Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans

Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked. Our study presents the first example of transcriptional vitamin-directed metabolic network rewiring to promote survival under vitamin deficiency. The ability to reroute propionate breakdown according to B12 availability may provide C. elegans with metabolic plasticity and thus a selective advantage on different diets in the wild. DOI: http://dx.doi. org/10.7554/eLife.17670. 001
An Adaptive Fuzzy Model for Personalization with Evolvable User Profiles

The paper discusses user attributes and their representation in user profiles for user-adaptive systems. It introduces an approach for representing multiple attributes in the user profile, and a technique that combines fuzzy programming and fuzzy relation networks to prioritize the impact of user attributes/requirements in personalizing the application through generating appropriate adaptation actions. The paper also presents a generic adaptation scenario using the proposed approach
Low complexity LFSR based bit-serial montgomery multiplier in GF(2m)

Montgomery multiplication in GF(2<sup>m</sup>) is defined as ABr<sup>-1</sup> mod f(α), where f(x) is the irreducible polynomial defining the field and r is a fixed field element. In this paper, a low complexity Montgomery multiplier in GF(2<sup>m</sup>) is proposed with r=α<sup>m-1</sup> or α<sup>m</sup>. Linear feedback shift register (LFSR) is adopted as the main module for the presented architecture. It is shown that the proposed multiplier has lower space complexity than any of the existing similar works we found in the literature. The time complexity of the proposed multiplier is slightly higher than the best result among the existing works.
RhoA‐ and RhoD‐dependent regulatory switch of Gα subunit signaling by PAR‐1 receptors in cellular invasion

Thrombin and proteinase‐activated receptors (PAR) specifically regulate several functions that markedly enhance the transformation phenotype such as inflammation, cell proliferation, tumor growth, and metastasis. We recently reported that thrombin inhibits cellular invasion induced by src, hepatocyte growth factor (HGF), and leptin in kidney and colonic epithelial cells via predominant activation of the pertussis toxin (PTx) ‐sensitive G‐proteins Gαo/Gαi. We provide pharmacological and biochemical evidence that in the presence of PTx, PAR‐1 induced cellular invasion through Gα12/Gα13‐ and RhoA/Rho kinase (ROCK) ‐dependent signaling. However, inhibition of the endogenous small GTPase RhoA by the C3 exoenzyme, dominant‐negative N19‐RhoA, activated G26VRhoD, and activators of the nitric oxide/cGMP pathways conferred invasive activity to PAR‐1 via a signaling cascade using Gαq, phospholipase C (PLC), Ca2+/ calmodulin myosin light chain kinase (CaM‐MLCK), and phosphorylation of MLC. We found that cellular invasion induced by the src oncogene is abrogated by inhibitors of the RhoA/ROCK pathway and is independent of PLC/CaM‐MLCK signaling. Our data demonstrate that the RhoA and RhoD small GTPases are acting as a molecular switch of cellular invasion and reveal a novel critical mechanism by which PAR‐1 bypass Gαo/i and RhoA inhibition via differential coupling to heterotrimeric G‐proteins linked to divergent or convergent biological responses. Our data also indicate that Rho GTPases and ROCK mediate a src‐dependent invasion signal in kidney and colonic cancer cells. We conclude that dynamic regulation of Rho GTPases activation and inactivation by oncogenes, growth factors, cGMP‐inducing agents, and adhesion molecules can initiate convergent invasion signals controlled by the thrombin PAR‐1 in cancer cells. —Nguyen, Q. ‐D. , Faivre, S. , Bruyneel, E. , Rivat, C. , Seto, M. , Endo, T. , Mareel, M. , Emami, S. , Gespach, C. RhoA‐ and RhoD‐dependent regulatory switch of Gα subunit signaling by PAR‐1 receptors in cellular invasion. FASEB J. 16, 565–576 (2002)
Foveal Wavelet-Based Color Active Contour

A framework for active contour segmentation in vector-valued images is presented. It is known that the standard active contour is a powerful segmentation method, yet it is susceptible to weak edges and image noise. The proposed scheme uses foveal wavelets for an accurate detection of the edges singularities of the image. The foveal wavelets introduced by Mallat (2000) are known by their high capability to precisely characterize the holder regularity of singularities. Therefore, image contours are accurately localized and are well discriminated from noise. Foveal wavelet coefficients are updated using the gradient descent algorithm to guide the snake deformation to the true boundaries of the objects being segmented. Thus, the curve flow corresponding to the proposed active contour holds formal existence, uniqueness, stability and correctness results in spite of the presence of noise where traditional snake approach may fail.
On grouped OFDM-IDMA

