Miracle-dz/UniFAR-FTUs huggingface dataset:
The Evolution and Adaptive Potential of Transcriptional Variation in Sticklebacks—Signatures of Selection and Widespread Heritability

Evidence implicating differential gene expression as a significant driver of evolutionary novelty continues to accumulate, but our understanding of the underlying sources of variation in expression, both environmental and genetic, is wanting. Heritability in particular may be underestimated when inferred from genetic mapping studies, the predominant “genetical genomics” approach to the study of expression variation. Such uncertainty represents a fundamental limitation to testing for adaptive evolution at the transcriptomic level. By studying the inheritance of expression levels in 10,495 genes (10,527 splice variants) in a threespine stickleback pedigree consisting of 563 individuals, half of which were subjected to a thermal treatment, we show that 74–98% of transcripts exhibit significant additive genetic variance. Dominance variance is also prevalent (41–99% of transcripts), and genetic sources of variation seem to play a more significant role in expression variance in the liver than a key environmental variable, temperature. Among-population comparisons suggest that the majority of differential expression in the liver is likely due to neutral divergence; however, we also show that signatures of directional selection may be more prevalent than those of stabilizing selection. This predominantly aligns with the neutral model of evolution for gene expression but also suggests that natural selection may still act on transcriptional variation in the wild. As genetic variation both within- and among-populations ultimately defines adaptive potential, these results indicate that broad adaptive potential may be found within the transcriptome.
To Bet or Not to Bet: Copper Price Uncertainty and Investment in Chile

A strand of research documents Chile's copper dependence hence significant exposure to terms of trade shocks. Copper prices' sharp decline and forecast uncertainty since the end of the commodity super-cycle has rekindled the debate on Chile's adjustment capacity to external shocks. Following Malz (2014), this paper builds a time-varying measure of copper price uncertainty using options contracts. VAR analysis shows that the investment response to an uncertainty shock of average magnitude in the sample is strong and persistent: the cumulative fall in investment from trend at a one-year horizon ranges 2-5.8 percentage points; and it takes between 11/2 and 2 years for investment to return to its trend level. Empirical ranges depend on alternative definitions for investment, uncertainty, and options' maturing time.
Full range active AC Filter with multilevel IGBT converter for transmission and distribution systems

The first active AC filter at an HVDC station was installed by Siemens in 1998 in the HVDC Converter Station of Tjele, in Denmark as a demonstration project. This active filter used a 0.6 MVA IGBT converter. This paper introduces the new full range active AC filter developed as a new standard product by the same company, four of them were commissioned at the converter stations of the Neptune Regional Transmission System USA in 2007. These active filters have a 22 MVA multilevel IGBT converter and open new possibilities for harmonic mitigation at HVDC stations but also in other AC applications where such ratings are required.
Quantitative delineation of how breathing motions open ligand migration channels in myoglobin and its mutants

Ligand migration and binding are central to the biological functions of many proteins such as myoglobin (Mb) and it is widely thought that protein breathing motions open up ligand channels dynamically. However, how a protein exerts its control over the opening and closing of these channels through its intrinsic dynamics is not fully understood. Specifically, a quantitative delineation of the breathing motions that are needed to open ligand channels is lacking. In this work, we present and apply a novel normal mode‐based method to quantitatively delineate what and how breathing motions open ligand migration channels in Mb and its mutants. The motivation behind this work springs from the observation that normal mode motions are closely linked to the breathing motions that are thought to open ligand migration channels. In addition, the method provides a direct and detailed depiction of the motions of each and every residue that lines a channel and can identify key residues that play a dominating role in regulating the channel. The all‐atom model and the full force‐field employed in the method provide a realistic energetics on the work cost required to open a channel, and as a result, the method can be used to efficiently study the effects of mutations on ligand migration channels and on ligand entry rates. Our results on Mb and its mutants are in excellent agreement with MD simulation results and experimentally determined ligand entry rates. Proteins 2015; 83:757–770. © 2015 Wiley Periodicals, Inc.
Promoter-Terminator Gene Loops Affect Alternative 3′-End Processing in Yeast*

