Miracle-dz/UniFAR-FTUs huggingface dataset:
Arabidopsis VILLIN1 and VILLIN3 Have Overlapping and Distinct Activities in Actin Bundle Formation and Turnover[W]

Villins are a class of actin-binding protein with multiple activities. This study uses single filament imaging techniques to evaluate and contrast the functions of Arabidopsis VILLIN1 (VLN1) and VLN3. Both isovariants are shown to bundle actin filaments, whereas VLN3 also severs filaments and can disassemble actin filament bundles in the presence of physiological calcium concentrations. Actin filament bundles are higher-order cytoskeletal structures that are crucial for the maintenance of cellular architecture and cell expansion. They are generated from individual actin filaments by the actions of bundling proteins like fimbrins, LIMs, and villins. However, the molecular mechanisms of dynamic bundle formation and turnover are largely unknown. Villins belong to the villin/gelsolin/fragmin superfamily and comprise at least five isovariants in Arabidopsis thaliana. Different combinations of villin isovariants are coexpressed in various tissues and cells. It is not clear whether these isovariants function together and act redundantly or whether they have unique activities. VILLIN1 (VLN1) is a simple filament-bundling protein and is Ca2+ insensitive. Based on phylogenetic analyses and conservation of Ca2+ binding sites, we predict that VLN3 is a Ca2+-regulated villin capable of severing actin filaments and contributing to bundle turnover. The bundling activity of both isovariants was observed directly with time-lapse imaging and total internal reflection fluorescence (TIRF) microscopy in vitro, and the mechanism mimics the “catch and zipper” action observed in vivo. Using time-lapse TIRF microscopy, we observed and quantified the severing of individual actin filaments by VLN3 at physiological calcium concentrations. Moreover, VLN3 can sever actin filament bundles in the presence of VLN1 when calcium is elevated to micromolar levels. Collectively, these results demonstrate that two villin isovariants have overlapping and distinct activities.
Efficient and compact coupling to slow light structures

In this study, we present several coupling structures designed for two different slow light photonic crystal waveguides (PCW). These slow light structures provide group indices of approximately 1200 and 950. For the first waveguide, very high coupling efficiency of 97% is declared from/to conventional waveguide to/from slow light PCW. The improvement lies on the optimization of the tapered input/output transition sections. Another novel coupling scheme for the second waveguide is proposed.
On the impact of hardware impairments on massive MIMO

Massive multi-user (MU) multiple-input multiple-output (MIMO) systems are one possible key technology for next generation wireless communication systems. Claims have been made that massive MU-MIMO will increase both the radiated energy efficiency as well as the sum-rate capacity by orders of magnitude, because of the high transmit directivity. However, due to the very large number of transceivers needed at each base-station (BS), a successful implementation of massive MU-MIMO will be contingent on of the availability of very cheap, compact and power-efficient radio and digital-processing hardware. This may in turn impair the quality of the modulated radio frequency (RF) signal due to an increased amount of power-amplifier distortion, phase-noise, and quantization noise. In this paper, we examine the effects of hardware impairments on a massive MU-MIMO single-cell system by means of theory and simulation. The simulations are performed using simplified, well-established statistical hardware impairment models as well as more sophisticated and realistic models based upon measurements and electromagnetic antenna array simulations.
Molecular and structural analysis of genetic variations in congenital cataract