A generalized version of orthogonal frequency division multiplexing interleave division multiple access (OFDM-IDMA) referred to as grouped OFDM-IDMA (G-OFDM-IDMA) is introduced in this paper. By dividing the users into several groups and transmitting each group's data only on part of the subcarriers, the G-OFDM-IDMA system is capable of having much lower decoding complexity compared with the conventional OFDM-IDMA while preserving the bandwidth efficiency and the bit error rate (BER) performance. We study the performance of the proposed scheme in terms of the decoding complexity and diversity order. We also extend the results to the multiple receive antennae case. Simulations are performed to corroborate the performance of the proposed G-OFDM-IDMA.
A comparison of three service composition approaches for end users

This paper compares user preferences for three alternative approaches to service composition, namely: control flow, data flow, and assisted composition approach. The end user perspective is gathered by organizing three focus groups that include discussions and subjective questionnaires, involving 35 non-technical participants. The comparison of alternative composition approaches yielded results confirming that users favour system-driven or assisted composition which deals with technological complexities such as service compatibility problems while allowing user control and involvement. The results also define the requirements for user-friendly design of a service composition tool, which is being developed in the EC-funded project SOA4 All.
The Influence of Culture on IT Governance: A Literature Review

IT governance is crucial for managers to regulate the decision rights and responsibilities that the desired IT behaviors and business objectives are aligned with each other. Additionally, culture in national, organizational or group level can play a role in IT governance and this role is rarely explored in academic research. This paper provides a literature review investigating the impact of culture on IT governance. It is aimed to find the linkage between these two concepts and to promote this area for future research. The literature review was done systematically and the findings are categorized by using an IT governance framework which includes three main components: structures, processes and relational mechanisms. The results indicate there is an influence from national and organizational culture on IT governance, especially on relational mechanisms. However, the number of studies is very few and there is still a lack of knowledge on how culture can influence IT governance.
Deciphering the story of software development through frequent pattern mining

Software teams record their work progress in task repositories which often require them to encode their activities in a set of edits to field values in a form-based user interface. When others read the tasks, they must decode the schema used to write the activities down. We interviewed four software teams and found out how they used the task repository fields to record their work activities. However, we also found that they had trouble interpreting task revisions that encoded for multiple activities at the same time. To assist engineers in decoding tasks, we developed a scalable method based on frequent pattern mining to identify patterns of frequently co-edited fields that each represent a conceptual work activity. We applied our method to our two years of our interviewee's task repositories and were able to abstract 83,000 field changes into just 27 patterns that cover 95% of the task revisions. We used the 27 patterns to render the teams' tasks in web-based English newsfeeds and evaluated them with the product teams. The team agreed with most of our patterns and English interpretations, but outlined a number of improvements that we will incorporate into future work.
Self-guided reconstruction for time-domain fluorescence molecular lifetime tomography

Abstract. Fluorescence probes have distinct yields and lifetimes when located in different environments, which makes the reconstruction of fluorescence molecular lifetime tomography (FMLT) challenging. To enhance the reconstruction performance of time-domain (TD) FMLT with heterogeneous targets, a self-guided L1 regularization projected steepest descent (SGL1PSD) algorithm is proposed. Different from other algorithms performed in time domain, SGL1PSD introduces a time-resolved strategy into fluorescence yield reconstruction. The algorithm consists of four steps. Step 1 reconstructs the initial yield map with full time gate strategy; steps 2–4 reconstruct the inverse lifetime map, the yield map, and the inverse lifetime map again with time-resolved strategy, respectively. The reconstruction result of each step is used as a priori for the reconstruction of the next step. Projected iterated Tikhonov regularization algorithm is adopted for the yield map reconstructions in steps 1 and 3 to provide a solution with iterative refinement and nonnegative constraint. The inverse lifetime map reconstructions in steps 2 and 4 are based on L1 regularization projected steepest descent algorithm, which employ the L1 regularization to reduce the ill-posedness of the high-dimensional nonlinear problem. Phantom experiments with heterogeneous targets at different edge-to-edge distances demonstrate that SGL1PSD can provide high resolution and quantification accuracy for TD FMLT.
Repulsive Affinity-Based Clustering

Clustering is a fundamental problem in machine learning that has applications in a wide variety of domains. It is concerned with finding groups of objects that are closely related under some dissimilarity measure. Most current clustering techniques suffer from a fundamental problem: they do not consider the data density between a point and its corresponding cluster center in the evaluation of the quality of a clustering. Instead, they only consider the dissimilarity between each point and its corresponding cluster center. As a result, they may fail to identify clusters that correspond to a wide mode in the data distribution, because in these clusters, points in the periphery of the mode are relatively far away from the center of the mode. This density problem hampers the performance of, e.g., k-means clustering and affinity propagation [1]. The density problem may be resolved by using (dis)similarities based on diffusion distances [3], as diffusion distances integrate over all paths in a neighborhood graph on the data. However, diffusion distances are computationally expensive to compute, and require the appropriate selection of parameters such as the number of steps in the random walks. Mixture models resolve the density problem by assuming a specific form of the clusters, which allows mixture models to deal with, e.g., elongated clusters. However, as a result of the assumption on the shape of the clusters, mixture models cannot successfully deal with the large variety in clusters shapes that characterizes real-world data.
Optimal Distributed Finite-Time Consensus On Unknown Undirected Graphs

