Miracle-dz/UniFAR-FTUs huggingface dataset:
Pyrosequencing of Haliotis diversicolor Transcriptomes: Insights into Early Developmental Molluscan Gene Expression

Background The abalone Haliotis diversicolor is a good model for study of the settlement and metamorphosis, which are widespread marine ecological phenomena. However, information on the global gene backgrounds and gene expression profiles for the early development of abalones is lacking. Methodology/Principal Findings In this study, eight non-normalized and multiplex barcode-labeled transcriptomes were sequenced using a 454 GS system to cover the early developmental stages of the abalone H. diversicolor. The assembly generated 35,415 unigenes, of which 7,566 were assigned GO terms. A global gene expression profile containing 636 scaffolds/contigs was constructed and was proven reliable using qPCR evaluation. It indicated that there may be existing dramatic phase transitions. Bioprocesses were proposed, including the ‘lock system’ in mature eggs, the collagen shells of the trochophore larvae and the development of chambered extracellular matrix (ECM) structures within the earliest postlarvae. Conclusion This study globally details the first 454 sequencing data for larval stages of H. diversicolor. A basic analysis of the larval transcriptomes and cluster of the gene expression profile indicates that each stage possesses a batch of specific genes that are indispensable during embryonic development, especially during the two-cell, trochophore and early postlarval stages. These data will provide a fundamental resource for future physiological works on abalones, revealing the mechanisms of settlement and metamorphosis at the molecular level.
Human PrimPol is a highly error-prone polymerase regulated by single-stranded DNA binding proteins

PrimPol is a recently identified polymerase involved in eukaryotic DNA damage tolerance, employed in both re-priming and translesion synthesis mechanisms to bypass nuclear and mitochondrial DNA lesions. In this report, we investigate how the enzymatic activities of human PrimPol are regulated. We show that, unlike other TLS polymerases, PrimPol is not stimulated by PCNA and does not interact with it in vivo. We identify that PrimPol interacts with both of the major single-strand binding proteins, RPA and mtSSB in vivo. Using NMR spectroscopy, we characterize the domains responsible for the PrimPol-RPA interaction, revealing that PrimPol binds directly to the N-terminal domain of RPA70. In contrast to the established role of SSBs in stimulating replicative polymerases, we find that SSBs significantly limit the primase and polymerase activities of PrimPol. To identify the requirement for this regulation, we employed two forward mutation assays to characterize PrimPol's replication fidelity. We find that PrimPol is a mutagenic polymerase, with a unique error specificity that is highly biased towards insertion-deletion errors. Given the error-prone disposition of PrimPol, we propose a mechanism whereby SSBs greatly restrict the contribution of this enzyme to DNA replication at stalled forks, thus reducing the mutagenic potential of PrimPol during genome replication.
District Leaders Engaged in School Turnaround: Identified Challenges and Espoused Responses

School turnaround initiatives have prioritized the school principal as the change lever. Little overall consideration about the critical role district leadership plays. In this study, we analyze the turnaround launch and, improvement plans of school district leaders participating in a university, turnaround program. We find that district leaders identify certain systems, levers as more significant challenges than other ones, but their espoused, ways to address these challenges are disparate if determined at all. Implications for districts and schools are discussed.
Graph Transformations on the UML Metamodel

The Unified Modeling Language UML is a rich language so that it seems not feasible to give a single semantics for the complete lang u ge in one step. In order to define the semantics, we propose to translate as ma ny UML language features as possible into UML itself. The part of UML wh ich cannot be treated in this way is called the UML core. The semantics of the non-core language features is given by a translation into the core, wh ereas a differ ent semantics (for example a set-theoretic one or a semantic s on the basis graphs) must be given to the UML core. It turns out that for the first step, namely the translation of UML language features into the UML core, graph transformations are an ideal language for expressing the re quired manipulations and the UML metamodel gives the necessary fundamental voc bulary and notions.
Online Feedback for Structure-from-Motion Image Acquisition