Objective To determine the relative contributions of mutations in congenital cataract cases in an Indian population by systematic screening of genes associated with cataract. Methods We enrolled 100 congenital cataract cases presenting at the Dr. R. P. Centre for Ophthalmic Sciences, a tertiary research and referral hospital (AIIMS, New Delhi, India). Crystallin, alpha A (CRYAA), CRYAB, CRYGs, CRYBA1, CRYBA4, CRYBB1, CRYBB2, CRYBB3, beaded filament structural protein 1 (BFSP1), gap function protein, alpha 3 (GJA3), GJA8, and heat shock transcription factor 4 gene genes were amplified. Protein structure differences analysis was performed using Discovery Studio (DS) 2.0. Results The mean age of the patients was 17.45±16.51 months, and the age of onset was 1.618±0.7181 months. Sequencing analysis of 14 genes identified 18 nucleotide variations. Fourteen variations were found in the crystallin genes, one in Cx-46 (GJA3), and three in BFSP1. Conclusions Congenital cataract shows marked clinical and genetic heterogeneity. Five nucleotide variations (CRYBA4:p.Y67N, CRYBB1:p.D85N, CRYBB1:p.E75K, CRYBB1:p.E155K, and GJA3:p.M1V) were predicted to be pathogenic. Variants in other genes might also be involved in maintaining lens development, growth, and transparency. The study confirms that the crystallin beta cluster on chromosome 22, Cx-46, and BFSP1 plays a major role in maintaining lens transparency. This study also expands the mutation spectrum of the genes associated with congenital cataract.
The People’s Web meets Linguistic Knowledge: Automatic Sense Alignment of Wikipedia and WordNet

We propose a method to automatically align WordNet synsets and Wikipedia articles to obtain a sense inventory of higher coverage and quality. For each WordNet synset, we first extract a set of Wikipedia articles as alignment candidates; in a second step, we determine which article (if any) is a valid alignment, i.e. is about the same sense or concept. In this paper, we go significantly beyond state-of-the-art word overlap approaches, and apply a threshold-based Personalized PageRank method for the disambiguation step. We show that WordNet synsets can be aligned to Wikipedia articles with a performance of up to 0.78 F1-Measure based on a comprehensive, well-balanced reference dataset consisting of 1,815 manually annotated sense alignment candidates. The fully-aligned resource as well as the reference dataset is publicly available.
Approximation and Compression With Sparse Orthonormal Transforms

We propose a new transform design method that targets the generation of compression-optimized transforms for next-generation multimedia applications. The fundamental idea behind transform compression is to exploit regularity within signals such that redundancy is minimized subject to a fidelity cost. Multimedia signals, in particular images and video, are well known to contain a diverse set of localized structures, leading to many different types of regularity and to nonstationary signal statistics. The proposed method designs sparse orthonormal transforms (SOTs) that automatically exploit regularity over different signal structures and provides an adaptation method that determines the best representation over localized regions. Unlike earlier work that is motivated by linear approximation constructs and model-based designs that are limited to specific types of signal regularity, our work uses general nonlinear approximation ideas and a data-driven setup to significantly broaden its reach. We show that our SOT designs provide a safe and principled extension of the Karhunen-Loeve transform (KLT) by reducing to the KLT on Gaussian processes and by automatically exploiting non-Gaussian statistics to significantly improve over the KLT on more general processes. We provide an algebraic optimization framework that generates optimized designs for any desired transform structure (multiresolution, block, lapped, and so on) with significantly better n-term approximation performance. For each structure, we propose a new prototype codec and test over a database of images. Simulation results show consistent increase in compression and approximation performance compared with conventional methods.
Partitioning Sparse Matrices for Parallel Preconditioned Iterative Methods

This paper addresses the parallelization of the preconditioned iterative methods that use explicit preconditioners such as approximate inverses. Parallelizing a full step of these methods requires the coefficient and preconditioner matrices to be well partitioned. We first show that different methods impose different partitioning requirements for the matrices. Then we develop hypergraph models to meet those requirements. In particular, we develop models that enable us to obtain partitionings on the coefficient and preconditioner matrices simultaneously. Experiments on a set of unsymmetric sparse matrices show that the proposed models yield effective partitioning results. A parallel implementation of the right preconditioned BiCGStab method on a PC cluster verifies that the theoretical gains obtained by the models hold in practice.
List Viterbi decoding algorithms with applications

