Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple connexins contribute to intercellular communication in the Xenopus embryo

To explore the role of gap junctional intercellular communication (GJIC) during Xenopus embryogenesis, we utilized the host-transfer and antisense techniques to specifically deplete Cx38, the only known maternally expressed connexin. Cx38-depleted embryos developed normally but displayed robust GJIC between blastomeres at 32-128 cell stages, suggesting the existence of other maternal connexins. Analysis of embryonic cDNA revealed maternal expression of two novel connexins, Cx31 and Cx43.4, and a third, Cx43, that had been previously identified as a product of zygotic transcription. Thus, the early Xenopus embryo contains at least four maternal connexins. Unlike Cx38, expression of Cx31, Cx43 and Cx43.4 continue zygotically. Of these, Cx43.4 is the most abundant, accumulating significantly in neural structures including the brain, the eyes and the spinal cord.
URC based accessible TV

This paper presents a new architecture to make TV sets accessible for all. Our proposal is based on the ISO/IEC 24752 Universal Remote Console Framework standard. This standard defines an abstract user interface layer called the "user interface socket" and allows the development of pluggable user interfaces for any type of user. Since this architecture is standards based, the development of compatible pluggable interfaces is open to any third party. Besides, a prototype of the proposed architecture has been built. In this prototype, the Universal Control Hub (UCH) has been used as the URC framework implementation, a PC with Windows Vista Media Center has been used as a TV Set-top box, and two pluggable UIs have been developed. These UIs consist of an accessible DHTML page for the visually impaired, and a multimodal client, which allows interaction via touch screen and speech. Finally, these two pluggable UIs have been validated with user groups with special needs and preliminary results show encouraging results.
The Max b-HLH-LZ Can Transduce into Cells and Inhibit c-Myc Transcriptional Activities

The inhibition of the functions of c-Myc (endogenous and oncogenic) was recently shown to provide a spectacular therapeutic index in cancer mouse models, with complete tumor regression and minimal side-effects in normal tissues. This was achieved by the systemic and conditional expression of omomyc, the cDNA of a designed mutant of the b-HLH-LZ of c-Myc named Omomyc. The overall mode of action of Omomyc consists in the sequestration of Max and the concomitant competition of the Omomyc/Max complex with the endogenous c-Myc/Max heterodimer. This leads to the inhibition of the transactivation of Myc target genes involved in proliferation and metabolism. While this body of work has provided extraordinary insights to guide the future development of new cancer therapies that target c-Myc, Omomyc itself is not a therapeutic agent. In this context, we sought to exploit the use of a b-HLH-LZ to inhibit c-Myc in a cancer cell line in a more direct fashion. We demonstrate that the b-HLH-LZ domain of Max (Max*) behaves as a bona fide protein transduction domain (PTD) that can efficiently transduce across cellular membrane via through endocytosis and translocate to the nucleus. In addition, we show that the treatment of HeLa cells with Max* leads to a reduction of metabolism and proliferation rate. Accordingly, we observe a decrease of the population of HeLa cells in S phase, an accumulation in G1/G0 and the induction of apoptosis. In agreement with these phenotypic changes, we show by q-RT-PCR that the treatment of HeLa cells with Max* leads to the activation of the transcription c-Myc repressed genes as well as the repression of the expression of c-Myc activated genes. In addition to the novel discovery that the Max b-HLH-LZ is a PTD, our findings open up new avenues and strategies for the direct inhibition of c-Myc with b-HLH-LZ analogs.
Looking heteronormatively good! Combining story completion with Bitstrips to explore understandings of sexuality and appearance

