Miracle-dz/UniFAR-FTUs huggingface dataset:
ZO-1 function in the assembly of tight junctions in MDCK epithelial cells

Zonula occludens-1 (ZO-1) was the first tight junction protein to be cloned, and has been implicated as an important scaffold protein. It contains multiple domains that bind a diverse set of junction proteins. However, the molecular functions of ZO-1 and related proteins such as ZO-2 and ZO-3 have remained unclear. We now show that gene silencing of ZO-1 causes a delay of ~3 hours in tight junction formation in MDCK epithelial cells, but mature junctions appear functionally normal even in the continuing absence of ZO-1. Depletion of ZO-2, cingulin, or occludin, proteins that can interact with ZO-1, had no discernable effects on tight junctions. Rescue of junction assembly using murine ZO-1 mutants demonstrated that the ZO-1 C-terminus is neither necessary nor sufficient for normal assembly. Moreover, mutation of the PDZ1 domain did not block rescue. However, point mutations in the SH3 domain almost completely prevented rescue. Surprisingly, the isolated SH3 domain of ZO-1 could also rescue junction assembly. These data reveal an unexpected function for the SH3 domain of ZO-1 in regulating tight junction assembly in epithelial cells, and show that cingulin, occludin, or ZO-2 are not limiting for junction assembly in MDCK monolayers. INTRODUCTION Epithelia form the archetypal polarized tissue of the Metazoa (Knust and Bossinger, 2002; Gibson and Perrimon, 2003; Nelson, 2003). Typically, they create a barrier between the extracellular environment and the interior of the organism. Epithelia organize into layered sheets of cells with apical-basal polarity and strong cell-cell adhesions. The tight junction is the most apical adhesion between epithelial cells and is a complex structure that functions both as a barrier to the paracellular diffusion of ions and molecules, and as a fence to separate the apical plasma membrane from the basolateral domain in polarized epithelia (D'Atri and Citi, 2002; Gonzalez-Mariscal et al., 2003; Matter and Balda, 2003). Tight junctions are fine-tuned to perform specific
On Combining Region-Growing with Non-Parametric Clustering for Color Image Segmentation

Region-based and clustering-based techniques are two of the most important segmentation methods, and both of them have their advantages and disadvantages. In this paper, we present a color image segmentation method combining region-growing with non-parametric clustering technique. First, a bottom-up region-merging technique is used to yield an intermediate result. This procedure takes into account simultaneously the spectral properties of pixels as well as their spatial information, which is not fully utilized in clustering technique. Second, a clustering technique based on mean shift algorithm is used to cluster similar image objects in the intermediate result. In the mean shift procedure, we adopt adaptive bandwidths instead of a single one over the entire feature space. The two steps of image segmentation are performed in an unsupervised way. The validity of the proposed method is verified on various color images.
Spatial R&D spillovers and economic growth: evidence from West Germany

The paper bases itself on recent theoretical writings in growth economics that empha-size the effects of both own R&D efforts and of interregional technology spillovers on regions´ productivity. We propose robust estimation techniques to evaluate the R&D spillovers across West German functional regions during the period 1976 - 1996. The findings suggest the existence of knowledge spillovers across functional regional boundaries. Moreover, significant spillovers are mainly found among geographically close regions. This finding confirms the hypothesis that proximity matters.
2-D pseudo-spectral viscoacoustic modeling in a distributed-memory multi-processor computer

Two pseudo-spectral implementations of 2-D viscoacoustic modeling are developed in a distributed-memory multi-processor computing environment. The first involves simultaneous computation of the response of one model to many source locations and, as it requires no interprocessor communication, is perfectly parallel. The second involves computation of the response, to one source, of a large model that is distributed across all processors. In the latter, local rather than global, Fourier transforms are used to minimize interprocessor communication and to eliminate the need for matrix transposition. In both algorithms, absorbing boundaries are defined as zones of decreased Q as part of the model, and so require no extra computation. An empirical method of determining sets of relaxation times for a broad range of Q values eliminates the need for iterative fitting of Q-frequency curves.
A Multi-Engine LUT-Based Synthesis Framework