The quality and completeness of 3D models obtained by Structure-fromMotion (SfM) heavily depend on the image acquisition process. If the user gets feedback about the reconstruction quality already during the acquisition, he can optimize this process. The goal of this paper is to support a user during image acquisition by giving online feedback of the current reconstruction quality. We propose an online SfM method that integrates wide-baseline still-images in an online fashion into a consistent reconstruction and we derive a surface model given the SfM point cloud. To guide the user to scene parts that are captured not very well, we colour the mesh according to redundancy and resolution information. In the experiments, we show that our approach makes the final SfM result predictable already during image acquisition. The method is suited for large-scale reconstructions as obtained by flying micro aerial vehicles as well as on small indoor environments. We propose a method that supports a user in the acquisition process in two ways: (a) sparse online SfM with accuracy close to offline methods and (b) surface extraction and quality visualization. The workflow of our method is shown in Figure 1.
Stemming for Arabic words similarity measures based on Latent Semantic Analysis model

One of the major problems of modern Information Retrieval (IR) systems is the vocabulary problem that concerns the discrepancies between terms used for describing documents and the terms used by the researchers to describe their information need. In this paper, we propose to use the well known abstractive model -Latent Semantic Analysis (LSA)- with a wide variety of distance functions and similarity measures to measure the similarity between Arabic words, such as the Euclidean Distance, Cosine Similarity, Jaccard Coefficient, and the Pearson Correlation Coefficient. LSA statistically analyze distribution of terms belonging to a large textual corpus to elaborate a semantic space in which each term is represented by a vector. In our experiments, we compare and analyze the effectiveness of this model with the different measures above in two cases: with and without Stemming, for two testing data: the first is composed of 252 documents from several categories (Economics, Politics, and Sports), and the second contains 257 politics documents only to test the influence of the variety of the used corpus. The obtained results show that, on the one hand, the variety of the corpus gives more accurate results; on the other hand, the use of the Stemming gives us more accuracy in some cases and the opposite in the others.
Species-specific variation in the phosphorus nutritional sources by microphytoplankton in a Mediterranean estuary

We investigated the species-specific phosphorus (P) nutrition sources in the microphytoplankton community in the Mahon estuary (Minorca, Western Mediterranean) in 2011, under two contrasting hydrographic scenarios. Estuarine flow, nutrient concentrations, phytoplankton community composition and enzyme-labeled fluorescence (ELF) were measured in June and October, corresponding to the beginning and the end of summer. Dissolved inorganic nitrogen (DIN) and inorganic phosphate (Pi) exhibited enhanced concentrations in the inner estuary where N:P molar ratios suggested P-limitation in both surveys. Pi was low and variable (0.09±0.02 μmol•l-1 in June and 0.06±0.02 μmol•l-1 in October), whereas organic phosphorus remained a more reliable P source. Even though ambient Pi concentrations were slightly higher on June, when the microphytoplankton assemblage was dominated by dinoflagellates, the percentage of cells expressing ELF labeling was notably higher (65% of total cells) than in October (12%), when the presence of diatoms characterized the microphytoplankton community. ELF was mainly expressed by dinoflagellate taxa, whereas diatoms only expressed significant AP in the inner estuary during the June survey. A P-addition bioassay in which response of AP to Pi enrichment was evaluated showed remarkable reduction in AP with increasing Pi. However, some dinoflagellate species maintained AP even when Pi was supplied in excess. We suggest that in the case of some dinoflagellate species AP is not as tightly controlled by ambient Pi as previously believed. AP activity in these species could indicate selective use of organic phosphorus, or slow metabolic response to changes in P forms, rather than physiological stress to low Pi availability. We emphasize the importance of identifying the links between the different P sources and the species-specific requirements, in order to understand the ecological response to anthropogenic biogeochemical perturbations.
Serie Research Memoranda Matching Unemployment and Vacancies in Regional Labour Markets ; an Empirical Analysls for the Netherlands

