Miracle-dz/UniFAR-FTUs huggingface dataset:
Methyl-CpG Binding Domain Protein 2 Represses Transcription from Hypermethylated π-Class Glutathione S-Transferase Gene Promoters in Hepatocellular Carcinoma Cells*

During the pathogenesis of human hepatocellular carcinoma (HCC), the CpG island encompassing the π-class glutathione S-transferase gene (GSTP1) becomes hypermethylated. Repression of transcription accompanying CpG island hypermethylation has been proposed to be mediated by methyl-CpG binding domain (MBD) proteins. We report here that inhibition of transcription from hypermethylatedGSTP1 promoters in Hep3B HCC cells, which fail to expressGSTP1 mRNA or GSTP1 polypeptides, appears to be mediated by MBD2. Treatment of Hep3B cells with 5-azadeoxycytidine (5-aza-dC), a methyltransferase inhibitor, activated GSTP1expression, whereas treatment with trichostatin A, a histone deacetylase inhibitor, had little effect. To more precisely assess the contribution of the pattern of GSTP1 CpG island methylation on GSTP1 mRNA expression, Hep3B cells were treated for 72 h with 5-aza-dC and then subjected to limiting dilution cloning. Bisulfite sequencing was used to map the methylation patterns of the GSTP1 promoter region inGSTP1-expressing and -non-expressing clones. In the clone that expressed GSTP1 mRNA determined by Northern blot analysis and quantitative reverse transcriptase (RT)-PCR, widespread demethylation of at least one GSTP1allele was evident. Chromatin immunoprecipitation experiments revealed the presence of MBD2, but not Sp1, at the GSTP1 promoter in Hep3B cells. In contrast, Sp1 was detected at the GSTP1promoter in a GSTP1-expressing Hep3B 5-aza-dC subclone. To test whether MBD2 might be responsible for the inhibition ofGSTP1 transcription from hypermethylated GSTP1promoters, siRNAs were used to reduce MBD2 polypeptide levels in Hep3B cells. SssI-catalyzed methylation ofGSTP1 promoter sequences resulted in diminished luciferase reporter activity after transfection into Hep3B cells. However, when hypermethylated GSTP1 promoter sequences were transfected into Hep3B cells that had been treated with siRNA-targetingMBD2 mRNA, no repression of luciferase reporter expression was evident. These findings implicate MBD2 in the repression of GSTP1 expression associated with GSTP1 CpG island hypermethylation in HCC cells.
EUS-Guided Routine Liver Biopsy in Selected Patients

TO THE EDITOR: The article by Sawhney et al. compares the prevalence of advanced colonic neoplasm in nonanemic patients and anemic patients with a variety of ferritin levels (1). While the use of odds ratios in Table 3 is correctly interpreted in the text, the likelihood ratios in Table 4 are not clearly discussed in the text. Guyatt et al. define an odds ratio as “a ratio of the odds of an event in an exposed group to the odds of the same event in a group that is not exposed” (2). Using the data from Table 3, Sawhney et al. correctly state patients with ferritin <50 ng/mL and ferritin 51–100 ng/mL are almost 5 times more likely to have advanced colonic neoplasia than those patients with ferritin >100 ng/mL or nonanemic controls. A likelihood ratio is defined by Guyatt et al. as the relative likelihood that a given test would be expected in a patient with as opposed to one without a disorder of interest (2). Fletcher and Wagner state likelihood ratios reflect the probability of that test result in people with the disease divided by the probability of the result in people without disease (3). Therefore, using the likelihood ratios in Table 4, the authors should have clarified in the text that a ferritin >100 ng/mL is 0.27 times as likely to occur in a patient with colonic neoplasm compared to a patient without colonic neoplasm. If a statement defining likelihood ratios was included, readers could more readily interpret the results. The likelihood ratio and the odds ratio could then be expressed to a patient in terms that the patient could understand and weigh the risks and benefits.
BIND: Binary Integrated Net Descriptors for Texture-Less Object Recognition