In this paper, we present a new synthesis framework. This framework, ASU-Synthesizer, is built for logic synthesis for LUT based FPGAs. The synthesis process is composed of logic optimization and technology mapping. We implemented the different categories of logic optimization algorithms. Then we used the well known technology mapping package, Flow-Map (Cong et al., 1996). We added to the framework, our online area estimator that we proposed before in (Hamed et al., 2004). This framework can be used to build any commercial synthesis tool for LUT-based designs
A TCAD approach to the physics-based modeling of frequency conversion and noise in semiconductor devices under large-signal forced operation

The paper presents a novel, unified technique to evaluate, through physics-based modeling, the frequency conversion and noise behavior of semiconductor devices operating in the large-signal periodic regime. Starting from the harmonic balance (HE) solution of the spatially discretized physics-based model under (quasi) periodic forced operation, frequency conversion at the device ports in the presence of additional input tones is simulated by application of the small-signal large-signal network approach to the model. Noise analysis under large-signal operation readily follows as a direct extension of classical approaches by application of the frequency conversion principle to the modulated microscopic noise sources and to the propagation of these to the external device terminals through a Green's function technique. An efficient numerical implementation is discussed within the framework of a drift-diffusion model and some examples are finally provided on the conversion and noise behavior of rf Si diodes.
Association Mapping and Nucleotide Sequence Variation in Five Drought Tolerance Candidate Genes in Spring Wheat

Functional markers are needed for key genes involved in drought tolerance to improve selection for crop yield under moisture stress conditions. The objectives of this study were to (i) characterize five drought tolerance candidate genes, namely dehydration responsive element binding 1A (DREB1A), enhanced response to abscisic acid (ERA1‐B and ERA1‐D), and fructan 1‐exohydrolase (1‐FEH‐A and 1‐FEH‐B), in wheat (Triticum aestivum L.) for nucleotide and haplotype diversity, Tajima's D value, and linkage disequilibrium (LD) and (ii) associate within‐gene single nucleotide polymorphisms (SNPs) with phenotypic traits in a spring wheat association mapping panel (n = 126). Field trials were grown under contrasting moisture regimes in Greeley, CO, and Melkassa, Ethiopia, in 2010 and 2011. Genome‐specific amplification and DNA sequence analysis of the genes identified SNPs and revealed differences in nucleotide and haplotype diversity, Tajima's D, and patterns of LD. DREB1A showed associations (false discovery rate adjusted probability value = 0.1) with normalized difference vegetation index, heading date, biomass, and spikelet number. Both ERA1‐A and ERA1‐B were associated with harvest index, flag leaf width, and leaf senescence. 1‐FEH‐A was associated with grain yield, and 1‐FEH‐B was associated with thousand kernel weight and test weight. If validated in relevant genetic backgrounds, the identified marker–trait associations may be applied to functional marker‐assisted selection.
Replacement of Retinyl Esters by Polyunsaturated Triacylglycerol Species in Lipid Droplets of Hepatic Stellate Cells during Activation

Activation of hepatic stellate cells has been recognized as one of the first steps in liver injury and repair. During activation, hepatic stellate cells transform into myofibroblasts with concomitant loss of their lipid droplets (LDs) and production of excessive extracellular matrix. Here we aimed to obtain more insight in the dynamics and mechanism of LD loss. We have investigated the LD degradation processes in rat hepatic stellate cells in vitro with a combined approach of confocal Raman microspectroscopy and mass spectrometric analysis of lipids (lipidomics). Upon activation of the hepatic stellate cells, LDs reduce in size, but increase in number during the first 7 days, but the total volume of neutral lipids did not decrease. The LDs also migrate to cellular extensions in the first 7 days, before they disappear. In individual hepatic stellate cells. all LDs have a similar Raman spectrum, suggesting a similar lipid profile. However, Raman studies also showed that the retinyl esters are degraded more rapidly than the triacylglycerols upon activation. Lipidomic analyses confirmed that after 7 days in culture hepatic stellate cells have lost most of their retinyl esters, but not their triacylglycerols and cholesterol esters. Furthermore, we specifically observed a large increase in triacylglycerol-species containing polyunsaturated fatty acids, partly caused by an enhanced incorporation of exogenous arachidonic acid. These results reveal that lipid droplet degradation in activated hepatic stellate cells is a highly dynamic and regulated process. The rapid replacement of retinyl esters by polyunsaturated fatty acids in LDs suggests a role for both lipids or their derivatives like eicosanoids during hepatic stellate cell activation.
Study of Data Mining Techniques for Software Quality Assurance

