Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon‐rich Analyses of Five Genes

Photosynthetic euglenids acquired chloroplasts by secondary endosymbiosis, which resulted in changes to their mode of nutrition and affected the evolution of their morphological characters. Mapping morphological characters onto a reliable molecular tree could elucidate major trends of those changes. We analyzed nucleotide sequence data from regions of three nuclear‐encoded genes (nSSU, nLSU, hsp90), one chloroplast‐encoded gene (cpSSU) and one nuclear‐encoded chloroplast gene (psbO) to estimate phylogenetic relationships among 59 photosynthetic euglenid species. Our results were consistent with previous works; most genera were monophyletic, except for the polyphyletic genus Euglena, and the paraphyletic genus Phacus. We also analyzed character evolution in photosynthetic euglenids using our phylogenetic tree and eight morphological traits commonly used for generic and species diagnoses, including: characters corresponding to well‐defined clades, apomorphies like presence of lorica and mucilaginous stalks, and homoplastic characters like rigid cells and presence of large paramylon grains. This research indicated that pyrenoids were lost twice during the evolution of phototrophic euglenids, and that mucocysts, which only occur in the genus Euglena, evolved independently at least twice. In contrast, the evolution of cell shape and chloroplast morphology was difficult to elucidate, and could not be unambiguously reconstructed in our analyses.
Independence of sensitivity to relative reinforcement rate and discriminability in signal detection.

Six pigeons were trained to detect differences between two white stimuli, S1 and S2, differing in duration and arranged probabilistically on the center key of a three-key chamber. Detection performance was measured at two levels of discriminability. At one level, S1 was five seconds and S2 was thirty seconds. At the other level, S1 was twenty seconds and S2 was thirty seconds. The procedure was a standard signal-detection yes-no design in which stimulus-presentation probability was varied from . 1 to . 9 at both discriminability levels. On completion of the center-key stimulus, a peck on the center key darkened the center-key light and turned on the two red side keys. A left-key response was "correct" on S1 trials, and a right-key response was "correct" on S2 trials. Correct responses produced food reinforcement on a variable-ratio 1.3 schedule. Incorrect responses produced three second blackout. Discriminability was higher for the five-second versus thirty-second conditions than for the twenty-second versus thirty-second conditions, but there were no differences in sensitivity of behavior to reinforcement variation for the two stimulus pairs. Response bias was a function of the relative reinforcement rate for correct choice responses.
A high performance four-parallel 128/64-point radix-24 FFT/IFFT processor for MIMO-OFDM systems

This paper presents a novel high-speed, low-complexity 128/64-point radix-24 FFT/IFFT processor for the applications in a high-throughput MIMO-OFDM systems. The high radix radix-24 multi-path delay feed-back (MDF) FFT architecture provides a higher throughput rate and low hardware complexity by using a four-parallel data-path scheme. The proposed processor not only supports the operation of FFT/IFFT in 128 points and 64 points but can also provide a high data processing rate by using a four-parallel data-path scheme. Furthermore, the proposed design has a less hardware complexity compared with traditional 128/64-point FFT/IFFT processors. The proposed FFT/IFFT processor was implemented using Xilinx Virtex-4 FPGA. Our proposed processor achieves a considerable performance, which has a high throughput rate of up to 560 M sample/s at 140 MHz.
Contribution of amygdala neurons containing peptides and calcium‐binding proteins to fear‐potentiated startle and exploration‐related anxiety in inbred Roman high‐ and low‐avoidance rats

The purpose of this study was to investigate amygdala‐related fear and anxiety in two inbred rat lines differing in emotionality (RHA/Verh and RLA/Verh), and to relate the behaviour of the animals to neuronal types in different nuclei of the amygdala. The behavioural tests used were the motility test, elevated plus‐maze and fear‐potentiated startle response. The neurons investigated were immunoreactive for the anxiogenic peptide corticotropin‐releasing factor (CRF‐ir), the anxiolytic peptide neuropeptide Y (NPY‐ir), and the calcium‐binding proteins parvalbumin (PARV‐ir) and calbindin (CALB‐ir). The NPY‐ir, PARV‐ir and CALB‐ir neurons studied were subpopulations of GABAergic neurons. RLA/Verh rats, which showed a significant fear‐potentiation of the acoustic startle response, had more CRF‐ir projection neurons in the central nucleus of the amygdala. The same RLA/Verh rats were either less or equally anxious in the motility test (similar to open field) and elevated plus‐maze as compared with RHA/Verh rats. In accordance with this behaviour, the RLA/Verh rats had more NPY‐ir neurons in the lateral, and more PARV‐ir neurons in basal nuclei of the amygdala than RHA/Verh rats, but no differences were detected in the number of CRF‐ir and CALB‐ir neurons of the basolateral complex. In conclusion, the RLA/Verh rats displayed an opposite behaviour in the fear‐potentiated startle model and the exploratory tests measuring anxiety based on choice behaviour. Thus, the anxiogenic systems in the central nucleus and anxiolytic systems in the basolateral complex of the amygdala might be differentially involved in the fear‐potentiated startle paradigm and exploratory tests in the Roman rat lines.
Iron and Fur Regulation in Vibrio cholerae and the Role of Fur in Virulence

