Miracle-dz/UniFAR-FTUs huggingface dataset:
Small-world hidden in differential evolution

Differential evolution is an effective population-based global optimizer which is used in many areas of research. The population consists of individuals, which are mutated, crossed and better of them survive to the next generation. In this paper, we look at this process as at the communication between individuals which can be modeled by the network where the individuals are represented by the nodes and the edges between them reflect the dynamics in the population, i.e. interactions between individuals. The main goal of this work is to find out if the differential evolution algorithm is able to create the networks where the small-world phenomenon (known as six degrees of separation) is observed. The secondary objective was to investigate the dependency between the type of the selected test function and the extent of this phenomenon. To evaluate the performance of the algorithm eleven test functions from the benchmark set CEC 2015 have been used. The analysis of the generated networks indicates that the differential evolution is able to create small-world networks in majority of test functions. As the result, the selected test functions can be classified into three categories which binds to the degree of cooperation between the individuals in the population.
The power of witness reduction

Recent results by M. Ogiwara and L.A. Hemachandra (1990) established a connection between functions being hard for a class of functions and functions interacting with the class to effect witness reduction. The author believes that the ability to achieve some form of witness reduction is what makes a function hard for a class of functions. To support this thesis he defines new function classes and obtains results analogous to those of Ogiwara and Hemachandra. He also introduces the notion of randomly hard functions and obtains similar results. <<ETX>>
Counting auxiliary pushdown automata and semi-unbounded arithmetic circuits

The author examines various counting measures on space bounded nondeterministic auxiliary pushdown machines. In the main theorem, it is shown how a NAuxPDA may be simulated efficiently by a uniform family of Boolean circuits, which preserve the number of accepting paths in the NAuxPDA as the number of accepting subtrees in the Boolean circuit. The techniques used simulate the NAuxPDA in a novel way by considering the height and reversal bounds of an AuxPDA. One of the highlights of the present work is an exact characterization of the important class DET. It is shown that DET is exactly the class of functions that can be computed as the difference between the outputs of two counting logspace machines. <<ETX>>
Data traffic differentiation and QoS on the train, in fast parameter varying, heterogeneous wireless networks

Although Internet on the train and train to wayside communication in general becomes more and more available for train operators, there are still a lot of challenges for future research. We previously developed a network platform that is responsible for an uninterrupted and seamless connectivity from the train to the wayside through heterogeneous wireless access technologies. This paper mainly focuses on the concept for providing sufficient Quality of Service (QoS) guarantees in a dynamic train environment. Within this network platform, IPv6 strategies are adopted for QoS, exploiting multi-homing and intelligent aggregation techniques. The implementation that has been done in the Click Modular Router programming environment will also be presented in details.
Multi-objective optimization with Proper Orthogonal Decomposition and Gaussian predictive distribution

A numerical study of multi-objective optimization with Proper Orthogonal Decomposition (POD) and Gaussian predictive distribution on the well known ZDT and DLZT benchmark set, is presented and discussed. Based on the algorithm, design optimization of the Global Trajectory Optimization Problems (GTOP) database based on trajectory models of real-world interplanetary space mission, Cassini is presented. The trajectory models are formulated as nonlinear optimization problems and are known to be difficult to solve. In this contribution, for part of the standard ZDT and DTLZ series problems, the proposed algorithm is able to solve these benchmarks to their optimal solutions within 20 generations.
Glycemic Control in Critically Ill Patients Before and After Institution of an Intensive Insulin Infusion Protocol: Circadian Rhythm and the Quality Duration Calculator