ABSTRACT This study sought to develop knowledge about understandings of sexuality and appearance by using a story completion task combined with an innovative visual methodology. Fifty-four (mainly female) participants were randomly assigned to complete a story about a fictional bisexual, lesbian, or heterosexual character who is going on a date, and then asked to build a Bitstrips online avatar of their character. Our social constructionist thematic analysis identified that looking good was a common feature of the stories and that this was understood in largely heteronormative terms. This imperative was also clear in stories of the date, which relied on traditional notions of gender and heterosexuality. Finally, individuality and authenticity were rewarded in participants’ stories, yet this was simultaneously constrained by (dominant) heteronormative narratives. We conclude that combining story completion with visual methods enabled deeper insights into representations of appearance, dating, and relationships, than a textual method alone.
Association of Linear Plasmid 28-1 with an Arthritic Phenotype of Borrelia burgdorferi

ABSTRACT Borrelia burgdorferi, the Lyme disease spirochete, has a genome comprised of a linear chromosome and up to 21 plasmids. Loss of plasmids is associated with decreased infectivity and pathogenicity. Sixteen transformants were generated by transforming the noninfectious clone 5A13 with the recombinant plasmid pBBE22. The transformants were classified into nine groups based on plasmid content analysis. An infectivity study revealed that all nine transformants examined, each of which represented one of the plasmid patterns, were infectious in mice with severe combined immunodeficiency (SCID) regardless of their genomic compositions. Tissue bacterial quantification revealed that the loss of plasmids significantly reduced the spirochete burden in the heart and joint tissues, not in the skin, suggesting virulence factors may be tissue specific. Four transformants containing lp28-1 induced severe arthritis in SCID mice, in contrast to the five transformants lacking lp28-1. These pathogenicity studies associated lp28-1 with an arthritic phenotype and further studies may identify factors that contribute to arthritic pathology.
MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis

SUMMARY MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way. It allows users to interpret and examine metabolic behavior in response to genetic and/or environmental modifications. As a result, quantitative in silico simulations of metabolic pathways can be carried out to understand the metabolic status and to design the metabolic engineering strategies. The main features of the program include a well-developed model construction environment, user-friendly interface for metabolic flux analysis (MFA), comparative MFA of strains having different genotypes under various environmental conditions, and automated pathway layout creation. AVAILABILITY http://mbel.kaist. ac.kr/ SUPPLEMENTARY INFORMATION A manual for MetaFluxNet is available as PDF file.
A Novel Model for Security Requirements Process

Nowadays, mostly security solutions are mainly focused on how to defend against various threats, including insider threats and outsider threats, instead of trying to solve security issues from their sources. In this paper, a security requirements engineering process is presented for security requirements elicitation and analysis. And the proposed process will deal with the security requirements at the earlier stages of system design in a systematic way. Thus critical security risks to the business will be considered in the development of the security requirements.
The Contributions of Image Content and Behavioral Relevancy to Overt Attention

During free-viewing of natural scenes, eye movements are guided by bottom-up factors inherent to the stimulus, as well as top-down factors inherent to the observer. The question of how these two different sources of information interact and contribute to fixation behavior has recently received a lot of attention. Here, a battery of 15 visual stimulus features was used to quantify the contribution of stimulus properties during free-viewing of 4 different categories of images (Natural, Urban, Fractal and Pink Noise). Behaviorally relevant information was estimated in the form of topographical interestingness maps by asking an independent set of subjects to click at image regions that they subjectively found most interesting. Using a Bayesian scheme, we computed saliency functions that described the probability of a given feature to be fixated. In the case of stimulus features, the precise shape of the saliency functions was strongly dependent upon image category and overall the saliency associated with these features was generally weak. When testing multiple features jointly, a linear additive integration model of individual saliencies performed satisfactorily. We found that the saliency associated with interesting locations was much higher than any low-level image feature and any pair-wise combination thereof. Furthermore, the low-level image features were found to be maximally salient at those locations that had already high interestingness ratings. Temporal analysis showed that regions with high interestingness ratings were fixated as early as the third fixation following stimulus onset. Paralleling these findings, fixation durations were found to be dependent mainly on interestingness ratings and to a lesser extent on the low-level image features. Our results suggest that both low- and high-level sources of information play a significant role during exploration of complex scenes with behaviorally relevant information being more effective compared to stimulus features.
Nitrate Contamination of Groundwater in Austria : D t i t d I di te erm nan s an n ca ors