ABSTRACT Regulation of iron uptake and utilization is critical for bacterial growth and for prevention of iron toxicity. In many bacterial species, this regulation depends on the iron-responsive master regulator Fur. In this study we report the effects of iron and Fur on gene expression in Vibrio cholerae. We show that Fur has both positive and negative regulatory functions, and we demonstrate Fur-independent regulation of gene expression by iron. Nearly all of the known iron acquisition genes were repressed by Fur under iron-replete conditions. In addition, genes for two newly identified iron transport systems, Feo and Fbp, were found to be negatively regulated by iron and Fur. Other genes identified in this study as being induced in low iron and in the fur mutant include those encoding superoxide dismutase (sodA), fumarate dehydratase (fumC), bacterioferritin (bfr), bacterioferritin-associated ferredoxin (bfd), and multiple genes of unknown function. Several genes encoding iron-containing proteins were repressed in low iron and in the fur mutant, possibly reflecting the need to reserve available iron for the most critical functions. Also repressed in the fur mutant, but independently of iron, were genes located in the V. cholerae pathogenicity island, encoding the toxin-coregulated pilus (TCP), and genes within the V. cholerae mega-integron. The fur mutant exhibited very weak autoagglutination, indicating a possible defect in expression or assembly of the TCP, a major virulence factor of V. cholerae. Consistent with this observation, the fur mutant competed poorly with its wild-type parental strain for colonization of the infant mouse gut.
Affective Characterization of Movie Scenes Based on Content Analysis and Physiological Changes

In this paper, we propose an approach for affective characterization of movie scenes based on the emotions that are actually felt by spectators. Such a representation can be used to characterize the emotional content of video clips in application areas such as affective video indexing and retrieval, and neuromarketing studies. A dataset of 64 different scenes from eight movies was shown to eight participants. While watching these scenes, their physiological responses were recorded. The participants were asked to self-assess their felt emotional arousal and valence for each scene. In addition, content-based audio- and video-based features were extracted from the movie scenes in order to characterize each scene. Degrees of arousal and valence were estimated by a linear combination of features from physiological signals, as well as by a linear combination of content-based features. We showed that a significant correlation exists between valence-arousal provided by the spectator's self-assessments, and affective grades obtained automatically from either physiological responses or from audio-video features. By means of an analysis of variance (ANOVA), the variation of different participants' self assessments and different gender groups self assessments for both valence and arousal were shown to be significant (p-values lower than 0.005). These affective characterization results demonstrate the ability of using multimedia features and physiological responses to predict the expected affect of the user in response to the emotional video content.
Outage performance of dual hop full-duplex MIMO relay networks with TAS/MRC over Rayleigh fading channels

In this paper, we investigate end-to-end (e2e) outage probability (OP) performance of dual hop full-duplex (FD) amplify-and-forward (AF) relay network with transmit antenna selection (TAS) and maximal-ratio combining (MRC) over independent identically distributed Rayleigh fading channels. In the network, source and destination are equipped with multiple antennas, and communicate with each other via a single relay, which is equipped with one receive and one transmit antennas. We assume that the direct link between the source and destination is not available. For signal transmission, TAS is used at the source by neglecting residual self-interference (RSI) effect and maximal-ratio combining (MRC) technique is employed at the destination for combining received signals. In order to simplify the theoretical derivations, we also investigate the e2e OP in case that the RSI is non-fading. OP expression is derived in integral form for the Rayleigh faded RSI effect. Moreover, in case of non-fading RSI effect, OP expression is derived in closed form. The analytical results are verified by the Monte Carlo simulations.
Adaptive Fault-Tolerant Control of Uncertain Nonlinear Large-Scale Systems With Unknown Dead Zone

In this paper, an adaptive neural fault-tolerant control scheme is proposed and analyzed for a class of uncertain nonlinear large-scale systems with unknown dead zone and external disturbances. To tackle the unknown nonlinear interaction functions in the large-scale system, the radial basis function neural network (RBFNN) is employed to approximate them. To further handle the unknown approximation errors and the effects of the unknown dead zone and external disturbances, integrated as the compounded disturbances, the corresponding disturbance observers are developed for their estimations. Based on the outputs of the RBFNN and the disturbance observer, the adaptive neural fault-tolerant control scheme is designed for uncertain nonlinear large-scale systems by using a decentralized backstepping technique. The closed-loop stability of the adaptive control system is rigorously proved via Lyapunov analysis and the satisfactory tracking performance is achieved under the integrated effects of unknown dead zone, actuator fault, and unknown external disturbances. Simulation results of a mass-spring-damper system are given to illustrate the effectiveness of the proposed adaptive neural fault-tolerant control scheme for uncertain nonlinear large-scale systems.
The unexpected mating system of the androdioecious barnacle Chelonibia testudinaria (Linnaeus 1758)