This paper presents BIND (Binary Integrated Net Descriptor), a texture-less object detector that encodes multi-layered binary-represented nets for high precision edge-based description. Our proposed concept aligns layers of object-sized patches (nets) onto highly fragmented occlusion resistant line-segment midpoints (linelets) to encode regional information into efficient binary strings. These lightweight nets encourage discriminative object description through their high-spatial resolution, enabling highly precise encoding of the objects edges and internal texture-less information. BIND achieved various invariant properties such as rotation, scale and edge-polarity through its unique binary logical-operated encoding and matching techniques, while performing remarkably well in occlusion and clutter. Apart from yielding efficient computational performance, BIND also attained remarkable recognition rates surpassing recent state-of-the-art texture-less object detectors such as BORDER, BOLD and LINE2D.
A dual technology femto cell architecture for robust communication using whitespaces

We propose WhiteCell - a dual technology femto cell architecture for wide-area wireless users that addresses some of the critical challenges being faced by the cellular industry today in better meeting surging demands. WhiteCell extends the traditional notion of a femto cell in which small, low-power, short-range access points are placed in homes to improve coverage, connectivity and spatial re-use in the cellular operator's own frequency and technology. In WhiteCell, each indoor access point is equipped with the ability to communicate over two separate blocks of spectrum - the cellular operator's own spectrum using the same technology as before, and the recently released swath of TV whitespace spectrum that allows opportunistic use under specific FCC guidelines in the US. The two spectrum blocks and their corresponding technologies complement each other very well. While whitespace spectrum allows us to add significant capacity to the otherwise constrained cellular spectrum, the cellular frequencies allows the system to support some minimal expectation of performance guarantee that whitespace alone cannot, due to license exclusivity. While this extension is conceptually simple, it provides dramatic performance gains for both the cellular operator and the end users who are putting increasing demands on the limited cellular spectrum. This paper describes the overall WhiteCell architecture, a system implementation, and various challenges addressed in efficiently utilizing whitespace spectrum including a collaborative approach in spectrum sensing, as well as in efficiently transitioning traffic across this dual technology structure. In addition, the paper demonstrates the significant performance advantages of the architecture through detailed evaluation of our WhiteCell prototype.
Overview of the NTCIR-12 IMine-2 Task

In this paper, we provide an overview of the NTCIR-12 IMine-2 task, which is a core task of NTCIR-12 and also a succeeding work of IMine@NTCIR-11, INTENT-2@NTCIR-10, and INTENT@NTCIR-9 tasks. IMine-2 comprises the Query Understanding subtask and the Vertical Incorporating subtask. 23 groups from diverse countries including China, France, India, Portugal, Ireland, and Japan registered to the task. Finally, IMine-2 attracted 9 participating teams; we received 42 runs for the Query Understanding subtask and 15 runs for the Vertical Incorporating subtask. We describe the subtasks, data, evaluation methods, and report the official results for each subtask.
Chromosome regions between centromeres and proximal crossovers are the physical sites of major effect loci for yield in potato: genetic analysis employing meiotic mutants.

Meiotic mutant (2n) gametes formed by first-division restitution without crossover (FDR-NCO) are expected to be superior to FDR with crossover (FDR-CO) because they transmit to the progeny, without disruption by recombination, almost 100% of the parental genotype. FDR-CO transfers approximately 80% of the parental heterozygosity and a large fraction of the epistatic interactions. Another genetic expectation associated with both FDR gametes is their equivalence for the phenotypic expression of traits controlled by genes residing between centromeres and proximal crossover sites. This set of unique cytogenetic features of FDR mutants was employed here as a tool to infer physical location of quantitative trait loci controlling total tuber yield (TTY) in potato. Two assays were conducted to verify the superiority of FDR-NCO over FDR-CO gametes for TTY by using progenies from 4x-2x factorial crosses. Male clones were 2n-pollen producers by either FDR-CO or FDR-NCO mechanisms. Compared with the 4x parents, TTY of the progenies ranged from 41% to 175% (i.e., high-parent heterosis). However, no significant TTY differences were observed between FDR-CO and FDR-NCO families. In addition, the size of variance components of males was smaller than females and near zero. Our results reinforce the hypothesis that genes controlling yielding ability have a predominant physical location between centromeres and proximal chiasmata. Quantitative trait loci in chromosome regions with reduced levels of recombination may provide a partial explanation for the slow progress in increasing TTY through conventional 4x-4x crosses and for the often high degree of heterosis obtained by introgressing genetic diversity via 4x-2x crosses in potato.
The Relationship between Visual Field Index and Estimated Number of Retinal Ganglion Cells in Glaucoma

