Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Origins of the Eukaryotic Shikimate Pathway: Gene Fusions, Horizontal Gene Transfer, and Endosymbiotic Replacements

ABSTRACT Currently the shikimate pathway is reported as a metabolic feature of prokaryotes, ascomycete fungi, apicomplexans, and plants. The plant shikimate pathway enzymes have similarities to prokaryote homologues and are largely active in chloroplasts, suggesting ancestry from the plastid progenitor genome. Toxoplasma gondii, which also possesses an alga-derived plastid organelle, encodes a shikimate pathway with similarities to ascomycete genes, including a five-enzyme pentafunctional arom. These data suggests that the shikimate pathway and the pentafunctional arom either had an ancient origin in the eukaryotes or was conveyed by eukaryote-to-eukaryote horizontal gene transfer (HGT). We expand sampling and analyses of the shikimate pathway genes to include the oomycetes, ciliates, diatoms, basidiomycetes, zygomycetes, and the green and red algae. Sequencing of cDNA from Tetrahymena thermophila confirmed the presence of a pentafused arom, as in fungi and T. gondii. Phylogenies and taxon distribution suggest that the arom gene fusion event may be an ancient eukaryotic innovation. Conversely, the Plantae lineage (represented here by both Viridaeplantae and the red algae) acquired different prokaryotic genes for all seven steps of the shikimate pathway. Two of the phylogenies suggest a derivation of the Plantae genes from the cyanobacterial plastid progenitor genome, but if the full Plantae pathway was originally of cyanobacterial origin, then the five other shikimate pathway genes were obtained from a minimum of two other eubacterial genomes. Thus, the phylogenies demonstrate both separate HGTs and shared derived HGTs within the Plantae clade either by primary HGT transfer or secondarily via the plastid progenitor genome. The shared derived characters support the holophyly of the Plantae lineage and a single ancestral primary plastid endosymbiosis. Our analyses also pinpoints a minimum of 50 gene/domain loss events, demonstrating that loss and replacement events have been an important process in eukaryote genome evolution.
Biomedicine as Culture: Instrumental Practices, Technoscientific Knowledge, and New Modes of Life

Foreword. Introduction Regula Valerie Burri and Joseph Dumit I. Social and Cultural Studies of Biomedicine 1. Medicalizing Culture(s) or Culturalizing Medicine(s) Stefan Beck 2. Metaphors of Medicine and the Culture of Healing: Historical Perspectives Jakob Tanner 3. Medicine as Practice and Culture: The Analysis of Border Regimes and the Necessity of a Hermeneutics of Physical Bodies Gesa Lindemann II. Epistemic Practices and Material Culture(s) 4. The Future Is Now: Locating Biomarkers for Dementia Margaret Lock 5. Embodied Action, Enacted Bodies: The Example of Hypoglycaemia Annemarie Mol and John Law 6. Sociotechnical Anatomy Regula Valerie Burri 7. Risk and Safety in the Operating Theater: An Ethnographic Study of Socio-technical Practices Cornelius Schubert III. Biomedical Knowledge in Context 8. Genomic Susceptibility as an Emergent Form of Life? Genetic Testing, Identity, and the Remit of Medicine Nikolas Rose 9. Susceptible Individuals and Risky Rights: Dimensions of Genetic Responsibility Thomas Lemke 10. "Pop Genes": An Investigation of "the Gene" in Popular Parlance Barbara Duden and Silja Samerski 11. Genetics and Its Publics: Crafting Genetic Literacy and Identity in the Early Twenty-first Century Karen-Sue Taussig 12. Constructing the Digital Patient: Patient Organizations and the Development of Health Web Sites Nelly Oudshoorn. Epilogue: Indeterminate Lives, Demands, Relations: Emergent Bioscapes Joseph Dumit and Regula Valerie Burri
Parked Cars are Excellent Roadside Units

A comprehensive implementation of the envisioned traffic safety and efficiency applications of the IEEE 802.11p and Wireless Access for Vehicular Environments (WAVE) standards assume the premise of the use of Dedicated Short-Range Communications (DSRC) technology both as on-board units and as roadside units (RSUs). The high cost associated with RSUs, however, has so far prevented massive deployment of RSUs. Finding alternative solutions to this longstanding problem is therefore very important. In this paper, we propose a self-organizing network approach to using parked cars in urban areas as RSUs. This self-organizing network approach enables parked cars to create coverage maps based on received signal strength and make important decisions, such as if and when a parked car should serve as an RSU. Our results show the feasibility and cost-effectiveness of the proposed approach, which is able to provide excellent coverage using only a small fraction of the cars parked in a city.
Online Efficiency Optimization of a Fuzzy Logic Controller Based IPMSM Drive