Androdioecy was first described by Darwin in his seminal work on barnacle diversity; he identified males and hermaphrodites in the same reproductive population. Today, we realize that many androdioecious plants and animals share astonishing similarities, particularly with regard to their evolutionary history and mating system. Notably, these species were ancestrally dioecious, and their mating system has the following characteristics: hermaphrodites self‐fertilize frequently, males are more successful in large mating groups, and males have a mating advantage. A male mating advantage makes androdioecy more likely to persist over evolutionary times. Androdioecious barnacles, however, appear to persist as an outlier with a different evolutionary trajectory: they originate from hermaphroditic species. Although sexual systems of androdioecious barnacles are known, no information on the mating system of androdioecious barnacles is available. This study assessed the mating system of the androdioecious barnacle Chelonibia testudinaria. In contrast to other androdioecious species, C. testudinaria does not self‐fertilize, males do not have a mating advantage over hermaphrodites, and the average mating group is quite small, averaging only three individuals. Mating success is increased by proximity to the mate and penis length. Taken together, the mating system of C. testudinaria is unusual in comparison with other androdioecious plants and animals, and the lack of a male mating advantage suggests that the mating system alone does not provide an explanation for the maintenance of androdioecy in this species. Instead, we propose that sex‐specific life history equalizes male and hermaphroditic overall fitness.
Scent may signal fighting ability in male Iberian rock lizards

Intrasexual competition favours the evolution of conspicuous fighting ability badges. However, in spite of the fact that chemoreception is important in sexual selection of many animals, such as lizards, the role of chemical signals in males' contests is relatively unknown. Here, we show that proportions of cholesterol in femoral gland secretions of male Iberian rock lizards were related to their body size (which confers a competitive advantage in fights). Males discriminated chemically and responded aggressively to cholesterol stimuli presented on swabs. Moreover, we experimentally increased cholesterol in the scent of males, and staged encounters in neutral cages between two unfamiliar and size-matched males. Focal males lost more agonisitic interactions against males manipulated with cholesterol than in control tests. We suggest that differences in scent composition may reliably signal fighting ability in many lizard species, which would help to avoid the costs of fighting.
Tax Evasion and the Marginal Cost of Public Funds

Tax evasion is analogous to deadweight loss in its effect upon the rules for cost-benefit analysis of public sector projects. Deadweight loss and tax evasion both cause the marginal cost of public funds to increase as tax payers attempt to reduce the tax base in response to increases in tax rates. In one case, the social cost is from the diversion of resources from highly taxed to less taxed activities. In the other, the social cost includes the expense of concealment of income from the tax collector, the cost to the public sector of detecting and punishing tax evasion, and the cost of punishment to the convicted tax evader. It follows that a complete theory of optimal taxation can be derived from the susceptibilities to evasion of the different means of taxation.
A protein–protein interaction map of the Caenorhabditis elegans 26S proteasome

The ubiquitin‐proteasome proteolytic pathway is pivotal in most biological processes. Despite a great level of information available for the eukaryotic 26S proteasome—the protease responsible for the degradation of ubiquitylated proteins—several structural and functional questions remain unanswered. To gain more insight into the assembly and function of the metazoan 26S proteasome, a two‐hybrid‐based protein interaction map was generated using 30 Caenorhabditis elegans proteasome subunits. The results recapitulate interactions reported for other organisms and reveal new potential interactions both within the 19S regulatory complex and between the 19S and 20S subcomplexes. Moreover, novel potential proteasome interactors were identified, including an E3 ubiquitin ligase, transcription factors, chaperone proteins and other proteins not yet functionally annotated. By providing a wealth of novel biological hypotheses, this interaction map constitutes a framework for further analysis of the ubiquitin‐proteasome pathway in a multicellular organism amenable to both classical genetics and functional genomics.
Improving program understanding by unfolding layers of interacting patterns

Reverse engineering of legacy systems is a cumbersome task. Some of its aspects can be automated reasonably well, others are better not touched or require the intervention of a human expert. In an attempt to improve our rearchitecturing methodology, COREM, we found that various patterns, software developers use or have to use when developing systems, can serve to support the program understanding part of the reverse engineering process. We depart from the widely accepted hypothesis that software developed by experts is not a mere sequence of relatively primitive statements, but rather the result of a set of interacting, time and situation specific problem, design, and language patterns. To support these considerations, the paper shows how different language paradigms influence the actual code even with a simple problem. The extension of these ideas to interacting high level design patterns is motivated.
Identification of a Hydrophobic Domain in Varicella-Zoster Virus ORF61 Necessary for ORF61 Self-Interaction, Viral Replication, and Skin Pathogenesis