Nitrogen is an important input to agricultural production but also detrimentally a ects the environmental quality of air, soil and water. Identifying the determinants of nitrate pollution and in turn de ning sensible performance indicators to design, enforce and monitor regulatory policies is therefore of utmost importance. Using data on more than 1000 Austrian municipalities, we provide a detailed econometric analysis of (1) the determinants of nitrate concentration in groundwater, and (2) the predictive abilities of one of the most commonly used agri-environmental indicators, the Nitrogen Balance. We nd that the proportion of cropland exerts a positive e ect on the nitrate content in groundwater. Additionally, environmental factors such as temperature and precipitation are found to be important. Higher average temperature leads to lower nitrate pollution of groundwater possibly due to increased evapotranspiration. Equally, higher average precipitation dilutes nitrate content in the soil, reducing nitrate concentration in groundwater. To assess the Nitrogen Balance, we link observed pollution levels to the theoretical indicator and evaluate its ability to measure nitrate pollution e ects. Indeed, the indicator proves to be a good predictor for nitrate pollution. We also show that its predictive power can be improved if average precipitation of a region is taken into account. If average precipitation is higher, the Nitrogen Balance predicts nitrate levels in groundwater more precisely.
Tunnel Effect in CNNs: Image Reconstruction From Max Switch Locations

In this letter, we show that reconstruction of an image passed through a neural network is possible, using only the locations of the max pool activations. This was demonstrated with an architecture consisting of an encoder and a decoder. The decoder is a mirrored version of the encoder, where convolutions are replaced with deconvolutions and poolings are replaced with unpooling layers. The locations of the max pool switches are transmitted to the corresponding unpooling layer. The reconstruction is computed only from these switches without the use of feature values. Using only the max switch location information of the pool layers, a surprisingly good image reconstruction can be achieved. We examine this effect in various architectures, as well as how the quality of the reconstruction is affected by the number of features. We also compare the reconstruction with an encoder with randomly initialized weights with an encoder pretrained for classification. Finally, we give recommendations for future architecture decisions.
Adaptive interval type-2 fuzzy control based on gradient descent algorithm

Fuzzy rule base and fuzzy variables are two crucial factors which decide the fuzzy controller performance. This paper presents the gradient descent learning algorithm to adaptively optimize free parameters of the interval type-2 fuzzy controller, which can overcome the divergence of another global optimization algorithms, such as GA, PSO and ACO, when they are employed to optimize the free parameters. A few numerical experiments are performed to evaluate our proposing approach. The experiment results verify the effectiveness.
Level-set segmentation with contour based object representation

In this paper we present an approach for contour based object representation. To this end we use a curvature signal gained by a level-set segmentation method. The advantage of that curvature signal is that it generates no computational overhead as it is a byproduct of standard level-set segmentation methods. Different methods for the description of the segmented objects, so called object descriptors are presented. The object descriptors are all invariant against translation, rotation and scale of the object. Furthermore we show a sparse and memory efficient representation of the descriptors for a series of objects. Finally an approach for classification of unknown objects based on “memorized” objects is proposed.
Performance analysis of Snort-based Intrusion Detection System

The most important purpose of intrusion detection system is to identify attacks against information systems. It is a security method attempting to identify various attacks. Snort is mostly used signature based IDS because it is an open source software. It is used world widely in intrusion detection and prevention domain. In this paper, we used IDEVAL data set we detect attacks using Snort on this dataset.
Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes

