Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying crosstalk in biochemical systems

Recent work has introduced biocircuit architectures that exhibit robust oscillatory behavior in organisms ranging from cyanobacteria to mammals. Complementary research in synthetic biology has introduced oscillators in vivo and in vitro suggesting that robust oscillation can be recapitulated using a small number of biochemical components. In this work, we introduce signaling crosstalk in biocircuits as a consequence of enzyme-mediated biochemical reactions. As a motivating example, we consider an in vitro oscillator with two types of crosstalk: crosstalk in production and degradation of RNA signals. We then propose a framework for quantifying crosstalk and use it to derive several dynamical constraints and suggest design techniques for ameliorating crosstalk in vitro biochemical systems. We demonstrate that the effects of crosstalk can be attenuated through the effective tuning of two key parameters in order to recover desired system dynamics. As an example, we show that by changing the balance between production and degradation crosstalk, we can tune a system to be stable or exhibit oscillatory behavior.
The Impact of Macroeconomic Uncertainty on Cash Holdings for Non-Financial Firms

This paper investigates the effects of macroeconomic volatility on non-financial firms' cash holding behavior. Using an augmented cash buffer-stock model, we demonstrate that an increase in macroeconomic volatility will cause the cross-sectional distribution of firms' cash-to-asset ratios to narrow. We test this prediction on a panel of non-financial firms drawn from the annual COMPUSTAT database covering the period 1957-2000, and find that as macroeconomic uncertainty increases, firms behave more homogeneously. Our results are shown to be robust to the inclusion of the levels of several macroeconomic factors.
Time-Optimal Real-Time Test Case Generation Using Prioritized Time Petri Nets

This paper discusses the application of modelchecking to test generation from specifications written inPrioritized Time Petri Nets. We demonstrate how toautomatically generate conformance test cases, specially timedtest cases with optimal execution time, using the model checkerselt and the path analysis tool plan of the TINA toolbox.Properties are described in the SE-LTL temporal logic. Testcases are generated using manually formulated test purposesor automatically from various coverage criteria of the model.
Individual Participant Data Meta-Analysis for a Binary Outcome: One-Stage or Two-Stage?

Background A fundamental aspect of epidemiological studies concerns the estimation of factor-outcome associations to identify risk factors, prognostic factors and potential causal factors. Because reliable estimates for these associations are important, there is a growing interest in methods for combining the results from multiple studies in individual participant data meta-analyses (IPD-MA). When there is substantial heterogeneity across studies, various random-effects meta-analysis models are possible that employ a one-stage or two-stage method. These are generally thought to produce similar results, but empirical comparisons are few. Objective We describe and compare several one- and two-stage random-effects IPD-MA methods for estimating factor-outcome associations from multiple risk-factor or predictor finding studies with a binary outcome. One-stage methods use the IPD of each study and meta-analyse using the exact binomial distribution, whereas two-stage methods reduce evidence to the aggregated level (e.g. odds ratios) and then meta-analyse assuming approximate normality. We compare the methods in an empirical dataset for unadjusted and adjusted risk-factor estimates. Results Though often similar, on occasion the one-stage and two-stage methods provide different parameter estimates and different conclusions. For example, the effect of erythema and its statistical significance was different for a one-stage (OR = 1.35, ) and univariate two-stage (OR = 1.55, ). Estimation issues can also arise: two-stage models suffer unstable estimates when zero cell counts occur and one-stage models do not always converge. Conclusion When planning an IPD-MA, the choice and implementation (e.g. univariate or multivariate) of a one-stage or two-stage method should be prespecified in the protocol as occasionally they lead to different conclusions about which factors are associated with outcome. Though both approaches can suffer from estimation challenges, we recommend employing the one-stage method, as it uses a more exact statistical approach and accounts for parameter correlation.
Joint beamforming and antenna selection for two-way amplify-and-forward MIMO relay networks

