Miracle-dz/UniFAR-FTUs huggingface dataset:
Paf1 Restricts Gcn4 Occupancy and Antisense Transcription at the ARG1 Promoter

ABSTRACT The conserved Paf1 complex negatively regulates the expression of numerous genes, yet the mechanisms by which it represses gene expression are not well understood. In this study, we use the ARG1 gene as a model to investigate the repressive functions of the Paf1 complex in Saccharomyces cerevisiae. Our results indicate that Paf1 mediates repression of the ARG1 gene independently of the gene-specific repressor, ArgR/Mcm1. Rather, by promoting histone H2B lysine 123 ubiquitylation, Paf1 represses the ARG1 gene by negatively affecting Gcn4 occupancy at the promoter. Consistent with this observation, Gcn5 and its acetylation sites on histone H3 are required for full ARG1 derepression in paf1Δ cells, and the repressive effect of Paf1 is largely maintained when the ARG1 promoter directs transcription of a heterologous coding region. Derepression of the ARG1 gene in paf1Δ cells is accompanied by small changes in nucleosome occupancy, although these changes are subtle in comparison to those that accompany gene activation through amino acid starvation. Additionally, conditions that stimulate ARG1 transcription, including PAF1 deletion, lead to increased antisense transcription across the ARG1 promoter. This promoter-associated antisense transcription positively correlates with ARG1 sense transcription. Finally, our results indicate that Paf1 represses other genes through mechanisms similar to those used at the ARG1 gene.
Microsatellites reveal substantial among-population genetic differentiation and strong inbreeding in the relict fern Dryopteris aemula.

BACKGROUND AND AIMS A previous study detected no allozyme diversity in Iberian populations of the buckler-fern Dryopteris aemula. The use of a more sensitive marker, such as microsatellites, was thus needed to reveal the genetic diversity, breeding system and spatial genetic structure of this species in natural populations. METHODS Eight microsatellite loci for D. aemula were developed and their cross-amplification with other ferns was tested. Five polymorphic loci were used to characterize the amount and distribution of genetic diversity of D. aemula in three populations from the Iberian Peninsula and one population from the Azores. KEY RESULTS Most microsatellite markers developed were transferable to taxa close to D. aemula. Overall genetic variation was low (H(T) = 0.447), but was higher in the Azorean population than in the Iberian populations of this species. Among-population genetic differentiation was high (F(ST) = 0.520). All loci strongly departed from Hardy-Weinberg equilibrium. In the population where genetic structure was studied, no spatial autocorrelation was found in any distance class. CONCLUSIONS The higher genetic diversity observed in the Azorean population studied suggested a possible refugium in this region from which mainland Europe has been recolonized after the Pleistocene glaciations. High among-population genetic differentiation indicated restricted gene flow (i.e. lack of spore exchange) across the highly fragmented area occupied by D. aemula. The deviations from Hardy-Weinberg equilibrium reflected strong inbreeding in D. aemula, a trait rarely observed in homosporous ferns. The absence of spatial genetic structure indicated effective spore dispersal over short distances. Additionally, the cross-amplification of some D. aemula microsatellites makes them suitable for use in other Dryopteris taxa.
The relationships among workaholism, proactivity, and locomotion in a work setting

We evaluated the relationship between workaholism and 2 individual difference variables relevant to an organizational context, namely: proactive personality and locomotion orientation. Specifically, we examined working excessively (WE), working compulsively (WC), and perceived self-efficacy, proactivity, and locomotion in a sample of nurses working in an Italian public hospital. Data were analyzed using confirmatory factor analysis and structural equation modeling. Because WE and WC were not distinct factors, a unitary workaholism factor was used when applying regression analysis. As expected, workaholism was related negatively to proactivity, and positively to locomotion. In contrast, its relationship with self-efficacy was nonsignificant. The practical implications of our findings and future research directions are discussed.
Using GIS and outranking multicriteria analysis for land-use suitability assessment

Land-use planners often make complex decisions within a short period of time when they must take into account sustainable development and economic competitiveness. A set of land-use suitability maps would be very useful in this respect. Ideally, these maps should incorporate complex criteria integrating several stakeholders' points of view. To illustrate the feasibility of this approach, a land suitability map for housing was realised for a small region of Switzerland. Geographical Information System technology was used to assess the criteria requested to define the suitability of land for housing. An example dealing with the evaluation of noise levels illustrates the initial steps of this procedure. Because the required criteria are heterogeneous and measured on various scales, an outranking multicriteria analysis method called ELECTRE-TRI was used. However, using it to assess the suitability of any point in a territory was impractical due to computational limitations. Therefore, a mathematical function to evaluate closeness relationships and classify the study area into homogeneous zones was used. This function is compatible with the outranking function of ELECTRE-TRI used to assess the suitability index. The resulting maps lend efficient support to negotiation and are very useful in dealing with inherent conflicts in land-use planning.
Evaluation of leflunomide for the treatment of BK viremia and biopsy proven BK nephropathy; a single center experience

