Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression

The half-a-tetratricopeptide repeat (HAT) motif is a helical repeat motif found in proteins that influence various aspects of RNA metabolism, including rRNA biogenesis, RNA splicing, and polyadenylation. This functional association with RNA suggested that HAT repeat tracts might bind RNA. However, RNA binding activity has not been reported for any HAT repeat tract, and recent literature has emphasized a protein binding role. In this study, we show that a chloroplast-localized HAT protein, HCF107, is a sequence-specific RNA binding protein. HCF107 consists of 11 tandem HAT repeats and short flanking regions that are also predicted to form helical hairpins. The minimal HCF107 binding site spans ∼11 nt, consistent with the possibility that HAT repeats bind RNA through a modular one repeat–1 nt mechanism. Binding of HCF107 to its native RNA ligand in the psbH 5′ UTR remodels local RNA structure and protects the adjacent RNA from exonucleases in vitro. These activities can account for the RNA stabilizing, RNA processing, and translational activation functions attributed to HCF107 based on genetic data. We suggest that analogous activities contribute to the functions of HAT domains found in ribonucleoprotein complexes in the nuclear–cytosolic compartment.
Protein palmitoylation in signal transduction of hematopoietic cells

Abstract The covalent attachment of palmitate to proteins can alter protein–lipid and protein–protein interactions thereby influencing protein function. Palmitoylation is a reversible post-translational modification. Thus, like protein phosphorylation, protein palmitoylation can function in activation-dependent signaling pathways. This review will provide an overview of the mechanisms and regulation of protein palmitoylation and focus on the role of palmitoylation in signal transduction pathways of lymphocytes and platelets.
Differential effects of peroxisome proliferator activator receptor-alpha and gamma ligands on intimal hyperplasia after balloon catheter-induced vascular injury in Zucker rats.

BACKGROUND Patients with type 2 diabetes mellitus have a higher rate of restenosis following angioplasty. Peroxisome proliferator activator receptor-alpha (PPAR) and gamma ligands such as fenofibrate and rosiglitazone, respectively, have been shown to have protective effects on the vessel wall. We studied the effect of fenofibrate and rosiglitazone on intimal hyperplasia in the Zucker rat, a model for insulin resistance and type 2 diabetes mellitus, following balloon catheter-induced injury. METHODS AND RESULTS Three groups of 13-week-old female fatty Zucker rats were administered an aqueous suspension of either 3 mg/kg/d rosiglitazone (n=7) or 150 mg/kg/d fenofibrate (n=6) by gavage, or served as controls (n=9). In addition, two groups of 13-week-old female lean Zucker rats were either administered 3 mg/kg/d rosiglitazone (n=6) or served as controls (n=6). Carotid balloon injury was induced 1 week after the drugs were started. The drug administration was continued for 3 weeks. A 2-mm balloon catheter was introduced through the femoral artery to the left carotid. The balloon was inflated to 4 atmospheres for 20 seconds and then was deflated to 2 atmospheres and dragged down to the aorta. The rats were killed 3 weeks after the injury. The carotid intima/media ratio was calculated. Intimal hyperplasia after carotid balloon-induced injury in the fatty Zucker rats was significantly reduced in the group treated with rosiglitazone (0.18 +/- 0.29) compared with the untreated group (0.97 +/- 0.13; P<.01). Plasma glucose, triglyceride, and insulin levels were elevated, indicative of the presence of insulin resistance; rosiglitazone treatment significantly reduced insulin and triglyceride levels without decreasing glucose. Rosiglitazone treatment also reduced, but to a lesser extent, the intimal hyperplasia in the lean Zucker rats (0.57 +/- 0.10 vs 1.06 +/- 0.12 treated and untreated, respectively; P<.01); however, it had no effect on insulin, triglyceride, or glucose levels in this group. The intimal hyperplasia in the fatty Zucker rats treated with fenofibrate was not reduced compared with controls (0.84 +/- 0.26 vs 0.97 +/- 0.13, respectively); fenofibrate reduced insulin and triglyceride, but not glucose levels, in these animals. CONCLUSIONS The PPAR-gamma ligand rosiglitazone, but not the PPAR-alpha ligand fenofibrate, decreases intimal hyperplasia following balloon injury in both fatty and lean Zucker rats. This effect of the PPAR-gamma ligand was independent of glycemia, insulin, and lipid levels, and was more pronounced in insulin-resistant rats.
Massive Actin Polymerization Induced by Phosphatidylinositol-4-phosphate 5-Kinase in Vivo*

