Miracle-dz/UniFAR-FTUs huggingface dataset:
bind thousands of sites in a cell type-specific manner Genistein and bisphenol A exposure cause estrogen receptor 1 to Material Supplemental

Material Supplemental http://genome.cshlp. org/content/suppl/2012/09/13/gr.135681. 111.DC1. html References http://genome.cshlp. org/content/22/11/2153.full. html#ref-list-1 This article cites 59 articles, 19 of which can be accessed free at: License Commons Creative . http://creativecommons.org/licenses/by-nc/3.0/ described at a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as ). After six months, it is available under http://genome.cshlp. org/site/misc/terms.xhtml first six months after the full-issue publication date (see This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the
Title Optimal rebalancing of portfolios with transaction costs

Rebalancing of portfolios with a concave utility function is considered. It is proved that transaction costs imply that there is a no-trade region where it is optimal not to trade. For proportional transaction costs it is optimal to rebalance to the boundary when outside the no-trade region. With flat transaction costs, the rebalance from outside the no-trade region should be to a state at an internal surface in the no-trade region but never a full rebalance. The standard optimal portfolio theory is extended to n-symmetric assets, general utility function, and more general stochastic processes. Examples are discussed. The paper studies rebalancing of portfolios with a general concave utility function. It is proved that transaction costs imply that there is a no-trade region in the state space where it is not optimal to perform trading. If the transaction costs are proportional, then it is optimal to rebalance when outside the no-trade region to a state at the boundary of this region. If the transaction costs have fixed or flat elements, then the rebalance from outside the no-trade region should be to a state at an internal surface in the no-trade region but never a full rebalance. This extends previous results by considering n-symmetric assets, using a general utility function, and a larger class of stochastic processes. We find an analytic approximation to the boundary of the no-trade region for a quadratic utility function. The results are illustrated with an explicit example and a numerical example with simulation. The paper is a natural extension of the optimal portfolio theory (Markowitz, (7)) since it includes transaction costs and handles more general stochastic processes and utility functions.
Seed fields for galactic dynamos by the magnetorotational instability

A linear but global numerical model for the magnetorotational instability (MRI) in a disk geometry is considered to estimate the instability parameters for galaxies. Similarity rules suggested by a local analysis are applied to reveal a uni- versal behavior of the results of global calculations for large magnetic Prandtl numbers. The findings are used to estimate the MRI characteristics for galaxies with their very large magnetic Prandtl numbers which cannot be attained in any numerical simulations. The resulting minimum field for the instability, Bmin � 10 −25 G, is small compared to any seed fields currently discussed. The growth times of MRI are estimated to be on the order of the rotation period of the inner rigidly-rotating core, i.e. ∼100 Myr. Global MRI excites preferentially magnetic field modes of quadrupolar symmetry.
U-HAUL: Efficient State Migration in NFV

Network function virtualization (NFV) enables dynamic scaling of resources to middlebox deployment and management. In NFV, state migration is an important task because operators often need to shift traffic and its associated flow states across NF instances for load balancing. Existing state migration schemes, however, exhibit long delays and high controller overhead. This paper presents U-HAUL, an efficient state migration system that reduces the state migration overhead. U-HAUL takes advantage of the fact that most flows are short-lived mice flows, and in many cases their processing states will expire before the state migration finishes. Rather than blindly moving states of all the flows, U-HAUL keeps the states of active mice flows on the original NF instance, and only migrates elephant flow states. By reducing the number of flow states to be migrated, U-HAUL greatly reduces the migration delay and its performance penalty. Our evaluation shows that U-HAUL reduces the average migration time by up to 87% and the latency to mice flows by up to 94% compared to OpenNF.
Electronic Voting Using Identity Based Cryptography

Today voting processes are the most important element of democracy as the society´s way to make decisions. Such processes have been influenced by information technologies until becoming be named electronic voting. This topic has been an active research area, on which, cryptographic primitives are used in order to propose secure protocols. Most of them use a Public Key Infrastructure. In this paper, we propose the use of Bilinear Pairings, first implementation of Identity Based Cryptography, in order to provide stronger security requirements than protocols based on Public Key Infastructure and without requiring the entire infrastructure needed by them. We make a comparative analysis of our proposal with previous proposals, which is based on the total number of needed key pairs and required authorities by those protocols.
A SEARCH FOR “DWARF” SEYFERT NUCLEI. VII. A CATALOG OF CENTRAL STELLAR VELOCITY DISPERSIONS OF NEARBY GALAXIES

