Miracle-dz/UniFAR-FTUs huggingface dataset:
Abnormal Auditory Experience Induces Frequency-Specific Adjustments in Unit Tuning for Binaural Localization Cues in the Optic Tectum of Juvenile Owls

Early auditory experience shapes the auditory spatial tuning of neurons in the barn owl's optic tectum in a frequency-dependent manner. We examined the basis for this adaptive plasticity in terms of changes in tuning for frequency-specific interaural time differences (ITDs) and level differences (ILDs), the dominant sound localization cues. We characterized broadband and narrowband ITD and ILD tuning in normal owls and in owls raised with an acoustic filtering device in one ear that caused frequency-dependent changes in sound timing and level. In normal owls, units were tuned to frequency-specific ITD and ILD values that matched those produced by sound sources located in their visual receptive fields. In contrast, in device-reared owls, ITD tuning at most sites was shifted from normal by ∼55 μsec toward open-ear leading for 4 kHz stimuli and 15 μsec toward the opposite-ear leading for 8 kHz stimuli, reflecting the acoustic effects of the device. ILD tuning was shifted in the adaptive direction by ∼3 dB for 4 kHz stimuli and 8 dB for 8 kHz stimuli, but these shifts were substantially smaller than expected based on the acoustic effects of the device. Most sites also exhibited conspicuously abnormal frequency–response functions, including a strong dependence on stimulus ITD and a reduction of normally robust responses to 6 kHz stimuli. The results demonstrate that the response properties of high-order auditory neurons in the optic tectum are adjusted during development to reflect the influence of frequency-specific features of the binaural localization cues experienced by the individual.
The EBNA3 Family of Epstein-Barr Virus Nuclear Proteins Associates with the USP46/USP12 Deubiquitination Complexes to Regulate Lymphoblastoid Cell Line Growth

The Epstein-Barr virus (EBV) nuclear proteins EBNA3A, EBNA3B, and EBNA3C interact with the cell DNA binding protein RBPJ and regulate cell and viral genes. Repression of the CDKN2A tumor suppressor gene products p16INK4A and p14ARF by EBNA3A and EBNA3C is critical for EBV mediated transformation of resting B lymphocytes into immortalized lymphoblastoid cell lines (LCLs). To define the composition of endogenous EBNA3 protein complexes, we generated lymphoblastoid cell lines (LCLs) expressing flag-HA tagged EBNA3A, EBNA3B, or EBNA3C and used tandem affinity purification to isolate each EBNA3 complex. Our results demonstrated that each EBNA3 protein forms a distinct complex with RBPJ. Mass-spectrometry revealed that the EBNA3A and EBNA3B complexes also contained the deubquitylation complex consisting of WDR48, WDR20, and USP46 (or its paralog USP12) and that EBNA3C complexes contained WDR48. Immunoprecipitation confirmed that EBNA3A, EBNA3B, and EBNA3C association with the USP46 complex. Using chromatin immunoprecipitation, we demonstrate that WDR48 and USP46 are recruited to the p14ARF promoter in an EBNA3C dependent manner. Mapping studies were consistent with WDR48 being the primary mediator of EBNA3 association with the DUB complex. By ChIP assay, WDR48 was recruited to the p14ARF promoter in an EBNA3C dependent manner. Importantly, WDR48 associated with EBNA3A and EBNA3C domains that are critical for LCL growth, suggesting a role for USP46/USP12 in EBV induced growth transformation.
The Burden of Diarrheal Diseases among Children under Five Years of Age in Arba Minch District, Southern Ethiopia, and Associated Risk Factors: A Cross-Sectional Study

Introduction. In Ethiopia diarrhea is the second cause for clinical presentation among under five-year child population next to pneumonia and it is also more common in rural than in urban areas. Methods. A community based cross-sectional study was conducted in Arba Minch District. Data were collected using structured questionnaire by trained data collectors. To identify predictors of diarrhea the negative binomial regression model was used to predict and control the effect of confounders. Results. The prevalence of diarrhea among under-five children was 30.5%. This study showed children whose mothers did not attend any formal education were 89% more likely to develop diarrhea (APR = 1.89, [95% CI: 1.35, 2.53]) compared to their counterparts. Similarly, children's being in age category 6-23 months (APR = 2.78 [95% CI: 1.72, 4.55]) and mothers' poor hand washing practice (APR = 2.33 [95% CI: 1.80, 4.15]) were found predictors of diarrhea. The study also showed that, out of 180 mothers whose child had got diarrhea, about 31% of mothers could not give anything to manage the diarrhea. Conclusions. In this study the prevalence of diarrhea was high which was significantly associated with maternal education level, age of the child, and personal hygiene practices. Therefore, women's education level of at least primary school and enhancing community based behavioral change communications using multiple channels (radio) and community health workers are recommended to reduce the occurrence and consequences of childhood diarrhea in the study area.
SAMER: Spectrum Aware Mesh Routing in Cognitive Radio Networks