A novel joint beamforming and antenna selection strategy is proposed and analyzed for two-way multiple-input multiple-output amplify-and-forward relay networks. Specifically, this strategy selects the optimal transmit precoding and receiver filtering vectors at the two source terminals, and an optimal transmit/receive antenna at the relay terminal based on minimizing the overall outage probability. The performance of this transmission strategy is quantified by first deriving the exact cumulative distribution function of the effective signal-to-noise ratio (SNR), and thereby, evaluating the overall outage probability, its asymptotically exact high SNR approximation and achievable diversity order. For a multiple relay scenario, a joint relay, beamforming, and antenna selection strategy is proposed and analyzed as well. Interestingly, our selection strategies are optimal in the sense of the overall outage probability, and hence, in the sense of achievable diversity order as well.
Structure and Function of the Haemophilus influenzae Autotransporters

Autotransporters are a large class of proteins that are found in the outer membrane of Gram-negative bacteria and are almost universally implicated in virulence. These proteins consist of a C-terminal β-domain that is embedded in the outer membrane and an N-terminal domain that is exposed on the bacterial surface and is endowed with effector function. In this article, we review and compare the structural and functional characteristics of the Haemophilus influenzae IgA1 protease and Hap monomeric autotransporters and the H. influenzae Hia and Hsf trimeric autotransporters. All of these proteins play a role in colonization of the upper respiratory tract and in the pathogenesis of H. influenzae disease.
An approach for designing management support systems: the design science research process and its outcomes

Design science research involves creating and evaluating innovative methods and approaches to be used in design practice. We present an approach to be used in the process of designing Management Support Systems (MSS). The nature of managerial work makes the design, development, and implementation of MSS a major challenge. The MSS literature suggests that determining MSS requirements and specification of MSS are the most critical phases in MSS design and development. We present an approach that can be used as a guide for MSS design, with a primary focus on MSS requirements determination and how requirements can be fulfilled using information and communication technologies (ICT). The approach builds on Quinn and associates' competing values model (CVM) of organizational effectiveness. The approach can guide MSS designers in designing MSS that support different managerial roles, i.e., the development of MSS that support managerial cognition, decision, and action.
Advanced Java bytecode instrumentation

Bytecode instrumentation is a valuable technique for transparently enhancing virtual execution environments for purposes such as monitoring or profiling. Current approaches to bytecode instrumentation either exclude some methods from instrumentation, severely restrict the ways certain methods may be instrumented, or require the use of native code. In this paper we compare different approaches to bytecode instrumentation in Java and come up with a novel instrumentation framework that goes beyond the aforementioned limitations. We evaluate our approach with an instrumentation for profiling which generates calling context trees of various platform-independent dynamic metrics.
Children's conceptions of trust in the context of social expectations.

Children's conceptions of trust were examined within the context of social ex pectations. Sixty children (30 girls, 30 boys) from the first, third, and fifth grades participated in the study. Assessments were made of children's evaluations and corresponding justifications of stories that depicted violations of three social ex pectations between friends: They involved deception, emotional support, and conventional dress. Judgments of the effects of the violations on friendships were also made. The results showed, across age groups, that children's concep tions of trust drew on moral reasoning; resulted, after a violation, in feelings of being let down, if not betrayed; excluded social-conventional expectations; and included differentiations between contingent and noncontingent obligations. With increasing age, children, across all three social expectations, gave impor tance to reciprocity in their friendship relations.
The Controversy, Challenges, and Potential Benefits of Putative Female Germline Stem Cells Research in Mammals

The conventional view is that female mammals lose their ability to generate new germ cells after birth. However, in recent years, researchers have successfully isolated and cultured a type of germ cell from postnatal ovaries in a variety of mammalian species that have the abilities of self-proliferation and differentiation into oocytes, and this finding indicates that putative germline stem cells maybe exist in the postnatal mammalian ovaries. Herein, we review the research history and discovery of putative female germline stem cells, the concept that putative germline stem cells exist in the postnatal mammalian ovary, and the research progress, challenge, and application of putative germline stem cells in recent years.
Determinants of preference for elective caesarean section in Hong Kong Chinese pregnant women.