Introduction: A circadian rhythm of blood glucose values has been recently reported in critically ill patients, but there are no reports of how this rhythm is altered by a continuous intensive insulin infusion therapy protocol (IIT). We wished to examine the effect of IIT on this rhythm as well as to describe the use of the quality duration calculator (QDC) for the evaluation of glycemic control before and after IIT. Methods: This was a retrospective multihospital observational study that took place in the medical and surgical intensive care units (ICUs) of 2 tertiary care hospitals. Cohorts of consecutively admitted critically ill patients from 2-year periods before and after institution of an IIT protocol were examined. Laboratory, demographic, and outcome data were extracted from hospital databases. Results: We studied 167,645 blood glucose measurements from 8,327 patients. We observed a circadian rhythm of blood glucose control in the pre-IIT cohort that was greatly attenuated in the post-IIT cohort. The difference between the morning and the average daily blood glucose in the pre-IIT cohort was 3.53 mg/dL (P < .001), and the difference between these values in the post-IIT cohort was 1.10 mg/dL (P = .031). In addition, the circadian nature of hyperglycemia incidence observed in the pre-IIT cohort was not seen in the post-IIT cohort. The amount of time spent in goal glycemic range increased from 23.69% (95% CI 23.01-24.38) in the pre-IIT cohort to 29.67% (95% CI 29.04-30.31) in the post-IIT cohort as estimated by the QDC. The amount of time spent in the hyperglycemic decreased from 20.17% (95% CI 19.33-20.99) in the pre-IIT cohort to 14.80% (95% CI 14.15-15.39) in the post-IIT cohort. Conclusions: The circadian rhythm of blood glucose control confirmed in our pre-IIT cohort was lost after institution of IIT. The morning blood glucose value appears to be a reasonable surrogate of overall glycemic control in a critically ill population on IIT, although this may vary based on the degree of control achieved. The QDC method is useful for analyzing glycemic control in patients on IIT.
Wafer-Scale Growth of Single-Crystal Monolayer Graphene on Reusable Hydrogen-Terminated Germanium

Smoothing Graphene Several methods have been reported for the growth of monolayer graphene into areas large enough for integration into silicon electronics. However, the electronic properties of the graphene are often degraded by grain boundaries and wrinkles. Lee et al. (p. 286, published online 3 April) showed that flat, single crystals of monolayer graphene can be grown by chemical-vapor deposition on silicon wafers covered by a germanium layer that aligns the grains. The graphene can be dry-transferred to other substrates, and the germanium layer can be reused for further growth cycles. Wafer-scale single-crystal monolayer graphene can be repeatedly grown on a hydrogen-terminated germanium (110) surface. The uniform growth of single-crystal graphene over wafer-scale areas remains a challenge in the commercial-level manufacturability of various electronic, photonic, mechanical, and other devices based on graphene. Here, we describe wafer-scale growth of wrinkle-free single-crystal monolayer graphene on silicon wafer using a hydrogen-terminated germanium buffer layer. The anisotropic twofold symmetry of the germanium (110) surface allowed unidirectional alignment of multiple seeds, which were merged to uniform single-crystal graphene with predefined orientation. Furthermore, the weak interaction between graphene and underlying hydrogen-terminated germanium surface enabled the facile etch-free dry transfer of graphene and the recycling of the germanium substrate for continual graphene growth.
Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages

Up and down go the cyanobacteria Plankton move together in strikingly coordinated daily patterns, sinking at night to avoid being eaten and rising to the surface in daylight to photosynthesize. Otteson et al. found similar activity patterns in even the smallest of planktonic organisms, such as photosynthetic bacteria (see the Perspective by Armbrust). Because it's hard to take regular samples in the open ocean, the authors built a robotic sampler and set it adrift for several days in the mid-Pacific. The captured bacteria showed immediate responses to changes in light, temperature, and salinity in ways that could affect the ocean's carbon and nitrogen cycles. Science, this issue p. 207; see also p. 134 Multispecies’ daily waves of gene transcription are observed in open ocean microplankton. [Also see Perspective by Armbrust] Oscillating diurnal rhythms of gene transcription, metabolic activity, and behavior are found in all three domains of life. However, diel cycles in naturally occurring heterotrophic bacteria and archaea have rarely been observed. Here, we report time-resolved whole-genome transcriptome profiles of multiple, naturally occurring oceanic bacterial populations sampled in situ over 3 days. As anticipated, the cyanobacterial transcriptome exhibited pronounced diel periodicity. Unexpectedly, several different heterotrophic bacterioplankton groups also displayed diel cycling in many of their gene transcripts. Furthermore, diel oscillations in different heterotrophic bacterial groups suggested population-specific timing of peak transcript expression in a variety of metabolic gene suites. These staggered multispecies waves of diel gene transcription may influence both the tempo and the mode of matter and energy transformation in the sea.
A secure and efficient key management scheme for wireless sensor networks