Cognitive radio technology holds great promises in enabling unlicensed operation in licensed bands, to meet the increasing demand for radio spectrum. The new open spectrum operation necessitates novel routing protocols to exploit the available spectrum opportunistically. In this paper we present SAMER, a routing solution for cognitive radio mesh networks. SAMER opportunistically routes traffic across paths with higher spectrum availability and quality via a new routing metric. It balances between long-term route stability and short-term opportunistic performance. SAMER builds a runtime forwarding mesh that is updated periodically and offers a set of candidate routes to the destination. The actual forwarding path opportunistically adapts to the dynamic spectrum conditions and exploits the link with the highest spectrum availability at the time. We evaluate SAMER through simulations, and show that it effectively exploits the available network spectrum and results in higher end-to-end performance.
Integration of stress and leptin signaling by CART producing neurons in the rodent midbrain centrally projecting Edinger-Westphal nucleus

Leptin targets the brain to regulate feeding, neuroendocrine function and metabolism. The leptin receptor is present in hypothalamic centers controlling energy metabolism as well as in the centrally projecting Edinger–Westphal nucleus (EWcp), a region implicated in the stress response and in various aspects of stress-related behaviors. We hypothesized that the stress response by cocaine- and amphetamine-regulated transcript (CART)-producing EWcp-neurons would depend on the animal’s energy state. To test this hypothesis, we investigated the effects of changes in energy state (mimicked by low, normal and high leptin levels, which were achieved by 24 h fasting, normal chow and leptin injection, respectively) on the response of CART neurons in the EWcp of rats subjected or not to acute restraint stress. Our data show that leptin treatment alone significantly increases CART mRNA expression in the rat EWcp and that in leptin receptor deficient (db/db) mice, the number of CART producing neurons in this nucleus is reduced. This suggests that leptin has a stimulatory effect on the production of CART in the EWcp under non-stressed condition. Under stressed condition, however, leptin blunts stress-induced activation of EWcp neurons and decreases their CART mRNA expression. Interestingly, fasting, does not influence the stress-induced activation of EWcp-neurons, and specifically EWcp-CART neurons are not activated. These results suggest that the stress response by the EWcp depends to some degree on the animal’s energy state, a mechanism that may contribute to a better understanding of the complex interplay between obesity and stress.
Image-based dress up system

In this work, we present an image based virtual dress up system according to user input model and garment image. At 'Registration' step, we asked the user manually setting the skeleton structure and matte out the alphamap from the image. Next step, our method automatically deforms the garment image corresponding to model's body. For the boundary fitting, our method uniformly sampled contour points and solves the optimization function. To enhance the more realistic scene, we reconstruct the 2D mesh to the 3D mesh according to a human's standard body shape. For the lighting effect we estimate the light position by using luminance value with the detected face region. Previous 3D scanner based virtual dress up system has expensive cost and under locational limitation issues, but our system integrates various image processing techniques and introduced an easy-to-use system for the general users. We present that our system produces a visually plausible and well-fitted virtual dress up results in a practical and usable way.
Metamaterial-based electric and magnetic loop antennas with polarization diversity

In order to reduce correlation between multiple antennas and enhance spatial efficiency, novel polarization diversity antennas based on metamaterials are proposed by overlapping two antennas; an electric loop antenna and a magnetic loop antenna. The electrical loop antenna is realized by a resonant wire antenna, while the magnetic loop antenna is realized by an open-ended CRLH TL with a metamaterial concept. Since the current distributions of two antennas are orthogonal each other, each one independently operates with polarization diversity, which leads to minimize correlation. The proposed antennas can produce maximum spatial efficiency by overlapping two antenna elements. In order to place the magnetic loop antenna inside the electric loop antenna, the magnetic loop antenna's size needs to be much smaller than 0. 25λ×0. 25λ, and thus spiral slots on the ground plane is used to reduce the size of magnetic loop antenna.
Performance analysis of a planar inverted-F antenna (PIFA) including human interaction

