Miracle-dz/UniFAR-FTUs huggingface dataset:
Traditional infrageneric classification of Gymnopilus is not supported by ribosomal DNA sequence data

The traditional classification of Gymnopilus (Agaricales) recognizes two primary groups, Annulati and Gymnopilus, based on the presence or absence of a membranous partial veil. While our analyses of DNA sequence data from the nuclear ribosomal ITS1–5.8S-ITS2 (ITS) gene supports the monophyly of the genus, these traditional subgroups were not recovered. Five well-supported clades within the genus were identified through these analyses: 1) the spectabilis-imperialis group; 2) nevadensis-penetrans group; 3) a clade formed by G. underwoodii, G. validipes and G. cf. flavidellus; 4) aeruginosus-luteofolius group; and 5) lepidotus-subearlei group. Relationships among these subgroups were not resolved.
A meta-analysis of working memory impairments in survivors of moderate-to-severe traumatic brain injury.

OBJECTIVES To establish the magnitude of deficits in working memory (WM) and short-term memory (STM) in those with moderate-to-severe traumatic brain injury (TBI) relative to age-matched, healthy controls and to explore the moderating effects of time since injury and age at injury on these impairments. METHOD Twenty-one studies that compared the WM and/or STM abilities of individuals with at least a moderate TBI relative to healthy controls were included in a random effects meta-analysis. Measures used to examine memory performance were categorized by modality (visuospatial, verbal) and memory system (WM, STM). RESULTS Individuals with TBI had significant deficits in verbal STM (Cohen's d = .41), visuospatial WM (Cohen's d = .69), and verbal WM (Cohen's d = .37) relative to controls. Greater decrements in verbal STM and verbal WM skills were associated with longer time postinjury. Larger deficits were observed in verbal WM abilities in individuals with older age at injury. CONCLUSION Evidence for WM impairments following TBI is consistent with previous research. Larger verbal STM and verbal WM deficits were related to a longer time postinjury, suggesting that these aspects of memory do not "recover" over time and instead, individuals might show increased rates of cognitive decline. Age at injury was associated with the severity of verbal WM impairments, with larger deficits evident for injuries that occurred later in life. Further research needs to chart the long-term effects of TBI on WM and to compare the effects of injury on verbal relative to visuospatial memory. (PsycINFO Database Record
Fruit and vegetable purchasing and the relative density of healthy and unhealthy food stores: evidence from an Australian multilevel study

Background Evidence of a relationship between residential retail food environments and diet-related outcomes is inconsistent. One reason for this may be that food environments are typically defined in terms of the absolute number of particular store types in an area, whereas a measure of the relative number of healthy and unhealthy stores may be more appropriate. Methods Using cross-sectional data from the VicLANES study conducted in Melbourne, Australia, multilevel logistic regression analysis was used to estimate the independent associations between absolute measures (numbers of healthy and unhealthy stores) and a relative measure (relative density of healthy stores) of the food environment, and self-reported variety of fruit and vegetable purchasing in local households. Purchasing behaviour was measured as the odds of purchasing above the median level of fruit and vegetables. Results Compared to households in areas where healthy food stores made up no more than 10% of all healthy and unhealthy stores, households in areas with 10.1–15.0% healthy food stores and >15% healthy stores had increased odds of healthier purchasing (OR=1.48 (95% CI 1.12 to 1.96) and OR=1.45 (95% CI 1.09 to 1.91), respectively). There was less evidence of an association between absolute numbers of healthy or unhealthy stores and fruit and vegetable purchasing. Conclusions We found strong evidence of healthier fruit and vegetable purchasing in households located in areas where the proportion of food stores that were healthy was greater. Policies aimed at improving the balance between healthy and unhealthy stores within areas may therefore be effective in promoting greater consumption of fruit and vegetables.
Relationship Between Selenium Accumulation and Mycelial Cell Composition in Lentinula edodes (Berk.) Cultures

