Miracle-dz/UniFAR-FTUs huggingface dataset:
Age‐associated changes in hippocampal‐dependent cognition in Diversity Outbred mice

Episodic memory impairment due to aging has been linked to hippocampal dysfunction. Evidence exists for alterations in specific circuits within the hippocampal system that are closely coupled to individual differences in the presence and severity of such memory loss. Here, we used the newly developed Diversity Outbred (DO) mouse that was designed to model the genetic diversity in human populations. Young and aged DO mice were tested in a hippocampal‐dependent water maze task. Young mice showed higher proficiency and more robust memory compared to the overall performance of aged mice. A substantial number of the older mice, however, performed on par with the normative performance of the younger mice. Stereological quantification of somatostatin‐immunoreactive neurons in the dentate hilus showed that high‐performing young and unimpaired aged mice had similar numbers of somatostatin‐positive interneurons, while aged mice that were impaired in the spatial task had significantly fewer such neurons. These data in the DO model tie loss of hilar inhibitory network integrity to age‐related memory impairment, paralleling data in other rodent models. © 2014 Wiley Periodicals, Inc.
Assessment of Tachykinin Receptor 3′ Gene Polymorphism rs3733631 in Rosacea

Background. Rosacea is a chronic skin disease, possibly following the neurogenic skin inflammation model. Neurokinin B, involved in the pathogenesis of Parkinson's disease, frequently coexisting with subsequent onset of rosacea, is an endogenous ligand of the tachykinin receptor 3 (TACR3). Methods. 128 rosacea patients and 121 matched controls were genotyped for rs3733631 by PCR-RFLP and analyzed by chi-square test. Results. We observed statistically significant predominance of the C/G or G/G genotype (p = 0.006) and of the G allele (p = 0.004) in the papulopustular (PP) form of rosacea and statistically marginal significance of the C/G or G/G genotype in erythematotelangiectatic (ET) rosacea (p = 0.052). Significantly higher frequency of the C/G or G/G genotype and G allele in PP rosacea (p = 0.021 and p = 0.008, resp.) was ascertained within male patients. Conclusion. TACR3 rs3733631 G allele possibly predisposes the evolution of the initial phase of rosacea to the PP and not the ET form in male patients.
Data Anamnesis: Admitting Raw Data into an Organization

Today’s internet offers a plethora of openly available datasets, bearing great potential for novel applications and research. Likewise, rich datasets slumber within organizations. However, all too often those datasets are available only as raw dumps and lack proper documentation or even a schema. Data anamnesis is the ﬁrst step of any effort to work with such datasets: It determines fundamental properties regarding the datasets’ content, structure, and quality to assess their utility and to put them to use appropriately. Detecting such properties is a key concern of the research area of data proﬁling, which has developed several viable instruments, such as data type recognition and foreign key discovery. In this article, we perform an anamnesis of the MusicBrainz dataset, an openly available and complex discographic database. In particular, we employ data proﬁling methods to create data summaries and then further analyze those summaries to reverse-engineer the database schema, to understand the data semantics, and to point out tangible schema quality issues. We propose two bottom-up schema quality dimensions, namely conciseness and normality, that measure the ﬁt of the schema with its data, in contrast to a top-down approach that compares a schema with its application requirements.
Democratic Participation in Early Childhood Education and Care - Serving the Best Interests of the Child

Abstract: The meaning of democratic participation in Early Childhood Education and Care (ECEC) remainsvague and difficult to implement. Thus, the aim of this paper is to contribute to this gap of knowledge by shed light on the meaning of democratic participation in relation to the best interests of the child, by analysing General Comment No. 14 (2013). The research uses theories on democracy in ECEC to discuss the results (Biesta, 2014, 2015; Moss, 2007, 2011; Pettersvold, 2014; Einarsdottir, Purola, Johansson, Broström, &Emilson, 2015). The study investigates how key terms (rights, participation, unity/collective, equality, influence and responsibility) relate to democratic participation. Findings indicate that these terms are used to align with ideas about the “best interests of the child”. Furthermore, the study identified specific groups of children who can be in vulnerable situations and their explicit right to express their views and to influence decisions affecting them in ECEC institutions. I therefore argue that understanding democracy in ECEC must focus on inclusion of children who can be in vulnerable situations because this is in the best interests of the child. Keywords: Best Interests of the Child, Democratic Participation, Document Analysis, General Comments
The Expected Value Premium

