Miracle-dz/UniFAR-FTUs huggingface dataset:
Measurement Protocols for Medium-Field Distance Perception in Large-Screen Immersive Displays

How do users of virtual environments perceive virtual space? Many experiments have explored this question, but most of these have used head-mounted immersive displays. This paper reports an experiment that studied large-screen immersive displays at medium-field distances of 2 to 15 meters. The experiment measured ego-centric depth judgments in a CAVE, a tiled display wall, and a real-world outdoor field as a control condition. We carefully modeled the outdoor field to make the three environments as similar as possible. Measuring egocentric depth judgments in large-screen immersive displays requires adapting new measurement protocols; the experiment used timed imagined walking, verbal estimation, and triangulated blind walking. We found that depth judgments from timed imagined walking and verbal estimation were very similar in all three environments. However, triangulated blind walking was accurate only in the out-door field; in the large-screen immersive displays it showed under-estimation effects that were likely caused by insufficient physical space to perform the technique. These results suggest using timed imagined walking as a primary protocol for assessing depth perception in large-screen immersive displays. We also found that depth judgments in the CAVE were more accurate than in the tiled display wall, which suggests that the peripheral scenery offered by the CAVE is helpful when perceiving virtual space.
Cardiac diffusion MRI without motion effects

We present a method for diffusion tensor MRI in the beating heart that is insensitive to cardiac motion and strain. Using a stimulated echo pulse sequence with two electrocardiogram (ECG) triggers, diffusion‐encoding bipolar gradient pulses are applied at identical phases in consecutive cardiac cycles. In this experiment, diffusion is encoded at a single phase in the cardiac cycle of less than 30 ms in duration. This encoding produces no phase shifts for periodic motion and is independent of intervening strains. Studies in a gel phantom with cyclic deformation confirm that by using this sequence we can map the diffusion tensor free of effects of cyclic motion. In normal human subjects, myocardial diffusion eigenvalues measured with the present method showed no significant change between acquisitions encoded at maximum contractile velocity (peak) vs. at myocardial standstill (end‐systole), demonstrating motion independence of in vivo diffusion measurements. Diffusion tensor images acquired with the present method agree with registered data acquired with a previous cardiac diffusion MRI method that was shown to be valid in the normal heart, strongly supporting the validity of MRI diffusion measurement in the beating heart. Myocardial sheet and fiber dynamics measured during systole showed that normal human myocardial sheet orientations tilt toward the radial during systole, and fiber orientations tilt toward the longitudinal, in qualitative agreement with previous invasive studies in canines. These results demonstrate the technique's ability to measure myocardial diffusion accurately at any point in the cardiac cycle free of measurable motion effect, as if the heart were frozen at the point of acquisition. Magn Reson Med 48:105–114, 2002. © 2002 Wiley‐Liss, Inc.
Opposing roles of IL‐17A and IL‐25 in the regulation of TSLP production in human nasal epithelial cells

To cite this article: Xu G, Zhang L, Wang DY, Xu R, Liu Z, Han DM, Wang XD, Zuo KJ, Li HB. Opposing roles of IL‐17A and IL‐25 in the regulation of TSLP production in human nasal epithelial cells. Allergy 2010; 65: 581–589.
The importance of chorismate mutase in the biocontrol potential of Trichoderma parareesei

Species of Trichoderma exert direct biocontrol activity against soil-borne plant pathogens due to their ability to compete for nutrients and to inhibit or kill their targets through the production of antibiotics and/or hydrolytic enzymes. In addition to these abilities, Trichoderma spp. have beneficial effects for plants, including the stimulation of defenses and the promotion of growth. Here we study the role in biocontrol of the T. parareesei Tparo7 gene, encoding a chorismate mutase (CM), a shikimate pathway branch point leading to the production of aromatic amino acids, which are not only essential components of protein synthesis but also the precursors of a wide range of secondary metabolites. We isolated T. parareesei transformants with the Tparo7 gene silenced. Compared with the wild-type, decreased levels of Tparo7 expression in the silenced transformants were accompanied by reduced CM activity, lower growth rates on different culture media, and reduced mycoparasitic behavior against the phytopathogenic fungi Rhizoctonia solani, Fusarium oxysporum and Botrytis cinerea in dual cultures. By contrast, higher amounts of the aromatic metabolites tyrosol, 2-phenylethanol and salicylic acid were detected in supernatants from the silenced transformants, which were able to inhibit the growth of F. oxysporum and B. cinerea. In in vitro plant assays, Tparo7-silenced transformants also showed a reduced capacity to colonize tomato roots. The effect of Tparo7-silencing on tomato plant responses was examined in greenhouse assays. The growth of plants colonized by the silenced transformants was reduced and the plants exhibited an increased susceptibility to B. cinerea in comparison with the responses observed for control plants. In addition, the plants turned yellowish and were defective in jasmonic acid- and ethylene-regulated signaling pathways which was seen by expression analysis of lipoxygenase 1 (LOX1), ethylene-insensitive protein 2 (EIN2) and pathogenesis-related protein 1 (PR-1) genes.
Generalizations of Cyclostationarity: A New Paradigm for Signal Processing for Mobile Communications, Radar, and Sonar