In the rapid progress of commercial communication applications the development of small integrated antenna has an important role. Planar inverted-F antennas (PIFAs) are commonly used as handset antennas. This paper presents the analysis on the performance of single band PIFA antenna for handsets. Different specifications of the proposed antenna are measured through computer simulation in free space as well as in the presence of human head model. The Specific Absorption Rate (SAR) is also measured for this antenna and how the antenna interacts with human body that is also observed. All simulation results are performed using the CST Microwave Studio.
Steady state and convergence characteristics of the fixed point RLS algorithm

The steady-state mean square prediction error is derived for the fixed point recursive-least-squares (RLS) algorithm, both for the exponentially windowed RLS (forgetting factor, gamma <1) and the prewindowed growing memory RLS ( gamma =1) for correlate inputs. It is shown that signal correlation enhances the excess error due to additive noise and roundoff noise in the desired signal prediction computation. However, correlation has no effect on the noise due to roundoff of the weight error update recursion, which is the error term leading to the divergence of the algorithm for gamma =1. It is shown that the convergence rate of the algorithm depends on the filter order, on the choice of the forgetting factor, and on the eigenvalue spread of the data. Convergence is slower if the data are highly correlated, i.e., have a large eigenvalue spread. <<ETX>>
Warp sculpting

The task of computer-based free-form shape design is fraught with practical and conceptual difficulties. Incorporating elements of traditional clay sculpting has long been recognized as a means of shielding the user from these complexities. We present warp sculpting, a variant of spatial deformation, which allows deformations to be initiated by the rigid body transformation or uniform scaling of volumetric tools. This is reminiscent of a tool imprinting, flexing, and molding clay. Unlike previous approaches, the deformation is truly interactive. Tools, encoded in a distance field, can have arbitrarily complex shapes. Although individual tools have a static shape, several tools can be applied simultaneously. We enhance the basic formulation of warp sculpting in two ways. First, deformation is toggled to automatically overcome the problem of "sticky" tools, where the object's surface clings to parts of a tool that are moving away. Second, unlike many other spatial deformations, we ensure that warp sculpting remains foldover-free and, hence, prevent self-intersecting objects.
Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13

Significance Here we report a method to rapidly examine the effect of nearly all possible single amino acid substitutions within a substrate fragment of the coagulation protein von Willebrand factor (VWF) on the efficiency of cleavage by its cognate protease, ADAMTS13. A substrate phage display library was generated containing ∼3.5 × 107 independent clones and uncleaved phages collected at multiple reaction time points after reaction with ADAMTS13. Analysis of these phages by high-throughput sequencing facilitated simultaneous calculations of kcat/KM values for multiple substitutions at each position of this protein fragment, providing a comprehensive picture of the substrate recognition landscape for the interaction between ADAMTS13 and VWF. This approach should be broadly applicable to many other protease/substrate pairs. Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1′ substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF.
A partial coherent detector for orthogonal modulations in two-way relay communications with physical network coding and fading

We present in this paper a partial coherent receiver for detecting (at the relay) the modulo-2 sum bit of the uplink orthogonal modulations in a two-way relay communication system with physical network coding and fading. The detector exploits the availability of implicit pilot symbols in every signaling interval of an orthogonal modulation and is able to provide reasonably accurate data recovery without the need of sending pilot symbols. Using the characteristic function approach, we were able to derive a tight analytical upper bound on the bit-error-rate (BER) of the detector. The first component in the upper bound tells us that when the uplink symbols from the two users are identical, the BER approaches that of conventional point-to-point coherent detection, i.e. the multiple-access interference arising from physical network coding has no effect on the BER when the two data bits are identical. On the other hand, the second component in the upper bound shows that when the data from the two users are different, the BER increases dramatically. In essence, the BER of the proposed partial coherent detector is the average of those of the coherent and non-coherent detectors. We also outline in the paper a simple technique for achieving full coherent detection at the relay without resorting to transmitting any pilot symbols.
A random graph approach to NMR sequential assignment

Nuclear magnetic resonance (NMR) spectroscopy allows scientists to study protein structure, dynamics, and interactions in solution. A necessary first step for such applications is determining the resonance assignment, mapping spectral data to atoms and residues in the primary sequence. Automated resonance assignment algorithms rely on information regarding connectivity (e.g. through-bond atomic interactions) and amino acid type, typically using the former to determine strings of connected residues and the latter to map those strings to positions in the primary sequence. Significant ambiguity exists in both connectivity and amino acid type, and different algorithms have combined the information in two phases (find short unambiguous strings then align) or simultaneously (align while extending strings). This paper focuses on the information content available in connectivity alone, allowing for ambiguity rather than handling only unambiguous strings, and complements existing work on the information content in amino acid type.In this paper, we develop a novel random-graph theoretic framework for algorithmic analysis of NMR sequential assignment. Our random graph model captures the structure of chemical shift degeneracy (a key source of connectivity ambiguity). We then give a simple and natural randomized algorithm for finding an optimum sequential cover. The algorithm naturally and efficiently reuses substrings while exploring connectivity choices; it overcomes local ambiguity by enforcing global consistency of all choices. We employ our random graph model to analyze our algorithm, and show that it can provably tolerate a relatively large ambiguity while still giving expected optimal performance in polynomial time. To study the algorithm's performance in practice, we tested it on experimental data sets from a variety of proteins and experimental set-ups. The algorithm was able to overcome significant noise and local ambiguity and consistently identify significant sequential fragments.
SWISS-MODEL: an automated protein homology-modeling server

