Miracle-dz/UniFAR-FTUs huggingface dataset:
The Heteromultimeric Debranching Enzyme Involved in Starch Synthesis in Arabidopsis Requires Both Isoamylase1 and Isoamylase2 Subunits for Complex Stability and Activity

Isoamylase-type debranching enzymes (ISAs) play an important role in determining starch structure. Amylopectin – a branched polymer of glucose – is the major component of starch granules and its architecture underlies the semi-crystalline nature of starch. Mutants of several species lacking the ISA1-subclass of isoamylase are impaired in amylopectin synthesis. Consequently, starch levels are decreased and an aberrant soluble glucan (phytoglycogen) with altered branch lengths and branching pattern accumulates. Here we use TAP (tandem affinity purification) tagging to provide direct evidence in Arabidopsis that ISA1 interacts with its homolog ISA2. No evidence for interaction with other starch biosynthetic enzymes was found. Analysis of the single mutants shows that each protein is destabilised in the absence of the other. Co-expression of both ISA1 and ISA2 Escherichia coli allowed the formation of the active recombinant enzyme and we show using site-directed mutagenesis that ISA1 is the catalytic subunit. The presence of the active isoamylase alters glycogen biosynthesis in E. coli, resulting in colonies that stain more starch-like with iodine. However, analysis of the glucans reveals that rather than producing an amylopectin like substance, cells expressing the active isoamylase still accumulate small amounts of glycogen together with a population of linear oligosaccharides that stain strongly with iodine. We conclude that for isoamylase to promote amylopectin synthesis it needs to act on a specific precursor (pre-amylopectin) generated by the combined actions of plant starch synthase and branching enzyme isoforms and when presented with an unsuitable substrate (i.e. E. coli glycogen) it simply degrades it.
Cross-Layer Design of Sequential Detectors in Sensor Networks

A network of sensors polled by a mobile agent (the SENMA paradigm) is used for detection purposes, with both the remote nodes and the mobile agent implementing Wald's sequential tests. When polled, each remote node transmits its local decision (if any) to the agent, and two network/agent communication schemes are considered. One of these is designed with specific care to the network's energy consumption. In both cases, collisions over the common communication channel are precluded by the sequentiality of the sensors' query. The system performances in terms of average decision time, error probability, and network energy consumption are derived in exact analytical form. A tradeoff exists between the amount and the reliability of the information that the rover may collect: At optimality, the decentralized system overcomes a single supernode by orders of magnitude in terms of decision time, while only 30% of the sensors encountered by the mobile agent spend energy to reveal themselves. The remaining sensors contribute to the detection process by their silence
Single image super-resolution using compressive sensing with learned overcomplete dictionary

This paper proposes a novel framework that unifies the concept of sparsity of a signal over a properly chosen basis set and the theory of signal reconstruction via compressed sensing in order to obtain a high-resolution image derived by using a single down-sampled version of the same image. First, we enforce sparse overcomplete representations on the low-resolution patches of the input image. Then, using the sparse coefficients as obtained above, we reconstruct a high-resolution output image. A blurring matrix is introduced in order to enhance the incoherency between the sparsifying dictionary and the sensing matrices which also resulted in better preservation of image edges and other textures. When compared with the similar techniques, the proposed method yields much better result both visually and quantitatively.
Adaptive evolution of baker's yeast in a dough‐like environment enhances freeze and salinity tolerance

We used adaptive evolution to improve freeze tolerance of industrial baker's yeast. Our hypothesis was that adaptation to low temperature is accompanied by enhanced resistance of yeast to freezing. Based on this hypothesis, yeast was propagated in a flour‐free liquid dough model system, which contained sorbitol and NaCl, by successive batch refreshments maintained constantly at 12°C over at least 200 generations. Relative to the parental population, the maximal growth rate (µmax) under the restrictive conditions, increased gradually over the time course of the experiment. This increase was accompanied by enhanced freeze tolerance. However, these changes were not the consequence of genetic adaptation to low temperature, a fact that was confirmed by prolonged selection of yeast cells in YPD at 12°C. Instead, the experimental populations showed a progressive increase in NaCl tolerance. This phenotype was likely achieved at the expense of others traits, since evolved cells showed a ploidy reduction, a defect in the glucose derepression mechanism and a loss in their ability to utilize gluconeogenic carbon sources. We discuss the genetic flexibility of S. cerevisiae in terms of adaptation to the multiple constraints of the experimental design applied to drive adaptive evolution and the technologically advantageous phenotype of the evolved population.
Casimir energy and a cosmological bounce