Many eukaryotic genes undergo alternative 3′-end poly(A)-site selection producing transcript isoforms with 3′-UTRs of different lengths and post-transcriptional fates. Gene loops are dynamic structures that juxtapose the 3′-ends of genes with their promoters. Several functions have been attributed to looping, including memory of recent transcriptional activity and polarity of transcription initiation. In this study, we investigated the relationship between gene loops and alternative poly(A)-site. Using the KlCYC1 gene of the yeast Kluyveromyces lactis, which includes a single promoter and two poly(A) sites separated by 394 nucleotides, we demonstrate in two yeast species the formation of alternative gene loops (L1 and L2) that juxtapose the KlCYC1 promoter with either proximal or distal 3′-end processing sites, resulting in the synthesis of short and long forms of KlCYC1 mRNA. Furthermore, synthesis of short and long mRNAs and formation of the L1 and L2 loops are growth phase-dependent. Chromatin immunoprecipitation experiments revealed that the Ssu72 RNA polymerase II carboxyl-terminal domain phosphatase, a critical determinant of looping, peaks in early log phase at the proximal poly(A) site, but as growth phase advances, it extends to the distal site. These results define a cause-and-effect relationship between gene loops and alternative poly(A) site selection that responds to different physiological signals manifested by RNA polymerase II carboxyl-terminal domain phosphorylation status.
THE ROLE OF INDIVIDUAL, MANAGER, AND EXECUTIVE IN EMPLOYEE ENGAGEMENT: CASE OF INDONESIA CENTER FOR SUSTAINABLE DEVELOPMENT BANDUNG

The purpose of this research is to identify factors that influence level of employee engagement in a consultant company named Indonesia Center for Sustainable Development Bandung. Researcher collected the data using ethnography method with two main tools that are in-depth interview and participant observation. The Domain Analysis by Spradley (1979) is used as the data analysis method to interpret the influential factors of employee engagement based on BlessingWhite (2011) theory. The researcher concluded that the most influential factor of employee engagement is manager that have specific tool to increase the engagement level by using “constructive bullying” approach. In addition, “client-server” relationship is the significant factor to improve employee engagement level. This research only focused on strategies of ICSDB in building employee engagement and did not discuss the measurement of employee engagement level. It also evaluated the existing theory of employee engagement that can be useful to enrich the understanding contextually. Based on several researches on employee engagement has been done, there is still few research done in a consultant company. Therefore, this study seeks to use a newly established consultant company as the research object that is still rarely done by other researchers. Keywords: Consultant, Employee Engagement, Qualitative Research
A temperature cline in copy number for 412 but not roo/B104 retrotransposons in populations of Drosophila simulans

The copy number of the retrotransposable element 412 of Drosophila simulans from populations collected worldwide shows a negative correlation with minimum temperature. No association was detected for the roo/B104 element. The possibility that selective pressures might regulate the 412 copy number in these natural populations is supported by detection of selection against the detrimental effects of 412 insertions (estimated by the proportion of insertions on the X chromosome in comparison with the autosomes) but not roo/B104. These data reveal different spatial patterns for two element families, and strongly suggest that some factors in the environment, such as temperature, may interfere with the control of retrotransposition, thus affecting important aspects of genomic evolution.
Power Play in the German Wine Business: Are German Wine Co-operatives able to Use their Power to manage their Business Relationships?