SWISS-MODEL (http://swissmodel.expasy.org) is a server for automated comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated modeling starting in 1993 and is the most widely-used free web-based automated modeling facility today. In 2002 the server computed 120 000 user requests for 3D protein models. SWISS-MODEL provides several levels of user interaction through its World Wide Web interface: in the 'first approach mode' only an amino acid sequence of a protein is submitted to build a 3D model. Template selection, alignment and model building are done completely automated by the server. In the 'alignment mode', the modeling process is based on a user-defined target-template alignment. Complex modeling tasks can be handled with the 'project mode' using DeepView (Swiss-PdbViewer), an integrated sequence-to-structure workbench. All models are sent back via email with a detailed modeling report. WhatCheck analyses and ANOLEA evaluations are provided optionally. The reliability of SWISS-MODEL is continuously evaluated in the EVA-CM project. The SWISS-MODEL server is under constant development to improve the successful implementation of expert knowledge into an easy-to-use server.
Rateless Coding for Gaussian Channels

A rateless code-i.e., a rate-compatible family of codes-has the property that codewords of the higher rate codes are prefixes of those of the lower rate ones. A perfect family of such codes is one in which each of the codes in the family is capacity-achieving. We show by construction that perfect rateless codes with low-complexity decoding algorithms exist for additive white Gaussian noise channels. Our construction involves the use of layered encoding and successive decoding, together with repetition using time-varying layer weights. As an illustration of our framework, we design a practical three-rate code family. We further construct rich sets of near-perfect rateless codes within our architecture that require either significantly fewer layers or lower complexity than their perfect counterparts. Variations of the basic construction are also developed, including one for time-varying channels in which there is no a priori stochastic model.
SIG1, a Sigma Factor for the Chloroplast RNA Polymerase, Differently Associates with Multiple DNA Regions in the Chloroplast Chromosomes in Vivo

Chloroplasts have their own DNA and gene expression systems. Transcription in chloroplasts is regulated by two types of RNA polymerase, nuclear-encoded plastid RNA polymerase (NEP) and plastid-encoded plastid RNA polymerase (PEP), and multiple sigma factors for PEP. To study transcriptional regulation in chloroplasts, a molecular genetic approach has extensively been used. However, this method may include indirect effects, and it cannot be applied to the analysis of factors essential to survival. These limitations make understanding specific regulation by transcription factors difficult. Chromatin immunoprecipitation (ChIP) is a powerful and useful tool for obtaining information on transcription-factor binding sites; it can directly detect dynamic changes in their interaction patterns in vivo. To further understand transcriptional regulation in chloroplasts, we here established a ChIP-based method in Arabidopsis thaliana and analyzed the binding pattern of a chloroplast sigma factor, SIG1. We found that SIG1 specifically binds to newly identified target promoters as well as to a set of promoters of genes whose mRNA expression is dependent on OsSIG1 in rice and that this binding changed in response to high-light stress. These results suggested that the ChIP-based approach is very useful in understanding transcriptional regulation of chloroplast genes and can overcome several problems posed by conventional methods.
Informing Eclipse API production and consumption

Application programming interfaces (APIs) inform application developers as to the functionality provided by a library and how to interact with it. APIs are a double-edged sword: if they do not permit the needed functionality to be accessed and adapted as needed, they are obstructing; if they permit all things to all people, they are complex, leading application developers to have difficulty understanding how to use them correctly. Thus, the developers of APIs have a delicate balance to strike between providing configurable functionality and simple interfaces. Inevitably, the wrong balance is sometimes chosen, as the actual usage is different from the expected usage; APIs need to evolve, or to be re-documented to account for this disparity. In this paper we propose a simple technique for quantitatively determining how existing APIs are used, and demonstrate its application to Eclipse. This technique would enable application developers to more easily understand how others have used the APIs and would allow API developers to more easily understand how their APIs are being used.