We present new central stellar velocity dispersion measurements for 428 galaxies in the Palomar spectroscopic survey of bright, northern galaxies. Of these, 142 have no previously published measurements, most being relatively late-type systems with low velocity dispersions (≲100 km s−1). We provide updates to a number of literature dispersions with large uncertainties. Our measurements are based on a direct pixel-fitting technique that can accommodate composite stellar populations by calculating an optimal linear combination of input stellar templates. The original Palomar survey data were taken under conditions that are not ideally suited for deriving stellar velocity dispersions for galaxies with a wide range of Hubble types. We describe an effective strategy to circumvent this complication and demonstrate that we can still obtain reliable velocity dispersions for this sample of well-studied nearby galaxies.
Integrable probability: From representation theory to Macdonald processes

These are lecture notes for a mini-course given at the Cornell Probability Summer School in July 2013. Topics include lozenge tilings of polygons and their representation theoretic interpretation, the (q,t)-deformation of those leading to the Macdonald processes, nearest neighbor dynamics on Macdonald processes, their limit to semi-discrete Brownian polymers, and large time asymptotic analysis of polymer's partition function.
Individual Variability of Hearing-Impaired Consonant Perception

Abstract The study of hearing impaired speech recognition at the consonant level allows for a detailed examination of individual variability. Use of low-context stimuli, such as consonants, aids in minimizing the influence of some variable cognitive abilities (e.g., use of context, memory) across listeners and focuses on differences in the processing or interpretation of the existing acoustic consonant cues. We show that hearing-impaired perception can vary across multiple tokens of the same consonant, in both noise robustness and confusion groups. Within-consonant differences in noise robustness are related to differences in intensity of the consonant cue region. For a single listener, high errors can exist for a small subset of test stimuli, while performance for the majority of test stimuli remains at ceiling. The existence of within-consonant differences in confusion groups entails that an average over multiple tokens of the same consonant results in a larger confusion group than for a single consonant token. For each consonant token, the same confusion group is consistently observed across a population of hearing-impaired listeners. Quantifying perceptual differences provides insight into the perception of speech under noisy conditions and characterizes each listener's hearing impairment.
Obtaining representable coimplications from aggregation and dual operators

The aim of this work is to study Ndual structures of representable implications generated from a set M of aggregation functions and pairs of mutual dual functions, founded on the isomorphism between the unit interval and special instances of the Goguen’s L-fuzzy sets. We discuss under which conditions representable functions preserve the main properties of their Ndual interval approach.
Syntaxin 1C, a soluble form of syntaxin, attenuates membrane recycling by destabilizing microtubules

Syntaxin 1C (STX1C), produced by alternative splicing of the stx1A gene, is a soluble syntaxin lacking a SNARE domain and a transmembrane domain. It is unclear how soluble syntaxin can control intracellular membrane trafficking. We found that STX1C affected microtubule (MT) dynamics through its tubulin-binding domain (TBD) and regulated recycling of intracellular vesicles carrying glucose transporter-1 (GLUT1). We demonstrated that the amino acid sequence VRSK of the TBD was important for the interaction between STX1C and tubulin and that wild-type STX1C (STX1C-WT), but not the TBD mutant, reduced the Vmax of glucose transport and GLUT1 translocation to the plasma membrane in FRSK cells. Moreover, by time-lapse analysis, we revealed that STX1C-WT suppressed MT stability and vesicle-transport motility in cells expressing GFP–α-tubulin, whereas TBD mutants had no effect. We also identified that GLUT1 was recycled in the 45 minutes after endocytosis and that GLUT1 vesicles moved along with MTs. Finally, we showed, by a recycling assay and FCM analysis, that STX1C-WT delayed the recycling phase of GLUT1 to PM, without affecting the endocytotic process of GLUT1. These data indicate that STX1C delays the GLUT1 recycling phase by suppressing MT stability and vesicle-transport motility through its TBD, providing the first insight into how soluble syntaxin controls membrane trafficking.
A Bayesian Approach to Large Scale Simultaneous Inference

We discuss Bayesian decision rules for highly multiple comparisons in the context of differential expression in microarray studies. Some of the advantages of our Bayesian approach include: flexible modeling of gene expressions, many options for decision rules to control either expectation or nonexpectation error rates, insensitivity to weak dependencies in the data, and pooling of results while retaining control of expected error rates. The proposed approach is demonstrated by the analysis of the spike-in HG-U133 data.
Transcriptional Profiling of ESTs from the Biocontrol Fungus Chaetomium cupreum

Comparative analysis was applied to two cDNA/ESTs libraries (C1 and C2) from Chaetomium cupreum. A total of 5538 ESTs were sequenced and assembled into 2162 unigenes including 585 contigs and 1577 singletons. BlastX analysis enabled the identification of 1211 unigenes with similarities to sequences in the public databases. MFS monosaccharide transporter was found as the gene expressed at the highest level in library C2, but no expression in C1. The majority of unigenes were library specific. Comparative analysis of the ESTs further revealed the difference of C. cupreum in gene expression and metabolic pathways between libraries. Two different sequences similar to the 48-KDa endochitinase and 46-KDa endochitinase were identified in libraries C1 and C2, respectively.
Process improvement of peer code review and behavior analysis of its participants