OBJECTIVE To find the clinical and socio-demographic determinants for Hong Kong Chinese women who preferred elective caesarean section. DESIGN Cross-sectional interview survey. SETTING University teaching hospital, Hong Kong. PARTICIPANTS A cohort of consecutive Hong Kong Chinese pregnant women (n=660) attending a government-funded obstetric unit catering deliveries in the New Territories in Hong Kong in 2002. MAIN OUTCOME MEASURES The clinical and socio-demographic determinants of preference for elective caesarean section, in women who could have a trial of vaginal delivery. RESULTS The overall prevalence for maternal preference for elective caesarean section was 16.7% (95% confidence interval, 13.8-19.6). The factors associated with preferring elective caesarean section were: previous elective caesarean section (odds ratio=7.6; 95% confidence interval, 2.0-28.7) and previous emergency caesarean section (3.8; 1.8-8.2). Among nulliparous women, the prevalence of preference for elective caesarean section was 16.8% (95% confidence interval, 13.0-20.6). Conception by in-vitro fertilisation was found to be significantly associated with preferring elective caesarean section in nulliparous women (odds ratio=5.2; 95% confidence interval, 1.0-26.4). CONCLUSION Previous caesarean section and conception by in-vitro fertilisation were determinants for women preferring elective caesarean section.
Significance of Tumor-Infiltrating Lymphocytes and the Expression of Topoisomerase IIα in the Prediction of the Clinical Outcome of Patients with Triple-Negative Breast Cancer after Taxane-Anthracycline-Based Neoadjuvant Chemotherapy

Purpose: The aim of this study was to determine factors able to predict chemotherapeutic responses and clinical outcomes in patients with triple-negative breast cancer (TNBC) after neoadjuvant chemotherapy (NAC). Methods: Fifty-two TNBC patients on taxane-anthracycline-based NAC were included. The expression of Ki67, topoisomerase IIα (TOPOIIα), and p53, as well as the presence of CD4+ tumor-infiltrating lymphocytes (TILs) and CD8+ TILs were evaluated in biopsy specimens by immunohistochemistry. The expression of Ki67, TOPOIIα, and p53, as well as CD4 and CD8 in TILs was calculated according to the pathological response to NAC, disease-free survival (DFS), and overall survival (OS). Results: Fourteen (26.9%) TNBC patients demonstrated a pathological complete response (pCR). According to univariate analyses, significant factors associated with pCR were high infiltration of CD4+ TILs (p = 0.004), high infiltration of CD8+ TILs (p = 0.010), and high expression of topoisomerase IIα (TOPOIIα) (p = 0.006). CD4+ TILs and TOPOIIα were significantly positively correlated with CD8+ TILs. Multivariate analyses indicated that TOPOIIα was an independent predictor of pCR. Although TNBC patients with high infiltration of CD4+ TILs, CD8+ TILs, or with high expression of TOPOIIα exhibited a significantly good 5-year DFS, only TNBC patients with a high infiltration of CD8+ TILs exhibited significantly positive 5-year OS probabilities. Conclusion: Our study demonstrated that CD4+ TILs and TOPOIIα in pretreated cancer tissues were significantly correlated with CD8+ TILs. CD4+ TILs, CD8+ TILs, and TOPOIIα expression were predictors of pCR and 5-year DFS of TNBC patients who were treated with NAC, and TOPOIIα was an independent predictor of pCR. CD8+ TILs were a key factor in the prediction of good 5-year OS rates of TNBC patients after taxane-anthracycline-based NAC.
Genetic polymorphisms in the ALDH2 gene and the risk of ischemic stroke in a Chinese han population