It was postulated that fractions enriched in selenium (Se) isolated from Lentinula edodes mycelium polysaccharide might possess higher biological activity than the non-enriched fractions currently used to treat cancer. In order to obtain Se-enriched mycelial preparations, L. edodes cultures were cultivated in media enriched with sodium selenite. In order to determine whether the concentration of Se in the culture medium affected the biosynthesis and composition of cell wall and cell membrane, concentrations of the exopolysaccharide (EPS), chitin, and sterol (ergosterol) were measured in harvested mycelia. In addition, the relationship between Se accumulation and content of polyphenols and vitamin D2 in L. edodes mycelium was examined. The effects of Se levels on the mycelium cell composition were determined in culture media enriched with Se at concentrations ranging from 0 to 30 μg/ml. In each culture mycelial growth, total Se and Se distribution were determined between mycelial fractions of different polarity. The EPS, polyphenolics, and ergosterol content in harvested mycelia rose in proportion to Se concentration in the culture medium. The chitin content in mycelia increased with Se concentrations in the range 0–5 μg/ml, but at higher concentrations chitin levels decreased. Data showed that Se in culture medium exerted potent effects on the composition of the mushroom cell wall and semipermeable membrane, and on the content of polyphenolics that are involved in detoxification processes. Our findings indicate the optimal concentration of Se required in the culture medium for maximal yield of immunostimulatory-active selenated exopolysaccharides.
Event-Triggered Protocol for the Consensus of Multi-Agent Systems With State-Dependent Nonlinear Coupling

This paper proposes an event-triggered protocol to achieve consensus in multi-agent system, in which neighboring agents are coupled via a nonlinear function with local passivity. It is mathematically proved that the proposed protocol guarantees average consensus in the system, excluding the existence of Zeno phenomenon. As a practical application, the scheme is applied to achieve synchronization in the Kuramoto oscillator network. Phase agreement is obtained for oscillators with identical natural frequency. For oscillators with non-identical natural frequencies, their phases are confined in a bounded range and their frequencies reach an average of their natural frequencies. To further demonstrate the generality of the scheme, another multi-agent system with coupling based on exponential and tangent functions is also presented. All the simulation results verify the condition of consensus and confirm the effectiveness of the scheme.
Communication skills training exploiting multimodal emotion recognition

ABSTRACT The teaching of communication skills is a labour-intensive task because of the detailed feedback that should be given to learners during their prolonged practice. This study investigates to what extent our FILTWAM facial and vocal emotion recognition software can be used for improving a serious game (the Communication Advisor) that delivers a web-based training of communication skills. A test group of 25 participants played the game wherein they were requested to mimic specific facial and vocal emotions. Half of the assignments included direct feedback and the other half included no feedback. It was investigated whether feedback on the mimicked emotions would lead to better learning. The results suggest the facial performance growth was found to be positive, particularly significant in the feedback condition. The vocal performance growth was significant in both conditions. The results are a significant indication that the automated feedback from the software improves learners’ communication performances.
Current challenges of lung cancer care in an aging population

Lung cancer is the most common cancer in the elderly with a high mortality rate. Despite the high incidence, the elderly are under-represented in clinical trials and under-treated in clinical practice. These patients have a higher prevalence of comorbid disease, higher polypharmacy interactions, and an increased risk of mortality and toxicity with cancer treatments, compared to younger patients. Often data about their treatments come from retrospective analysis including patients who do not reflect the general elderly population. However, elderly patients can often receive cancer treatment similar to younger patients and an active treatment should not be denied based on older age.
Direct activator/co‐activator interaction is essential for bacteriophage T4 middle gene expression

The bacteriophage T4 AsiA protein is a bifunctional regulator that inhibits transcription from the major class of bacterial promoters and also serves as an essential co‐activator of transcription from T4 middle promoters. AsiA binds the primary σ factor in Escherichia coli, σ70, and modifies the promoter recognition properties of the σ70‐containing RNA polymerase (RNAP) holoenzyme. In its role as co‐activator, AsiA directs RNAP to T4 middle promoters in the presence of the T4‐encoded activator MotA. According to the current model for T4 middle promoter activation, AsiA plays an indirect role in stabilizing the activation complex by facilitating interaction between DNA‐bound MotA and σ70. Here we show that AsiA also plays a direct role in T4 middle promoter activation by contacting the MotA activation domain. Furthermore, we show that interaction between AsiA and the β‐flap domain of RNAP is important for co‐activation. Based on our findings, we propose a revised model for T4 middle promoter activation, with AsiA organizing the activation complex via three distinct protein–protein interactions.
Metazoan Parasites of the European Sea Bass Dicentrarchus labrax (Linnaeus 1758) (Pisces: Teleostei) from Corsica