Fama and French (2002) estimate the equity premium using dividend growth rates to measure the expected rate of capital gain. We use similar methods to study the value premium. From 1941 to 2002, the expected HML return is on average 5.1% per annum, consisting of an expected-dividend-growth component of 3.5% and an expected-dividend-to-price component of 1.6%. The ex-ante HML return is also countercyclical: a positive, one-standard-deviation shock to real consumption growth rate lowers this premium by about 0.45%. Unlike the equity premium, there is only mixed evidence suggesting that the value premium has declined over time.
An information-theoretic measure to evaluate parsing difficulty across treebanks

With the growing interest in statistical parsing, special attention has recently been devoted to the problem of comparing different treebanks to assess which languages or domains are more difficult to parse relative to a given model. A common methodology for comparing parsing difficulty across treebanks is based on the use of the standard labeled precision and recall measures. As an alternative, in this article we propose an information-theoretic measure, called the expected conditional cross-entropy (ECC). One important advantage with respect to standard performance measures is that ECC can be directly expressed as a function of the parameters of the model. We evaluate ECC across several treebanks for English, French, German, and Italian, and show that ECC is an effective measure of parsing difficulty, with an increase in ECC always accompanied by a degradation in parsing accuracy.
Implementation and Analysis of an Image-Based Global Illumination Framework for Animated Environments

We describe a new framework for efficiently computing and storing global illumination effects for complex, animated environments. The new framework allows the rapid generation of sequences representing any arbitrary path in a "view space" within an environment in which both the viewer and objects move. The global illumination is stored as time sequences of range-images at base locations that span the view space. We present algorithms for determining locations for these base images, and the time steps required to adequately capture the effects of object motion. We also present algorithms for computing the global illumination in the base images that exploit spatial and temporal coherence by considering direct and indirect illumination separately. We discuss an initial implementation using the new framework. Results and analysis of our implementation demonstrate the effectiveness of the individual phases of the approach; we conclude with an application of the complete framework to a complex environment that includes object motion.
Reproducibility and Agreement of Tissue Tracking versus Feature Tracking for Strain Measurement on Cardiac MR Images in Patients with Repaired Tetralogy of Fallot.

Purpose To evaluate differences in strain measurements by using tissue-tracking (TT) and feature-tracking (FT) software on cardiovascular MR images in patients with repaired tetralogy of Fallot (TOF). Materials and Methods In this retrospective cross-sectional study of 25 patients with repaired TOF (median age, 33.1 years; interquartile range, 25.3-38.3 years) from 2008 through 2014, left ventricular (LV) and right ventricular (RV) global circumferential and longitudinal strain were measured from cardiac MR images by using TT and FT software. Time to process was measured from opening the study to acceptance of contours. Intra- and interobserver reproducibility were evaluated with Bland-Altman analysis, coefficient of variation, and intraclass correlation coefficient. Results Time to process was slightly longer for TT (10.2 minutes ± 3.1 [standard deviation] vs 9.0 minutes ± 1.7, P = .04). Fewer patients required contour revision with TT than with FT. Both TT and FT measurements had similar moderate-to-strong correlations with LV and RV ejection fractions; correlation of RV longitudinal strain with RV ejection fraction did not reach significance by using either method. With the exception of LV circumferential strain, strain measurements were lower with FT relative to TT. Intra- and interobserver reproducibility were lower with FT for longitudinal strain measurements. Conclusion TT and FT have systematic differences in strain values and reproducibility, particularly for longitudinal strain. Software-specific normative data are necessary, as are studies to evaluate correlation with clinical outcomes for each modality. © RSNA, 2019.
Two faces of human happiness: Explicit and implicit life satisfaction

Evidence is provided for implicit aspects of life satisfaction. In study 1 the implicit life satisfaction measure (ILS): (i) showed moderate reliability as well as convergent and incremental validity; (ii) appeared to be affected by temporary mood and social desirability to a lesser extent than explicit measures; and (iii) showed cultural invariance in contrast to explicit measures that revealed cross-cultural differences, as found in previous research. Study 2 showed that the ILS replicated theoretically expected differences between those known to have encountered chronically negative life experiences (North Korean defectors) and those without such experiences (South Koreans). Implications of these findings for explicit and ILS are discussed.
Exploring Collaboratively Annotated Data for Automatic Annotation