Background Previous studies have shown that aldehyde dehydrogenase 2 (ALDH2) plays a role in ischemic stroke progression. In recent years, the activation of the ALDH2 pathway have been reported serving as a useful index in the identification of stroke-prone participants, and the ALDH2 pathway may be a potential target for the therapeutic intervention in ischemic stroke. Materials and Methods We evaluated six tagging single-nucleotide polymorphisms (SNPs) of the ALDH2 gene in a case–control study from Hainan of China (488 cases, 503 controls). We used SPSS version 17.0 statistical software, Excel software and other analysis software to explore associations between SNPs and the risk of ischemic stroke various genetic models (additive, dominant, and recessive). Results Through statistical analysis, we found that ALDH2 rs886205 [odds ratio (OR) = 6.39; 95% confidence interval (CI) = 1.19-34.38; p = 0.03] and rs7296651 (OR = 9.29; 95% CI = 1.37-63.21; p = 0.02) were associated with increased risk of ischemic stroke in recessive model analysis. In addition, we established that the “AA” genotype (OR = 5.99; 95% CI = 1.11-32.23; p = 0.037) for rs886205 and the “AA” genotype (OR = 8.93; 95% CI = 1.31-60.78; p = 0.025) for rs7296651 were associated with increased ischemic stroke risk. Conclusions Our results provide evidence that variants of ALDH2 gene polymorphisms influence the risk of developing ischemic stroke in Han Chinese population.
Developing an integrative Modelling Language for enhancing road traffic simulations

Road traffic is a pervasive aspect in modern societies that affects millions people. The study of its multiple aspects is a very demanding task. Due to its complexity, traffic simulations become a key tool. Their development demands multidisciplinary teams, where communication problems are frequent. Model-driven engineering alleviates this situation providing graphical instruments for designing Modelling Languages (MLs) and semi-automatic transformations. This work presents a model-driven infrastructure composed by an integrative ML, a model editor, and a code generator. The ML is based on related literature and facilitates modelling different theories and simulations based on them. It considers the roles of individuals involved in road traffic, and partially adopts agent-based methodologies to model their decision-making. A case study shows how to produce a simulation specification adapting an existing traffic theory to the ML, and adjust this specification to a simulation platform for testing. It provides the basis for comparison with related work.
Specular color imaging on a metallic substrate

We propose a full reproduction workflow for printing color images on metallic substrates. It relies on an ink spreading enhanced cellular Yule-Nielsen modified spectral Neugebauer model, calibrated with 35 color samples printed on the metal film and measured under specular reflection. The calibration accounts for the different phenomena contributing to the reflectance of halftone prints on metal: specular reflection by the metal film substrate of light traveling across the inks, illumination and viewing geometry, shadowing effect induced by the ink and difference in surface structure between the inked and non-inked metal halftone elements. The model enables predicting printable colors with an average CIELAB âˆ†E94 error of 1.7. Thanks to the model, the metal print gamut is established and a 3D table provides the correspondence between printable metallic colors viewed under specular reflection and the corresponding ink surface coverages. The input sRGB gamut is mapped into the print gamut. At halftone image generation time, surface coverages of the inks yielding the desired gamut mapped input colors are obtained from the 3D table. These ink surface coverages yield the ink separations that are halftoned and printed. The resulting color images printed on a silver substrate viewed under specular reflection reproduce the hues at a high degree of fidelity. The luminance of metallic prints under specular observation is generally higher than the luminance of paper under the same illuminating conditions. Therefore, the printed metallic colors appear more colorful. Such metal prints are attractive for design, art and publicity. Their high brightness immediately strikes the observer and transmits the message incorporated into the reproduced picture or artwork.
Poisson NL means: Unsupervised non local means for Poisson noise

An extension of the non local (NL) means is proposed for images damaged by Poisson noise. The proposed method is guided by the noisy image and a pre-filtered image and is adapted to the statistics of Poisson noise. The influence of both images can be tuned using two filtering parameters. We propose an automatic setting to select these parameters based on the minimization of the estimated risk (mean square error). This selection uses an estimator of the MSE for NL means with Poisson noise and Newton's method to find the optimal parameters in few iterations.
Simulation on Crowd Mobility of Moving Objects Using Multi-Agent and ClearPath