The relative motion between transmitter and receiver introduces nonstationarity to stationary signals and modifies the nonstationarity of nonstationary signals. Several Doppler channel models of interest transform almost-cyclostationary (ACS) processes, which are an appropriate nonstationary model for modulated signals adopted in communications, radar, sonar, and telemetry, into generalized ACS (GACS) processes or spectrally correlated (SC) processes. Both classes of processes include the ACS processes as special cases. A review of these new classes of nonstationary processes is presented. The problems of probabilistic characterization, statistical function estimation, and determining the effects of time-sampling on these models are addressed. The impact of these models on signal detection and source location problems is discussed.
Morphological instability and dynamics of fronts in bacterial growth models with nonlinear diffusion.

Depending on the growth condition, bacterial colonies can exhibit different morphologies. As argued by Ben-Jacob et al. there is biological and modeling evidence that a nonlinear diffusion coefficient of the type D(b)=D(0)b(k) is a basic mechanism that underlies almost all of the patterns and generates a long-wavelength instability. We study a reaction-diffusion system with a nonlinear diffusion coefficient and find that a unique planar traveling front solution exists whose velocity is uniquely determined by k and D=D(0)/D(n), where D(n) is the diffusion coefficient of the nutrient. Due to the fact that the bacterial diffusion coefficient vanishes when b-->0, in the front solution b vanishes in a singular way. As a result the standard linear stability analysis for fronts cannot be used. We introduce an extension of the stability analysis that can be applied to singular fronts, and use the method to perform a linear stability analysis of the planar bacteriological growth front. We show that a nonlinear diffusion coefficient generates a long-wavelength instability for k>0 and D0 and k--> infinity the dynamics of the growth zone essentially reduces to that of a sharp interface problem that is reminiscent of a so-called one-sided growth problem where the growth velocity is proportional to the gradient of a diffusion field ahead of the interface. The moving boundary approximation that we derive in these limits is quite accurate but surprisingly does not become a proper asymptotic theory in the strict mathematical sense in the limit D-->0, due to lack of full separation of scales on all dynamically relevant length scales. Our linear stability analysis and sharp interface formulation will also be applicable to other examples of interface formation due to nonlinear diffusion, like in porous media or in the problem of vortex motion in superconductors.
Learning to Teach Culturally Diverse Learners: Charting Change in Preservice Teachers' Thinking about Effective Teaching

We explored the use of 2 measurement strategies-concept maps and surveys-to assess the effects of a multicultural education course on the cognitions of individuals and groups of preservice teachers. Participants included 17 preservice teachers enrolled in a 5-week multicultural education course required as part of a 1-year M.Ed. and credential program at a public university. Data were gathered before and after the course to assess preservice teachers' beliefs and conceptual changes in their representations of effective teaching for culturally diverse learners. Results suggested that 2 groups of students began the course with distinct beliefs and conceptualizations in this area, as indicated by differences in the density of their concept maps. Results also suggested that multiple indicators of cognitive change must be used to better understand the effect of these courses on preservice teachers' cognitions. Group B students had lower-density maps prior to the course than after the course. Specifically, although the density of Group B students' conceptualizations of effective teaching increased after the course-a pattern that has been traditionally associated with more complex understanding-other indicators of conceptual change showed that these students did not actively reorganize their conceptualizations. Group A students exhibited the opposite pattern. Moreover, the qualitative data analysis indicated that each group of students emphasized a distinct view of teaching. These findings suggest that teacher educators and others working in this field can use concept maps and surveys to assess cognitive transformations in individuals and groups of teachers. This is best achieved through the analysis of both quantitative and qualitative indicators of cognitive changes.
Cortical networks subserving pursuit and saccadic eye movements in humans: An FMRI study