Purpose To evaluate the relationship between visual field index (VFI) and the estimated number of retinal ganglion cells (RGCs) in glaucoma. Methods A multicenter study of 1,245 healthy, glaucomatous and suspected glaucomatous eyes of 1,245 subjects recruited from the Diagnostic Innovations in Glaucoma Study (DIGS) and African Descent and Glaucoma Evaluation Study (ADAGES). All eyes underwent standard automated perimetry (SAP) and time-domain optical coherence tomography (TD-OCT). Estimates of RGC count and percentage of RGCs remaining, compared to age-matched healthy eyes, were calculated from TD-OCT using a previously described formula. Smoothing spline curves were fitted to examine the relationship between VFI and the percent remaining RGCs. The first derivative (i.e., slopes) of these curves was used to explore the relationship between changes in these measures. Results The relationships between the VFI and both estimated RGC counts and the percent remaining RGCs were nonlinear. A unit number of VFI loss corresponded to substantially greater loss of estimated RGCs and estimated percentage of RGCs remaining in early compared to late disease. Conclusions The relationship between VFI and estimated RGC counts is nonlinear and the index substantially underestimates the amount of neural loss early in the disease. Disease severity should be taken into account when interpreting rates of VFI change over time.
Mushroom body miscellanea: transgenic Drosophila strains expressing anatomical and physiological sensor proteins in Kenyon cells

The fruit fly Drosophila melanogaster represents a key model organism for analyzing how neuronal circuits regulate behavior. The mushroom body in the central brain is a particularly prominent brain region that has been intensely studied in several insect species and been implicated in a variety of behaviors, e.g., associative learning, locomotor activity, and sleep. Drosophila melanogaster offers the advantage that transgenes can be easily expressed in neuronal subpopulations, e.g., in intrinsic mushroom body neurons (Kenyon cells). A number of transgenes has been described and engineered to visualize the anatomy of neurons, to monitor physiological parameters of neuronal activity, and to manipulate neuronal function artificially. To target the expression of these transgenes selectively to specific neurons several sophisticated bi- or even multipartite transcription systems have been invented. However, the number of transgenes that can be combined in the genome of an individual fly is limited in practice. To facilitate the analysis of the mushroom body we provide a compilation of transgenic fruit flies that express transgenes under direct control of the Kenyon-cell specific promoter, mb247. The transgenes expressed are fluorescence reporters to analyze neuroanatomical aspects of the mushroom body, proteins to restrict ectopic gene expression to mushroom bodies, or fluorescent sensors to monitor physiological parameters of neuronal activity of Kenyon cells. Some of the transgenic animals compiled here have been published already, whereas others are novel and characterized here for the first time. Overall, the collection of transgenic flies expressing sensor and reporter genes in Kenyon cells facilitates combinations with binary transcription systems and might, ultimately, advance the physiological analysis of mushroom body function.
Quantitative differences in tissue surface tension influence zebrafish germ layer positioning