Social tagging, as a collaborative form of annotation process, has grown in popularity on the web due to its effectiveness in organizing and accessing web resources. This paper addresses the issue of automatic annotation, which aims to predict social tags for web resources automatically to help future navigation, filtering or search. We explore the collaboratively annotated data in social tagging services, in which collaborative annotations (i.e., combined social tags of many users) serve as a description of web resources from the crowds’ point of views, and analyze its three important properties. Based on these properties, we propose an automatic annotation approach by leveraging a probabilistic topic model, which captures the relationship between resources and annotations. The topic model is an extension of conventional LDA (Latent Dirichlet Allocation), referred as Word-Tag LDA, which effectively reflects the generative process of the collaboratively annotated data and models the conditional distribution of annotations given resources. Experiments are carried out on a real-world annotation data set sampled from del.icio. us. Results demonstrate that our approach can significantly outperform the other baseline methods in automatic annotation.
Population Genetic Analysis of Propionibacterium acnes Identifies a Subpopulation and Epidemic Clones Associated with Acne

The involvement of Propionibacterium acnes in the pathogenesis of acne is controversial, mainly owing to its dominance as an inhabitant of healthy skin. This study tested the hypothesis that specific evolutionary lineages of the species are associated with acne while others are compatible with health. Phylogenetic reconstruction based on nine housekeeping genes was performed on 210 isolates of P. acnes from well-characterized patients with acne, various opportunistic infections, and from healthy carriers. Although evidence of recombination was observed, the results showed a basically clonal population structure correlated with allelic variation in the virulence genes tly and camp5, with pulsed field gel electrophoresis (PFGE)- and biotype, and with expressed putative virulence factors. An unexpected geographically and temporal widespread dissemination of some clones was demonstrated. The population comprised three major divisions, one of which, including an epidemic clone, was strongly associated with moderate to severe acne while others were associated with health and opportunistic infections. This dichotomy correlated with previously observed differences in in vitro inflammation-inducing properties. Comparison of five genomes representing acne- and health-associated clones revealed multiple both cluster- and strain-specific genes that suggest major differences in ecological preferences and redefines the spectrum of disease-associated virulence factors. The results of the study indicate that particular clones of P. acnes play an etiologic role in acne while others are associated with health.
Comparative Genomics of Gene Regulation—conservation and Divergence of Cis-regulatory Information This Review Comes from a Themed Issue on Genomes and Evolution Edited Main Text Conflict of Interest

We recently witnessed a tremendous increase in genomics studies on gene regulation and in entirely sequenced genomes from closely related species. This has triggered analyses that suggest a wide range of evolutionary dynamics of gene regulation, from rapid turnover of transcription-factor binding sites to conservation of enhancer function across large evolutionary distances. Many examples show that enhancers can evolve beyond recognizable sequence similarity while retaining function. However, bioinformatics approaches are increasingly able to detect conserved regulatory elements through characteristic evolutionary sequence signatures. Cis-regulatory changes are also a major source of morphological evolution, which might be facilitated by many biochemically functional elements that are selectively neutral and by the buffering function of redundant enhancers and 'shadow' enhancers. Introduction The basis for multicellular life is the ability to create functional specialization and distinct cell types through differentially regulated gene expression. The information that underlies this regulation is encoded in the genome and is 'read' by sequence-specific transcription factors (TFs). To date, we only know a small fraction of any animal's regulatory sequences and deciphering the sequences' spa-tio-temporal activity has remained one of the greatest – and most fascinating – challenges of today's biology. The past few years have seen tremendous progress in the genome-wide assessment of gene expression and of transcription factor DNA binding. Similarly, the sequencing of entire genomes from closely related species has enabled comparative studies of known regulatory sequences and regulator binding sites. Combined with detailed dissections of individual regulatory sequences, this has answered old questions but created new ones and – in particular – fuelled the controversy over the evolutionary conservation of regulatory sequences. In this review, we will discuss current work on the conservation and divergence of regulatory sequences. The genome encodes gene-regulatory information in the form of modular cis-regulatory sequences or enhancers, each of which contributes certain parts of a gene's overall expression pattern in an additive fashion (e.g. [1]). Enhancers have been found thousands of base pairs upstream or downstream of the regulated gene, in the gene's or in neighboring genes' introns, and even work across intervening genes (e.g. [2,3]). While this indicates that the relative location of enhancers can be highly variable, some enhancers' positions are constrained, such as a distal enhancer of brinker in Drosophila and mosquitoes [3], or the Hox gene cluster (see discussion in [3]). Each enhancer contains binding sites for specific sets of TFs and is thus only active in …
What Influences DNA Replication Rate in Budding Yeast?