We review different computation methods for the renormalized energy–momentum tensor of a quantized scalar field in an Einstein static universe. For the extensively studied conformally coupled case, we check their equivalence; for different couplings, we discuss violation of different energy conditions. In particular, there is a family of masses and couplings which violate the weak and strong energy conditions but do not lead to spacelike propagation. Amongst these cases is that of a minimally coupled massless scalar field with no potential. We also point out a particular coupling for which a massless scalar field has vanishing renormalized energy–momentum tensor. We discuss the backreaction problem and in particular the possibility that this Casimir energy could both source a short inflationary epoch and avoid the big bang singularity through a bounce.
Comparison of online social relations in volume vs interaction: a case study of cyworld

Online social networking services are among the most popular Internet services according to Alexa.com and have become a key feature in many Internet services. Users interact through various features of online social networking services: making friend relationships, sharing their photos, and writing comments. These friend relationships are expected to become a key to many other features in web services, such as recommendation engines, security measures, online search, and personalization issues. However, we have very limited knowledge on how much interaction actually takes place over friend relationships declared online. A friend relationship only marks the beginning of online interaction. Does the interaction between users follow the declaration of friend relationship? Does a user interact evenly or lopsidedly with friends? We venture to answer these questions in this work. We construct a network from comments written in guestbooks. A node represents a user and a directed edge a comments from a user to another. We call this network an activity network. Previous work on activity networks include phone-call networks [34, 35] and MSN messenger networks [27]. To our best knowledge, this is the first attempt to compare the explicit friend relationship network and implicit activity network. We have analyzed structural characteristics of the activity network and compared them with the friends network. Though the activity network is weighted and directed, its structure is similar to the friend relationship network. We report that the in-degree and out-degree distributions are close to each other and the social interaction through the guestbook is highly reciprocated. When we consider only those links in the activity network that are reciprocated, the degree correlation distribution exhibits much more pronounced assortativity than the friends network and places it close to known social networks. The k-core analysis gives yet another corroborating evidence that the friends network deviates from the known social network and has an unusually large number of highly connected cores. We have delved into the weighted and directed nature of the activity network, and investigated the reciprocity, disparity, and network motifs. We also have observed that peer pressure to stay active online stops building up beyond a certain number of friends. The activity network has shown topological characteristics similar to the friends network, but thanks to its directed and weighted nature, it has allowed us more in-depth analysis of user interaction.
Chapter 3 | Validation of Two Outcome Measures

Background: Transparency in psychiatry can be increased by the use of routine outcome monitoring (ROM) instruments. Instruments should be easy to use and take very little time to complete; they also need to have psychometric qualities, about interpersonal and social functioning. Aim: To investigate to what extent the Dutch translation of the combination of the Health of the Nation Outcome Scales (HoNOS) and Outcome Questionnaire (OQ) meets the above-mentioned quality criteria and to examine how the combination relates to the Symptoms CheckList (SCL-90). Method: Data for 148 patients collected at three measurement time-points were available for analysis. The psychometric qualities of the instruments and their sensitivity to change were carefully monitored. Results: The three scales showed high values for internal consistency (Cronbach's alpha). The HoNOS total score and the subscales of the OQ correlated reasonably well with the SCL-90 total score (convergent validity). At the first measurements, patients with a comorbid diagnosis had the lowest scores (discriminant validity). The clinically significant change between T1 and T2 and between T2 and T3 was sufficiently high for all measurement instruments. Conclusion: The combination of the HoNOS rating scale and the self-report list OQ seems to be suitable for ROM in psychiatry.
Mutuality in the management of human resources: assessing the quality of alignment in employment relationships

How can managers improve the alignment of organisational and individual interests in the management of human resources? This article integrates a diverse set of literatures to propose three tests of mutuality in employment relationships: (a) the quality of the match between the organisation's needs for human capabilities and the individual's needs to deploy and develop them; (b) the extent to which the organisation's dual needs for commitment and flexibility are aligned with the needs of individuals for security and community; and (c) the extent to which both parties feel they are making a worthwhile return on their investment. These tests form a starting point for assessing and modelling the quality of employment relationships in particular contexts.
Fear in Horses Responses to Novelty and Habituation