Wireless sensor networks consist of a huge number of battery-powered and low-cost devices, called (sensor) nodes. To guarantee secure communication in wireless sensor networks, secret keys should be securely established between sensor nodes. Recently, the random key management approaches have been proposed for pair-wise key establishment in sensor networks. However, all of them have the following problem : if sensor nodes are captured by an attacker, some pair-wise keys of non-captured nodes can be compromised. In this paper, we propose a key distribution scheme which improves the resilience against node capture and reduces communication cost.
Enforcing Business Collaboration Consistency in Business Transaction Net

Managing business collaboration is about coordinating the flow of information among organizations and linking their business processes into a cohesive whole. A consistent outcome is expected within and among involving organization. However, inadequate coordination onthe autonomous, heterogeneous, and long-lasting cross-organizational business processes can lead to inconsistent execution in loosely-coupled environment, e.g., Service Oriented Computing (SOC). Therefore, a model that describes business collaboration to enforce consistency for each partner as well as consistency for thecollaboration as a whole becomes essential. Previously we proposed a Business Transaction Net(BTx-Net) as a theoretical model to describe business collaboration during design time and manage consistency at run-time execution. In this paper, we will further explore the BTx-Net's enforceability for managing consistency by performingTransactional Management Actions(TMAs) which are needed to be taken during the occurrence of runtime faults and exceptions.
Real-Time Recognition and Profiling of Appliances through a Single Electricity Sensor

Sensing, monitoring and actuating systems are expected to play a key role in reducing buildings overall energy consumption. Leveraging sensor systems to support energy efficiency in buildings poses novel research challenges in monitoring space usage, controlling devices, interfacing with smart energy meters and communicating with the energy grid. In the attempt of reducing electricity consumption in buildings, identifying individual sources of energy consumption is key to generate energy awareness and improve efficiency of available energy resources usage. Previous work studied several non-intrusive load monitoring techniques to classify appliances; however, the literature lacks of an comprehensive system that can be easily installed in existing buildings to empower users profiling, benchmarking and recognizing loads in real-time. This has been a major reason holding back the practice adoption of load monitoring techniques. In this paper we present RECAP: RECognition of electrical Appliances and Profiling in real-time. RECAP uses a single wireless energy monitoring sensor easily clipped to the main electrical unit. The energy monitoring unit transmits energy data wirelessly to a local machine for data processing and storage. The RECAP system consists of three parts: (1) Guiding the user for profiling electrical appliances within premises and generating a database of unique appliance signatures; (2) Using those signatures to train an artificial neural network that is then employed to recognize appliance activities (3) Providing a Load descriptor to allow peer appliance benchmarking. RECAP addresses the need of an integrated and intuitive tool to empower building owners with energy awareness. Enabling real-time appliance recognition is a stepping-stone towards reducing energy consumption and allowing a number of major applications including load-shifting techniques, energy expenditure breakdown per appliance, detection of power hungry and faulty appliances, and recognition of occupant activity. This paper describes the system design and performance evaluation in domestic environment.
Disruption of Pichia pastoris PMR1 gene decreases its folding capacity on human serum albumin and interferon‐α2b fusion protein