A list Viterbi decoding algorithm (LVA) produces a rank ordered list of the L globally best candidates after a trellis search. The authors present two such algorithms, (i) a parallel LVA that simultaneously produces the L best candidates and (ii) a serial LVA that iteratively produces the k/sup th/ best candidate based on knowledge of the previously found k-1 best paths. The application of LVA to a concatenated communication system consisting of an inner convolutional code and an outer error detecting code is considered in detail. Analysis as well as simulation results show that significant improvement in error performance is obtained when the inner decoder, which is conventionally based on the Viterbi algorithm (VA), is replaced by the LVA. An improvement of up to 3 dB is obtained for the additive white Gaussian noise (AWGN) channel due to an increase in the minimum Euclidean distance. Ever larger gains are obtained for the Rayleigh fading channel due to an increase in the time diversity. It is also shown that a 10% improvement in throughput is obtained along with significantly reduced probability of a decoding failure for a hybrid FEC/ARQ scheme with the inner code being a rate compatible punctured convolutional (RCPC) code. >
Cultural influence of social information use in pedestrian road-crossing behaviours

Social information use is common in a wide range of group-living animals, notably in humans. The role it plays in decision-making could be a key to understanding how social groups make collective decisions. The observation of road-crossing behaviours in the presence of other individuals is an ideal means to study the influence of social information on decision-making. This study investigated the influence of culture on social information used by pedestrians in a potentially dangerous scenario, namely road crossing. We scored the collective crossing of pedestrians at four locations in Nagoya (Japan) and three locations in Strasbourg (France). French pedestrians cross against the lights much more often (41.9%) than Japanese ones (2.1%). Individuals deciding to cross the road were strongly influenced by the behaviour and the presence of other pedestrians, especially in Japan, where a stronger conformism was noted. However, Japanese pedestrians were half as likely to be influenced by social information as their French counterparts when crossing at the red light, as they were more respectful of rules. Men show riskier behaviour than women (40.6% versus 25.7% of rule-breaking, respectively), deciding quickly and setting off earlier than women. Further related studies could help target specific preventive, culture-specific solutions for pedestrian safety.
A Delay-Flexible Stereo Acoustic Echo Cancellation for DFT-Based In-Car Communication (ICC) Systems

In-car communication (ICC) systems supporting speech communication in noise by reproducing amplified speech from the car cabin in the car cabin ask for low-delay acoustic echo cancellation (AEC). In this paper we propose a delay-flexible DFTbased stereo AEC capable of cancelling also the echoes stemming from the audio player or FM radio. For the price of a somewhat higher complexity we are able to reduce the 32 ms delay of the baseline down to 4 ms, loosing only 1 dB in ERLE while even preserving system distance properties.
Phenotypic Analysis of a Family of Transcriptional Regulators, the Zinc Cluster Proteins, in the Human Fungal Pathogen Candida glabrata

Candida glabrata is the second most important human fungal pathogen. Despite its formal name, C. glabrata is in fact more closely related to the nonpathogenic budding yeast Saccharomyces cerevisiae. However, less is known about the biology of this pathogen. Zinc cluster proteins form a large family of transcriptional regulators involved in the regulation of numerous processes such as the control of the metabolism of sugars, amino acids, fatty acids, as well as drug resistance. The C. glabrata genome encodes 41 known or putative zinc cluster proteins, and the majority of them are uncharacterized. We have generated a panel of strains carrying individual deletions of zinc cluster genes. Using a novel approach relying on tetracycline for conditional expression in C. glabrata at the translational level, we show that only two zinc cluster genes are essential. We have performed phenotypic analysis of nonessential zinc cluster genes. Our results show that two deletion strains are thermosensitive whereas two strains are sensitive to caffeine, an inhibitor of the target of rapamycin pathway. Increased salt tolerance has been observed for eight deletion strains, whereas one strain showed reduced tolerance to salt. We have also identified a number of strains with increased susceptibility to the antifungal drugs fluconazole and ketoconazole. Interestingly, one deletion strain showed decreased susceptibility to the antifungal micafungin. In summary, we have assigned phenotypes to more than half of the zinc cluster genes in C. glabrata. Our study provides a resource that will be useful to better understand the biological role of these transcription factors.
Resistant image watermarking in the phases of the Complex Hadamard Transform coefficients