Crowd simulation is the simulation process of movement on a large number of agents in a virtual environment and simulated in the form of animation. The object's tranquility is not just a collection of some individuals but the crowd of objects illustrating how individual's movements can be affected by other individual movements in the crowd. It is necessary then to set the direction and velocity of the object as it moves. The purpose of this research is to simulate the multi agency of movement between objects by using ClearPath. The output generated from this simulation is the simulation process time and the number of collisions that occur during the simulation process. The results obtained from several trials of three simulation models show that ClearPath is capable of handling simulations that require multiple objects, ClearPath can direct objects to avoid static obstacles, increasing number of objects will enhance the number of collisions occurring and simulation time.
Highly similar piggyBac transposase‐like sequences from various Bactrocera (Diptera, Tephritidae) species

The piggyBac transposable element is currently the vector of choice for transgenesis, enhancer trapping, gene discovery and gene function determination in both insects and mammals. However, the recent discovery of sequences with similarity to piggyBac in a wide diversity of organisms suggests that piggyBac may be horizontally transferred to distantly related species. This has raised concern on the wide‐range application of piggyBac‐based transformation vectors and their stability. In this paper, the presence of sequences homologous to the piggyBac transposase was investigated in 17 species belonging to six genera within the Tephritidae family, including many pest species for which transformation has already been achieved. piggyBac‐like sequences, with a high degree of similarity to the original Trichoplusia ni transposase sequence were identified only in six species of the Bactrocera genus.
Fast Multiclass Segmentation using Diffuse Interface Methods on Graphs

Abstract : We present two graph-based algorithms for multiclass segmentation of high-dimensional data. The algorithms use a diffuse interface model based on the Ginzburg-Landau functional, related to total variation compressed sensing and image processing. A multiclass extension is introduced using the Gibbs simplex, with the functional's double-well potential modified to handle the multiclass case. The first algorithm minimizes the functional using a convex splitting numerical scheme. The second algorithm is a uses a graph adaptation of the classical numerical Merriman-Bence-Osher (MBO) scheme, which alternates between diffusion and thresholding. We demonstrate the performance of both algorithms experimentally on synthetic data, grayscale and color images and several benchmark data sets such as MNIST, COIL and WebKB. We also make use of fast numerical solvers for finding the eigenvectors and eigenvalues of the graph Laplacian, and take advantage of the sparsity of the matrix. Experiments indicate that the results are competitive with or better than the current state-of-the-art multiclass segmentation algorithms.
On power law distributions in large-scale taxonomies

In many of the large-scale physical and social complex systems phenomena fat-tailed distributions occur, for which different generating mechanisms have been proposed. In this paper, we study models of generating power law distributions in the evolution of large-scale taxonomies such as Open Directory Project, which consist of websites assigned to one of tens of thousands of categories. The categories in such taxonomies are arranged in tree or DAG structured configurations having parent-child relations among them. We first quantitatively analyse the formation process of such taxonomies, which leads to power law distribution as the stationary distributions. In the context of designing classifiers for large-scale taxonomies, which automatically assign unseen documents to leaf-level categories, we highlight how the fat-tailed nature of these distributions can be leveraged to analytically study the space complexity of such classifiers. Empirical evaluation of the space complexity on publicly available datasets demonstrates the applicability of our approach.
Improved Check Node Decomposition for Linear Programming Decoding

For the linear programming decoding (LPD) proposed by Feldman et al., the number of constraints increases exponentially with check degrees. By decomposing a high-degree check node into a number of degree-3 check nodes, the number of constraints grows linearly with check degrees. In this letter, we show that the size of the LPD can be reduced by decomposing a high-degree check node into a number of degree-4 check nodes. The LPD using the degree-4 decomposition leads to almost the same number of constraints as using the degree-3 decomposition, while the number of auxiliary variable nodes is less than half of the one using the degree-3 decomposition. Moreover, when decomposing a high degree check node into a number of check nodes with degree d, d>4, the number of constraints increases rapidly and the size of the LPD becomes larger than the degree-4 decomposition. It is demonstrated on an LDPC code and a BCH code that the decoding time of the degree-4 decomposition is the smallest among the different decomposition methods.