Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic Reconstruction of the Building Blocks of Molecular Interaction Networks

(ABSTRACT) High-throughput whole-genome biological assays are highly intricate and difficult to interpret. The molecular interaction networks generated from evaluation of those experiments suggest that cellular functions are carried out by modules of interacting molecules. Reverse-engineering the modular structure of cellular interaction networks has the promise of significantly easing their analysis. We hypothesize that: (i) cellular wiring diagrams can be decomposed into overlapping modules, where each module is a set of coherently-interacting molecules and (ii) a cell responds to a stress or a stimulus by appropriately modulating the activities of a subset of these modules. Motivated by these hypotheses, we develop models and algorithms that can reverse-engineer molecular modules from large-scale functional genomic data. We address two major problems: (I) Given a wiring diagram and genome-wide gene expression data measured after the application of a stress or in a disease state, compute the active network of molecular interactions perturbed by the stress or the disease. (II) Given the active networks for multiple stresses, stimuli, or diseases, compute a set of network legos, which are molecular modules with the property that each active network can be expressed as an appropriate combination of a subset of modules. To address the first problem, we propose an approach that computes the most-perturbed subgraph of a curated pathway of molecular interactions in a disease state. Our method is based on a novel score for pathway perturbation that incorporates both differential gene expression and the interaction structure of the pathway. We apply our method to a compendium of cancer types. We show that the significance of the most perturbed sub-pathway is frequently larger than that of the entire pathway. We identify an association that suggests that IL-2 infusion may have a similar therapeutic effect in bladder cancer as it does in melanoma. We propose two models to address the second problem. First, we formulate a Boolean model for constructing network legos from a set of active networks. We reduce the problem of computing network legos to that of constructing closed biclusters in a binary matrix. Applying this method to a compendium of 13 stresses on human cells, we automatically detect that about four–six hours after treatment with chemicals cause endoplasmic reticulum stress, fibroblasts shut down the cell cycle far more aggressively than fibroblasts or HeLa cells do in response to other treatments. Our second model represents each active network as an additive combination of network legos. We …
Make or buy in a mature industry? models of client - supplier relationships under TCT and RBV perspectives

In this paper, we use the transaction cost theory [ TCT] and the resource-based view [RBV] to discuss three propositions on the models of client-supplier relat ionships in mature industries. The two theories see m to advance different organizational forms of the clien t-supplier relationships, and in some instances are contradictory. How should firms organize to prosper and grow, namely in the international markets? Thr ough the case study of three Portuguese packaging firms, wit h primary (interviews) and secondary data, we discu ss how the three firms deploy three distinct strategic org anization models in a mature industry. One firm uti lizes marketbased governance mechanisms, and concentrates its production in a few selected locations. Another firm vertically integrates almost the entire value chain of the product to provide full service to its clie nts. The third firm operates in a model of integrated outsourcing, with the installation wall to wall with its clients. The clientsupplier models adopted by these firms are based on efficient, stable, and trustworthy relationships t hat permit them to focus on their core competences and reduce transaction costs. The superior performance of firm s requires a proper alignment of hierarchical and rel ational governance, taking the dimensions of their transactions into consideration.
PPM: Preamble and Postamble-Based Multi-Packet Reception for Green ZigBee Communication

ZigBee, a low-power wireless communication technology, has been used in various applications, such as smart health/home/buildings. The proliferation of ZigBee-based applications (and thus devices), however, makes the concurrent transmissions—i.e., multiple transmitters send packets to the same receiver at the same time—common in practice, leading to inevitable collisions. Either retransmissions caused by collisions or the collision avoidance mechanism, e.g., CSMA/CA, introduces plenty of energy consumption. To facilitate the green and concurrent transmissions of ZigBee, we design pre/post-amble-based multi-packet reception (PPM), a method that recovers the collided ZigBee messages by exploiting their collision-free chips and the overlapped chips in their pre/post-ambles. We elaborately attach short postamble to standard ZigBee packet by manipulating the ZigBee payload, which can be compatible with standard ZigBee and only introduce negligible energy overhead. We further propose two design enhancements, cross-validation and reference chips calibration, to ensure the accuracy of PPM. Such a collision recovery of PPM reduces the retransmissions caused by collisions and eliminates the energy overhead of CSMA/CA simultaneously, facilitating the realization of green ZigBee. We have prototyped and evaluated PPM with USRP, showing PPM recovers the collided messages with bit-error-rates in the order of ${10}^{-6}$ , which is magnitudes lower than state-of-the-art methods. Experimental results show that PPM can achieve packet reception ratio more than 90% and less than 20 retransmissions in a concurrent transmission experiment with 400 packets resulting in negligible packet retransmission cost of energy.
Improved inter-modality image registration using normalized mutual information with coarse-binned histograms