This study provides direct functional evidence that differential adhesion, measurable as quantitative differences in tissue surface tension, influences spatial positioning between zebrafish germ layer tissues. We show that embryonic ectodermal and mesendodermal tissues generated by mRNA‐overexpression behave on long‐time scales like immiscible fluids. When mixed in hanging drop culture, their cells segregate into discrete phases with ectoderm adopting an internal position relative to the mesendoderm. The position adopted directly correlates with differences in tissue surface tension. We also show that germ layer tissues from untreated embryos, when extirpated and placed in culture, adopt a configuration similar to those of their mRNA‐overexpressing counterparts. Down‐regulating E‐cadherin expression in the ectoderm leads to reduced surface tension and results in phase reversal with E‐cadherin‐depleted ectoderm cells now adopting an external position relative to the mesendoderm. These results show that in vitro cell sorting of zebrafish mesendoderm and ectoderm tissues is specified by tissue interfacial tensions. We perform a mathematical analysis indicating that tissue interfacial tension between actively motile cells contributes to the spatial organization and dynamics of these zebrafish germ layers in vivo.
Robust H∞ control for switched singular systems with linear fractional uncertainties: A strict LMI approach

In this paper, for a class of switched linear singular systems with linear fractional uncertainty, the robust H∞ control problem is investigated by using a strict linear matrix inequality (LMI) appoach. First of all, for the unforced system, a sufficient condition is given for generalized robust stabilization with prescribed disturbance attenuation level only by switching. Then, the robust H∞ control synthesis via switched state feedback is solved by LMI approach. The obtained results generalize and improve the previous works on switched singular systems and switched state-space systems.
A Mission for Computational Natural Language Learning

In this presentation, I will look back at 10 years of CoNLL conferences and the state of the art of machine learning of language that is evident from this decade of research. My conclusion, intended to provoke discussion, will be that we currently lack a clear motivation or "mission" to survive as a discipline. I will suggest that a new mission for the field could be found in a renewed interest for theoretical work (which learning algorithms have a bias that matches the properties of language? , what is the psycholinguistic relevance of learner design issues? ), in more sophisticated comparative methodology, and in solving the problem of transfer, reusability, and adaptation of learned knowledge.
Author's Personal Copy Statistics and Probability Letters Characterizing the Variance Improvement in Linear Dirichlet Random Effects Models

An alternative to the classical mixed model with normal random effects is to use a Dirichlet process to model the random effects. Such models have proven useful in practice, and we have observed a noticeable variance reduction, in the estimation of the fixed effects, when the Dirichlet process is used instead of the normal. In this paper we formalize this notion, and give a theoretical justification for the expected variance reduction. We show that for almost all data vectors, the posterior variance from the Dirichlet random effects model is smaller than that from the normal random effects model.
Bayesian Active Distance Metric Learning

Distance metric learning is an important component for many tasks, such as statistical classification and content-based image retrieval. Existing approaches for learning distance metrics from pairwise constraints typically suffer from two major problems. First, most algorithms only offer point estimation of the distance metric and can therefore be unreliable when the number of training examples is small. Second, since these algorithms generally select their training examples at random, they can be inefficient if labeling effort is limited. This paper presents a Bayesian framework for distance metric learning that estimates a posterior distribution for the distance metric from labeled pair-wise constraints. We describe an efficient algorithm based on the variational method for the proposed Bayesian approach. Furthermore, we apply the proposed Bayesian framework to active distance metric learning by selecting those unlabeled example pairs with the greatest uncertainty in relative distance. Experiments in classification demonstrate that the proposed framework achieves higher classification accuracy and identifies more informative training examples than the non-Bayesian approach and state-of-the-art distance metric learning algorithms.
The relevance of mid-Holocene Arctic warming to the future