In this paper we analyze regional developments in unemployment and vacancies in the Netherlands during the eighties. Our purpose is to establish to what extent the differences in unemployment and vacancy rates are due to differences in regional labour market performance. We do not use traditional UV-analysis in our empirical investigation since a necessary condjtjon to apply this approach is not fulfilled: there is no constant flow of filled vacancies. Therefore, we perform the analysis by looking at the dynamics of the labour market using the concept of the matching function. We find a constant returns to scale matching function with coefficients of 0.25 on unemployment and 0.75 on vacancies. Efficiency rises significantly during the recession at the beginning of the eighties. Regional differences in efficiency appear to be modest, suggesting that the reduction of regional unemployment can only be achieved by stimulating regional labour demand.
Natural Sunlight Shapes Crude Oil-Degrading Bacterial Communities in Northern Gulf of Mexico Surface Waters

Following the Deepwater Horizon (DWH) spill in 2010, an enormous amount of oil was observed in the deep and surface waters of the northern Gulf of Mexico. Surface waters are characterized by intense sunlight and high temperature during summer. While the oil-degrading bacterial communities in the deep-sea plume have been widely investigated, the effect of natural sunlight on those in oil polluted surface waters remains unexplored to date. In this study, we incubated surface water from the DWH site with amendments of crude oil, Corexit dispersant, or both for 36 days under natural sunlight in the northern Gulf of Mexico. The bacterial community was analyzed over time for total abundance, density of alkane and polycyclic aromatic hydrocarbon degraders, and community composition via pyrosequencing. Our results showed that, for treatments with oil and/or Corexit, sunlight significantly reduced bacterial diversity and evenness and was a key driver of shifts in bacterial community structure. In samples containing oil or dispersant, sunlight greatly reduced abundance of the Cyanobacterium Synechococcus but increased the relative abundances of Alteromonas, Marinobacter, Labrenzia, Sandarakinotalea, Bartonella, and Halomonas. Dark samples with oil were represented by members of Thalassobius, Winogradskyella, Alcanivorax, Formosa, Pseudomonas, Eubacterium, Erythrobacter, Natronocella, and Coxiella. Both oil and Corexit inhibited the Candidatus Pelagibacter with or without sunlight exposure. For the first time, we demonstrated the effects of light in structuring microbial communities in water with oil and/or Corexit. Overall, our findings improve understanding of oil pollution in surface water, and provide unequivocal evidence that sunlight is a key factor in determining bacterial community composition and dynamics in oil polluted marine waters.
Brain-Derived Neurotrophic Factor Activation of CaM-Kinase Kinase via Transient Receptor Potential Canonical Channels Induces the Translation and Synaptic Incorporation of GluA1-Containing Calcium-Permeable AMPA Receptors

Glutamatergic synapses in early postnatal development transiently express calcium-permeable AMPA receptors (CP-AMPARs). Although these GluA2-lacking receptors are essential and are elevated in response to brain-derived neurotrophic factor (BDNF), little is known regarding molecular mechanisms that govern their expression and synaptic insertion. Here we show that BDNF-induced GluA1 translation in rat primary hippocampal neurons requires the activation of mammalian target of rapamycin (mTOR) via calcium calmodulin-dependent protein kinase kinase (CaMKK). Specifically, BDNF-mediated phosphorylation of threonine 308 (T308) in AKT, a known substrate of CaMKK and an upstream activator of mTOR-dependent translation, was prevented by (1) pharmacological inhibition of CaMKK with STO-609, (2) overexpression of a dominant-negative CaMKK, or (3) short hairpin-mediated knockdown of CaMKK. GluA1 surface expression induced by BDNF, as assessed by immunocytochemistry using an extracellular N-terminal GluA1 antibody or by surface biotinylation, was impaired following knockdown of CaMKK or treatment with STO-609. Activation of CaMKK by BDNF requires transient receptor potential canonical (TRPC) channels as SKF-96365, but not the NMDA receptor antagonist d-APV, prevented BDNF-induced GluA1 surface expression as well as phosphorylation of CaMKI, AKTT308, and mTOR. Using siRNA we confirmed the involvement of TRPC5 and TRPC6 subunits in BDNF-induced AKTT308 phosphorylation. The BDNF-induced increase in mEPSC was blocked by IEM-1460, a selected antagonist of CP-AMPARs, as well as by the specific repression of acute GluA1 translation via siRNA to GluA1 but not GluA2. Together these data support the conclusion that newly synthesized GluA1 subunits, induced by BDNF, are readily incorporated into synapses where they enhance the expression of CP-AMPARs and synaptic strength.
Bilateral Economic Relations in a Global Political Economy: Australia and Japan