Satisfying the customer requirements is the ultimate goal of producing or developing any product. The quality of the product is decided on the bases of the level of customer satisfaction. There are different techniques which have been reported during the survey which enhance the quality of the product through software defect prediction and by locating the missing software requirements. Some mining techniques were proposed to assess the individual performance indicators in collaborative environment to reduce errors at individual level. The basic intention is to produce a product with zero or few defects thereby producing a best product quality wise. In the analysis of survey the techniques like Genetic algorithm, artificial neural network, classification and clustering techniques and decision tree are studied. After analysis it has been discovered that these techniques contributed much to the improvement and enhancement of the quality of the product.
Molecular Characterization of the Tumor Suppressor Candidate 5 Gene: Regulation by PPARγ and Identification of TUSC5 Coding Variants in Lean and Obese Humans

Tumor suppressor candidate 5 (TUSC5) is a gene expressed abundantly in white adipose tissue (WAT), brown adipose tissue (BAT), and peripheral afferent neurons. Strong adipocyte expression and increased expression following peroxisome proliferator activated receptor γ (PPARγ) agonist treatment of 3T3-L1 adipocytes suggested a role for Tusc5 in fat cell proliferation and/or metabolism. However, the regulation of Tusc5 in WAT and its potential association with obesity phenotypes remain unclear. We tested the hypothesis that the TUSC5 gene is a bona fide PPARγ target and evaluated whether its WAT expression or single-nucleotide polymorphisms (SNPs) in the TUSC5 coding region are associated with human obesity. Induction of Tusc5 mRNA levels in 3T3-L1 adipocytes by troglitazone and GW1929 followed a dose-response consistent with these agents' binding affinities for PPARγ. Chromatin immunoprecipitation (ChIP) experiments confirmed that PPARγ protein binds a ∼ −1.1 kb promotor sequence of murine TUSC5 transiently during 3T3-L1 adipogenesis, concurrent with histone H3 acetylation. No change in Tusc5 mRNA or protein levels was evident in type 2 diabetic patients treated with pioglitazone. Tusc5 expression was not induced appreciably in liver preparations overexpressing PPARs, suggesting that tissue-specific factors regulate PPARγ responsiveness of the TUSC5 gene. Finally, we observed no differences in Tusc5 WAT expression or prevalence of coding region SNPs in lean versus obese human subjects. These studies firmly establish the murine TUSC5 gene locus as a PPARγ target, but the significance of Tusc5 in obesity phenotypes or in the pharmacologic actions of PPARγ agonists in humans remains equivocal.
Social Network Analysis in Military Headquarters using CAVALIER

Social Network Analysis is a branch of mathematical social science (focusing on the relationships between people and/or groups) which we intend to apply to military organisations (in particular military headquarters). In this paper, we discuss the use of Social Network Analysis in analysing such organisations in order to make recommendations about work practices, and to suggest new placements of staff within a physical headquarters setting.
Measuring information on mobile devices usage: An entropy-based approach