The last 20 years of advancement in DNA sequencing technologies have led to the sequencing of thousands of microbial genomes, creating mountains of genetic data. While our efficiency in generating the data improves almost daily, applying meaningful relationships between the taxonomic and genetic entities requires a new approach. Currently, the knowledge is distributed across a fragmented landscape of resources from government-funded institutions such as NCBI and Uniprot to topic-focused databases like the ODB3 database of prokaryotic operons, to the supplemental table of a primary publication. A major drawback to large scale, expert curated databases is the expense of maintaining and extending them over time. No entity apart from a major institution with stable long-term funding can consider this, and their scope is limited considering the magnitude of microbial data being generated daily. Wikidata is an, openly editable, semantic web compatible framework for knowledge representation. It’s a project of the Wikimedia Foundation and offers knowledge integration capabilities ideally suited to the challenge of representing the exploding body of information about microbial genomics. We are developing a microbial specific data model, based on Wikidata’s semantic web compatibility, that represents bacterial species, strains and the gene and gene products that define them. Currently, we have loaded 1736 gene items and 1741 protein items for two strains of the human pathogenic bacteria Chlamydia trachomatis and used this subset of data as an example of the empowering utility of this model. In our next phase of development we will expand by adding another 118 bacterial genomes and their gene and gene products, totaling over ~900,000 additional entities. This aggregation of knowledge will be a platform for community-driven collaboration, allowing the networking of microbial genetic data through the sharing of knowledge by both the data and domain expert.
Knowledge Management and Knowledge Agents in Campiello

The area of ‚Knowledge Management‘ is closely related to CSCW as it involves collaboration in various ways. In this paper we outline our ideas for using collaborative filtering as one element of a knowledge management service in the project Campiello. We also detail what different types of agents we envision for the knowledge management and collaboration service in Campiello and briefly present the current status of the Knowledge Agents Platform which we build for supporting the development and the operation of this agent set.
On the motion of rotating bodies in field gravity theory and general relativity

On the basis of Lagrangian formalism of relativistic field theory post-Newtonian equations of motion for a rotating body are derived in the frame of Feynman's quantum field gravity theory (FGT) and compared with corresponding geodesic equations in general relativity (GR). It is shown that in FGT the trajectory of a rotating test body does not depend on a choice of a coordinate system. The equation of translational motion of a gyroscope is applied to description of laboratory experiments with free falling rotating bodies and rotating bodies on a balance scale. Post-Newtonian relativistic effect of periodical modulation of the orbital motion of a rotating body is discussed for the case of planets of the solar system and for binary pulsars PSR B1913+16 and PSR B1259-63. In the case of binary pulsars with known spin orientations this effect gives a possibility to measure radiuses of neutron stars.
Complex regional pain syndrome (CRPS) impairs visuospatial perception,whereas post-herpetic neuralgia does not: possible implications for supraspinal mechanism of CRPS.

INTRODUCTION Complex regional pain syndrome (CRPS) patients show impaired visuospatial perception in the dark, as compared to normal patients with acute nociceptive pain. The purpose of this study is 2-fold: (i) to ascertain whether this distorted visuospatial perception is related to the chronicity of pain, and (ii) to analyse visuospatial perception of CRPS in comparison with another neuropathic pain condition. MATERIALS AND METHODS We evaluated visual subjective body-midline (vSM) representation in 27 patients with post-herpetic neuralgia (PHN) and 22 with CRPS under light and dark conditions. A red laser dot was projected onto a screen and moved horizontally towards the sagittal plane of the objective body-midline (OM). Each participant was asked to direct the dot to a position where it crossed their vSM. The distance between the vSM and OM was analysed to determine how and in which direction the vSM deviated. RESULTS Under light condition, all vSM judgments approximately matched the OM. However, in the dark, CRPS patients, but not PHN patients, showed a shifted vSM towards the affected side. CONCLUSION We demonstrated that chronic pain does not always impair visuospatial perception. The aetiology of PHN is limited to the peripheral nervous system, whereas the distorted visuospatial perception suggests a supraspinal aetiology of CRPS.
Pharmacological Screening Using an FXN-EGFP Cellular Genomic Reporter Assay for the Therapy of Friedreich Ataxia