This paper argues that despite the internationalisation of economic activity, and a concomitant diminution of economic policy-making autonomy, national policy settings continue to display a surprising degree of divergence and remain important determinants of economic outcomes. Similarly, there are distinctively different and enduring patterns of corporate organisation across nations which confer specific competitive advantages. Important theoretical and practical questions are raised, therefore, about the potential efficacy of national economic policies and their capacity to accommodate such divergent practices. This paper examines the bilateral relationship between Australia and Japan, and assesses the effectiveness of Australia's predominantly neoliberal economic policy framework in the light of such national and organisational variation. It will be suggested that Australian policy-makers' faith in market mechanisms caused them to underestimate the significance of Japanese commercial practices and regional production strategies, rendering attempts to transform the relationship largely unsuccessful.
Generating Explicit Orderings for Non-monotonic Logics

For non-monotonic reasoning, explicit orderings over formulae offer an important solution to problems such as 'multiple extensions'. However, a criticism of such a solution is that it is not clear, in general, from where the orderings should be obtained. Here we show how orderings can be derived from statistical information about the domain which the formulae cover. For this we provide an overview of prioritized logics--a general class of logics that incorporate explicit orderings over formulae. This class of logics has been shown elsewhere to capture a wide variety of proof-theoretic approaches to non-monotonic reasoning, and in particular, to highlight the role of preferences-both implicit and explicit--in such proof theory. We take one particular prioritized logic, called SF logic, and describe an experimental approach for comparing this logic with an important example of a logic that does not use explicit orderings of preference-namely Horn clause logic with negation-as-failure. Finally, we present the results of this companson, showmg how SF logic is more skeptical and more accurate than negation-as-failure.
Monte Carlo simulations of the broad‐band X‐ray continuum of SS433

We develop a Monte Carlo technique based on L.B. Lucy's indivisible photon packets method to calculate X-ray continuum spectra of Comptonized thermal plasma in arbitrary geometry and apply it to describe the broad-band X-ray continuum of the galactic superaccreting microquasar SS433 observed by INTEGRAL. A physical model of the X-ray emitting region is proposed that includes thermal emission from the accretion disc, jets and hot corona where the photons of different origin are Comptonized. From comparison with INTEGRAL observations, we estimate physical parameters of the complex X-ray emitting region in SS433 and present model spectra for different viewing angles of the object.
The effect of acute consumption of non-specific COX-inhibitors on neuromuscular fatigue and exercise performance

II Acknowledgments . IV Tables of contents . VII List of tables . IX List of figures . X List of abbreviations . XV Declaration, publications and communications . XVIII Chapter 1: Introduction . 1 Chapter 2: Literature review . 8 2.1 Measuring exercise-induced fatigue . 10 2.2 Multi-faceted, task-dependent nature of fatigue . 17 2.3 Group III/IV muscle afferents and fatigue . 31 2.4 Contralateral limb fatigue . 39 2.5 COX-inhibitors and exercise performance . 42 2.6 Study aims and hypotheses . 54 Chapter 3: General methods . 56 3.1 Pre-test procedures . 56 3.2 Apparatus, procedures & measurements . 58 3.3 Measurements . 61 3.4 Statistical analyses . 68 Chapter 4: Acute acetaminophen ingestion improves performance and muscle activation during maximal intermittent knee extensor exercise . 69 Abstract . 70. 70 Introduction . 71 Methods . 73 Results . 80 Discussion . 89
Optimization of floor cleaning coverage performance of a random path-planning mobile robot