Over the last decade, mobile devices have been widely used in numerous aspects. Thanks to mobile applications platforms that deliver millions of mobile applications for end users anytime and anywhere. Lately, research on mobile devices and mobile applications have been gaining more attention. However, the research to date has tended to focus on technical aspects or adoption behavior of mobile applications. There is still very little scientific understanding on how to measure the level of information in mobile device usage. Therefore, this study demonstrates an approach based on Shannon's entropy for the measurement of the information level and uncertainty in mobile applications usage. The initial findings confirmed that the purposed method could measure the level of information in the mobile device usage. The different number of mobile applications and the frequency of each mobile application usage would generate different bits of entropy values, which mean it can use to indicate the level of information and uncertainty. The results of this paper will serve as indicators for the direction of our planned future research in this field.
Programmable data parallel accelerator for mobile computer vision

The demand for high performance yet extremely low-power multimedia accelerators for mobile communication is ever growing. To meet this challenge a novel approach with a very low-power programmable TTA processor is proposed in this paper. The processor is benchmarked with two OpenCL computer vision applications; depth estimation and face detection. The former is an excellent example of a highly parallel algorithm that suits our TTA processor extremely well whereas the latter is an example of a more serial algorithm that poses a challenge for GPU-style parallel platforms. Both algorithms are also implemented and optimized for a high throughput AMD Radeon HD 7750 GPU, Qualcomm Adreno 330 mobile GPU and Intel Core i5-480M for a fair comparison of performance and energy efficiency. These platforms are chosen because they all can be programmed with OpenCL with equivalent programming efforts. In this paper we show that our novel approach can achieve real-time requirements and easily outperform both GPUs as well as the CPU in terms of throughput per watt criterion, making it an excellent candidate for power-constrained mobile platforms.
New data sets and improved models of highway traffic

In this paper we report progress on the use of novel data sets to calibrate and improve car-following models of highway traffic. These models describe vehicles as discrete entities moving in continuous time and space, and use plausible behavioural assumptions to derive systems of differential equations which must be solved for vehicles’ trajectories. To date, there has been little or no systematic attempt to fit these models to quantative microscopic (at the level of individual vehicles) highway data. Our recent work has involved the analysis of two such data sets: • MIDAS (Motorway Incident Detection and Automatic Signalling) IVD (Individual Vehicle Data), and • aerial video pictures. Each of these data sets has been kindly provided by the Highways Agency. The MIDAS (Motorway Incident Detection and Automatic Signalling) system consists of double inductance loops which record the lane number, time headway and wall-clock time of passing vehicles, as well as estimating their lengths and speeds. This data has been collected by TRL. We have applied novel statistical techniques to the pattern matching of vehicle length measurements at different loops, and thus we are able to track individual vehicles down the motorway. In particular, we may: • obtain accurate estimates for individual vehicles’ travel times between loops; • estimate lane changing rates. However, presently MIDAS loops may not be used to estimate vehicles’ accelerations. We describe how image analysis and pattern matching techniques have been used to automatically follow vehicles across a sequence of aerial video frames. Projective transformations can then be applied to build full time series of vehicles’ displacements, from which headway, velocity, and acceleration information can be extracted.
Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses

Calcification is one of the most distinctive traits of scleractinian corals. Their hard skeletons form the substratum of reef ecosystems and confer on corals their remarkable diversity of shapes. Corallimorpharians are non-calcifying, close relatives of scleractinian corals, and the evolutionary relationship between these two groups is key to understanding the evolution of calcification in the coral lineage. One pivotal question is whether scleractinians are a monophyletic group, paraphyly being an alternative possibility if corallimorpharians are corals that have lost their ability to calcify, as is implied by the “naked-coral” hypothesis. Despite major efforts, relationships between scleractinians and corallimorpharians remain equivocal and controversial. Although the complete mitochondrial genomes of a range of scleractinians and corallimorpharians have been obtained, heterogeneity in composition and evolutionary rates means that mitochondrial sequences are insufficient to understand the relationship between these two groups. To overcome these limitations, transcriptome data were generated for three representative corallimorpharians. These were used in combination with sequences available for a representative range of scleractinians to identify 291 orthologous single copy protein-coding nuclear markers. Unlike the mitochondrial sequences, these nuclear markers do not display any distinct compositional bias in their nucleotide or amino-acid sequences. A range of phylogenomic approaches congruently reveal a topology consistent with scleractinian monophyly and corallimorpharians as the sister clade of scleractinians.
MMSE subcarrier equalization for filter bank based multicarrier systems

