has been solved at 2.13-Å resolution. The enzyme is a chromosomally encoded broad-spectrum β-lactamase with low specific activity on cefotaxime. Specific features of the active site of the class A β-lactamase from M. fortuitum are consistent with its specificity profile. Arg278 and Ser237 favor cephalosporinase activity and could explain its broad substrate activity. The MFO active site presents similarities with the CTX-M type extended-spectrum β-lactamases but lacks a specific feature of these enzymes, the VNYN motif (residues 103 to 106), which confers on CTX-M-type extended-spectrum β-lactamases a more efficient cefotaximase activity.
Using cause-related events to fulfil the strategic objectives of social partnerships : a thesis presented in partial fulfilment of the requirements for the degree of Master of Business Studies in Marketing at Massey University, Albany, New Zealand

iii Acknowledgements. v List of Figures . xiii List of Tables . xv Chapter 1: Introduction . 1 Chapter 2: Literature Review . 5 2.1 What are social partnerships? 5 2.1.1 Defining social partnerships . 6 2.1.2 Corporate and NFP strategic objectives . 7 2.1.3 Stakeholder theory . 8 2.1.3.1 Descriptive: Who is a stakeholder and what constitutes a ‘stake’? 9 2.1.3.2 Normative: How should firms behave in terms of stakeholder relationships? 11 2.1.3.3 Instrumental: What are the strategic outcomes of a stakeholderoriented approach? 12 2.2 Why are social partnerships formed? 13 2.2.1 External drivers of social partnership formation . 13 2.2.1.1 The fundamental influence of social values and ethics . 14 2.2.1.2 The interrelationship of business and society . 14 2.2.1.3 Changes in the business environment and emerging issues–the rise of CSR . 15 2.2.2 Internal drivers of social partnership formation . 19 2.2.2.1 Value for corporate . 20 2.2.2.2 Value for NFP . 20 2.3 How are social partnerships formed and governed? 21 2.3.1 Key characteristics of partnership formation and governance . 22 2.3.1.1 Collective strength . 22 2.3.1.2 Interdependencies . 24 2.3.1.3 Inter-partner conflict . 25 2.3.2 Negotiating partnership conditions . 26 2.3.3 Planning and implementing activities . 27
A Gaussian Particle Filter Approach for Sensors to Track Multiple Moving Targets

In a variety of problems, the number and state of multiple moving targets are unknown and are subject to be inferred from their measurements obtained by a sensor with limited sensing ability. This type of problems is raised in a variety of applications, including monitoring of endangered species, cleaning, and surveillance. Particle filters are widely used to estimate target state from its prior information and its measurements that recently become available, especially for the cases when the measurement model and the prior distribution of state of interest are non-Gaussian. However, the problem of estimating number of total targets and their state becomes intractable when the number of total targets and the measurement-target association are unknown. This paper presents a novel Gaussian particle filter technique that combines Kalman filter and particle filter for estimating the number and state of total targets based on the measurement obtained online. The estimation is represented by a set of weighted particles, different from classical particle filter, where each particle is a Gaussian distribution instead of a point mass.
Associations between Single Nucleotide Polymorphisms in Iron-Related Genes and Iron Status in Multiethnic Populations

The existence of multiple inherited disorders of iron metabolism suggests genetic contributions to iron deficiency. We previously performed a genome-wide association study of iron-related single nucleotide polymorphisms (SNPs) using DNA from white men aged ≥25 y and women ≥50 y in the Hemochromatosis and Iron Overload Screening (HEIRS) Study with serum ferritin (SF) ≤12 µg/L (cases) and controls (SF >100 µg/L in men, SF >50 µg/L in women). We report a follow-up study of white, African-American, Hispanic, and Asian HEIRS participants, analyzed for association between SNPs and eight iron-related outcomes. Three chromosomal regions showed association across multiple populations, including SNPs in the TF and TMPRSS6 genes, and on chromosome 18q21. A novel SNP rs1421312 in TMPRSS6 was associated with serum iron in whites (p = 3.7×10−6) and replicated in African Americans (p = 0.0012). Twenty SNPs in the TF gene region were associated with total iron-binding capacity in whites (p<4.4×10−5); six SNPs replicated in other ethnicities (p<0.01). SNP rs10904850 in the CUBN gene on 10p13 was associated with serum iron in African Americans (P = 1.0×10−5). These results confirm known associations with iron measures and give unique evidence of their role in different ethnicities, suggesting origins in a common founder.
Epigenetics mechanisms and degenerative diseases

Epigenetic regulations are heritable changes in gene expression that occur in the absence of alterations in DNA sequences. Various epigenetic mechanisms include histone modifications and DNA methylations. In this review, we examine methods to study DNA methylations and their contribution to degenerative diseases by mediating the complex gene-by-environment interactions. Such epigenetic modifications despite being heritable and stably maintained are also potentially reversible and there is scope for the development of epigenetic therapies for this disease.
Hybrid neuro-fuzzy inference systems and their application for on-line adaptive learning of nonlinear dynamical systems

In this paper, an adaptive neuro-fuzzy system, called HyFIS, is proposed to build and optimise fuzzy models. The proposed model introduces the learning power of neural networks into the fuzzy logic systems and provides linguistic meaning to the connectionist architectures. Heuristic fuzzy logic rules and input-output fuzzy membership functions can be optimally tuned from training eramples by a hybrid learning scheme composedof two phases: the phase of rule generation from data, and the phase of rule tuning by using the error backpropagation learning scheme for a neural fuzzy system. In order to illustrate the performance and applicability of the proposedneuro-fuzzy hybrid model, extensive . simulation studies of nonlinear complex dynamics are carried out. The proposed method can be applied to on-line incremental adaptive learning for the purpose of prediction and control of nonlinear dynamical systems. Keywords-Neuro-fuzzy systems, Neural networks, Fuzzy logic, Parameter and structure learning, Knowledge acquisition, Adaptation, Time series. *TR-99-65, Department of Information Science, University of Otago, PO Box 56, Dunedin, New Zealand. Submitted and revised to Neural Networks, 15 March, 1999. H yF IS: Adaptive Neuro-Fuzzy Inference Systems 2
BEP Analysis of OFDM Relay Links with Nonlinear Power Amplifiers

This paper studies the performance of a two-hop infrastructure-based relay link. The relay operates in a half-duplex mode using an amplify-and-forward protocol. Considering transmission of OFDM signals with nonlinear power amplifiers (PAs), we determine exact closed-form expressions for end-to-end bit error probabilities (BEPs). The expressions allow us to analyze the effect of nonlinear distortion as well as the special case of linear PAs. Furthermore, we derive asymptotic BEP floor values which illustrate how the end-to-end performance is limited by both the nonlinear PA distortion and the weakest hop. Our discussion indicates that the influence of the nonlinear distortion can be mitigated by properly adjusting the PA back-offs.
Herding on Ending Digits in Security Trading

This article complements prior literature by distinguishing between buys and sells, and taking a new approach in testing for herding on ending digits. Using a sample of nearly 100 million stock trades, it provides strong evidence in favor of herding on ending digits, particularly in round numbers. Our investigation of what drives investor herding behavior over ending digits finds that the herding effect has a weak but positive association with past returns over a longer horizon. This finding implies that investor preference for round numbers is not only a result of price clustering, but also a consequence of momentum trading.