Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic Repression of RARRES1 Is Mediated by Methylation of a Proximal Promoter and a Loss of CTCF Binding

Background The cis-acting promoter element responsible for epigenetic silencing of retinoic acid receptor responder 1 (RARRES1) by methylation is unclear. Likewise, how aberrant methylation interplays effectors and thus affects breast neoplastic features remains largely unknown. Methodology/Principal Findings We first compared methylation occurring at the sequences (−664∼+420) flanking the RARRES1 promoter in primary breast carcinomas to that in adjacent benign tissues. Surprisingly, tumor cores displayed significantly elevated methylation occurring solely at the upstream region (−664∼−86), while the downstream element (−85∼+420) proximal to the transcriptional start site (+1) remained largely unchanged. Yet, hypermethylation at the former did not result in appreciable silencing effect. In contrast, the proximal sequence displayed full promoter activity and methylation of which remarkably silenced RARRES1 transcription. This phenomenon was recapitulated in breast cancer cell lines, in which methylation at the proximal region strikingly coincided with downregulation. We also discovered that CTCF occupancy was enriched at the unmethylayed promoter bound with transcription-active histone markings. Furthermore, knocking-down CTCF expression hampered RARRES1 expression, suggesting CTCF positively regulated RARRES1 transcription presumably by binding to unmethylated promoter poised at transcription-ready state. Moreover, RARRES1 restoration not only impeded cell invasion but also promoted death induced by chemotherapeutic agents, denoting its tumor suppressive effect. Its role of attenuating invasion agreed with data generated from clinical specimens revealing that RARRES1 was generally downregulated in metastatic lymph nodes compared to the tumor cores. Conclusion/Significance This report delineated silencing of RARRES1 by hypermethylation is occurring at a proximal promoter element and is associated with a loss of binding to CTCF, an activator for RARRES1 expression. We also revealed the tumor suppressive roles exerted by RARRES1 in part by promoting breast epithelial cell death and by impeding cell invasion that is an important property for metastatic spread.
Assessment of Drama Courses from the Preschoolers' Point of View

Creative drama which interconnects with the concepts of play, theatre, animation and role playing is a field which can only be learnt and expressed through experiencing. This study about assessment of the drama teaching in preschools by children was conducted in 3 preschools in Ankara with participation of 12 children of 6 ages who had taken drama learning courses. Qualitative research approach and semi-structured interviewing technique were employed. The results of the study indicated that all of 12 children defined drama as a game and entertainment. Keywords—Creative drama, preschoolers, drama courses
A comparison of music performance anxiety to a laboratory stressor

This study extends previous work investigating the cardiovascular reactivity to stress obtained in response to laboratory-based tasks to cardiovascular reactivity measured in response to a musical performance. Heart rate (HR) reactivity and psychological responses were measured in 52 female and 18 male healthy classically trained graduate students in two settings: during a standardized laboratory stressor (Stroop) and prior to a jury assessed musical performance of two pieces. HR and state anxiety (SAI) were assessed. Results indicate that while both conditions increased HR significantly, there was no difference in the magnitude of change in response to the musical performance and the laboratory stressors. However, the musical performance produced significantly higher levels of perceived anxiety between conditions. A greater correlation was observed for HR in between conditions compared with the relationship observed in the SAI responses. Some support is provided for the view that the Stroop could be used to identify higher HR responders to musical performance, although its efficacy to self perceptions of anxiety are less compelling.
Microsatellite variation among diverging populations of Drosophila mojavensis