Background: BK virus reactivation is a significant complication following renal transplantation that can result in graft failure. Reduction of immunosuppression and substitution of leflunomide for mycophenolate mofetil (MMF) has been used to treat this entity. Objectives: To evaluate the use of leflunomide in BK viremia (BKV) and biopsy proven BK nephropathy (BKN) in kidney and kidney-pancreas transplant recipients. Patients and Methods: We retrospectively reviewed 28 kidney and kidney-pancreas transplant recipients who had received leflunomide for BKV from January 2006 to November 2012. Demographics, time to BKV diagnosis, biopsy findings, rejection episodes, and laboratory data were recorded. Results: The average (mean ± SD) time to BKV from time of transplant was 316.1 ± 368.0 days (62-1708 days). At time of diagnosis, 64% of patients had their maintenance immunosuppression reduced. The indications for leflunomide administration were; BKV and biopsy proven acute rejection (BPAR) (50%), biopsy proven BKN (18%), or persistent BKV (25%). Therapeutic levels (50-100 mcg/mL) were achieved in only 54% of patients, and 60% of them had required a leflunomide dose of at least 60 mg/day. BK virus was cleared from the serum on average of 151 ± 145.2 days (17-476 days). At study commencement, 29% of patients had remained on leflunomide due to persistent BKV. Conclusions: In our study, most patients required at least a 60 mg daily dose of leflunomide to achieve therapeutic levels and to clear the virus compared to the standard 40 mg daily dose. Delaying therapy may result in progressive BKV and BKN.
Optimal threshold estimation for binary classifiers using game theory

Many bioinformatics algorithms can be understood as binary classifiers. They are usually compared using the area under the receiver operating characteristic ( ROC) curve. On the other hand, choosing the best threshold for practical use is a complex task, due to uncertain and context-dependent skews in the abundance of positives in nature and in the yields/costs for correct/incorrect classification. We argue that considering a classifier as a player in a zero-sum game allows us to use the minimax principle from game theory to determine the optimal operating point. The proposed classifier threshold corresponds to the intersection between the ROC curve and the descending diagonal in ROC space and yields a minimax accuracy of 1-FPR. Our proposal can be readily implemented in practice, and reveals that the empirical condition for threshold estimation of “specificity equals sensitivity” maximizes robustness against uncertainties in the abundance of positives in nature and classification costs.
Social Factors in Policy Compliance -- Evidence Found in Literature to Assist the Development of Policies in Information Security Management

Researchers and practitioners of Information Systems Security (ISS) operate semi-disconnected. Standards and frameworks born out of the cumulated best-practice experiences have filled this gap. But without the rigor of the scientific process their validity is in question. To aid in building the required scientific foundation, existing empirical evidence needs to be processed further than the scope of a single research endeavor may allow. Other fields of science, such as medicine, have long recognized the need for higher level analyses of research. In our paper we perform an exhaustive literature research in the realm of empirical ISS research. As one of the research hotspots of recent years, we then perform a systematic review of research results in Information Security Policy (ISP) compliance. We analyze and discuss the heterogeneity of research results and suggest a presentation format that may allow ISS practitioners to base their ISP design decisions on.
Focus on opportunities as a boundary condition of the relationship between job control and work engagement: A multi-sample, multi-method study

The concept of focus on opportunities describes how many new goals, options, and possibilities employees believe to have in their personal future at work. In this multi-sample, multi-method study, the authors investigated relationships between focus on opportunities and general and daily work engagement and the moderating role of focus on opportunities on between- and within-person relationships between job control and work engagement. Based on a social cognitive theory framework on the motivating potential of a future temporal focus, it was hypothesized that focus on opportunities is positively related to work engagement. Further, consistent with the notion of compensatory resources, it was expected that job control is not related to work engagement among employees with a high focus on opportunities, whereas job control, as an external resource of the work environment, is positively related to work engagement among employees with a low focus on opportunities. Both a cross-sectional survey study (N=174) and a daily diary study (N=64) supported the hypotheses. The study contributes to research on the job demands-resources model as it emphasizes the role of focus on opportunities as a motivational factor in the relationship between job control and work engagement.
Time-resolved step-scan Fourier transform infrared spectroscopy of the CO adducts of bovine cytochrome c oxidase and of cytochrome bo(3) from Escherichia coli.