In the paper a new method is presented for digital content protection based on watermark data insertion in the image transform domain. For this, the still digital image is transformed using Complex Hadamard Transform (CHT), and the watermark data is then inserted in the imaginary part of the transform coefficients. The selection of the suitable for watermarking transform coefficients is done in accordance with pre-defined rules. The so inserted watermark is perceptually invisible. The method permits the insertion of relatively large amount of data, retaining the high quality of the protected image. The main advantages of the algorithm for digital watermarking, based on the CHT are that it is resistant against attacks, based on high-frequency filtration (JPEG compression); it permits the insertion of significant amount of data, and the watermark detection could be done without using the original image.
Angular Motion Estimation Using Dynamic Models in a Gyro-Free Inertial Measurement Unit

In this paper, we summarize the results of using dynamic models borrowed from tracking theory in describing the time evolution of the state vector to have an estimate of the angular motion in a gyro-free inertial measurement unit (GF-IMU). The GF-IMU is a special type inertial measurement unit (IMU) that uses only a set of accelerometers in inferring the angular motion. Using distributed accelerometers, we get an angular information vector (AIV) composed of angular acceleration and quadratic angular velocity terms. We use a Kalman filter approach to estimate the angular velocity vector since it is not expressed explicitly within the AIV. The bias parameters inherent in the accelerometers measurements' produce a biased AIV and hence the AIV bias parameters are estimated within an augmented state vector. Using dynamic models, the appended bias parameters of the AIV become observable and hence we can have unbiased angular motion estimate. Moreover, a good model is required to extract the maximum amount of information from the observation. Observability analysis is done to determine the conditions for having an observable state space model. For higher grades of accelerometers and under relatively higher sampling frequency, the error of accelerometer measurements is dominated by the noise error. Consequently, simulations are conducted on two models, one has bias parameters appended in the state space model and the other is a reduced model without bias parameters.
TIDE: A User-centric Tool for Identifying Energy Hungry Applications on Smartphones

Today, many smartphone users are unaware of what applications (apps) they should stop using to prevent their battery from running out quickly. The problem is identifying such apps is hard due to the fact that there exist hundreds of thousands of apps and their impact on the battery is not well understood. We show via extensive measurement studies that the impact of an app on battery consumption depends on both environmental (wireless) factors and usage patterns. Based on this, we argue that there exists a critical need for a tool that allows a user to (a) identify apps that are energy hungry, and (b) understand why an app is consuming energy, on her phone. Towards addressing this need, we present TIDE, a tool to detect high energy apps on any particular smartphone. TIDE's key characteristic is that it accounts for usage-centric information while identifying energy hungry apps from among a multitude of apps that run simultaneously on a user's phone. Our evaluation of TIDE on a testbed of Android-based smartphones, using weeklong smartphone usage traces from 17 real users, shows that TIDE correctly identifies over 94% of energy-hungry apps and has a false positive rate of <; 6%.
Protein-Protein Interaction of Zinc Finger LIM Domains with Protein Kinase C*

The LIM domain comprising two zinc-finger motifs is found in a variety of proteins and has been proposed to direct protein-protein interactions. During the identification of protein kinase C (PKC)-interacting proteins by a yeast two-hybrid assay, a novel protein containing three LIM domains, designated ENH, was shown to associate with PKC in an isoform-specific manner. Deletion analysis demonstrated that any single LIM domain of ENH associates with the NH2-terminal region of PKC. ENH associated with PKC in COS-7 cells and was phosphorylated by PKC in vitro. Upon treatment of the cells with phorbol ester, ENH in the membrane fraction was translocated to the cytosol fraction in vivo. Other LIM domain-containing proteins, such as Enigma and LIM-kinase 1, also interacted with PKC through their LIM domains. These results suggest that the LIM domain is one of the targets of PKC and that the LIM-PKC interaction may shed light on undefined roles of LIM domain-containing proteins.
When Emotion Intensifies Memory Interference