Due to the pyramidal-hierarchical structure of supply chain networks power is an essential part of them and the fact that it is very often unequally distributed among the participants is quite obvious, which might represent great difficulties for member-owned enterprise coops. By clarifying the concept of power and identifying its five different sources, we were able to build hypotheses of how power affects cooperation and coordination - the two main elements of chain management in wine business. The first aim of our research is to elaborate on the question of power. Furthermore, we will construct some hypotheses regarding the use of power as a chain management instrument. Our second aim is to apply our general findings to the wine production chain, analysing the power play between cooperatives and retailers, and between cooperatives and their members. Due to the explorative nature of our study, we based the elaboration of our second aim on oral interviews, which were conducted in 2009, as well as in 2010, at five major international food and beverage fairs (twice ProWein, Anuga, and twice Fruit Logistica) in Germany. In addition, we conducted a comprehensive review of the Lebensmittelzeitung - the leading German food and beverage newspaper - for the last five years. Discussing our hypotheses in the context of the German wine sector, in which cooperatives are still of high importance, we were able to show that power is a very useful tool for managing strictly- coordinated chains. However, depending on which source the power originates from, its effect may be completely different.
Carbamazepine Enhances Discriminative Memory in a Rat Model of Epilepsy

Summary: Purpose: Seizures and antiepileptic drugs (AEDs) are the main causes for cognitive impairment in persons with epilepsy. It is still a matter of debate whether carbamazepine (CBZ) improves cognition because of its own psychotropic effects or because it is more effective to treat temporal epilepsy. Our objective was to analyze the performance of CBZ‐treated or nontreated pilocarpine epileptic rats in an object‐recognition test.
Evidence Linking Chondrocyte Lipid Peroxidation to Cartilage Matrix Protein Degradation

Reactive oxygen species (ROS) are implicated in both cartilage aging and the pathogenesis of osteoarthritis. We developed an in vitro model to study the role of chondrocyte-derived ROS in cartilage matrix protein degradation. Matrix proteins in cultured primary articular chondrocytes were labeled with [3H]proline, and the washed cell matrix was returned to a serum-free balanced salt solution. Exposure to hydrogen peroxide resulted in oxidative damage to the cell matrix as established by monitoring the release of labeled material into the medium. Calcium ionophore treatment of chondrocytes, in a dose-dependent manner, significantly enhanced the release of labeled matrix, suggesting a chondrocyte-dependent mechanism of matrix degradation. Antioxidant enzymes such as catalase or superoxide dismutase did not influence matrix release by the calcium ionophore-activated chondrocytes. However, vitamin E, at physiological concentrations, significantly diminished the release of labeled matrix by activated chondrocytes. The fact that vitamin E is a chain-breaking antioxidant indicates that the mechanism of matrix degradation and release is mediated by the lipid peroxidation process. Lipid peroxidation was measured in chondrocytes loaded withcis-parinaric acid. Both resting and activated cells showed constitutive and enhanced levels of lipid peroxidation activity, which were significantly reduced in the presence of vitamin E. In an immunoblot analysis, malondialdehyde and hydroxynonenal adducts were observed in chondrocyte-matrix extracts, and the amount of adducts increased with calcium ionophore treatment. Furthermore, vitamin E diminished aldehyde-protein adduct formation in activated extracts, which suggests that vitamin E has an antioxidant role in preventing protein oxidation. This study provides in vitro evidence linking chondrocyte lipid peroxidation to cartilage matrix protein (collagen) oxidation and degradation and suggests that vitamin E has a preventive role. These observations indicate that chondrocyte lipid peroxidation may have a role in the pathogenesis of cartilage aging and osteoarthritis.
An Improved Subdomain Model for Predicting Magnetic Field of Surface-Mounted Permanent Magnet Machines Accounting for Tooth-Tips