The Rho family GTP-binding proteins have been known to mediate extracellular signals to the actin cytoskeleton. Although several Rho interacting proteins have been found, downstream signals have yet to be determined. Many actin-binding proteins are known to be regulated by phosphatidylinositol 4,5-bisphosphate in vitro Rho has been shown to enhance the activity of phosphatidylinositol-4-phosphate 5-kinase (PI4P5K), the phosphatidylinositol 4,5-bisphosphate synthesizing enzyme. Recently we isolated several isoforms of type I PI4P5K. Here we report that PI4P5K Iα induces massive actin polymerization resembling “pine needles” in COS-7 cells in vivo When truncated from the C terminus to amino acid 308 of PI4P5K Iα, both kinase activity and actin polymerizing activity were lost. Although the dominant negative form of Rho, RhoN19, alone decreased actin fibers, those induced by PI4P5K were not affected by the coexpression of RhoN19. These results suggest that PI4P5K is located downstream from Rho and mediates signals for actin polymerization through its phosphatidylinositol-4-phosphate 5-kinase activity.
Economic evaluation of healthcare technology improving the quality of social life: the case of assistive technology for the disabled and elderly

ABSTRACT Public investments in healthcare technology for the disabled and elderly to improve the quality of social life have been vigorous, but the economic evaluation of the assistive technology is still lacking. Under this circumstance, the purpose of this study is to analyse the socio-economic value of developing assistive technologies with the potential to improve the quality of social life, especially for disabled and elderly individuals. Based on a survey of 400 respondents, the spike model, a special form of the contingent valuation method (CVM) is applied to assess the value of assistive technologies. In Korea, a household’s willingness-to-pay (WTP) for the development of assistive technologies is US$4.26 per year, on average, in the form of a government-levied tax; although many people express zero WTP for the development of these technologies, people with higher household savings, higher levels of education and higher levels of charity donations have a higher WTP for the development of assistive technology. We conclude that although assistive technologies have considerable economic value many people express zero WTP for the development of these technologies. Therefore, political and social educational efforts are necessary to reach social consensus on the government investment in such technologies.
Characterization of intermediates in the process of plant peroxisomal protein import

A hybrid protein in which the immunoglobulin G‐binding domain of Staphylococcus aureus protein A replaced the N‐terminal 43 amino acids of glycolate oxidase (a peroxisomal protein) was affinity purified after expression in Escherichia coli and used to study peroxisomal protein import in vitro. The fusion protein, which co‐purifies with the bacterial chaperones dnaK and groEL, binds to glyoxysomes and is partially translocated in an ATP‐dependent reaction which is independent of eukaryotic cytosol. Both binding and translocation are dependent upon the amount of glyoxysomes present. The partially translocated species has a transmembrane location and is extractable by salt, indicating that it is held in the membrane by ionic interactions. In the absence of ATP, the fusion protein binds to the surface of the glyoxysomes and competes the binding of authentic matrix proteins. The surface‐bound protein can be chased to the transmembrane species upon the addition of ATP. These results indicate that the surface‐bound form is a true translocation intermediate. The availability of this fusion protein in milligram quantities offers the possibility to use the intermediate formed in the absence of ATP and the transmembrane species to probe interactions with the peroxisome import machinery.
Probing nanoparticle translocation across the permeable endothelium in experimental atherosclerosis

Significance This study shows that an endothelialized microfluidic chip with controllable permeability can serve as a model for nanoparticle translocation across the permeable endothelium. Integration of this in vitro model and an in vivo rabbit model revealed that the extravasation of nanoparticles across the endothelium in atherosclerotic plaques depends on microvascular permeability. This approach represents a unique method for the assessment of nanoparticle behavior across the atherosclerotic endothelium, and may also serve as a valuable tool to study nanomedicine accumulation in a variety of other diseases. Therapeutic and diagnostic nanomaterials are being intensely studied for several diseases, including cancer and atherosclerosis. However, the exact mechanism by which nanomedicines accumulate at targeted sites remains a topic of investigation, especially in the context of atherosclerotic disease. Models to accurately predict transvascular permeation of nanomedicines are needed to aid in design optimization. Here we show that an endothelialized microchip with controllable permeability can be used to probe nanoparticle translocation across an endothelial cell layer. To validate our in vitro model, we studied nanoparticle translocation in an in vivo rabbit model of atherosclerosis using a variety of preclinical and clinical imaging methods. Our results reveal that the translocation of lipid–polymer hybrid nanoparticles across the atherosclerotic endothelium is dependent on microvascular permeability. These results were mimicked with our microfluidic chip, demonstrating the potential utility of the model system.
Regional Snow Parameters Estimation for Large‐Domain Hydrological Applications in the Western United States