SUMMARY In this paper we extend the method of inter-modality image registration using the maximization of normalized mutual information (NMI) for the registration of [ 18 F]-2-fluoro-deoxy-D-glucose (FDG)positron emission tomography (PET) with T1-weighted magnetic resonance (MR) volumes. We investigate the impact on the NMI maximization with respect to using coarse-to-fine grained B-spline bases and to the number of bins required for the voxel intensity histograms of each volume. Our results demonstrate that the efficiency and accuracy of elastic, as well as rigid body, registration is improved both through the use of a reduced number of bins in the PET and MR histograms, and of a limited coarse-to-fine grain interpolation of the volume data. To determine the appropriate number of bins prior to registration, we consider the NMI between the two volumes, the mutual information content of the two volumes, as a function of the binning of each volume. Simulated data sets are used for validation and the registration improves that obtained with a standard approach based on the Statistical Parametric Mapping software. Copyright q 2008 John Wiley & Sons, Ltd.
An exact theory of the industrial evolution and national recovery

Preface We started this work in a case study for graduate students, convinced that an exact theory of economic growth with forecasting quality must and can be found. Subsequently most of our decisions in industrial research and development had to be made without academic backing. Some of them led us to question fundamental assumptions. For instance, we learned that technical progress cannot be responsible for the pace of macroeconomic growth. The level of education and the last century's reservoir of relevant but unused patents and prototypes were convincing and growing, although the real long term national growth rates per capita of leading nations decreased since 1955. The investment question of how long China would continue to grow with real 10 percent p.a. per capita got us back into the fundamental problems of economic growth theory. We solved some of them with the discovery of a causal connection between the depth of a disaster and the stability of recovery. The necessary and sufficient conditions for success were complete renormalization of the economy, social coherence, and evolution in peace. Our theory and first predictions were published 12 years ago although we did not understand why just 3 decisive parameters determined long term growth, and what kept them constant from 1800 to date. Their continued constancy is decisive for the quality of predictions. Back in academia this work benefited from the discovery of an S-functional parallelism between the mean life expectancy and the envelope of the best real GDPs per capita above all political and financial disasters. This identified the decisive parameters as genetically stabilized constants of the human species. Therefore the present version of our natural theory has full forecasting power unless global resources supersede human biology in limiting the pace of economic growth per capita. In retrospect this was to be expected for a species at the end of the food chain guided by natural science.
Indoor RFID alignment system for service station

Nowadays, motorized vehicles are essential in our daily lives. Therefore, fuel supply services should be efficient and easily accessible. Fuel supplying may encounter some difficulties, such as queues, non-continuous availability of fuel, and fraud. The problems of long waiting queues and non-continuous availability of fuel can be solved by going to another near fuel station. However, fraud is a more serious issue that is more difficult to solve. We developed, by research, an intelligent system for fuel supply management to solve this problem. For safety reasons, we must avoid the risk of causing a spark in the fueling environment. In particular, an electric system close to the pump, the hose, or the vehicle fuel tank may be a risk. We opted for the RFID (Radio Frequency IDentification) technology and the use of passive tags, since semi-passive or active tags involve a battery, on one hand, and are significantly more expensive, on the other hand. A motorized vehicle is identified by a passive RFID tag; two other passive RFID tags are used for the fueling nozzle of each fuel pump. Our work consists of the design, by research, of the required system and focuses on the optimization of the topology of antennas and tags so that frauds are prevented. The technique is based on the alignment of tags.
CA4IOT: Context Awareness for Internet of Things

Internet of Things (IoT) will connect billions of sensors deployed around the world together. This will create an ideal opportunity to build a sensing-as-a-service platform. Due to large number of sensor deployments, there would be number of sensors that can be used to sense and collect similar information. Further, due to advances in sensor hardware technology, new methods and measurements will be introduced continuously. In the IoT paradigm, selecting the most appropriate sensors which can provide relevant sensor data to address the problems at hand among billions of possibilities would be a challenge for both technical and non-technical users. In this paper, we propose the Context Awareness for Internet of Things (CA4IOT) architecture to help users by automating the task of selecting the sensors according to the problems/tasks at hand. We focus on automated configuration of filtering, fusion and reasoning mechanisms that can be applied to the collected sensor data streams using selected sensors. Our objective is to allow the users to submit their problems, so our proposed architecture understands them and produces more comprehensive and meaningful information than the raw sensor data streams generated by individual sensors.
humanaquarium: A Participatory Performance System

humanaquarium is a self-contained, transportable performance environment that is used to stage technology-mediated interactive performances in public spaces. Drawing upon the creative practices of busking and street performance, humanaquarium incorporates live musicians, real-time audiovisual content generation, and frustrated total internal reflection (FTIR) technology to facilitate participatory interaction by members of the public.
Small Molecule-Based Promotion of PKCα-Mediated β-Catenin Degradation Suppresses the Proliferation of CRT-Positive Cancer Cells