As in many parts of the world, aquaculture production in the Mediterranean has been expanding rapidly over recent years (Basurco & Lovatelli, 2005). The continuous decline of ocean fisheries stocks has provided impetus for rapid growth in aquaculture. Global production of farm fish has more than doubled in the past 20 years with the growing demands of an expanding population, and it seems that grow is set to continue. It has been the fastest growing food production sector since 1970, with an increase at a compounded rate about 9.2% per year (Guo & Woo, 2009; Naylor et al., 2000). Alongside, and perhaps partly due to this rapid expansion, the welfare of farmed fish has received increasing attention. Fish welfare is an important issue for the industry, not just for public perception, marketing and product acceptance, but also often in terms of production efficiency, quality and quantity (Ashley, 2006). Many factors influenced the rapid increase in the production of cultured fish species in the last two decades (FAO, 2010). One of the most important factors is the great development and diffusion of sea-cage culture. The success of the sea-cage farming is essentially correlated with the possibility to reduce production cost. On the other hand, aquaculture of fish is not without problems. Cages constitute an open system, which allow free exchange between wild and caged organisms, leading to the emergence of characteristic diseases (Ghittino et al., 2003; Merella et al., 2006). The maintenance of a good health is a major problem in animal populations. Rapid development of fish culture in marine cages has been associated with an emergence of parasitic diseases (Fioravanti et al., 2006; Nowak, 2007). The difficulty of managing disease within sea-cages is regarded as a major drawback (Mladineo, 2006). Fish parasites are a major component of aquatic biodiversity, and their monitoring is considered an essential element of the management of the health for animals. Parasites that have low rates of infestation and minor pathological effects on their hosts under natural conditions can easily spread in populations confined to rearing systems, causing serious outbreaks and epizootics diseases resulting in significant economical losses (Combes, 1990; Ghittino et al., 2003; Johnson et al., 2004; Naylor et al., 2000). The environmental conditions in culture systems, in particular increased density of fish, repeated introduction of hosts, homogeneous host populations, fast growth and a potential decrease in genetic diversity have an important effect on commercial production
Performance Analysis of an Expanding-Search Algorithm for Coarse Acquisition of DSSS Signals

For coarse acquisition of Direct Sequence Spread Spectrum (DSSS) signals, a search of the possible code phases is required. In cases such as signal reacquisition, where a priori information is available, the serial search may be abandoned in favor of an expanding search. In this paper, an expanding-search algorithm is presented and compared to the expanding-sweep algorithms which have been treated in the literature. Performance results for the serial-search and the expanding-search algorithms are given. A discussion of the optimality of the serial-search and the expanding-search algorithms is presented. Performance comparisons of the serial search and the expanding search are made for different a priori code phase probability density functions (pdfs) and the results are discussed. A technique for determining when the expanding search is an optimal search algorithm is developed and applied to the performance curves shown previously. The results indicate that the expanding search provides a quantifiable improvement over the serial search when the pdf is somewhat peaked. The results also indicate that in many cases the expanding search may be a more effective search algorithm than the more common expanding sweep.
Superoxide-Mediated Protection of Escherichia coli from Antimicrobials

ABSTRACT Antimicrobial lethality is promoted by reactive oxygen species (ROS), such as superoxide, peroxide, and hydroxyl radical. Pretreatment with subinhibitory concentrations of plumbagin or paraquat, metabolic generators of superoxide, paradoxically reduced killing for oxolinic acid, kanamycin, and ampicillin. These pretreatments also reduced an oxolinic acid-mediated ROS surge. Defects in SoxS MarA or AcrB eliminated plumbagin- and paraquat-mediated MIC increases but maintained protection from killing. Thus, superoxide has both protective and detrimental roles in response to antimicrobial stress.
Development of high speed composite flywheel rotors for energy storage systems