High‐field (3 Tesla) functional magnetic resonance imaging (MRI) was used to investigate the cortical circuitry subserving pursuit tracking in humans and compare it to that for saccadic eye movements. Pursuit performance, relative to visual fixation, elicited activation in three areas known to contribute to eye movements in humans and in nonhuman primates: the frontal eye field, supplementary eye field, and intraparietal sulcus. It also activated three medial regions not previously identified in human neuroimaging studies of pursuit: the precuneus and the anterior and posterior cingulate cortices. All six areas were also activated during saccades. The spatial extent of activation was similar for saccades and pursuit in all but two regions: spatial extent was greater for saccades in the superior branch of the frontal eye field and greater for pursuit in posterior cingulate cortex. This set of activations for smooth pursuit parallels the network of oculomotor areas characterized in nonhuman primates and complements recent studies showing that common cortical networks subserve oculomotor functions and spatial attention in humans. Hum. Brain Mapping 8:209–225, 1999. © 1999 Wiley‐Liss, Inc.
An extensive enhancer-promoter map generated by genome-scale analysis of enhancer and gene activity patterns

Massive efforts have documented hundreds of thousands of putative enhancers in the human genome. A pressing genomic challenge is to identify which of these enhancers are functional and map them to the genes they regulate. We developed a novel method for inferring enhancer-promoter (E-P) links based on correlated activity patterns across many samples. Our method, called FOCS, uses rigorous statistical validation tailored for zero-inflated data, identifying the most important E-P links in each gene model. We applied FOCS to the wide epigenomic and transcriptomic datasets recorded by the ENCODE, Roadmap Epigenomics and FANTOM5 projects, together covering 2,630 samples of human primary cells, tissues and cell lines. In addition, building on expression of enhancer RNAs (eRNAs) as an exquisite mark of enhancer activity and on the robust detection of eRNAs by the GRO-seq technique, we compiled a compendium of eRNA and gene expression profiles based on public GRO-seq data from 245 samples and 23 human cell types. Applying FOCS to this compendium further expanded the coverage of our inferred E-P map. Benchmarking against gold standard E-P links from ChIA-PET and eQTL data, we demonstrate that FOCS prediction of E-P links outperforms extant methods. Collectively, we inferred >300,000 cross-validated E-P links spanning ~16K known genes. Our study presents an improved method for inferring regulatory links between enhancers and promoters, and provides an extensive resource of E-P maps that could greatly assist the functional interpretation of the noncoding regulatory genome. FOCS and our predicted E-P map are publicly available at http://acgt.cs. tau.ac. il/focs.
The clinicopathological significance of hMLH1 hypermethylation in non-small-cell lung cancer: a meta-analysis and literature review

The hMLH1 gene plays an essential role in DNA repair. Methylation of the hMLH1 gene is common in many types of cancer and can lead to the loss of hMLH1 expression. However, the association and clinicopathological significance between hMLH1 promoter hypermethylation and non-small-cell lung cancer (NSCLC) is elusive. Here, we investigated the correlation of hMLH1 promoter hypermethylation and NSCLC using 13 studies by comprising 1,056 lung cancer patients via a meta-analysis. We observed that 1) loss of hMLH1 protein expression was significantly associated with its promoter hypermethylation, 2) hMLH1 gene inactivation through hypermethylation contributed to the tumorigenesis of NSCLC, which could be a decisive factor for the pathogenesis of NSCLC due to its high occurrence in NSCLC tissues compared to normal lung tissues, 3) a correlation exists between histologic subtypes/disease stages (TNM I+II vs III+IV) and hypermethylation status of hMLH1 gene, and 4) NSCLC patients with hMLH1 hypermethylation and subsequent low expression levels of hMLH1 have a short overall survival period than those patients with normal expression of hMLH1 gene. hMLH1 mRNA predicts patient survival in lung cancer, and this was confirmed by using a public database. We then discussed the tumor suppressor function of hMLH1 and the clinicopathological significance of hMLH1 in NSCLC. We concluded that hMLH1 hypermethylation should be an early diagnostic marker for NSCLC and also a prognostic index for NSCLC. hMLH1 is an interesting therapeutic target in human lung cancers.
Social Skills, Stressful Life Events, and the Development of Psychosocial Problems