In an attempt to increase the secretion capacity of Pichia pastoris (Pp), PpPMR1 gene was disrupted with GS115 as parent strain, and the resultant mutant was designated as Pppmr1. Pppmr1 displayed a Ca2+‐dependent growth defect, which was consistent with the PMR1 mutation in other yeasts. HSA–L5–IFNα2b, a human serum albumin (HSA) and inferferon‐α2b (IFNα2b) fusion protein with a flexible linker of 5 amino acid residues, was employed as a reporter to study the effects of PpPMR1 disruption on the secretion of heterologous protein. Because of its decreased viability after induction, Pppmr1 secreted more HSA–L5–IFNα2b only during the early phase (the first 15 hours) of induction. Although HSA–L5–IFNα2b secreted from GS115 and Pppmr1 had similar antiviral activity, the latter was heterogeneous (migrated as doublets on non‐reducing SDS–PAGE) and unstable (prone to aggregation at neutral to mild alkaline pH). Site‐directed mutagenesis revealed that the heterogeneity of HSA–L5–IFNα2b secreted from Pppmr1 was originated from the incomplete disulphide bridge pairing between Cys1 and Cys98 of IFNα2b. To be secreted homogeneously from Pppmr1 and to be stable in aqueous solution, the linker of the fusion protein should be extended to 10 amino acid residues. Copyright © 2008 John Wiley & Sons, Ltd.
New interacting partners of the F‐box protein Ufo1 of yeast

The yeast F‐box protein Ufo1 recruits proteins for ubiquitylation by the SCF ubiquitin ligase complex preparing them for proteasomal degradation. Ufo1 has a role in maintenance of genome stability; its substrates include Ho endonuclease and Rad30 polymerase of error‐prone DNA repair. Ufo1 is an unusual F‐box protein, as it has three ubiquitin interacting motifs (UIMs). Deletion of the genomic UIMs is lethal; ectopic expression of UFO1ΔUIMs extends protein half‐life and arrests the cell cycle. A whole‐genome study employing a TAP tag fused to the C‐terminal UIMs did not identify Ufo1‐interacting proteins. Here we therefore used stabilized N‐terminally tagged Ufo1ΔUIM as a strategy to identify Ufo1‐interacting proteins by mass spectroscopy. We identified proteins that function in transcription, and an indirect interaction with Hsp70 molecular chaperones via the Skp1 adaptor; we also show that Ufo1 interacts with the 19S regulatory particle of the proteasome. Thus, our data augment the current network of known Ufo1 interacting proteins. We show directly that the UIMs are crucial for Ufo1 ubiquitylation in vivo, indicating that they facilitate turnover of SCFUfo1 complexes. This allows recycling of the core subunits of the SCF complex and cell cycle progression. Copyright © 2008 John Wiley & Sons, Ltd.
Targeted enhancement of cortical-hippocampal brain networks and associative memory

Brain stimulation to improve human memory The hippocampus is a crucial brain area for certain types of memory. Working with humans, Wang et al. found that a specific type of non-invasive brain stimulation improved memory tests and enhanced information flow between the hippocampus and a number of other brain regions. This increased connectivity was highly specific for the individual target areas selected for each participant. Science, this issue p. 1054 Noninvasive stimulation of the brain can improve memories for episodes by boosting the connectivity between cortical regions. The influential notion that the hippocampus supports associative memory by interacting with functionally distinct and distributed brain regions has not been directly tested in humans. We therefore used targeted noninvasive electromagnetic stimulation to modulate human cortical-hippocampal networks and tested effects of this manipulation on memory. Multiple-session stimulation increased functional connectivity among distributed cortical-hippocampal network regions and concomitantly improved associative memory performance. These alterations involved localized long-term plasticity because increases were highly selective to the targeted brain regions, and enhancements of connectivity and associative memory persisted for ~24 hours after stimulation. Targeted cortical-hippocampal networks can thus be enhanced noninvasively, demonstrating their role in associative memory.
A framework for implementing business agility through knowledge management systems