This paper presents an online loss minimization algorithm (LMA) for a fuzzy logic controller (FLC) based interior permanent magnet synchronous motor (IPMSM) drive to yield high efficiency and high dynamic performance over wide speed range. The loss minimization algorithm is developed based on the motor model. In order to minimize the controllable electrical losses of the motor and thereby maximize the operating efficiency the d-axis armature current is controlled optimally according to the operating speed and load conditions. For vector control purpose, a fuzzy logic controller (FLC) is used as a speed controller which enables the utilization of the reluctance torque to achieve high dynamic performance as well as to operate the motor over a wide speed range. In order to test the performance of the proposed drive in real-time, the complete drive is experimentally implemented using DSP board DS1104 for a prototype laboratory 5 hp motor. The performance of the proposed loss minimization based FLC for IPMSM drive is tested in both simulation and experiment at different operating conditions. A performance comparison of the drive with and without the proposed LMA based FLC is also provided. It is found from the results that the proposed LMA and FLC based drive demonstrates higher efficiency and better dynamic responses over FLC based IPMSM drive without LMA.
An Adaptive Multiagent Approach to Protection Relay Coordination With Distributed Generators in Industrial Power Distribution System

This paper presents new explorations into the use of agent technology applied to the protection coordination of power systems. The impact of distributed generators on protection coordination is first discussed. Then, a coordination multiagent system is proposed with the functions of the agents described. In the proposed system, communication will play an important role to provide more information for the relay coordination besides the relay settings. Communication simulation has been carried out on the Java Agent Development Framework platform. The information communication process shows that adaptive coordination can be achieved.
Overexpression of Glutathione Reductase but Not Glutathione Synthetase Leads to Increases in Antioxidant Capacity and Resistance to Photoinhibition in Poplar Trees

A poplar hybrid, Populus tremula x Populus alba, was transformed with the bacterial genes for either glutathione reductase (GR) (gor) or glutathione synthetase (GS) (gshll). When the gor gene was targeted to the chloroplasts, leaf GR activities were up to 1000 times greater than in all other lines. In contrast, targeting to the cytosol resulted in 2 to 10 times the GR activity. GR mRNA, protein, and activity levels suggest that bacterial GR is more stable in the chloroplast. When the gshll gene was expressed in the cytosol, GS activities were up to 100 times greater than in other lines. Overexpression of GR or GS in the cytosol had no effect on glutathione levels, but chloroplastic-GR expression caused a doubling of leaf glutathione and an increase in reduction state. The high-chloroplastic-GR expressors showed increased resistance to photoinhibition. The herbicide methyl viologen inhibited CO2 assimilation in all lines, but the increased leaf levels of glutathione and ascorbate in the high-chloroplastic-GR expressors persisted despite this treatment. These results suggest that overexpression of GR in the chloroplast increases the antioxidant capacity of the leaves and that this improves the capacity to withstand oxidative stress.
Towards understanding IT security professionals and their tools

We report preliminary results of our ongoing field study of IT professionals who are involved in security management. We interviewed a dozen practitioners from five organizations to understand their workplace and tools. We analyzed the interviews using a variation of Grounded Theory and predesigned themes. Our results suggest that the job of IT security management is distributed across multiple employees, often affiliated with different organizational units or groups within a unit and responsible for different aspects of it. The workplace of our participants can be characterized by their responsibilities, goals, tasks, and skills. Three skills stand out as significant in the IT security management workplace: inferential analysis, pattern recognition, and bricolage.
Ten-year anniversary of the Maintenance Act 99 of 1998 - a time to reflect on improvements, shortcomings and the way forward

Through qualitative research as well as a literature review, this article examines whether the innovations of the Maintenance Act 99 of 1998 and certain government initiatives implemented since the enactment of this Act have succeeded in improving the operation of South Africa's maintenance system. First, the innovations of the Act (such as the appointment of maintenance investigators, maintenance payments by way of a lump sum, orders by default against recalcitrant maintenance debtors, the civil execution of maintenance orders and the shift in the onus to prove lack of means upon criminal prosecution) and the government initiatives (such as the transunion ITC information support service, Operation Isondlo, the Justice Deposit Account System (JDAS) and the Electronic Funds Transfer (EFT) system) are set out. Secondly, the qualitative research undertaken at grass-roots level in maintenance courts across the country and the results thereof (as obtained from questionnaires to regional heads, accounts clerks, maintenance officers and maintenance investigators) are explained. Lastly, certain findings and recommendations are made - although the South African maintenance system has improved greatly over the past ten years, areas relating to manpower, practices and procedures, training, infrastructure, attitudes and the dynamics between different court officials still need more attention.
THE EMPIRICAL INSTITUTIONS-GROWTH LITERATURE: IS SOMETHING AMISS AT THE TOP?