A composite flywheel rotor was developed. The rotor was designed, which was based on the finite element analysis, and fabricated to achieve the peripheral speed of 1300 m/s. The rotor consisted of a composite rim and aluminum alloy hub. The inner diameter of the rim was 340 mm, the outer diameter was 400 mm and thickness was 25 mm. The rim comprised press fitted multiple concentric rings(multi-ring) to prevent radial tensile failures at high rotational speed. Rings were fabricated by a filament winding process using high strength carbon fiber. The configuration of the hub was like a steering wheel with 4 spokes. The cross-section area of these spokes was changed to withstand a centrifugal force. Spin tests of flywheel rotors were performed, using an air turbine driven spin tester in a vacuum chamber. The rotor was spun to maximum peripheral speed at 1310 m/s, whose stored energy was 354 Wh, and the specific energy density was 195 Wh/kg.
Peroxisome Proliferator‐Activated Receptor &ggr; Regulates the V‐Ets Avian Erythroblastosis Virus E26 Oncogene Homolog 1/microRNA‐27a Axis to Reduce Endothelin‐1 and Endothelial Dysfunction in the Sickle Cell Mouse Lung

&NA; Pulmonary hypertension (PH), a serious complication of sickle cell disease (SCD), causes significant morbidity and mortality. Although a recent study determined that hemin release during hemolysis triggers endothelial dysfunction in SCD, the pathogenesis of SCD‐PH remains incompletely defined. This study examines peroxisome proliferator‐activated receptor &ggr; (PPAR&ggr;) regulation in SCD‐PH and endothelial dysfunction. PH and right ventricular hypertrophy were studied in Townes humanized sickle cell (SS) and littermate control (AA) mice. In parallel studies, SS or AA mice were gavaged with the PPAR&ggr; agonist, rosiglitazone (RSG), 10 mg/kg/day, or vehicle for 10 days. In vitro, human pulmonary artery endothelial cells (HPAECs) were treated with vehicle or hemin for 72 hours, and selected HPAECs were treated with RSG. SS mice developed PH and right ventricular hypertrophy associated with reduced lung levels of PPAR&ggr; and increased levels of microRNA‐27a (miR‐27a), v‐ets avian erythroblastosis virus E26 oncogene homolog 1 (ETS1), endothelin‐1 (ET‐1), and markers of endothelial dysfunction (platelet/endothelial cell adhesion molecule 1 and E selectin). HPAECs treated with hemin had increased ETS1, miR‐27a, ET‐1, and endothelial dysfunction and decreased PPAR&ggr; levels. These derangements were attenuated by ETS1 knockdown, inhibition of miR‐27a, or PPAR&ggr; overexpression. In SS mouse lung or in hemin‐treated HPAECs, activation of PPAR&ggr; with RSG attenuated reductions in PPAR&ggr; and increases in miR‐27a, ET‐1, and markers of endothelial dysfunction. In SCD‐PH pathogenesis, ETS1 stimulates increases in miR‐27a levels that reduce PPAR&ggr; and increase ET‐1 and endothelial dysfunction. PPAR&ggr; activation attenuated SCD‐associated signaling derangements, suggesting a novel therapeutic approach to attenuate SCD‐PH pathogenesis.
Next‐generation technologies for spatial proteomics: Integrating ultra‐high speed MALDI‐TOF and high mass resolution MALDI FTICR imaging mass spectrometry for protein analysis

MALDI imaging mass spectrometry is a powerful analytical tool enabling the visualization of biomolecules in tissue. However, there are unique challenges associated with protein imaging experiments including the need for higher spatial resolution capabilities, improved image acquisition rates, and better molecular specificity. Here we demonstrate the capabilities of ultra‐high speed MALDI‐TOF and high mass resolution MALDI FTICR IMS platforms as they relate to these challenges. High spatial resolution MALDI‐TOF protein images of rat brain tissue and cystic fibrosis lung tissue were acquired at image acquisition rates >25 pixels/s. Structures as small as 50 μm were spatially resolved and proteins associated with host immune response were observed in cystic fibrosis lung tissue. Ultra‐high speed MALDI‐TOF enables unique applications including megapixel molecular imaging as demonstrated for lipid analysis of cystic fibrosis lung tissue. Additionally, imaging experiments using MALDI FTICR IMS were shown to produce data with high mass accuracy (<5 ppm) and resolving power (∼75 000 at m/z 5000) for proteins up to ∼20 kDa. Analysis of clear cell renal cell carcinoma using MALDI FTICR IMS identified specific proteins localized to healthy tissue regions, within the tumor, and also in areas of increased vascularization around the tumor.
Hedging quantity risks with standard power options in a competitive wholesale electricity market