Many of our most vivid memories are of emotional events; in research studies, emotional events or items are often more likely to be remembered than neutral events or items. However, as pointed out in this chapter, the same characteristics that make emotional information memorable can also make it more subject to interference effects in memory. Thus: (1) being reminded of some emotional memories interferes with other memories evoking the same emotion; (2) it is more difficult to update one’s memory of the context of emotional items than of neutral items; (3) it is harder to learn a new association to something that was previously associated with an emotional item; and (4) frequent reexposure to a cue to a negative memory increases forgetting of that negative
Glamour : A Wide-Area Filesystem Middleware Using NFSv 4

In this paper we describe the design and implementation of Glamour, a federated filesystem layer that enables clients to seamlessly navigate data that is spread across multiple heterogeneous widely distributed file servers. Glamour is not a globally distributed filesystem. Instead, it enables a set of loosely coupled file servers to behave as one. It provides the common enterprise-wide namespace and data management operations as a wide-area distributed filesystem would, while relying completely on standard off-the-shelf clients, filesystems and client-server protocols. Glamour provides data management with flexible granularity and supports transparent replication and data migration. Using our testbed, we demonstrate the various features of Glamour and report on overheads.
Localized modes in nonlinear binary kagome ribbons.

The localized mode propagation in binary nonlinear kagome ribbons is investigated with the premise to ensure controlled light propagation through photonic lattice media. Particularity of the linear system characterized by the dispersionless flat band in the spectrum is the opening of new minigaps due to the "binarism. " Together with the presence of nonlinearity, this determines the guiding mode types and properties. Nonlinearity destabilizes the staggered rings found to be nondiffracting in the linear system, but can give rise to dynamically stable ringlike solutions of several types: unstaggered rings, low-power staggered rings, hour-glass-like solutions, and vortex rings with high power. The type of solutions, i.e., the energy and angular momentum circulation through the nonlinear lattice, can be controlled by suitable initial excitation of the ribbon. In addition, by controlling the system "binarism" various localized modes can be generated and guided through the system, owing to the opening of the minigaps in the spectrum. All these findings offer diverse technical possibilities, especially with respect to the high-speed optical communications and high-power lasers.
Synergistic genetic defect in B-lymphocyte function. I. Defective responses to B-cell stimulants and their genetic basis

CBA/N female mice, which express an X-linked defect in B-lymphocyte function, were mated with C3H/HeJ male mice, which are unresponsive to lipopolysaccharide (LPS). The resulting F1 hybrid females were mated to C3H/HeJ males. Approximately one-half of the backcross (BC.1) males obtained from this mating expressed a more profound immunologic defect than either of the parental strains. Spleen cells from these mice were unresponsive to a series of B-cell mitogens including LPS prepared from Escherichia coli K235 and from E. coli 0111:B4, lipoprotein mitogen from E. coli, and Nocardia water-soluble mitogen (NWSM). They failed to give in vitro antibody responses to the thymus-independent type 2 (TI- 2) antigen trinophenylated Ficoll and most were unresponsive to the TI- 1 antigens trinitrophenylated Brucella abortus, trinitrophenylated LPS, and trinitrophenylated NWSM. This synergistic defect in B-lymphocyte function depended on the presence of the CBA/N xid gene but the critical gene(s) from the C3H strain was not the defective Lps gene (Lpsd). These mice should provide a valuable tool for the elucidation of B-lymphocyte ontogeny, heterogeneity, and function.