The initial publication of the Fraser Institute’s Economic Freedom of the World index prompted an explosion of empirical research on the institutions-growth relationship. To date, little of this research has appeared in the top economics journals. Subsequently, a number of empirical growth studies using alternative sources of data on institutions have appeared in top journals. This paper explores the two tracks of empirical research on the institutions-growth relationship—one track that recognizes all the relevant literature, and one that seems wanting in that respect.
A Personalised Thermal Comfort Model Using a Bayesian Network

In this paper, we address the challenge of predicting optimal comfort temperatures of individual users of a smart heating system. At present, such systems use simple models of user comfort when deciding on a set point temperature. These models generally fail to adapt to an individual user's preferences, resulting in poor estimates of a user's preferred temperature. To address this issue, we propose a personalised thermal comfort model that uses a Bayesian network to learn and adapt to a user's individual preferences. Through an empirical evaluation based on the ASHRAE RP-884 data set, we show that our model is consistently 17.5- 23.5% more accurate than current models, regardless of environmental conditions and the type of heating system used. Our model is not limited to a single metric but can also infer information about expected user feedback, optimal comfort temperature and thermal sensitivity at the same time, which can be used to reduce energy used for heating with minimal comfort loss.
Detecting Changes in Simulated Events Using Partial-Interval Recording and Momentary Time Sampling III: Evaluating Sensitivity as a Function of Session Length

In a series of two studies, we graphed simulated data representing continuous duration recording and continuous frequency recording into ABAB reversal designs depicting small, moderate, and large behavior changes during 10‐min, 30‐min, and 60‐min sessions. Data sets were re‐scored using partial‐ interval recording and momentary time sampling with interval sizes set at 10s, 20s, 30s, 1min, and 2min. In study 1, we visually inspected converted data for experimental control and compared the conclusion with those from the respective continuous duration recording or continuous frequency recording data to test for false negatives. In study 2, we evaluated the extent to which interval methods that were sensitive to changes in study 1 produced false positives. In part, the results show that momentary time sampling with interval sizes up to 30s detected a wide range of changes in duration events and frequency events during lengthier observation periods. The practical implications of the findings are briefly discussed. Copyright © 2011 John Wiley & Sons, Ltd. Since its inception, the field of applied behavior analysis has been interested in the accurate measurement of behavior (Baer, Wolf, & Risley, 1968). Although research on various behavioral recording methods is now in its fourth decade, a number of important issues have yet to be addressed. From a practical standpoint, discontinuous recording methods may offer some advantages over continuous recording methods, such as lower response effort and greater ease for scoring multiple target events; however, the former may not detect the same behavior changes as the latter. Historically, the use of discontinuous forms of data collection in the behavior‐ analytic literature has been quite high (Kelly, 1977; Rapp et al., 2007). Although numerous studies have compared discontinuous recording methods to continuous
Can We Understand Researcher Grant Needs without Direct Communication?

We study a light-weight but intensive observation method to understand researchers' needs for funding opportunities. Our method assumes that access logs of grant search engines reflect researchers' needs. Through an analysis of university grant search engine access logs, we present (1) the features of popular grants for researchers, (2) the reasons for grant needs, and (3) the timing of grant seeking. The results suggest that researchers' needs for funding opportunities can be comprehensively and cost-effectively investigated using access logs to improve research administration services without direct communication with the researchers.
Differential Signaling and Tumor Necrosis Factor Receptor–Associated Factor (Traf) Degradation Mediated by Cd40 and the Epstein-Barr Virus Oncoprotein Latent Membrane Protein 1 (Lmp1)

Latent membrane protein 1 (LMP1) plays a critical role in B cell transformation by Epstein-Barr virus (EBV) and appears to mimic a constitutively active CD40 receptor. Intracellular tumor necrosis factor (TNF) receptor–associated factor (TRAF) adapter proteins, shown to contribute to signaling by both CD40 and LMP1, were recruited by both molecules to lipid-enriched membrane rafts. However, we found that TRAFs 2 and 3 were subsequently degraded after CD40- but not LMP1-induced signaling. This degradation was proteasome-dependent and required direct TRAF binding by CD40. Using a model system designed to directly compare the signaling potency of the cytoplasmic domains of LMP1 and CD40 in B lymphocytes, we found that LMP1 more potently activates c-Jun kinase and nuclear factor κB and induces higher levels of several B cell effector functions than does CD40. This suggests that LMP1 utilizes a modified CD40 signaling pathway. Failure to regulate TRAFs may contribute to the enhanced capacity of LMP1 to activate B cells as well as promote B cell transformation.
An In-Depth Analysis of the Uses of Imagery by High-Level Slalom Canoeists and Artistic Gymnasts