The paper developed an improved analytical subdomain model for predicting the open-circuit magnetic field in surface-mounted permanent magnet machines accounting for the tooth-tips in the slots. The whole field domain is divided into four types of simple subdomains, viz. magnets, air-gap, slot openings, and slots. The analytical expression of each subdomain is derived and the field solution is obtained by applying the boundary conditions and interface conditions between subdomains. Compared with the conventional subdomain models, the subdomain model accounting for tooth-tips can accurately predict the flux density inside the slots. Based on the developed field model, the cogging torque is computed by the Maxwell stress tensor. The finite element analysis is carried out to validate the analytical model. It shows that the developed subdomain model accounting for tooth-tips is more accurate, especially for the machines having larger slot opening width compared with tooth-tip height.
From 0 to 60: The Case Study of a School of Education's Successful “Online Start-Up”

This chapter reports findings from the case study of a school of education that had not previously engaged in online education and within two years was able to offer a total of 61 online courses (ranging from hybrid to fully online) as part of its existing programs, with high student and faculty satisfaction as well as limited upfront investments. With the goal of informing academic leaders planning similar online initiatives, the chapter examines how this start-up was realized, with a focus on how the school secured quality online instructors, other key resources and infrastructures, student and faculty buy-in, consistent policies and expectations about online courses, as well as how decisions were made about the specific courses to be offered online. This study was informed by entrepreneurship as a theoretical lens to study innovations
Big Data and Sexual Surveillance

pressive tool to control women’s bodies and is closely related to colonial modes of managing populations. Big data, metadata and the technologies used to collect, store and analyse them are by no means neutral, but come with their own exclusions and biases. This paper highlights the gendered and racialised effects of data practices; outlines the overlapping nature of state, commercial and peer surveillance; and maps the challenges and opportunities women and queers encounter on the nexus between data, surveillance, gender and sexuality. Vulnerable communities as well as sexual rights activists are at heightened risk of data-driven modes
ABC50, a novel human ATP-binding cassette protein found in tumor necrosis factor-alpha-stimulated synoviocytes.

We have used the recently developed technique of differential display polymerase chain reaction to seek for new genes modulated by tumor necrosis factor-alpha (TNF-alpha) in cultured synoviocytes. One PCR fragment was shown to correspond to a new gene that was mapped by high-resolution fluorescence in situ hybridization to band 6p21.33. The cDNA of this gene was cloned, and the deduced amino acid sequence revealed consensus motifs for the nucleotide binding folds of the ATP-binding cassette (ABC) family of proteins. However, a hydropathy curve showed that the polypeptide does not contain the transmembrane domains that are typical of the subfamily of ABC transporters and are associated with transporter/channel functions. The new gene, called ABC50, is the first human and mammalian ABC protein found to lack transmembrane domains. Homology with some yeast ABC proteins suggests that ABC50 codes for a new human ribosomal protein involved in translation of mRNA. It could therefore play a role in the enhancement of protein synthesis that follows TNF-alpha treatment of synoviocytes and thus participate in the inflammatory processes mediated by this cytokine. Furthermore, since TNF-alpha also modulates the expression of MHC class I genes, and these genes are known to map to 6p21.33, it is hypothesized that ABC50 and MHC class I are part of the same chromatin expression domain.
Correlation lengths, porosity and water adsorption in TiO2 thin films prepared by glancing angle deposition

This paper reports a thorough microstructural characterization of glancing angle deposited (GLAD) TiO2 thin films. Atomic force microscopy (afm), grazing-incidence small-angle x-ray scattering (GISAXS) and water adsorption isotherms have been used to determine the evolution of porosity and the existence of some correlation distances between the nanocolumns constituting the basic elements of the film’s nanostructure. It is found that the deposition angle and, to a lesser extent, the film thickness are the most important parameters controlling properties of the thin film. The importance of porosity and some critical dimensions encountered in the investigated GLAD thin films is highlighted in relation to the analysis of their optical properties when utilized as antireflective coatings or as hosts and templates for the development of new composite materials.
Experiments with Monte Carlo Othello

In this paper, we report on our experiments with using Monte Carlo simulation (specifically the UCT algorithm) as the basis for an Othello playing program. Monte Carlo methods have been used for other games in the past, most recently and notably in successful Go playing programs. We show that Monte Carlo-based players have potential for Othello, and that evolutionary algorithms can be used to improve their strength.
The effect of substances releasing intracellular calcium ions on sodium‐dependent calcium efflux from guinea‐pig auricles.