ABSTRACT The varicella-zoster virus (VZV) ORF61 protein is necessary for normal replication in vitro and virulence in human skin xenografts in the severe combined immunodeficiency mouse model in vivo. These experiments identify a hydrophobic domain that mediates ORF61 self-interaction. While not needed to inhibit host cell defenses, disruption of this domain (residues 250 to 320) severely impairs VZV growth, transactivation of the immediate early 63 and glycoprotein E genes, and the pathogenesis of VZV skin infection in vivo.
Enhancing performance through best HRM practices, organizational learning and knowledge management

Purpose – The purpose of this paper is to explore the relationships between best human resource management (HRM) practices, knowledge management (KM), organization learning and organizational capabilities (OC) and their impact on organizational performance. The proposed framework intends to add to the understanding of the specific processes that mediate between best HRM practices and organizational performance.Design/methodology/approach – A range of relevant literature is explored and a conceptual model is proposed and discussed.Findings – This paper proposes an answer to “how” best HRM practices can influence performance. It is suggested that KM and organizational learning (OL) play their own unique role in creating OC, which lead to superior performance.Practical implications – The paper can help human resource managers to understand better the importance of OL and KM processes and the way best HRM practices, through the integration of these two processes, lead to superior and sustainable performance.O.
Association between maternal intimate partner violence and incident obesity in preschool-aged children: results from the Fragile Families and Child Well-being Study.

OBJECTIVE To examine the impact of chronicity of maternal intimate partner violence (IPV) on obesity risk among preschool-aged children. DESIGN Prospective cohort study. SETTING Several large US cities. PARTICIPANTS A subsample of the Fragile Families and Child Well-being Study participants (n = 1595), who were children born between 1998 and 2000 and their parents interviewed at baseline and at 12, 36, and 60 months. MAIN EXPOSURE Maternal report of restrictive, sexual, and physical abuse from an intimate partner. Chronic IPV was defined as any maternal IPV exposure during both pregnancy or infancy (0-12 months) and early childhood (36-60 months). MAIN OUTCOME MEASURE Repeated measures of child body mass index. RESULTS Among the 1595 children, 16.5% were obese at age 5 years and 49.4% of the mothers reported some form of IPV. Compared with those who had no IPV exposure, children whose mothers reported chronic IPV had an elevated risk for obesity at age 5 years (adjusted odds ratio = 1.80; 95% confidence interval, 1.24-2.61). Stratified analyses indicated increased risk for obesity among girls with a maternal history of chronic IPV (adjusted odds ratio = 2.21; 95% confidence interval, 1.30-3.75) compared with boys (adjusted odds ratio = 1.66; 95% confidence interval, 0.94-2.93) and a larger effect of any maternal IPV on obesity among children living in less safe neighborhoods (adjusted odds ratio = 1.56; 95% confidence interval, 1.03-2.36). CONCLUSIONS Chronic maternal IPV is associated with increased risk of obesity among preschool-aged children. Preventing family violence and improving community safety may help reduce childhood obesity.
Murine cytomegalovirus open reading frame m29.1 augments virus replication both in vitro and in vivo.

Murine cytomegalovirus mutant Rc29, with a premature stop codon mutation in the m29 open reading frame (ORF), produced no apparent phenotype in cell culture or following infection of BALB/c mice. In contrast, a similar mutant virus, Rc29.1, with a premature stop codon mutation in its m29.1 ORF, showed reduced virus yields (2-3 log(10) p.f. u. ml(-1)) in tissue culture. Mutant virus yields in BALB/c mice were delayed, reduced ( approximately 1 log(10) p.f. u. per tissue) and persisted less well in salivary glands compared with wild-type (wt) and revertant (Rv29.1) virus. In severe combined immunodeficiency mice, Rc29.1 virus showed delayed and reduced replication initially in all tissues (liver, spleen, kidneys, heart, lung and salivary glands). This delayed death until 31 days post-infection (p.i.) compared with wt (23 days p.i.) but at death virus yields were similar to wt. m29 gene transcription was initiated at early times post-infection, while production of a transcript from ORF m29.1 in the presence of cycloheximide indicated that it was an immediate-early gene. ORFs m29.1 and M28 are expressed from a bicistronic message, which is spliced infrequently. However, it is likely that each ORF expresses its own protein, as antiserum derived in rabbits to the m29.1 protein expressed in bacteria from the m29.1 ORF detected only one protein in Western blot analysis of the size predicted for the m29.1 protein. Our results suggest that neither ORF is essential for virus replication but m29.1 is important for optimal viral growth in vitro and in vivo.