We have used cryogenic difference FTIR and time-resolved step-scan Fourier transform infrared (TR-FTIR) spectroscopies to explore the redox-linked proton-pumping mechanism of heme-copper respiratory oxidases. These techniques are used to probe the structure and dynamics of the heme a(3)-Cu(B) binuclear center and the coupled protein structures in response to the photodissociation of CO from heme Fe and its subsequent binding to and dissociation from Cu(B). Previous cryogenic (80 K) FTIR CO photodissociation difference results were obtained for cytochrome bo(3), the ubiquinol oxidase of Escherichia coli [Puustinen, A. , et al. (1997) Biochemistry 36, 13195-13200]. These data revealed a connectivity between Cu(B) and glutamic acid E286, a residue which has been implicated in proton pumping. In the current work, the same phenomenon is observed using the CO adduct of bovine cytochrome aa(3) under cryogenic conditions, showing a perturbation of the equivalent residue (E242) to that in bo(3). Furthermore, using time-resolved (5 micros resolution) step-scan FTIR spectroscopy at room temperature, we observe the same spectroscopic perturbation in both cytochromes aa(3) and bo(3). In addition, we observe evidence for perturbation of a second carboxylic acid side chain, at higher frequency in both enzymes at room temperature. The high-frequency feature does not appear in the cryogenic difference spectra, indicating that the perturbation is an activated process. We postulate that the high-frequency IR feature is due to the perturbation of E62 (E89 in bo(3)), a residue near the opening of the proton K-channel and required for enzyme function. The implications of these results with respect to the proton-pumping mechanism are discussed. Finally, a fast loss of over 60% of the Cu(B)-CO signal in bo(3) is observed and ascribed to one or more additional conformations of the enzyme. This fast conformer is proposed to account for the uninhibited reaction with O(2) in flow-flash experiments.
A Case Study on the Critical Role of Geometric Regularity in Machine Learning

An important feature of many problem domains in machine learning is their geometry. For example, adjacency relationships, symmetries, and Cartesian coordinates are essential to any complete description of board games, visual recognition, or vehicle control. Yet many approaches to learning ignore such information in their representations, instead inputting flat parameter vectors with no indication of how those parameters are situated geometrically. This paper argues that such geometric information is critical to the ability of any machine learning approach to effectively generalize; even a small shift in the configuration of the task in space from what was experienced in training can go wholly unrecognized unless the algorithm is able to learn the regularities in decision-making across the problem geometry. To demonstrate the importance of learning from geometry, three variants of the same evolutionary learning algorithm (NeuroEvolution of Augmenting Topologies), whose representations vary in their capacity to encode geometry, are compared in checkers. The result is that the variant that can learn geometric regularities produces a significantly more general solution. The conclusion is that it is important to enable machine learning to detect and thereby learn from the geometry of its problems.
Effect of Timing Jitter on Sigma Delta ADC for SDR Mobile Receiver

Jitter is the limiting effect for high speed analog-to-digital converters with high resolution and wide digitization bandwidth, which are required in receivers in order to support high data rates. The rapid development of digital wireless system has led to a need of high resolution and high speed analog to digital converter. The performance of a data converter is dependent upon the accuracy and stability of the clock supplied to the circuits. When data converter employ a high sampling rate, clocking issues become magnified and significant distortion can be result. This paper describes minimizing the effect of Timing error such as aperture jitter and clock jitter on the performance of sigma delta ADC Model and Present analytical evaluation of the performance in terms of achievable signal to noise ratio and also draw mean error power spectrum due to aperture jitter and clock jitter.
Underwater Glider Model Parameter IdentiÞcation

An underwater glider is a buoyancy-propelled, Þxedwing vehicle with attitude controlled completely, or in part, by means of internal mass redistribution. We have developed a physics-based nonlinear model of the dynamics of an underwater glider and adapted it to model the SLOCUM glider’s geometry, rudder, ballast pump and internal movable mass. In this paper we identify the model parameters to match the steady glides in new sight test data from the SLOCUM glider. In the process we also estimate the
Structuring Typical Evolutions Using Temporal-Driven Constrained Clustering