Divergence and speciation may occur by various means, depending on the particular history, selective environments, and genetic composition of populations. In Drosophila mojavensis, a good model of incipient speciation, understanding the population genetic structure within this group facilitates our ability to understand the context in which reproductive isolation among populations is developing. Here we report the genetic structure and relationships of D. mojavensis populations at nuclear loci. We surveyed 29 populations throughout the distribution of D. mojavensis for four microsatellite loci to differentiation among populations of this species. These loci reveal four distinct geographical regions of D. mojavensis populations in the south‐western United States and north‐western Mexico – (i) Baja California peninsula (Baja), (ii) Sonora, Mexico–southern Arizona, United States (Sonora), (iii) Mojave Desert and Grand Canyon (Mojave), and (iv) Santa Catalina Island (Catalina). While all regions show strong isolation, Mojave and Catalina are highly diverged from other regions. Within any region, populations are largely homogenous over broad geographical distances. Based on the population structure, we find clear geographical barriers to gene flow appear to have a strong effect in isolating populations across regions for this species.
Combining multi-source far distance speech recognition strategies: beamforming, blind channel and confusion network combination

Interest within the automatic speech recognition (ASR) research community has recently focused on the recognition of speech captured with a microphone located in the medium field, rather than being mounted on a headset and positioned next to the speaker’s mouth. The capacity to recognize such speech is a primary requirement in making ASR a viable modality for socalled ubiquitous computing. This is a natural application for multiple microphones whose signals can be combined in different ways: On the signal side, combination can be accomplished by beamforming techniques using a microphone array or by blind source separation. On the word hypothesis side, combination can be achieved through confusion network combination. In this work, we compare the effectiveness of the several combination techniques, and compare their performance to that achieved with a close talking microphone.
A Comprehensive Morphological Analyzer for Swedish

SWETWOL is implemented in the framework of Koskenniemi’s (1983) two-level model. It contains a 48,000 item lexicon and a full inflectional description. Special attention was paid to the design of a computational analysis of productive Swedish compounds. Recall (coverage) and precision of SWETWOL meet high standards. SWETWOL has been extensively tested on various types of texts.
Large dispersion, averaging and attractors: three 1D paradigms

The effect of rapid oscillations, related to large dispersion terms, on the dynamics of dissipative evolution equations is studied for the model examples of the 1D complex Ginzburg–Landau and the Kuramoto–Sivashinsky equations. Three different scenarios of this effect are demonstrated. According to the first scenario, the dissipation mechanism is not affected and the diameter of the global attractor remains uniformly bounded with respect to the very large dispersion coefficient. However, the limit equation, as the dispersion parameter tends to infinity, becomes a gradient system. Therefore, adding the large dispersion term actually suppresses the non-trivial dynamics. According to the second scenario, neither the dissipation mechanism, nor the dynamics are essentially affected by the large dispersion and the limit dynamics remains complicated (chaotic). Finally, it is demonstrated in the third scenario that the dissipation mechanism is completely destroyed by the large dispersion, and that the diameter of the global attractor grows together with the growth of the dispersion parameter.
Evolving fuzzy neural networks for supervised/unsupervised online knowledge-based learning

This paper introduces evolving fuzzy neural networks (EFuNNs) as a means for the implementation of the evolving connectionist systems (ECOS) paradigm that is aimed at building online, adaptive intelligent systems that have both their structure and functionality evolving in time. EFuNNs evolve their structure and parameter values through incremental, hybrid supervised/unsupervised, online learning. They can accommodate new input data, including new features, new classes, etc., through local element tuning. New connections and new neurons are created during the operation of the system. EFuNNs can learn spatial-temporal sequences in an adaptive way through one pass learning and automatically adapt their parameter values as they operate. Fuzzy or crisp rules can be inserted and extracted at any time of the EFuNN operation. The characteristics of EFuNNs are illustrated on several case study data sets for time series prediction and spoken word classification. Their performance is compared with traditional connectionist methods and systems. The applicability of EFuNNs as general purpose online learning machines, what concerns systems that learn from large databases, life-long learning systems, and online adaptive systems in different areas of engineering are discussed.
Thermodynamic control and dynamical regimes in protein folding

Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be single exponential in nature, while the second regime is typical of sequences longer than 80 amino acids and the folding performance achievable is sensitive to target conformation. The extent to which stability, as measured by the energy of a sequence in the target, is an essential requirement and affects the folding dynamics of protein molecules in the first regime is investigated. The folding dynamics of sequences whose design stage was restricted to a certain fraction of randomly selected amino acids shows that while some degree of stability is a necessary and sufficient condition for successful folding, designing sequences that provide the lowest energy in the target seems to be a superfluous constraint. By studying the dynamics of under annealed but otherwise freely designed sequences we explore the relation between stability and kinetic accessibility. We find that there is no one-to-one correspondence between having low energy and folding quickly to the target, as only a small fraction of the most stable sequences were also found to fold relatively quickly.
Communication via gap junctions underlies early functional and beneficial interactions between grafted neural stem cells and the host

How grafted neural stem cells (NSCs) and their progeny integrate into recipient brain tissue and functionally interact with host cells is as yet unanswered. We report that, in organotypic slice cultures analyzed by ratiometric time-lapse calcium imaging, current-clamp recordings, and dye-coupling methods, an early and essential way in which grafted murine or human NSCs integrate functionally into host neural circuitry and affect host cells is via gap-junctional coupling, even before electrophysiologically mature neuronal differentiation. The gap junctions, which are established rapidly, permit exogenous NSCs to influence directly host network activity, including synchronized calcium transients with host cells in fluctuating networks. The exogenous NSCs also protect host neurons from death and reduce such signs of secondary injury as reactive astrogliosis. To determine whether gap junctions between NSCs and host cells may also mediate neuroprotection in vivo, we examined NSC transplantation in two murine models characterized by degeneration of the same cell type (Purkinje neurons) from different etiologies, namely, the nervous and SCA1 mutants. In both, gap junctions (containing connexin 43) formed between NSCs and host cells at risk, and were associated with rescue of neurons and behavior (when implantation was performed before overt neuron loss). Both in vitro and in vivo beneficial NSC effects were abrogated when gap junction formation or function was suppressed by pharmacologic and/or RNA-inhibition strategies, supporting the pivotal mediation by gap-junctional coupling of some modulatory, homeostatic, and protective actions on host systems as well as establishing a template for the subsequent development of electrochemical synaptic intercellular communication.
Robust common carotid artery lumen detection in B-mode ultrasound images using local phase symmetry

This paper presents a new method for automatic common carotid artery detection in B-mode ultrasonography. The proposed method is based on the location of phase symmetry patterns at apropriate scale of analysis. The local phase information is derived from the monogenic signal and isotropic log-normal band-pass filters, and the resulting common carotid artery is located using a dynamic programming optimization algorithm. The experiments show that the proposed method is more robust to noise than previous approaches, although additional research is required for robust common carotid artery detection on the more complicated cases.
On the kinematic deconvolution of the local neighbourhood luminosity function

ABSTRA C T A method for inverting the statistical star counts equation, including proper motions, is presented; in order to break the degeneracy in that equation, it uses the supplementary constraints required by dynamical consistency. The inversion gives access to both the kinematics and the luminosity function of each population in three regimes: the singular ellipsoid, the constant ratio Schwarzschild ellipsoid plane-parallel models and the epicyclic model. This more realistic model is tailored to account for the local neighbourhood density and velocity distribution. The first model is fully investigated, both analytically and by means of a non-parametric inversion technique, while the second model is shown to be formally its equivalent. The effect of noise and incompleteness in apparent magnitude is investigated. The third model is investigated by a 5D 1 2D non-parametric inversion technique where positivity of the underlying luminosity function is explicitly accounted for. It is argued that its future application to data such as the Tycho catalogue (and in the upcoming satellite GAIA ) could lead - provided that the vertical potential and or the asymmetric drift or w( are known - to a non-parametric determination of the local neighbourhood luminosity function without any reference to stellar evolution tracks. It should also yield the proportion of stars for each kinematic component and a kinematic diagnostic to split the thin disc from the thick disc or the halo.
Simple improved confidence intervals for comparing matched proportions