Christensen, J.W. , 2005. Fear responses in horses. Licentiate thesis. ISSN 1652-750X, ISBN 91-576-6887-6 Fear is generally considered to be an undesirable emotional state that may reduce welfare, growth and reproductive performance in animals. Fear in horses is additionally problematic, because fear reactions can cause serious injury to both horse and human. Horses are primarily used for sports and leisure for a large number of children and young women. Unfortunately, horse riding ranks as one of the most dangerous sports in terms of the number and seriousness of accidents, and the ability of a horse to habituate to a range of otherwise frightening stimuli greatly increases safety in the horse-human relationship. However, there is a lack of research on fear reactions and no published research on basic habituation processes in horses. This licentiate project aimed to investigate the types of fear responses horses show towards novel stimuli acting on different senses, and to study how horses learn to be confident with an otherwise frightening stimulus using classical learning theory techniques. The experiments were conducted on two different groups of naïve stallions (n=24 and n=27). The first experiment showed that horses responded differently towards an olfactory stimulus compared to auditory and visual stimuli. The heart rate responses correlated between tests and probably reflected a non-differentiated activation of the sympathetic nervous system, while the behavioural responses were linked to the type of stimulus. The second experiment showed that gradual habituation was the most effective training method for horses to learn to react calmly to an otherwise frightening stimulus, compared to classic habituation and associative learning. Heart rate data revealed that horses may show physiological responses even when their behavioural response towards the stimulus has ceased. Choice of training method is likely to be especially important for the most fearful horses.
Searching for Autocoherence in the Cortical Network with a Time-Frequency Analysis of the Local Field Potential

Gamma-band peaks in the power spectrum of local field potentials (LFP) are found in multiple brain regions. It has been theorized that gamma oscillations may serve as a ‘clock’ signal for the purposes of precise temporal encoding of information and ‘binding’ of stimulus features across regions of the brain. Neurons in model networks may exhibit periodic spike firing or synchronized membrane potentials that give rise to a gamma-band oscillation that could operate as a ‘clock’. The phase of the oscillation in such models is conserved over the length of the stimulus. We define these types of oscillations to be ‘autocoherent’. We investigated the hypothesis that autocoherent oscillations are the basis of the experimentally observed gamma-band peaks: the autocoherent oscillator (ACO) hypothesis. To test the ACO hypothesis, we developed a new technique to analyze the autocoherence of a time-varying signal. This analysis used the continuous Gabor transform to examine the time evolution of the phase of each frequency component in the power spectrum. Using this analysis method, we formulated a statistical test to compare the ACO hypothesis with measurements of the LFP in macaque primary visual cortex, V1. The experimental data were not consistent with the ACO hypothesis. Gamma-band activity recorded in V1 did not have the properties of a ‘clock’ signal during visual stimulation. We propose instead that the source of the gamma-band spectral peak is the resonant V1 network driven by random inputs.
Re‐examining mimetic isomorphism

Purpose – In this study the aim is to analyze multiple decisions in mergers and acquisitions (M&As) strategy to verify whether isomorphism appears in these decisions when a firm imitates others and to determine under what conditions the link between imitation and the degree of similarity in M&As is weakened.Design/methodology/approach – With a sample of 4,881 completed M&As in the financial service industry, the authors adopt the generalized multivariate regression model to test the hypothesized effects of the independent variables on the degree of similarity in M&As.Findings – Support is found for the mimetic isomorphism argument. Furthermore, firm experience and local market segmentation weaken the positive relationship between imitation and the degree of similarity in M&As.Originality/value – This study enhances the understanding of mimetic isomorphism by not only verifying the relationship between imitation and isomorphism, but also integrating the role of organizational active agency (firm experience.
Neural Reactivation Reveals Mechanisms for Updating Memory

Our ability to remember new information is often compromised by competition from prior learning, leading to many instances of forgetting. One of the challenges in studying why these lapses occur and how they can be prevented is that it is methodologically difficult to “see” competition between memories as it occurs. Here, we used multi-voxel pattern analysis of human fMRI data to measure the neural reactivation of both older (competing) and newer (target) memories during individual attempts to retrieve newer memories. Of central interest was the following: (1) whether older memories were reactivated during retrieval of newer memories; (2) how reactivation of older memories related to retrieval performance; and (3) whether neural mechanisms engaged during the encoding of newer memories were predictive of neural competition experienced during retrieval. Our results indicate that older and newer visual memories were often simultaneously reactivated in ventral temporal cortex—even when target memories were successfully retrieved. Importantly, stronger reactivation of older memories was associated with less accurate retrieval of newer memories, slower mnemonic decisions, and increased activity in anterior cingulate cortex. Finally, greater activity in the inferior frontal gyrus during the encoding of newer memories (memory updating) predicted lower competition in ventral temporal cortex during subsequent retrieval. Together, these results provide novel insight into how older memories compete with newer memories and specify neural mechanisms that allow competition to be overcome and memories to be updated.
The Management Performance of the U.S. States