In this paper, we propose a new time-aware dissimilarity measure that takes into account the temporal dimension. Observations that are close in the description space, but distant in time are considered as dissimilar. We also propose a method to enforce the segmentation contiguity, by introducing, in the objective function, a penalty term inspired from the Normal Distribution Function. We combine the two propositions into a novel time-driven constrained clustering algorithm, called TDCK-Means, which creates a partition of coherent clusters, both in the multidimensional space and in the temporal space. This algorithm uses soft semi-supervised constraints, to encourage adjacent observations belonging to the same entity to be assigned to the same cluster. We apply our algorithm to a Political Studies dataset in order to detect typical evolution phases. We adapt the Shannon entropy in order to measure the entity contiguity, and we show that our proposition consistently improves temporal cohesion of clusters, without any significant loss in the multidimensional variance.
Synaptic Characteristics of Ag/AgInSbTe/Ta-Based Memristor for Pattern Recognition Applications

The memristor, a promising candidate for synaptic interconnections in artificial neural network, has gained significant attention for application to neuromorphic systems. One common method is using two memristors as one synapse to represent the positive and negative weights. In this paper, the synaptic behavior of a Ag/AgInSbTe/Ta (AIST)-based memristor is experimentally demonstrated. In addition, a neural architecture using one AIST memristor as a synapse is proposed, where both the plus and minus weights of the neural synapses are realized in a single memristive array. Moreover, the memristor-based neural network is extended to a multilayer architecture, and modified memristor-based backpropagation learning rules are implemented on-chip to achieve pattern recognition. The effects of device variations and input noise on the performance of a memristor-based multilayer neural network (MNN) are also described. The proposed MNN is capable of pattern recognition with high success rates and exhibits several advantages, such as good accuracy, high robustness, and noise immunity.
Control of hysteretic base-isolated structures: an adaptive backstepping approach

A hybrid seismic control system for building structures is considered, which combines a class of passive nonlinear base isolator with an active control system. The objective of the active control component applied to the structural base is to keep the base displacement relative to the ground, the interstory drift and the absolute acceleration within a reasonable range according to the design of the base isolator. We use the adaptive backstepping approach for the control design. The base isolator device exhibits a hysteretic nonlinear behavior which is described analytically by the Bouc-Wen model. The control problem is formulated representing the system dynamics in two alternative coordinates: absolute (with respect to an inertial frame) and relative to the ground. A comparison between both strategies is presented by means of numerical simulations.
Understanding pre‐service teachers’ construct of disability: a metacognitive process

This study identified pre‐service teachers’ understanding of disability as it relates to students they might teach and people they might meet in public, and determined the development of their understanding. Participants’ voices were elicited through semi‐structured interviews. Themes uncovered included: (a) many people with disabilities were ‘hidden away’; (b) participants were afraid of people with disabilities; (c) participants lacked self‐efficacy in teaching people with disabilities; (d) participants believed that people with disabilities lacked the ability to learn the same syllabus as typical students; and (e) participants also felt people with disabilities belonged and had rights in society. Conclusions drawn include the fact that in this Asian context, having a close relative with a disability did not presume that the participants would have a positive outlook on people with disabilities. Furthermore, there is a need for acceptance of people with disabilities in daily life activities, including in schools and other recreational activities.
Adaptation, Punctuation, and Rate Distortion: Non-cognitivèlearning Plateaus' in Evolutionary Process

Extending recent information-theoretic phase transition approaches to evolutionary and cognitive process via the Rate Distortion Theorem in the circumstance of interaction with a structured environment suggests that learning plateaus in cognitive systems and punctuated equilibria in evolutionary process are formally analogous, even though evolution is most certainly not cognitive. The result is curiously direct , and implies that evolutionary theories which do not produce punctuation are likely to be seriously incomplete. for identiication only. This material has been submitted for publication and is protected by copyright.
Support of Collaborative Business Process Networks in Aec

SUMMARY: Projects in the building industry are extremely dynamic, driven by external conditions, modified user requirements and frequently changing business partners. Therefore, common principles should be established throughout the construction industry, which flexibly support the management of construction project information and processes. New members should be supported to easily join and leave the project consortium while still using their own ICT-applications. The need to rapidly set up such organizational structures and effectively manage these collaborative networks places high demands on the methods and models that are used to establish a common, homogeneous project structure. Therefore, this article presents an architecture for dynamic cross-enterprise processes' planning, execution and controlling on a conceptual and application level. It is based on a Collaborative Business Process Management Lifecycle for virtual enterprises. For the adaptation of the architecture to the specific requirements of the AEC&FM-domain, a feasible Construction Network Scheme for the representation of strategic inter-organizational construction project information is introduced. Within this architecture, collaborative business process modeling will be achieved by the use of pre-defined process modules. Finally, the realization of the proposed models and methods are demonstrated in an example. KEYWORDS: collaborative business processes, process modules, collaboration architecture, virtual enterprises .