Aberrant accumulation of intracellular β-catenin is a well recognized characteristic of several cancers, including prostate, colon, and liver cancers, and is a potential target for development of anticancer therapeutics. Here, we used cell-based small molecule screening to identify CGK062 as an inhibitor of Wnt/β-catenin signaling. CGK062 promoted protein kinase Cα (PKCα)-mediated phosphorylation of β-catenin at Ser33/Ser37, marking it for proteasomal degradation. This reduced intracellular β-catenin levels and consequently antagonized β-catenin response transcription (CRT). Pharmacological inhibition or depletion of PKCα abrogated CGK062-mediated phosphorylation and degradation of β-catenin. In addition, CGK062 repressed the expression of the genes encoding cyclin D1, c-myc, and axin-2, β-catenin target genes, and thus inhibited the growth of CRT-positive cancer cells. Furthermore, treatment of nude mice bearing PC3 xenograft tumors with CGK062 at doses of 50 mg/kg and 100 mg/kg (i.p.) significantly suppressed tumor growth. Our findings suggest that CGK062 exerts its anticancer activity by promoting PKCα-mediated β-catenin phosphorylation/degradation. Therefore, CGK062 has significant therapeutic potential for the treatment of CRT-positive cancers.
Drosophila QVR/SSS Modulates the Activation and C-Type Inactivation Kinetics of Shaker K+ Channels

The quiver/sleepless (qvr/sss) gene encodes a small, glycosylphosphatidylinositol-anchored protein that plays a critical role in the regulation of sleep in Drosophila. Loss-of-function mutations in qvr/sss severely suppress sleep and effect multiple changes in in situ Shaker K+ currents, including decreased magnitude, slower time-to-peak, and cumulative inactivation. Recently, we demonstrated that SLEEPLESS (SSS) protein modulates Shaker channel activity, possibly through a direct interaction at the plasma membrane. We show here that SSS accelerates the activation of heterologously expressed Shaker channels with no effect on deactivation or fast N-type inactivation. Furthermore, this SSS-induced acceleration is sensitive to the pharmacological disruption of lipid rafts and sufficiently accounts for the slower time-to-peak of in situ Shaker currents seen in qvr/sss mutants. We also find that SSS decreases the rate of C-type inactivation of heterologously expressed Shaker channels, providing a potential mechanism for the cumulative inactivation phenotype induced by qvr/sss loss-of-function mutations. Kinetic modeling based on the in vitro results suggests that the SSS-dependent regulation of channel kinetics accounts for nearly 40% of the decrease in Shaker current magnitude in flies lacking SSS. Sleep duration in qvr/sss-null mutants is restored to normal by a qvr/sss transgene that fully rescues the Shaker kinetic phenotypes but only partially rescues the decrease in current magnitude. Together, these results suggest that the role of SSS in the regulation of sleep in Drosophila correlates more strongly with the effects of SSS on Shaker kinetics than current magnitude.
Relationship Dissolution Understood in Terms of Learning Barriers

Research on the ending of relationships has been conducted in the areas of businessto-business, business-to-consumer, romantic or personal, marketing channels, clientagency relationships in advertising and accounting, joint ventures, and strategic alliances. Business relationship dissolution can be considered in terms of definitions, outcomes, antecedents, and processes (Tahtinen and Halinen-Kaila (2002)). External or internal factors may increase the likelihood of dissolution, though this can be mediated by actor, dyad, or network factors (Tahtinen and Halinen-Kaila (1997)). A dynamic perspective considers relationship dissolution as a process. Tahtinen and Halinen-Kaila (1997) and Tahtinen (2002) proposed a model of the process of business net dissolution, with six interconnected stages, from intra-company to network levels. Researchers have considered the dissolution of both vertical and horizontal relationships among actors. It is fair to say that the majority of these studies have 1 Telephone 00 47 67 55 70 00, E-mail: lena.bygballe@bi.no or debbie.harrison@bi.no
A Personal Paradigm for Computer-Aided Visualization

We consider visualization to be a creative human endeavour and explore how the computer can assist this process, beyond mere image production. We propose a computer-aided visualization system which is driven by the unique abilities of each user. From an initial specification, the system provides a wide variety of visual representations by making combinations of components. From this range of choices, the user makes selections based on personal criteria for meaningfulness. These selections determine the fitness of the displayed representations and this information is used to provide new alternatives for display, consideration and selection. In this way, the space of all available visual representations can be effectively navigated under the user’s control. The operation of this computerized tool complements the process of human inventive thought, as described by many scholars.
Correlation of the COMT Val158Met polymorphism with latitude and a hunter-gather lifestyle suggests culture-gene coevolution and selective pressure on cognition genes due to climate