For multiagent networks described by undirected connectivity graphs, the problem of optimal distributed consensus without prior knowledge of global connectivity is considered. The problem is formulated as a decentralized linear quadratic game, and a linear dynamic feedback scheme that couples the tasks of learning the network topology and driving the network state is shown to solve the game and achieve a Nash equilibrium. This solution results in finite-time consensus in minimum time, and optimizes the transient behavior on the way to consensus with respect to a quadratic global performance measure.
Development of context cards: a bus-specific ideation tool for co-design workshops

The importance of context is widely studied in design practice. Still, design workshops often take place in meeting rooms, with the help of generic design materials. To support the participants' understanding of the context of products or services, context-specific design materials can be utilized. The aim of this study was to gain design-relevant insights on how to support ideation with context-specific card-based design tool. Thus, this paper presents Context Cards - a bus-specific ideation cards for co-design workshops. We present the four-phase process of the card tool development in our study of early stage co-design of digital services for the bus context. The findings reveal that the developed Context Cards aided the participants' ability to ideate new services for the specific context. As a concrete outcome of our design research study, we present the final version of the cards, and insights on how they can be used.
Exercise and Pharmacotherapy in the Treatment of Major Depressive Disorder

Objective: To assess whether patients receiving aerobic exercise training performed either at home or in a supervised group setting achieve reductions in depression comparable to standard antidepressant medication (sertraline) and greater reductions in depression compared to placebo controls. Methods: Between October 2000 and November 2005, we performed a prospective, randomized controlled trial (SMILE study) with allocation concealment and blinded outcome assessment in a tertiary care teaching hospital. A total of 202 adults (153 women; 49 men) diagnosed with major depression were assigned randomly to one of four conditions: supervised exercise in a group setting; home-based exercise; antidepressant medication (sertraline, 50–200 mg daily); or placebo pill for 16 weeks. Patients underwent the structured clinical interview for depression and completed the Hamilton Depression Rating Scale (HAM-D). Results: After 4 months of treatment, 41% of the participants achieved remission, defined as no longer meeting the criteria for major depressive disorder (MDD) and a HAM-D score of <8. Patients receiving active treatments tended to have higher remission rates than the placebo controls: supervised exercise = 45%; home-based exercise = 40%; medication = 47%; placebo = 31% (p = .057). All treatment groups had lower HAM-D scores after treatment; scores for the active treatment groups were not significantly different from the placebo group (p = .23). Conclusions: The efficacy of exercise in patients seems generally comparable with patients receiving antidepressant medication and both tend to be better than the placebo in patients with MDD. Placebo response rates were high, suggesting that a considerable portion of the therapeutic response is determined by patient expectations, ongoing symptom monitoring, attention, and other nonspecific factors. BDI = Beck Depression Inventory; CI = confidence interval; HAM-D = Hamilton Depression Rating Scale; ITT = intention-to-treat; MDD = major depressive disorder; SD = standard deviation; SSRIs = selective serotonin reuptake inhibitors; TSH = thyroid stimulating hormone.
Catheter-Related Infections: Diagnosis and Intravascular Treatment