Abstract. There remain substantial uncertainties in future projections of Arctic climate change. There is a potential to constrain these uncertainties using a combination of paleoclimate simulations and proxy data, but such a constraint must be accompanied by physical understanding on the connection between past and future simulations. Here, we examine the relevance of an Arctic warming mechanism in the mid-Holocene (MH) to the future with emphasis on process understanding. We conducted a surface energy balance analysis on 10 atmosphere and ocean general circulation models under the MH and future Representative Concentration Pathway (RCP) 4.5 scenario forcings. It is found that many of the dominant processes that amplify Arctic warming over the ocean from late autumn to early winter are common between the two periods, despite the difference in the source of the forcing (insolation vs. greenhouse gases). The positive albedo feedback in summer results in an increase in oceanic heat release in the colder season when the atmospheric stratification is strong, and an increased greenhouse effect from clouds helps amplify the warming during the season with small insolation. The seasonal progress was elucidated by the decomposition of the factors associated with sea surface temperature, ice concentration, and ice surface temperature changes. We also quantified the contribution of individual components to the inter-model variance in the surface temperature changes. The downward clear-sky longwave radiation is one of major contributors to the model spread throughout the year. Other controlling terms for the model spread vary with the season, but they are similar between the MH and the future in each season. This result suggests that the MH Arctic change may not be analogous to the future in some seasons when the temperature response differs, but it is still useful to constrain the model spread in the future Arctic projection. The cross-model correlation suggests that the feedbacks in preceding seasons should not be overlooked when determining constraints, particularly summer sea ice cover for the constraint of autumn–winter surface temperature response.
Inverse correlation between quasiparticle mass and Tc in a cuprate high-Tc superconductor

Contrary to what is expected near a quantum critical point, pressure decreases the quasiparticle mass of a high-Tc superconductor. Close to a zero-temperature transition between ordered and disordered electronic phases, quantum fluctuations can lead to a strong enhancement of electron mass and to the emergence of competing phases such as superconductivity. A correlation between the existence of such a quantum phase transition and superconductivity is quite well established in some heavy fermion and iron-based superconductors, and there have been suggestions that high-temperature superconductivity in copper-oxide materials (cuprates) may also be driven by the same mechanism. Close to optimal doping, where the superconducting transition temperature Tc is maximal in cuprates, two different phases are known to compete with superconductivity: a poorly understood pseudogap phase and a charge-ordered phase. Recent experiments have shown a strong increase in quasiparticle mass m* in the cuprate YBa2Cu3O7-δ as optimal doping is approached, suggesting that quantum fluctuations of the charge-ordered phase may be responsible for the high-Tc superconductivity. We have tested the robustness of this correlation between m* and Tc by performing quantum oscillation studies on the stoichiometric compound YBa2Cu4O8 under hydrostatic pressure. In contrast to the results for YBa2Cu3O7-δ, we find that in YBa2Cu4O8, the mass decreases as Tc increases under pressure. This inverse correlation between m* and Tc suggests that quantum fluctuations of the charge order enhance m* but do not enhance Tc.
Screening for Quorum-Sensing Inhibitors (QSI) by Use of a Novel Genetic System, the QSI Selector

ABSTRACT With the widespread appearance of antibiotic-resistant bacteria, there is an increasing demand for novel strategies to control infectious diseases. Furthermore, it has become apparent that the bacterial life style also contributes significantly to this problem. Bacteria living in the biofilm mode of growth tolerate conventional antimicrobial treatments. The discovery that many bacteria use quorum-sensing (QS) systems to coordinate virulence and biofilm development has pointed out a new, promising target for antimicrobial drugs. We constructed a collection of screening systems, QS inhibitor (QSI) selectors, which enabled us to identify a number of novel QSIs among natural and synthetic compound libraries. The two most active were garlic extract and 4-nitro-pyridine-N-oxide (4-NPO). GeneChip-based transcriptome analysis revealed that garlic extract and 4-NPO had specificity for QS-controlled virulence genes in Pseudomonas aeruginosa. These two QSIs also significantly reduced P. aeruginosa biofilm tolerance to tobramycin treatment as well as virulence in a Caenorhabditis elegans pathogenesis model.
Learning the Scope of Hedge Cues in Biomedical Texts

Identifying hedged information in biomedical literature is an important subtask in information extraction because it would be misleading to extract speculative information as factual information. In this paper we present a machine learning system that finds the scope of hedge cues in biomedical texts. The system is based on a similar system that finds the scope of negation cues. We show that the same scope finding approach can be applied to both negation and hedging. To investigate the robustness of the approach, the system is tested on the three subcorpora of the BioScope corpus that represent different text types.