This three-wave panel study sought to determine the extent to which social skills and stressful life events predict the development of psychosocial problems. At Time 1, 142 students completed a laboratory interaction and measures of social skills and depression, loneliness, and social anxiety. At Time 2 (four months later) and Time 3 (nine months later) participants again completed measures of psychosocial problems and a measure of stressful life events. Results indicated that poor social skills are causally linked, in small magnitude, to loneliness and anxiety, but less so to depression. All psychosocial problems worsened over time as a function of experiencing stressful life events. There was no evidence to suggest that social skills worsen over time as a function of experiencing depression, loneliness, or social anxiety.
A Flexible Framework for Defeasible Logics

Logics for knowledge representation suffer from over-specialization: while each logic may provide an ideal representation formalism for some problems, it is less than optimal for others. A solution to this problem is to choose from several logics and, when necessary, combine the representations. In general, such an approach results in a very difficult problem of combination. However, if we can choose the logics from a uniform framework then the problem of combining them is greatly simplified. In this paper, we develop such a framework for defeasible logics. It supports all defeasible logics that satisfy a strong negation principle. We use logic meta-programs as the basis for the framework.
A literature review of parents' online behavior

The purpose of this literature review was to compile and analyze the research that has been conducted on parents’ use of the Internet and determine what we know about how parents use the Internet in everyday life. A comprehensive literature review focusing on studies that have asked parents about their Internet use was conducted to include research published through December 2011. This yielded 27 studies. Articles were summarized and then organized by content. Three main themes emerged: what parents are doing online, social support online, and the digital divide. This literature review revealed that parents go online to search for parenting information and social support and generally report satisfaction with the resources they find on the Internet. Parents still express hesitation in trusting various online resources, though, and desire greater education in Internet searching and deciphering the credibility of online information. In addition, this review also exposes gaps in current research, provides direction for future research, and has implications for how to effectively reach parents using the Internet.
Philosophy of Sport: Core Readings

throughout the text, provides a much stronger and insightful thread of content. The ‘breakthrough kinesis’ and ‘collective kinetic blueprint’ ideas are described robustly in the early chapters and continue to find exposure later on in ways that are applied with personal anecdotes at times and with academic theory at other times. This connection provides helpful new insight into therapy, play, sport, human movement, and kinesiology. Overall, each section offers theoretical and practical relevance. Every chapter provides ways in which a reader can find inspiration to live better. Some of this motivation is theoretical, encouraging the reader to better understand all of the multi-disciplinary concepts that are a part of the experience of human movement. And some of this motivation is practical, encouraging the reader to spend more time engaged in physical activity and play that the author so obviously believes is such a central component of the good life. For this inspiration alone, the author has provided helpful scholarship.
Towards the automated generation of abstract test cases from requirements models

In a testing process, the design, selection, creation and execution of test cases is a very time-consuming and error-prone task when done manually, since suitable and effective test cases must be obtained from the requirements. This paper presents a model-driven testing approach for conceptual schemas that automatically generates a set of abstract test cases, from requirements models. In this way, tests and requirements are linked together to find defects as soon as possible, which can considerably reduce the risk of defects and project reworking. The authors propose a generation strategy which consists of: two meta-models, a set of transformations rules which are used to generate a Test Model, and the Abstract Test Cases from an existing approach to communication-oriented Requirements Engineering; and an algorithm based on Breadth-First Search. A practical application of our approach is included.
Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically ‘entangled’ helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints. To encourage interactivity, simulations launched as immediate jobs are automatically stopped after a few seconds and return adapted recommendations. Users can then choose to continue incomplete simulations using the batch queuing system or go back and modify suggested options in their initial query. Detailed output provide (i) a series of low free energy structures, (ii) an online animated folding path and (iii) a programmable trajectory plot focusing on a few helices of interest to each user. The service can be accessed at .
Peer Interactions and Friendship Opportunities Between Elementary Students With and Without Autism or Developmental Disability

Abstract This article describes a qualitative examination of the interactions between 2 students, 1 with autism and 1 with a developmental disability, and their peers without disabilities in 2 inclusive, public school elementary classrooms in the northeastern United States. Data were collected by naturalistic observation, semi-structured observation, and semi-structured interviews. Examining the quality and quantity of interactions, as well as the facilitating effects of educators, the goal was to identify conditions that support the development of friendship opportunities. The findings indicated that inclusive education and having classmates who accepted them were not enough to result in consistent friendship opportunities for the 2 focal students. Findings included (a) the identification of missed opportunities for educator intervention to support friendship opportunities, and (b) the success of several educator strategies to facilitate friendship opportunities. Implications and considerations to improv.