This paper addresses quantity risk in the electricity market and explores several ways of managing such risk. The paper also addresses the hedging problem of a load‐serving entity, which provides electricity service at a regulated price in electricity markets with price and quantity risk. Exploiting the correlation between consumption volume and spot price of electricity, an optimal zero‐cost hedging function characterized by payoff as a function of spot price is derived. It is then illustrated how such a hedging strategy can be implemented through a portfolio of forward contracts and call and put options. © 2006 Wiley Periodicals, Inc. Naval Research Logistics 2006
Different mechanisms to explain the reversed effects of mental health on work characteristics.

OBJECTIVES The number of longitudinal studies reporting evidence for reversed effects of strain on work is growing, but evidence regarding the mechanisms underlying such effects is scarce. In this study, earlier longitudinal findings were reviewed, and the following four mechanisms for reversed effects were proposed that reflect within-person or environmental changes: (i) the rosy perception mechanism, (ii) the gloomy perception mechanism, (iii) the upward selection mechanism, and (iv) the drift mechanism. METHODS These mechanisms were tested using structural equation modeling and longitudinal data from a Dutch four-phase study (N=1588 participants). RESULTS The results revealed that work characteristics and mental health influenced each other reciprocally and longitudinally. The reversed effects were examined in more detail, and it was found that these could be accounted for by both within-person and environmental change mechanisms. The rosy perception mechanism was found to explain the positive effects from health on job demands; the upward selection mechanism explained the positive (environmental) effects from health on job control; the gloomy perception mechanism explained the reversed (evaluation) effects from health on supervisory social support. No support was found for the drift mechanism. CONCLUSIONS Mechanisms that may explain reversed causation are yet poorly understood. The main contribution of the present study lies in the fact that it proposes (i) a conceptual framework with which to analyze the effects of health on work characteristics and (ii) methods for testing these mechanisms. The study revealed that there is good reason to pursue research on reversed causality.
NP‐313, 2‐acetylamino‐3‐chloro‐1,4‐naphthoquinone, a novel antithrombotic agent with dual inhibition of thromboxane A2 synthesis and calcium entry

1,4‐Naphthoquinones exhibit antiplatelet activity both in vivo and in vitro. In the present study, we investigated the antiplatelet effect of a novel naphthoquinone derivative NP‐313, 2‐acetylamino‐3‐chloro‐1,4‐naphthoquinone and its mechanism of action.
Signaling Lymphocyte Activation Molecule Family 5 Enhances Autophagy and Fine-Tunes Cytokine Response in Monocyte-Derived Dendritic Cells via Stabilization of Interferon Regulatory Factor 8

Signaling lymphocyte activation molecule family (SLAMF) receptors are essential regulators of innate and adaptive immune responses. The function of SLAMF5/CD84, a family member with almost ubiquitous expression within the hematopoietic lineage is poorly defined. In this article, we provide evidence that in human monocyte-derived dendritic cells (moDCs) SLAMF5 increases autophagy, a degradative pathway, which is highly active in dendritic cells (DCs) and plays a critical role in orchestration of the immune response. While investigating the underlying mechanism, we found that SLAMF5 inhibited proteolytic degradation of interferon regulatory factor 8 (IRF8) a master regulator of the autophagy process by a mechanism dependent on the E3-ubiquitin ligase tripartite motif-containing protein 21 (TRIM21). Furthermore, we demonstrate that SLAMF5 influences the ratio of CD1a+ cells in differentiating DCs and partakes in the regulation of IL-1β, IL-23, and IL-12 production in LPS/IFNγ-activated moDCs in a manner that is consistent with its effect on IRF8 stability. In summary, our experiments identified SLAMF5 as a novel cell surface receptor modulator of autophagy and revealed an unexpected link between the SLAMF and IRF8 signaling pathways, both implicated in multiple human pathologies.