For binary matched‐pairs data, this article discusses interval estimation of the difference of probabilities and an odds ratio for comparing ‘success’ probabilities. We present simple improvements of the commonly used Wald confidence intervals for these parameters. The improvement of the interval for the difference of probabilities is to add two observations to each sample before applying it. The improvement for estimating an odds ratio transforms a confidence interval for a single proportion. Copyright © 2005 John Wiley & Sons, Ltd.
A low-complexity message recovery method for Compute-and-Forward relaying

The Compute-and-Forward relaying strategy aims to achieve high computation rates by decoding linear combinations of transmitted messages at intermediate relays. However, if the involved relays independently choose which combinations of the messages to decode, there is no guarantee that the overall system of linear equations is solvable at the destination. In this article it is shown that, for a Gaussian fading channel model with two transmitters and two relays, always choosing the combination that maximizes the computation rate often leads to a case where the original messages cannot be recovered. It is further shown that by limiting the relays to select from carefully designed sets of equations, a solvable system can be guaranteed while maintaining high computation rates. The proposed method has a constant computational complexity and requires no information exchange between the relays.
Thai Connected Digit Speech Recognition Using Hidden Markov Models

A Connected digit speech recognition is important in many applications such as voice-dialing telephone, automated banking system, automatic data entry, PIN entry, etc. This research presents speech recognition system of speaker-independent Thai connected digit. The system employs mel frequency cepstrum coefficient (MFCC), delta MFCC, delta-delta MFCC, delta energy and delta-delta energy as features, and applies continuous density hidden Markov model (CDHMM) in the recognition process. The Viterbi beam search algorithm is used in decoding process. In training set, we use 100 speakers (50 females, 50 males) for 2000 utterances within the range of 20-28 years old. For the experiment, we used 50 speakers (25 females, 25 males) as testing set. The average recognition rate is 75.25 % for known length strings and 70.33 % for unknown length strings.
Comparative Genomics of NAD Biosynthesis in Cyanobacteria

ABSTRACT Biosynthesis of NAD(P) cofactors is of special importance for cyanobacteria due to their role in photosynthesis and respiration. Despite significant progress in understanding NAD(P) biosynthetic machinery in some model organisms, relatively little is known about its implementation in cyanobacteria. We addressed this problem by a combination of comparative genome analysis with verification experiments in the model system of Synechocystis sp. strain PCC 6803. A detailed reconstruction of the NAD(P) metabolic subsystem using the SEED genomic platform (http://theseed.uchicago.edu/FIG/index.cgi ) helped us accurately annotate respective genes in the entire set of 13 cyanobacterial species with completely sequenced genomes available at the time. Comparative analysis of operational variants implemented in this divergent group allowed us to elucidate both conserved (de novo and universal pathways) and variable (recycling and salvage pathways) aspects of this subsystem. Focused genetic and biochemical experiments confirmed several conjectures about the key aspects of this subsystem. (i) The product of the slr1691 gene, a homolog of Escherichia coli gene nadE containing an additional nitrilase-like N-terminal domain, is a NAD synthetase capable of utilizing glutamine as an amide donor in vitro. (ii) The product of the sll1916 gene, a homolog of E. coli gene nadD, is a nicotinic acid mononucleotide-preferring adenylyltransferase. This gene is essential for survival and cannot be compensated for by an alternative nicotinamide mononucleotide (NMN)-preferring adenylyltransferase (slr0787 gene). (iii) The product of the slr0788 gene is a nicotinamide-preferring phosphoribosyltransferase involved in the first step of the two-step nondeamidating utilization of nicotinamide (NMN shunt). (iv) The physiological role of this pathway encoded by a conserved gene cluster, slr0787-slr0788, is likely in the recycling of endogenously generated nicotinamide, as supported by the inability of this organism to utilize exogenously provided niacin. Positional clustering and the cooccurrence profile of the respective genes across a diverse collection of cellular organisms provide evidence of horizontal transfer events in the evolutionary history of this pathway.
Global budgets for local recommendations