In snow‐dominated regions, a key source of uncertainty in hydrologic prediction and forecasting is the magnitude and distribution of snow water equivalent (SWE). With ensemble simulations, this work demonstrates that SWE variability across the mountain ranges of the western United States (represented by 246 Snow Telemetry stations) can largely be captured at the daily time scale by a simple mass and energy‐balance snow model with four physically reasonable parameters—three snow albedo parameters and one snow temperature threshold for precipitation partitioning. The model skill is lower in the maritime Pacific Northwest where SWE variability is more sensitive to errors associated with simulated energy balance (e.g., downward radiation fluxes) and the temperature‐only precipitation partitioning approach. Poor model skill in high‐altitude, windy locations in the Northern Rockies can be attributed to precipitation undercatch and underrepresented wind processes. For the purpose of large‐domain hydrologic applications, regional snow parameters were developed for eight ecoregions characterized by a distinct hydroclimatic regime across the western United States. Results suggest that regionally coherent snow parameterizations are able to capture daily variations in SWE at most Snow Telemetry stations, suggesting that areas with a similar hydroclimate share a similar snow regime. While the three albedo parameters show limited spatial variability across all regions, the regional snow temperature threshold (Ts) shows marked spatial variation correlated with relative humidity; the Ts values increase from 0.2 °C in the higher‐humidity Pacific Northwest to 4.0 °C in the colder, lower‐humidity Rocky Mountains.
Hotel guests’ perception of best green practices: A content analysis of online reviews

The primary purpose of this study is to investigate guests’ perception of green hotels through a content analysis of online hotel reviews. A total of 7370 comments were collected, and 737 green comments were analyzed based on TripAdvisor’s top 10 green hotels. Our results indicate that the majority of hotel green practices are perceived as positive. Hotel guests consider some green practices, such as a reflective roofing system, a storm water management system, and guest training, as sincere efforts by hotels to be green and they complement them. However, some hotel guests assert that hotels may just be using green practices as a marketing tool or to gain financial benefits. Some green practices, such as temperature control, low water pressure, and degradable utensils, are actually not positively perceived. Therefore, our results suggest to hotel operators how they should implement being a sincere green hotel and how green practices should be approached to build environmental friendly branding strategies.
Do Probiotics Improve Eradication Response to Helicobacter Pylori on Standard Triple or Sequential Therapy?

Background: The standard triple therapy for the eradication of Helicobacter pylori consists of a combination of a proton pump inhibitor at a standard dose together with two antibiotics (amoxicillin 1000 mg plus either clarithromycin 500 mg or metronidazole 400 mg) all given twice daily for a period of 7-14 days. Recent reports have shown a dramatic decline in the rate of H. pylori eradication utilizing standard triple therapy from 95% down to 70-80%. Aims: Our study was designed to evaluate the effect of adding a probiotic as an adjuvant to common regimens used for H. pylori eradication. Materials and Methods: An open label randomized observational clinical study was designed to test three different regimens of H. pylori eradication treatment: Standard triple therapy with a concomitant probiotic added at the same time (n = 100), starting the probiotic for 2 weeks before initiating standard triple therapy along with the probiotic (n = 95), and the third regimen consists of the probiotic given concomitantly to sequential treatment (n = 76). The three arms were compared to a control group of patients treated with the traditional standard triple therapy (n = 106). Results: The eradication rate for the traditional standard therapy was 68.9%, and adding the probiotic “Bifidus infantis” to triple therapy, led to a successful rate of eradication of 83% (P < 0.001). Pre-treatment with 2 weeks of B. infantis before adding it to standard triple therapy increased the success rate of eradication to 90.5%. Similar improvement in eradication rate was noted when B. infantis was added as an adjuvant to the sequential therapy leading to an eradication rate of 90.8%. Conclusion: Adding B. infantis as an adjuvant to several therapeutic regimens commonly used for the eradication of H. pylori infection significantly improves the cure rates.
Salicylate Biosynthesis in Pseudomonas aeruginosa