Floor cleaning is a typical robot application. There are several mobile robots aviable in the market for domestic applications most of them with random path-planning algorithms. In this paper we study the cleaning coverage performances of a random path-planning mobile robot and propose an optimized control algorithm, some methods to estimate the are of the room, the evolution of the cleaning and the time needed for complete coverage.
A Critical Analysis of Privacy Design Strategies

The upcoming General Data Protection Regulation is quickly becoming of great concern to organizations which process personal data of European citizens. It is however nontrivial to translate these legal requirements into privacy friendly designs. One recently proposed approach to make 'privacy by design' more practical is privacy design strategies. This paper improves the strategy definitions and suggests an additional level of abstraction between strategies and privacy patterns: 'tactics'. We have identified a collection of such tactics based on an extensive literature review, in particular a catalogue of surveyed privacy patterns. We explore the relationships between the concepts we introduce and similar concepts used in software engineering. This paper helps bridge the gap between data protection requirements set out in law, and system development practice.
Player Adaptive Entertainment Computing (PAEC): Mechanism to model user satisfaction by using Neuro Linguistic Programming (NLP) techniques

The concept of Player Adaptive Entertainment Computing (PAEC) is introduced to provide personalized experiences when interacting with the entertainment media. Two of the important areas in PAEC are to create specific targeted strategies to cater for individual user, and to perform personalization. To accomplish this, a suitable mechanism to model user experience is required. This is explored in a case study using neuro linguistic programming (NLP) that models the NLP spatial anchors of experiences of a sample group of users during game play. These NLP anchors are reconstructed during game play of a second group of users allowing them to experience the same level satisfaction as the first sample group.
Finding Time-Lagged 3D Clusters

Existing 3D clustering algorithms on gene × sample × time expression data do not consider the time lags between correlated gene expression patterns. Besides, they either ignore the correlation on time subseries, or disregard the continuity of the time series, or only validate pure shifting or pure scaling coherent patterns instead of the general shifting and-scaling patterns. In this paper, we propose a novel 3D cluster model, S2D3 Cluster, to address these problems, where S2 reflects the shifting-and-scaling correlation and D3 the 3-Dimensional gene × sample × time data. Within the S2D3 Cluster model, expression levels of genes are shifting-and-scaling coherent in both sample subspace and time subseries with arbitrary time lags. We develop a 3D clustering algorithm, LagMiner, for identifying interesting S2D3 Clusters that satisfy the constraints of regulation (γ), coherence (γ), minimum gene number (MinG), minimum sample subspace size (MinS) and minimum time periods length (MinT). Experimental results on both synthetic and real-life datasets show that LagMiner is effective, scalable and parameter-robust. While we use gene expression data in this paper, our model and algorithm can be applied on any other data where both spatial and temporal coherence are pursued.
The process of forming a mobile media habit: results of a longitudinal study in a real-world setting

ABSTRACT Media habits are central constructs in audience research. Yet, little is known about the formation of (media) habits. Based on theoretical elaboration and the results of a longitudinal study on the formation of a mobile media application habit—specifically the smartphone application of the Union of European Football Associations for the European soccer championship 2016—in a real-world setting, this article develops a comprehensive framework of media habit formation. The framework focuses on the core process of habit formation: Habits form with (regular) repetition of a behavior in a specific context that is perceived as rewarding. Yet, the findings of the study show that regularity in behavior performance and stable external circumstances are less crucial for the formation of a mobile media habit. Instead, gateway behaviors are proposed as relevant context features for the formation of mobile media habits.