Friedreich ataxia (FRDA) is an autosomal recessive disorder characterized by neurodegeneration and cardiomyopathy. The presence of a GAA trinucleotide repeat expansion in the first intron of the FXN gene results in the inhibition of gene expression and an insufficiency of the mitochondrial protein frataxin. There is a correlation between expansion length, the amount of residual frataxin and the severity of disease. As the coding sequence is unaltered, pharmacological up-regulation of FXN expression may restore frataxin to therapeutic levels. To facilitate screening of compounds that modulate FXN expression in a physiologically relevant manner, we established a cellular genomic reporter assay consisting of a stable human cell line containing an FXN-EGFP fusion construct, in which the EGFP gene is fused in-frame with the entire normal human FXN gene present on a BAC clone. The cell line was used to establish a fluorometric cellular assay for use in high throughput screening (HTS) procedures. A small chemical library containing FDA-approved compounds and natural extracts was screened and analyzed. Compound hits identified by HTS were further evaluated by flow cytometry in the cellular genomic reporter assay. The effects on FXN mRNA and frataxin protein levels were measured in lymphoblast and fibroblast cell lines derived from individuals with FRDA and in a humanized GAA repeat expansion mouse model of FRDA. Compounds that were established to increase FXN gene expression and frataxin levels included several anti-cancer agents, the iron-chelator deferiprone and the phytoalexin resveratrol.
ERG signaling in prostate cancer is driven through PRMT5-dependent methylation of the Androgen Receptor

The TMPRSS2:ERG gene fusion is common in androgen receptor (AR) positive prostate cancers, yet its function remains poorly understood. From a screen for functionally relevant ERG interactors, we identify the arginine methyltransferase PRMT5. ERG recruits PRMT5 to AR-target genes, where PRMT5 methylates AR on arginine 761. This attenuates AR recruitment and transcription of genes expressed in differentiated prostate epithelium. The AR-inhibitory function of PRMT5 is restricted to TMPRSS2:ERG-positive prostate cancer cells. Mutation of this methylation site on AR results in a transcriptionally hyperactive AR, suggesting that the proliferative effects of ERG and PRMT5 are mediated through attenuating AR’s ability to induce genes normally involved in lineage differentiation. This provides a rationale for targeting PRMT5 in TMPRSS2:ERG positive prostate cancers. Moreover, methylation of AR at arginine 761 highlights a mechanism for how the ERG oncogene may coax AR towards inducing proliferation versus differentiation. DOI: http://dx.doi. org/10.7554/eLife.13964. 001
A New Sub-Canopy Soil Moisture Estimation Method Study Using PolinSAR

How to estimate soil moisture beneath vegetation using SAR data is an important study topic for SAR applications. The Polarimetric SAR Interferometry (PolinSAR) has a very promising application for solving this key problem. At this paper, based on spaceborne SIR-C L band PolinSAR data, a new sub-canopy soil moisture estimation method for ground-forest terrain is proposed. Firstly, from PolinSAR random Volume+Ground two layer coherent scattering model, using full maximum likelihood inversion method, the ground polarimetric covariance matrices of ground-forest terrain is reconstructed; Secondly, from ground backscatter polarimetric matrices, the Freeman Alpha is obtained; Thirdly, using surface and dihedral scattering model, the soil dielectric constants is estimated from Freeman Alpha; finally, sub-canopy soil moisture is obtained from Dobsen Model. The preliminary result indicates that the reasonable and promising result has been obtained, the future work will focus on method refine and further result validation using new data and ground truth.
A review on analysis of EEG signals

Electroencephalography (EEG) enlighten about the state of the brain i.e. about the electrical bustle going on in the brain. The electrical activity measured as voltage at different points of brain act as basis of EEG. These signals are generally time-varying and non-stationary in nature. These signals can be scrutinized using various signal processing techniques. In this paper, few statistical approaches to analyze EEG data are conversed.