The software industry is urging on universities and colleges to cultivate software engineers who can write high quality programs. Peer code review (PCR) is accepted as an ideal way to maximize the learning outcome of students in writing quality code. Using this learning process, students improve their skills while scientific and efficient management removes the extra burden from instructors such as checking programs written by every student. In this paper, the previous PCR process was improved and the definitions of the relevant roles and documents were refined as well. After implementing this process in two academic years, some problems were found. By means of summarizing the email submissions by the students and also interviewing a few students, the behavior of all participants was preliminarily analyzed. With regards to the further quality assurance and high efficiency, a web-based management information system with a built-in blind review mechanism was discussed for solving the problems with process control, and also a game theory model was proposed for addressing the ethical issues in the whole PCR process.
An iterative feature selection method for GRNs inference by exploring topological properties

An important problem in bioinformatics is the inference of gene regulatory networks (GRN) from temporal expression profiles. In general, the main limitations faced by GRN inference methods is the small number of samples with huge dimensionalities and the noisy nature of the expression measurements. In face of these limitations, alternatives are needed to get better accuracy on the GRNs inference problem. This work addresses this problem by presenting an alternative feature selection method that applies prior knowledge on its search strategy, called SFFS-BA. The proposed search strategy is based on the Sequential Floating Forward Selection (SFFS) algorithm, with the inclusion of a scale-free (Barab\'asi-Albert) topology information in order to guide the search process to improve inference. The proposed algorithm explores the scale-free property by pruning the search space and using a power law as a weight for reducing it. In this way, the search space traversed by the SFFS-BA method combines a breadth-first search when the number of combinations is small ( >= 3), being guided by the scale-free prior information. Experimental results show that the SFFS-BA provides a better inference similarities than SFS and SFFS, keeping the robustness of the SFS and SFFS methods, thus presenting very good results.
ON-LINE AUTOMATIC HELP GENERATION SYSTEMS

The design of good user interfaces enhances the acceptance and use of computers, basically in environments in which their users are not familiar with computers. In this paper we concentrate on the design and development of intelligent interaction systems that provide active context-sensitive assistance to the user. We seek a compromise solution between development simplicity and power. To reach this objective, we propose the application of techniques from knowledge engineering to the development of active on-line assistance systems, establishing total independence between the knowledge on the interaction domain, the data, and the control of the communication acts.
Novel signal representation of descriptors dependency in information retrieval based on wavelet spectral analysis

The representation of texts in the current methods of information extraction, and TextMining in general, does not always reflect the dependencies between descriptors. In the vector representation, for example, descriptors related are often considered to be either totally independent or totally similar. This type of approach can be considered as a coarse resolution of the document. We propose in this paper a new method of information retrieval based on signal representation and spectral processing at different levels of resolution of documents. It is a new way to exploit the power and properties of the multiresolution analysis of wavelet transform. To illustrate the interest that could present this approach, we have applied it to an Arabic corpus. Our approach in this context demonstrates an ability to achieve higher accuracy compared to the standard vector representation.
Plant root distributions and nitrogen uptake predicted by a hypothesis of optimal root foraging

CO2-enrichment experiments consistently show that rooting depth increases when trees are grown at elevated CO2 (eCO2), leading in some experiments to increased capture of available soil nitrogen (N) from deeper soil. However, the link between N uptake and root distributions remains poorly represented in forest ecosystem and global land-surface models. Here, this link is modeled and analyzed using a new optimization hypothesis (MaxNup) for root foraging in relation to the spatial variability of soil N, according to which a given total root mass is distributed vertically in order to maximize annual N uptake. MaxNup leads to analytical predictions for the optimal vertical profile of root biomass, maximum rooting depth, and N-uptake fraction (i.e., the proportion of plant-available soil N taken up annually by roots). We use these predictions to gain new insight into the behavior of the N-uptake fraction in trees growing at the Oak Ridge National Laboratory free-air CO2-enrichment experiment. We also compare MaxNup with empirical equations previously fitted to root-distribution data from all the world's plant biomes, and find that the empirical equations underestimate the capacity of root systems to take up N.
Checking for Nonresponse Bias in Web-Only Surveys of Special Populations using a Mixed-Mode (Web-with-Mail) Design