Filter bank based multicarrier systems (FBMC) offer a number of benefits over conventional orthogonal frequency division multiplexing (OFDM) with cyclic prefix (CP). One benefit is the improved spectral efficiency by not using a redundant CP and by having much better control of out-of-band emission. Another advantage is the ease of accommodating multiple users in an FDMA fashion especially in the uplink, i. e. the multiple access channel (MAC). On the other hand, more elaborate equalization concepts are needed compared to the single-tap per-subcarrier equalizer sufficient in the OFDM with CP case. In this contribution we will present an efficient linear minimum mean square error (MMSE) equalization concept. Since FBMC systems employ offset-quadrature-amplitude-modulation (OQAM), a fractionally spaced per-subcarrier equalizer will be derived, which takes into account the inter-subcarrier interference due to frequency selective multipath fading. Still this is handled with decoupled per-subcarrier equalizers. Simulation results will show that OQAMFBMCs allow for savings in transmit power which have to be paid with a practicable amount of computational overhead.
Evaluation of BRCAPRO Risk Assessment Model in Patients with Ductal Carcinoma In situ Who Underwent Clinical BRCA Genetic Testing

The authors retrospectively aimed to determine which of the following three scenarios, related to DCIS entry into BRCAPRO, predicted BRCA mutation status more accurately: (1) DCIS as an invasive breast cancer (IBC) entered using the actual age of diagnosis, (2) DCIS as IBC entered with 10 years added to the actual age of diagnosis, and (3) DCIS entered as no cancer. Of the 85 DCIS patients included in the study, 19% (n = 16) tested positive for a BRCA mutation, and 81% (n = 69) tested negative. DCIS patients who tested positive for a BRCA mutation had a higher BRCAPRO risk estimation (34.61%) than patients who tested negative (11.4%) when DCIS was entered at the actual age of diagnosis. When DCIS was entered with 10 years added to the actual age at diagnosis, the BRCAPRO estimate was still higher amongst BRCA positive patients (25.4%) than BRCA negative patients (7.1%). When DCIS was entered as no cancer, the BRCAPRO estimate remained higher among BRCA positive patients (2.56%) than BRCA negative patents (1.98%). In terms of accuracy of BRCA positivity, there was no statistically significant difference between DCIS at age at diagnosis, DCIS at 10 years later than age at diagnosis, and DCIS entered as no cancer (AUC = 0.77, 0.784, 0.75, respectively: p = 0.60). Our results indicate that regardless of entry approach into BRCAPRO, there were no significant differences in predicting BRCA mutation in patients with DCIS.
Gap junctional communication modulates agonist-induced calcium oscillations in transfected HeLa cells

Gap junctional communication modulates intercellular calcium signaling in many cell types. We have investigated whether gap junctional communication modulates calcium oscillatory behavior of cells responding to an agonist. Extracellular UTP induced calcium oscillations in 70% of HeLa cells cultured in monolayer, and neighboring cells oscillated independently of each other. In HeLa cell transfectants expressing connexin43 (HeLa/Cx43), extracellular UTP induced calcium transients, but calcium oscillations occurred in only 10% of cells. Inhibition of gap junctional communication with anandamide in HeLa/Cx43 transfectants substantially restored oscillations (55% of cells). In HeLa/Cx45 transfectants, UTP initiated calcium oscillations similar to those seen in HeLa cells (63% of cells), but HeLa/Cx46 transfectants demonstrated calcium oscillations that were dampened compared to those of the parental HeLa cells, and occurred in only 40% of cells. These experiments demonstrate that gap junctional communication modulates calcium oscillatory behavior in cell monolayers, presumably by allowing cells to share a small molecule such as inositol trisphosphate. These studies suggest that gap junctional communication may alter the nature of signals induced by calcium mobilizing agonists in a connexin-dependent fashion by modulating calcium oscillatory behavior.