1. 45‐Ca efflux and resting tension were measured in isolated guinea‐pig auricles under conditions known to change the intracellular free Ca ion concentration. 2. In the presence of [Na]o, caffeine (2mM) increases 45‐Ca efflux, but does not produce a contracture, while in the absence of [Na]o and [Ca]o caffeine causes a contracture without increasing 45‐Ca efflux. Adrenaline (10‐minus5–10‐minus 4M) with or without theophylline (0–5‐1‐0mM) has no effect on either 45‐Ca efflux or resting tension. 3. In the presence of caffeine the rate of net efflux of Ca depends on [Na]o‐2. Caffeine contractures of muscles in Na‐free solution relax upon the addition of [Na]o. Relaxation is correlated with the increase in net efflux of Ca. 4. Cyanide (2mM) produces a variable increase in 45‐Ca efflux without a concomitant contracture in Na‐containing solutions, but in Na, Ca‐free solutions a large contracture occurs without significant increase in 45‐Ca efflux. 5. A large increase in 45‐Ca efflux and a contracture were observed with the ‘Ca‐ionophore’ X 537 A. 6. Changes in membrane potential (K‐depolarization) in hypertonic solutions have no significant effect on Na‐dependent 45‐Ca efflux, which is an agreement with an electroneutral 2:1 Na‐Ca exchange. 7. Cyanide and X 537 A both cause a considerable release of Ca ions from isolated guinea‐pig heart mitochondria, while caffeine has no effect. 8. The results suggest a powerful role of the Na‐Ca exchange system in reducing the intracellular Ca concentration after Ca release from intracellular stores.
Damping Torques of Multi-Machine Power Systems During Transient Behaviors

A Weierstrass-based numerical method for computing damping torque of a 3-machine power system during transient period is proposed and evaluated. Numerical studies were performed to demonstrate mutual impacts of generators on the damping torque, when one of the generators is presented by a detailed model. The relationship between the averaged self-damping torque coefficient of the detailed model and the damping coefficient of the classical model is numerically studied. One interesting observation from our studies is that the damping torque coefficients tend to become zero at the end of transient stability period if all the generators are represented by the detailed model. This observation can be useful to determine the duration of transient stability period. One application of the proposed Weierstrass-based method is to determine appropriate and accurate damping terms for power system dynamic simulation.
ActA from Listeria monocytogenes Can Interact with Up to Four Ena/VASP Homology 1 Domains Simultaneously* 210

The facultative intracellular human pathogenic bacterium Listeria monocytogenes actively recruits host actin to its surface to achieve motility within infected cells. The bacterial surface protein ActA is solely responsible for this process by mimicking fundamental steps of host cell actin dynamics. ActA, a modular protein, contains an N-terminal actin nucleation site and a central proline-rich motif of the 4-fold repeated consensus sequence FPPPP (FP4). This motif is specifically recognized by members of the Ena/VASP protein family. These proteins additionally recruit the profilin-G-actin complex increasing the local concentration of G-actin close to the bacterial surface. By using analytical ultracentrifugation, we show that a single ActA molecule can simultaneously interact with four Ena/VASP homology 1 (EVH1) domains. The four FP4 sites have roughly equivalent affinities with dissociation constants of about 4 μm. Mutational analysis of the FP4 motifs indicate that the phenylalanine is mandatory for ActA-EVH1 interaction, whereas in each case exchange of the third proline was tolerated. Finally, by using sedimentation equilibrium centrifugation techniques, we demonstrate that ActA is a monomeric protein. By combining these results, we formulate a stoichiometric model to describe how ActA enables Listeriato utilize efficiently resources of the host cell microfilament for its own intracellular motility.