Background DNA replication begins at specific locations called replication origins, where helicase and polymerase act in concert to unwind and process the single DNA filaments. The sites of active DNA synthesis are called replication forks. The density of initiation events is low when replication forks travel fast, and is high when forks travel slowly. Despite the potential involvement of epigenetic factors, transcriptional regulation and nucleotide availability, the causes of differences in replication times during DNA synthesis have not been established satisfactorily, yet. Methodology/Principal Findings Here, we aimed at quantifying to which extent sequence properties contribute to the DNA replication time in budding yeast. We interpreted the movement of the replication machinery along the DNA template as a directed random walk, decomposing influences on DNA replication time into sequence-specific and sequence-independent components. We found that for a large part of the genome the elongation time can be well described by a global average replication rate, thus by a single parameter. However, we also showed that there are regions within the genomic landscape of budding yeast with highly specific replication rates, which cannot be explained by global properties of the replication machinery. Conclusion/Significance Computational models of DNA replication in budding yeast that can predict replication dynamics have rarely been developed yet. We show here that even beyond the level of initiation there are effects governing the replication time that can not be explained by the movement of the polymerase along the DNA template alone. This allows us to characterize genomic regions with significantly altered elongation characteristics, independent of initiation times or sequence composition.
Random matrix route to image denoising

We make use of recent results from random matrix theory to identify a derived threshold, for isolating noise from image features. The procedure assumes the existence of a set of noisy images, where denoising can be carried out on individual rows or columns independently. The fact that these are guaranteed to be correlated makes the correlation matrix an ideal tool for isolating noise. The random matrix result provides lowest and highest eigenvalues for the Gaussian random noise for which case, the eigenvalue distribution function is analytically known. This provides an ideal threshold for removing Gaussian random noise and thereby separating the universal noisy features from the non-universal components belonging to the specific image under consideration.
Remote usability testing

Imagine being able to collect data lie static and full motion screen images, user video, and user comments , through your computer. Think about observing from your office or lab as an evaluation participant worked in their own o&e. What if you could sample from an intercity, interregional, or international user base without having to leave your office or lab? Thanks to recent developments in the areas of information sharing and collabora-tive work tools, each of these objectives is now attainable Usability evaluators can now view computer networks and modem connections as frameworks upon which distributed usability labs can be constructed, and all network or modem accessible machines as potential windows into remote test sites. These remote test sites can range from a machine down the hall to one on the other side of the world. The technological building blocks needed to create remote testing facilities are now available, in varying degrees, on all major computing platforms (i.e., Unix, MS Windows, Macintosh, OS/2). With computer-to-computer video conferencing tools product development teams can now both see and listen to evaluation participants sitting in front of properly equipped computers anywhere in the world. They can observe evaluation participants as they examine and annotate screen shots or g documentation using shared whiteboard tools. Observers can also watch full motion images of f the participant's screen from remote locations H g as participants use their products. By mixing p and matching these technological building i blocks, usability specialists can conduct a myri-ad of usability engineering activities remotely.
Divergent Expression Patterns in Two Vernicia Species Revealed the Potential Role of the Hub Gene VmAP2/ERF036 in Resistance to Fusarium oxysporum in Vernicia montana

Tung oil tree (Vernicia fordii) is a promising industrial oil crop; however, this tree is highly susceptible to Fusarium wilt disease. Conversely, Vernicia montana is resistant to the pathogen. The APETALA2/ethylene-responsive element binding factor (AP2/ERF) transcription factor superfamily has been reported to play a significant role in resistance to Fusarium oxysporum. In this study, comprehensive analysis identified 75 and 81 putative Vf/VmAP2/ERF transcription factor-encoding genes in V. fordii and V. montana, respectively, which were divided into AP2, ERF, related to ABI3 and VP1 (RAV) and Soloist families. After F. oxysporum infection, a majority of AP2/ERF superfamily genes showed strong patterns of repression in both V. fordii and V. montana. We then identified 53 pairs of one-to-one orthologs in V. fordii and V. montana, with most pairs of orthologous genes exhibiting similar expression in response to the pathogen. Further investigation of Vf/VmAP2/ERF gene expression in plant tissues indicated that the pairs of genes with different expression patterns in response to F. oxysporum tended to exhibit different tissue profiles in the two species. In addition, VmAP2/ERF036, showing the strongest interactions with 666 genes, was identified as a core hub gene mediating resistance. Moreover, qRT-PCR results indicated VmAP2/ERF036 showed repressed expression while its orthologous gene VfAP2/ERF036 had the opposite expression pattern during pathogen infection. Overall, comparative analysis of the Vf/VmAP2/ERF superfamily and indication of a potential hub resistance gene in resistant and susceptible Vernicia species provides valuable information for understanding the molecular basis and selection of essential functional genes for V. fordii genetic engineering to control Fusarium wilt disease.