In this paper we have developed a research model that illustrates the role of IT and knowledge management in building an agile operation. Acknowledging that there is more than one dimension to business agility, we focus on operational agility as a catalyst to enforce quality, cost effectiveness, and delivery, thereby meeting organizational objectives. To develop our model of agility, we build on existing theoretical constructs and identify absorptive capacity and dynamic capabilities as enablers of operational agility. Further, we recognize major IT knowledge management capabilities that are instrumental in building absorptive capacity and thus enhancing dynamic capabilities. We will utilize surveys of key decision makers to validate our model and have provided a rough outline of the type of questions that we will employ.
Selection of cell death‐deficient p53 mutants in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae is a useful system for the detection and transcriptional evaluation of mutant p53 in cancer. In previous work we showed that the overexpression of wild‐type p53 induces yeast cell death on minimal medium; however, the R248W p53 mutant was completely inactive, and we suggested that ROS production is a key event in p53‐induced yeast cell death. In this study we explored the effect of other p53 mutants, such as the hot‐spot mutant R282W and the double mutant N268S::I332V. Unexpectedly, both mutants behaved inversely to R248W, as they completely inhibited yeast growth on minimal medium and induced ROS production. This phenotype ‘yeast cell death on minimal medium’ allowed for the subsequent screening of intragenic p53‐inactivating mutations. In all cases, the ‘revertant yeast clones’ display a complete p53 inactivation through either gross deletion or nonsense mutations. More interestingly, missense mutations were also found: the deletion of I255 or substitution of R337G completely inactivated the p53 mutant R282W in the yeast context. Taken together, these results suggest that p53 tumour‐derived mutants could be classified according to their ability to induce yeast cell death and not uniquely by their transcriptional activity on a selected target reporter gene. Copyright © 2009 John Wiley & Sons, Ltd.
Yap4 PKA‐ and GSK3‐dependent phosphorylation affects its stability but not its nuclear localization

Yap4 is a nuclear‐resident transcription factor induced in Saccharomyces cerevisiae when exposed to several stress conditions, which include mild hyperosmotic and oxidative stress, temperature shift or metal exposure. This protein is also phosphorylated. Here we report that this modification is driven by PKA and GSK3. In order to ascertain whether Yap4 is directly or indirectly phosphorylated by PKA, we searched for stress and PKA‐related kinases that could phosphorylate Yap4. We show that phosphorylation is independent of the kinases Rim15, Yak1, Sch9, Slt2, Ste20 and Ptk2. In addition, we showed that Yap4 phosphorylation is also abrogated in the triple GSK3 mutant mck1 rim11 yol128c. Furthermore, our data reveal that Yap4 nuclear localization is independent of its phosphorylation state. This protein has several putative phosphorylation sites, but only the mutation of residues T192 and S196 impairs its phosphorylation under different stress conditions. The ability of the non‐phosphorylated forms of Yap4 to partially rescue the hog1 severe sensitivity phenotype is not affected, suggesting that Yap4 activity is maintained in the absence of phosphorylation. However, this modification seems to be required for stability of the protein, as the non‐phosphorylated form has a shorter half‐life than the phosphorylated one. Copyright © 2009 John Wiley & Sons, Ltd.
Genetic evidence for a role of Saccharomyces cerevisiae Mph1 in recombinational DNA repair under replicative stress

In yeast as in human, DNA helicases play critical roles in assisting replication fork progression. The Saccharomyces cerevisiae MPH1 gene, homologue of human FANCM, has been involved in homologous recombination and DNA repair. We describe a synthetic growth defect of an mph1 deletion if combined with an srs2 deletion that can result—depending on the genetic background—in synthetic lethality. The lethality is suppressed by mutations in homologous recombination (rad51, rad52, rad55, rad57) and in the DNA damage checkpoint (rad9, rad24, rad17). Importantly, rad54 and mph1, epistatic for damage sensitivity, are subadditive for spontaneous mutator phenotype. Therefore, Mph1 could be placed at the Rad51‐mediated strand invasion process, with a function distinct from Rad54. Moreover, siz1 mutation is viable with mph1 and additive for DNA damage sensitivity. mph1 srs2 double mutants, isolated in a background where they are viable, are synergistically sensitive to DNA damage. Moderate overexpression of SGS1 partially suppresses this sensitivity. Finally, we observe an epistatic relationship in terms of sensitivity to camptothecin of mms4 or mus81 to mph1. Overall, our results support a role of Mph1 in assisting replication progression. We propose two models for the resumption of DNA synthesis under replicative stress where Mph1 is placed at the sister chromatid interaction step. Copyright © 2009 John Wiley & Sons, Ltd.