A fuel composition comprising a hydrogenated material obtained by hydrogenating a reaction mixture ranging from C11 to C16 containing mainly compounds which comprise butadiene and cyclopentadiene as basic structural units, produced by reacting an acyclic conjugated diene with cyclopentadiene, dicyclopentadiene, an alkyl-substituted cyclopentadiene, or an alkyl-substituted dicyclopentadiene in accordance with Diels-Alder reaction an isomeric material prepared by isomerizing the hydrogenated material or the mixture of the hydrogenated material and the isomeric material.
3D reconstruction from 360/spl times/360 mosaics

We are studying the geometry of a 360/spl times/360 mosaic image formation. A 360/spl times/360 mosaic camera model and a calibration procedure are proposed. It is shown that only one point correspondence is needed in order to acquire epipolar rectified images. The 360/spl times/360 mosaic camera model is therefore determined by only one intrinsic parameter It is shown that the relation between coordinates estimated with different values of intrinsic 360/spl times/360 mosaic camera parameters is a scaling of all scene point coordinates with additional nonlinear changes in the z coordinates of the scene points. Experimental results verifying the reconstruction of real scene points are presented.
Transference of PIM Research Prototype Concepts to the Mainstream: Successes or Failures

Personal Information Management (PIM) refers to the practice and the study of how people acquire, organize, maintain, retrieve, archive and discard information for various reasons in physical and digital worlds. Many PIM tools are available for managing information on our desktop computers while many research prototypes have tried to augment or replace them. The development of these tools was based on knowledge drawn from the fields of psychology, human–computer interaction, information retrieval, knowledge management and research in the PIM field. Different metaphors and ways of organizing were introduced. However, the prevailing beliefs are that most of these prototypes were not extensively tested and that the radical design (not addressing real-world issues) and quick abandonment of prototypes prevented transfer to mainstream products. This paper looks at what has been developed and learnt, what has been transferred to mainstream applications, discusses the possible reasons behind these trends and challenges some parts of the above-mentioned beliefs.
Exploiting Lexical Dependencies from Large-Scale Data for Better Shift-Reduce Constituency Parsing

This paper proposes a method to improve shift-reduce constituency parsing by using lexical dependencies. The lexical dependency information is obtained from a large amount of auto-parsed data that is generated by a baseline shift-reduce parser on unlabeled data. We then incorporate a set of novel features defined on this information into the shift-reduce parsing model. The features can help to disambiguate action conflicts during decoding. Experimental results show that the new features achieve absolute improvements over a strong baseline by 0.9% and 1.1% on English and Chinese respectively. Moreover, the improved parser outperforms all previously reported shift-reduce constituency parsers. Title and Abstract in Chinese 利用大规模数据词汇依存关系改进移进-归约成分句法分析 本文提出了一种利用词汇依存关系改进移进-归约成分句法分析的方法。 首先,我们利用 基准系统在大规模无标注数据上进行自动句法分析并从分析结果中抽取词汇依存关系。 其 后,我们在词汇依存信息的基础上定义了一组新特征并将这些特征整合到移进-归约句法 分析模型 中。 新特征用于帮助消除移进-归约过程中的动作歧义。 实验结果表明,新特征 在英文和中文数据上分别取得了0.9% 和1.1%的性能改进。 最终得到的句法分析器的性能 优于相关研究工作中所报告的移进-归约句法分析器的性能。
Disruption of the Paternal Necdin Gene Diminishes TrkA Signaling for Sensory Neuron Survival

Necdin is a multifunctional signaling protein that stabilizes terminal differentiation of postmitotic neurons. The human necdin gene in chromosome 15q11-q12 is maternally imprinted, paternally transcribed, and not expressed in Prader-Willi syndrome, a human genomic imprinting-associated neurodevelopmental disorder. Although necdin-deficient mice display several abnormal phenotypes reminiscent of this syndrome, little is known about molecular mechanisms that lead to the neurodevelopmental defects. Here, we demonstrate that paternally expressed necdin is required for physiological development of nerve growth factor (NGF)-dependent sensory neurons. Mouse embryos defective in the paternal necdin allele displayed absent necdin expression in the dorsal root ganglia, in which the tropomyosin-related kinase A (TrkA) receptor tyrosine kinase and the p75 neurotrophin receptor were expressed in a normal manner. Necdin interacted with both TrkA and p75 to facilitate the association between these receptors. NGF-induced phosphorylation of TrkA and mitogen-activated protein kinase was significantly diminished in the necdin-null sensory ganglia. Furthermore, the mice lacking the paternal necdin allele displayed augmented apoptosis in the sensory ganglia in vivo and had a reduced population of substance P-containing neurons. These mutant mice showed significantly high tolerance to thermal pain, which is often seen in individuals with Prader-Willi syndrome. These results suggest that paternally expressed necdin facilitates TrkA signaling to promote the survival of NGF-dependent nociceptive neurons.