Abstract The diagnosis of catheter-related infections relies on the presence of clinical manifestations of infection and the evidence of colonization of the catheter tip by bacteria, mycobacteria or fungi. The reference method to confirm the latter requires the withdrawal of the catheter for culturing, which frequently turns out to be inconvenient, unnecessary and costly. New methods try to avoid these inconveniences and to assess the presence of tip colonization without withdrawal. One of these methods uses quantitative blood cultures with a jump (>5) in colony counts between blood obtained from the catheter lumen and simultaneously from a peripheral vein. It has a high sensitivity (>80%) and specificity (94%-100%) but is cumbersome and requires both an easy backflow of blood in the catheter and the existence of bacteremia. Cytocentrifugation and acridine orange staining of blood withdrawn from an infected catheter lumen has a sensitivity and a specificity of over 90% for the diagnosis of tip colonization. “Superficial cultures” consist in the semiquantitative culture of the hub, of the skin surrounding the catheter entrance and of the first (1 cm) subcutaneous portion of the catheter after swabbing. Sensitivity of this method is >90% and specificity is >80%, and positive and negative predictive values for catheters (considering together those with and without clinical data of infection) are 66% and 97%, respectively. Endoluminal brushing has turned out to be an impractical and unreliable procedure, at least in our experience. New methods based on the speed of bacterial growth to detectable levels of microorganisms in conventional blood cultures are a new and interesting way of assessing catheter-related infections. Besides, as use of antimicrobial-coated catheters becomes more prevalent, the existing definitions of catheter colonization and catheter-related infection may need to be modified, because such coatings may lead to false-negative culture results. Many catheter infections, diagnosed without catheter withdrawal, can be handled nowadays with the so-called “antibiotic lock-in technique”, which consists in locking the infected catheter lumen with a solution containing antibiotics. A high proportion of infected catheters, mainly those with coagulase-neg-ative staphylococci, can be maintained in place and sterilized with this technique, including catheters in patients with therapeutic failure after receiving conventional intravenous antibiotic therapy. New diagnostic and therapeutic techniques may avoid the unnecessary withdrawal of thousands of efficient, difficult to replace and expensive intravascular lines.
Evaluation of Alcohol-Related Personalized Normative Feedback With and Without an Injunctive Message.

OBJECTIVE Personalized normative feedback (PNF) has been used extensively to reduce alcohol consumption, particularly among heavy drinkers. However, the majority of PNF studies have used only descriptive norms (real or perceived pervasiveness of a given behavior). The purpose of the current study was to explore the efficacy of PNF both with and without an injunctive message indicating approval or disapproval based on the participants' standing relative to other students' drinking levels. This randomized trial evaluated two brief web-based alcohol intervention conditions (descriptive-norms-feedback-only condition versus a descriptive-plus-injunctive-message condition relative to an assessment-only control condition). METHOD Participants included 176 students who had reported at least one heavy drinking episode in the past month. Participants completed baseline and follow-up assessments of perceived norms and drinking. Follow-up assessments were completed at 2 weeks post-intervention by 165 (94%) participants. RESULTS Analyses were conducted using zero-inflated negative binomial regression models. As expected, the descriptive-norms-only condition was effective in reducing drinking among heavier baseline drinkers at follow-up relative to the control condition. However, contrary to expectations, the descriptive-plus-injunctive-message condition did not predict less drinking at follow-up. CONCLUSIONS This study was unique in using an injunctive message as an adjunct to descriptive-norms feedback within the context of drinking. Findings highlight the need for additional research into the role of defensiveness, which may serve as an impediment to using injunctive norms/messages in interventions for problematic substance use and other potentially stigmatizing behaviors.
[An experimental study of the Sabatier CO2 reduction subsytem for space station].

Objective. To develop and fabricate a prototype Sabatier CO2 reduction subsystem for long duration manned space missions. Method. The rationale, equipment and function of the Sabatier CO2 reduction subsystem were introduced. Groundbased experiments with CO2 flows equivalent to a crewsize of 3 persons were conducted to verify the operation performance of the prototype. Result. The start-up temperature is less than 165 degrees C when the start-up time is 14 min; the lean component H2/CO2 conversion efficiency is over 95 percent when H2/CO2 molar ratios is 1.9-5.0; The water produced is nearly colorless and neutral. Conclusion. The prototype Sabatier CO2 reduction subsystem is simple in operation and the test results showed that design goals were achieved.
Reduced-reference video QoE assessment method based on image feature information

This paper discusses how to assess video Quality of Experience (QoE) with image feature information which includes texture and saliency information. In order to compress and transmit the feature information, wavelet transform is conducted and the high-frequency component histograms are fitted using generalized Gaussian distribution. At end user side, the video distortion is measured by using Kullback-Leibler Divergence (KLD) and therefore MOS is evaluated using neural network fitting. The LIVE Video Quality Database is used for testing the performance of proposed method. result confirms that the proposed method is competitive and suitable for assessing the QoE of real-time video service.
A ProbabiUstic Approach to Japanese Lexical Analysis

We report on a project to develop a stochastic lexical analyzer for Japanese and to compare the accuracy of this approach with the results obtained using conventional rule-based methods. In contrast with standard, knowledge intensive methods, the stochastic approach to lexical analysis uses statistical techniques that are based on probabilistic models. This approach has not previously been applied to unrestricted Japanese text and promises to yield insights into word formation and other morphological processes in Japanese. An experiment designed to assess the accuracy of a simple statistical technique for segmenting hiragana strings showed that this method was able to perform the task with a relatively low rate of error. A debate is being waged in the field of machine translation about the degree to which rationalist and empiricist approaches to linguistic knowledge should be used in MT systems. While most participants in the debate seem to agree that both methods are useful, albeit for different tasks, few have compared the limits of knowledge based and statistics based techniques in the various stages of translation.