This study employed a qualitative methodology to examine the ways in which imagery is used by high-level slalom canoeists (n = 3) and artistic gymnasts (n = 3). Participants were interviewed about their imagery use and experiences in different environments. Athletes’ responses were analyzed using inductive and deductive procedures. A total of 43 raw data themes formed 10 first order and 3 second order dimensions, characterizing the athletes’ uses of imagery. Participants reported using imagery in a variety of different environments for cognitive and motivational purposes. Data showed several differences between the canoeists’ and gymnasts’ uses of imagery, reflecting the differing task demands of each sport. The experience of imagery was unique to each individual, and athletes were able to emphasize certain aspects or manipulate the content of their images for specific cognitive or motivational functions.
A new binarization algorithm based on maximum gradient of histogram

This paper studies several binarization algorithms in Chinese cheque recognition preprocessing. After analyzing the histograms of gray images of 2000 cheques, we found a clue, which can be used for segmenting image. With the clue, we developed a new binarization algorithm based on the maximum gradient of the histogram, making the target object stand out in the binary image. Comparing several other commonly used binarization algorithms, the algorithm proposed by the paper has been proven in the simulating tests to be more feasible and advanced.
Subnuclear localization of the trans-activating protein of human T-cell leukemia virus type I

Human T-cell leukemia virus type I is associated with human lymphoid malignancies. The p40xI protein encoded by the x gene of this virus is believed to play some role in virally mediated transformation. This gene is known to encode a transcriptional trans activator which previous studies have shown to be a nuclear protein. Further characterization of the intracellular kinetics of this protein showed that it migrated into the nucleus very soon after synthesis. Within the nucleus, p40xI was distributed almost equally between the nucleoplasm and the nuclear matrix. Given the proposed role of the nuclear matrix in RNA transcription, the association of p40xI with the matrix places it in an appropriate cellular compartment to exercise an effect on transcription.
Vascular Stiffness and Increased Pulse Pressure in the Aging Cardiovascular System

Aging leads to a multitude of changes in the cardiovascular system, including systolic hypertension, increased central vascular stiffness, and increased pulse pressure. In this paper we will review the effects of age-associated increased vascular stiffness on systolic blood pressure, pulse pressure, augmentation index, and cardiac workload. Additionally we will describe pulse wave velocity as a method to measure vascular stiffness and review the impact of increased vascular stiffness as an index of vascular health and as a predictor of adverse cardiovascular outcomes. Furthermore, we will discuss the underlying mechanisms and how these may be modified in order to change the outcomes. A thorough understanding of these concepts is of paramount importance and has therapeutic implications for the increasingly elderly population.
Assessing, through reporting, the outcomes of scientific investigations

Summary The problem of practical coursework assessment and, in particular, that of whole investigations has been the subject of wide concern, particularly in the UK with the introduction of GCSE Of prime concern is the obtaining of a valid measure of the outcomes of investigative tasks without the need to resort to individual observations by the class teacher. The findings of this study in Singapore suggest that this is possible by using a certain type of written report produced by the student after doing the investigation. The problem entails keeping a balance between going for an open‐ended (uncued) form of reporting by the students and a specifically cued reporting style. The former does not provide any hint as to what is expected of the student, while the latter delves into each fine point expected from the conduct of a specific investigation. The study found a broad‐cued reporting style that depended upon the stages of progress through an investigative task to be the most reliable and valid measure o.
US teenagers’ perceptions and awareness of digital technology: a focus group approach

Scholars have recently begun investigating teenagers’ perceptions of digital devices and awareness of the functions they serve in their lives (Campbell, 2007: Cheong, 2008; Heim et al., 2007; Ling, 2004). This article aligns with research on adolescents’ uses of digital media devices by conducting focus groups with 80 middle- and high-school teenagers. The chief objective of this research was to further our understanding of what young people think about digital devices (e.g. cell phones, video game systems, the internet) and the functions they serve in their lives. Four themes emerged from 11 focus group interviews: (1) an awareness of digital devices; (2) a sense of temporal displacement; (3) social functions; and (4) a palpable sense of risk associated with using them. These themes resonate with the current literature.
Kin Discrimination and the Benefit of Helping in Cooperatively Breeding Vertebrates

In many cooperatively breeding vertebrates, a dominant breeding pair is assisted in offspring care by nonbreeding helpers. A leading explanation for this altruistic behavior is Hamilton's idea that helpers gain indirect fitness benefits by rearing relatives (kin selection). Many studies have shown that helpers typically provide care for relatives, but relatively few have shown that helpers provide closer kin with preferential care (kin discrimination), fueling the suggestion that kin selection only poorly accounts for the evolution of cooperative breeding in vertebrates. We used meta-analysis to show that (i) individuals consistently discriminate between kin, and (ii) stronger discrimination occurs in species where the benefits of helping are greater. These results suggest a general role for kin selection and that the relative importance of kin selection varies across species, as predicted by Hamilton's rule.