Dual-inheritance theory posits that the genotype has an impact on the evolution of human behavior and that cultural traits can be constrained by genetic imperatives. A large body of studies pro- vides evidence that the functional catechol-O-methyltransferase (COMT) Val158Met polymorphism is associated with executive function, working memory (WM), and intelligence. A survey of the popu- lation genetics database provides evidence that COMT gene frequencies vary across populations. The aim of the present study was to test the hypothesis that the COMT gene has an impact on cultural evo- lution, specifically on the adoption of an agricultural vs. a hunter-gatherer lifestyle. Statistically sig- nificant differences in COMT allele frequencies between hunter-gatherer and agricultural societies were found. Ethnic groups whose economy is based on farming have higher frequencies of the Met allele (symbol: A), whereas societies based on a hunter-gatherer economy have very low frequencies of the Met allele and a disproportionate predominance of the Val allele. Moreover, the frequency of the Met allele was positively correlated to the populations' IQ (r = 0.57). The FNBP1L gene (rs236330) is associated with childhood and adult intelligence and it varies in frequency across popu- lations. Frequency of rs236330 was also significantly correlated with the populations' IQ (r = 0.81). COMT and FNBP1L had fairly similar geographical distributions (r = 0.44) although the result did not reach statistical significance. The results suggest that the genotype of a population influences its cul- tural development in fairly specific and predictable ways. Met allele frequency was positively corre- lated with latitude (r = 0.56), suggesting selective pressure due to climate.
Educated for migration? Blind spots around labor market conditions, competence building, and international mobility

Young European graduates are crossing borders to work abroad more often than in the past. This trend is particularly evident in Southern Europe, where recent economic downturn has significantly diminished professional opportunities and career prospects. This study will investigate Spain, a country where unemployment has increased dramatically since 2008, as a case study to examine recent graduate’s experiences to develop a professional career in Germany. In particular, this study will draw upon various sources: official statistics; review literature; and education and training policies throughout the European Union. The investigation features an interview with Spanish graduates working in Germany to offer insight into the experiences of perhaps the best-prepared generation of the Spanish workforce. Our results indicate that young Spaniards, leaving the country to work out of necessity rather than choice, learn through the benefits and challenges of a career abroad. We finish our article by discussing the notions of education, competencies and adaptation, and how citizen and professional identities are redefined after the experience of working abroad.
Bank lending standards, the cost channel and inflation dynamics

If firms borrow working capital to finance production, then nominal interest rates have a direct influence on inflation dynamics, which appears to be the case empirically. However, interest rates may only partly mirror the cost of working capital. In this paper we explore the role of bank lending standards as a potential additional cost source and evaluate their empirical importance in explaining inflation dynamics in the US and in the euro area.
A Fast Algorithm for Undedetermined Mixing Matrix Identification Based on Mixture of Guassian (MoG) Sources Model

This paper proposes a new fast method for identifying the mixing matrix based on a binary state mixture of Gaussian (MoG) source model. First, a necessary discussion for solving the mixing matrix detection is offered under the multiple dominant circumstance. Second, a density detection method is presented to improve the identification performance. Simulations are given to demonstrate the effectiveness of our proposed approach.
Receptor Occupancy and Channel-opening Kinetics

AMPA glutamate ion channels are tetrameric receptors in which activation to form the open channel depends on the binding of possibly multiple glutamate molecules. However, it is unclear whether AMPA receptors bound with a different number of glutamate molecules (i.e. one being the minimal and four being the maximal number of glutamate molecules) open the channels with different kinetic constants. Using a laser pulse photolysis technique that provides microsecond time resolution, we investigated the channel-opening kinetic mechanism of a nondesensitizing AMPA receptor, i.e. GluR1Qflip L497Y or a leucine-to-tyrosine substitution mutant, in the entire range of glutamate concentrations to ensure receptor saturation. We found that the minimal number of glutamate molecules required to bind to the receptor and to open the channel is two (or n = 2), and that the entire channel-opening kinetics can be adequately described by just one channel-opening rate constant, kop, which correlates to n = 2. This result suggests that higher receptor occupancy (n = 3 and 4) does not give rise to different kop values or, at least, not appreciably if the kop values are different. Furthermore, compared with the wild-type receptor (Li, G., and Niu, L. (2004) J. Biol. Chem. 279, 3990-3997), the channel-opening and channel-closing rate constants of the mutant are 1.5- and 13-fold smaller, respectively. Thus, the major effect of this mutation is to decrease the channel-closing rate constant by stabilizing the open channel conformation.