The Maxwell School's Government Performance Project rated the management successes of the 50 states in several areas, such as capital management, human resources and information technology in 1998 and 2000. Variability among the states was significant. Viewing the Maxwell School data as something to be explained, we focus on political institutions, social characteristics and the economic environments in the states. We review hypotheses that predict management performance, and we test them empirically. We find that states high in social capital, states with professional legislatures, and states with vibrant entrepreneurial economies are more likely to be better managed. A state’s tax burden and the governor’s powers seem unrelated to the Maxwell School scores. States with a high density of “good government” groups tend to be poor performers, presumably because citizens join such groups hoping to improve their unsatisfactory state governments. Please note: The larger study that this paper discusses will be published in a book by The Brookings Institution in early 2005.
An Investigation of the Importance of Mechanisms and Parameters in a Multicellular Developmental System

Multicellular organisms in biology possess invaluable characteristics, which artificial systems in engineering lack, such as adaptivity and robustness. Modeling biologically inspired multicellular developmental systems in evolutionary computation have been considered for a number of years, and there exist many developmental simulations that capture multicellular characteristics of biological organisms. However, the relative importance of many mechanisms in such models is still poorly understood. This paper undertakes a detailed investigation of the importance of many mechanisms and parameters on the organizational behavior of a gene regulatory network based artificial developmental system via classical pattern matching experiments. The work leads to an improved understanding of artificial multicellular development, which will assist in its utilization in the application of evolutionary computation. It may also provide a better understanding of mechanisms of biological development.
Symmetric eigenfilters for partial shortening in ADSL DMT transceivers

A partial shortening method of equalization for xDSL is presented. The novel method is suitable for FDD systems, shortening the effective channel impulse response and, additionally, achieving out-of-band noise reduction. A family of solutions based on linear phase FIR equalizers is described. The mathematical framework for all symmetric filters is developed. Channel shortening and bit rate simulation results for several VDSL test loops, show that the novel method yields a similar performance and reduces the out-of-band noise, with a considerably lower mathematical complexity and a simpler implementation.
Unsaturated fatty acid regulation of cytochrome P450 expression via a CAR-dependent pathway

The liver is responsible for key metabolic functions, including control of normal homoeostasis in response to diet and xenobiotic metabolism/detoxification. We have shown previously that inactivation of the hepatic cytochrome P450 system through conditional deletion of POR (P450 oxidoreductase) induces hepatic steatosis, liver growth and P450 expression. We have exploited a new conditional model of POR deletion to investigate the mechanism underlying these changes. We demonstrate that P450 induction, liver growth and hepatic triacylglycerol (triglyceride) homoeostasis are intimately linked and provide evidence that the observed phenotypes result from hepatic accumulation of unsaturated fatty acids, which mediate these phenotypes by activation of the nuclear receptor CAR (constitutive androstane receptor) and, to a lesser degree, PXR (pregnane X receptor). To our knowledge this is the first direct evidence that P450s play a major role in controlling unsaturated fatty acid homoeostasis via CAR. The regulation of P450s involved in xenobiotic metabolism by this mechanism has potentially significant implications for individual responses to drugs and environmental chemicals.
Dynamic Pricing and Inventory Control in a Make-to-Stock Queue With Information on the Production Status

This paper addresses the dynamic pricing problem of a single-item, make-to-stock production system. Demand arrives according to Poisson processes with changeable arrival rate dependent on the selling price. Item processing times follow an Erlang distribution, which allows to use the information on the production status in a tractable way. The objective is to identify a dynamic control policy that decides production and adjusts the price to maximize the long-run total discounted profit. An optimal policy is based on the so-called work-storage level that captures the information of the inventory level and the status of ongoing production process. Specifically, we show that: 1) the finished goods inventory is optimally managed by a critical stage level policy: when the inventory is below a certain work-storage level, production is started if the system is currently idle and 2) the price is optimally set by threshold levels: a certain price is posted when the work-storage level is at or below a threshold corresponding to that level of price. Moreover, we develop an efficient algorithm to compute the optimal policy.
Data Aggregation at the Level of Molecular Pathways Improves Stability of Experimental Transcriptomic and Proteomic Data

High throughput technologies opened a new era in biomedicine by enabling massive analysis of gene expression at both RNA and protein levels. Unfortunately, expression data obtained in different experiments are often poorly compatible, even for the same biological samples. Here, using experimental and bioinformatic investigation of major experimental platforms, we show that aggregation of gene expression data at the level of molecular pathways helps to diminish cross- and intra-platform bias otherwise clearly seen at the level of individual genes. We created a mathematical model of cumulative suppression of data variation that predicts the ideal parameters and the optimal size of a molecular pathway. We compared the abilities to aggregate experimental molecular data for the five alternative methods, also evaluated by their capacity to retain meaningful features of biological samples. The bioinformatic method OncoFinder showed optimal performance in both tests and should be very useful for future cross-platform data analyses.