We present the design, implementation and evaluation of a new geotagging service, Gloe, that makes it easy to find, rate and recommend arbitrary on-line content in a mobile setting. The service automates the content search process by taking advantage of geographic and social context, while using crowdsourced expertise to present a personalized feed of targeted information ranked by a novel geo-aware rating and incentive mechanism. Users rate the relevance of recommendations for particular locations using a limited, global voting budget. This budget is, in turn, increased by accurately predicting local content popularity. One of the key goals of our mechanism is to encourage ratings, and in an evaluation of the live system we found that the rating to click ratio was 107 times higher than the ratio for videos on YouTube, 34 times higher than the ratio for applications on the Android Market, and 3 times higher than the ratio for Web pages on Digg. To investigate whether our mechanism also had qualitative effects on the ratings we conducted a number of experiments on Amazon Mechanical Turk, with 500 users, comparing our mechanism to the de-facto 5-star ratings commonly in use on the Web. Our results show that budgets improved the ranking and incentives improved the aggregate rating of a series of location-dependent Web pages.
Chapter 17 Graph-Theoretic Analysis of Finite Markov Chains

Markov chains arise frequently in the modeling of physical and conceptual processes that evolve over time. For example, the diffusion of liquids across a semiporous membrane, the spread of disease within a population, and the flow of personnel within the ranks of an organization can all be modeled using Markov chains. In each of these cases, the system can be found in any of a finite number of states, and transitions between states occur at discrete instants according to specified probabilities.
Pregnancy Dose Tdap and Postpartum Cocooning to Prevent Infant Pertussis: A Decision Analysis

BACKGROUND: Infants <2 months of age are at highest risk of pertussis morbidity and mortality. Until recently, the US Advisory Committee on Immunization Practices (ACIP) recommended protecting young infants by “cocooning” or vaccination of postpartum mothers and other close contacts with tetanus toxoid, reduced diphtheria toxoid, and acellular pertussis, adsorbed (Tdap) booster vaccine. ACIP recommends pregnancy vaccination as a preferred and safe alternative to postpartum vaccination. The ACIP cocooning recommendation has not changed. METHODS: We used a cohort model reflecting US 2009 births and the diphtheria-tetanus-acellular pertussis schedule to simulate a decision and cost-effectiveness analysis of Tdap vaccination during pregnancy compared with postpartum vaccination with or without vaccination of other close contacts (ie, cocooning). We analyzed infant pertussis cases, hospitalizations, and deaths, as well as direct disease, indirect, and public health costs for infants in the first year of life. All costs were updated to 2011 US dollars. RESULTS: Pregnancy vaccination could reduce annual infant pertussis incidence by more than postpartum vaccination, reducing cases by 33% versus 20%, hospitalizations by 38% versus 19%, and deaths by 49% versus 16%. Additional cocooning doses in a father and 1 grandparent could avert an additional 16% of cases but at higher cost. The cost per quality-adjusted life-year saved for pregnancy vaccination was substantially less than postpartum vaccination ($414 523 vs $1 172 825). CONCLUSIONS: Tdap vaccination during pregnancy could avert more infant cases and deaths at lower cost than postpartum vaccination, even when postpartum vaccination is combined with additional cocooning doses. Pregnancy dose vaccination is the preferred alternative to postpartum vaccination for preventing infant pertussis.
GMM-Based Hidden Markov Random Field for Color Image and 3D Volume Segmentation

In this project, we first study the Gaussian-based hidden Markov random field (HMRF) model and its expectation-maximization (EM) algorithm. Then we generalize it to Gaussian mixture model-based hidden Markov random field. The algorithm is implemented in MATLAB. We also apply this algorithm to color image segmentation problems and 3D volume segmentation problems.