Isochorismate pyruvate-lyase (IPL), the second enzyme of pyochelin biosynthesis and the product of thepchB gene, was purified to homogeneity fromPseudomonas aeruginosa. In the reaction catalyzed by this enzyme, isochorismate → salicylate + pyruvate, no cofactors appear to be required. At the pH optimum (pH 6.8), the enzyme displayed Michaelis-Menten kinetics, with an apparent K m of 12.5 μm for isochorismate and ak cat of 106 min−1, calculated per monomer. The native enzyme behaved as a homodimer, as judged by molecular sieving chromatography, electrophoresis under nondenaturing conditions, and cross-linking experiments. PchB has approximately 20% amino acid sequence identity with AroQ-class chorismate mutases (CMs). Chorismate was shown to be converted to prephenate by purified PchBin vitro, with an apparent K m of 150 μm and a k cat of 7.8 min−1. An oxabicyclic diacid transition state analog and well characterized inhibitor of CMs competitively inhibited both IPL and CM activities of PchB. Moreover, a CM-deficient Escherichia coli mutant, which is auxotrophic for phenylalanine and tyrosine, was functionally complemented by the cloned P. aeruginosa pchB gene for growth in minimal medium. A mutant form of PchB, in which isoleucine 88 was changed to threonine, had no detectable IPL activity, but retained wild-type CM activity. In conclusion, the 11.5-kDa subunit of PchB appears to contain a single active site involved in both IPL and CM activity.
Sylvian fissure morphology and asymmetry in men and women: Bilateral differences in relation to handedness in men

The anatomy of the sylvian fissure in the human brain was studied to develop reliable criteria for anatomical landmarks of the posterior part of the fissure for use in its definition and measurement; to quantify right‐left asymmetries in segments of the sylvian fissure; to assess whether any anatomical features are associated with hand preference (selected as one index of hemispheric functional asymmetry) and whether structure‐function relationships are similar in men and women.
The application of chromogenic media in clinical microbiology

Since 1990, a wide range of chromogenic culture media has been made commercially available providing useful tools for diagnostic clinical microbiology. By the inclusion of chromogenic enzyme substrates targeting microbial enzymes, such media are able to target pathogens with high specificity. Examples of target pathogens include Staphylococcus aureus, Streptococcus agalactiae, Salmonella spp. and Candida spp. The inclusion of multiple chromogenic substrates into culture media facilitates the differentiation of polymicrobial cultures, thus allowing for the development of improved media for diagnosis of urinary tract infections and media for the enhanced discrimination of yeasts. The purpose of this review is to provide some insight into how such media work and appraise their utility in routine clinical diagnostics, in comparison with conventional media.
Adaptive NN control of uncertain nonaffine pure-feedback systems with unknown time-delay

Adaptive dynamic surface control is presented for a class of nonaffine pure-feedback systems with unknown time-delay using neural networks. The problem of "explosion of complexity" in the traditional backstepping algorithm is avoided using dynamic surface control (DSC). The effects of unknown time-delays are eliminated by using appropriate Lyapunov-Krasovskii functionals in the design procedure. The proposed control scheme guarantees that all the signals in the closed-loop system are semi-globally uniformly ultimately bounded. A simulation example is presented to demonstrate the method.
Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors

The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs’ embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess–as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.
Design, Packaging and Characterization of a Two-Port Bulk Wave Langasite Viscometer

A two-port monolithic crystal filter (MCF) viscosity sensor has been developed using high coupling langasite material and advanced packaging techniques. The present work details the evaluation of quartz and langasite MCF elements with varying shapes, contours and electrode designs. Additional work on protective coatings has made the sensor reliable for a wide range of harsh conditions. The study has resulted in a candidate design on 10.25 mm blanks, housed in a TO-8 header with support circuitry contained in a 3/4" NPT bolt. The sensor elements are presently operable over the MIL temperature range and packaging improvements are underway to allow operation to 200degC or higher.
Interpretation, Interaction, and Scalability for Structural Decomposition Trees

Structural Decomposition Trees (SDTs) have been proposed as a completely novel display approach to tackling the research problem of visualizing high-dimensional data. SDTs merge the two distinct classes of relation and value visualizations into a single integrated strategy. The method is promising; however, statements regarding its meaningful application are still missing, constraining its broad adoption. This paper introduces solutions for still-existing issues in the application of SDTs with regard to interpretation, interaction, and scalability. SDTs provide a well-designed initial projection of the data to meaningfully represent its properties, but not much is known about how to interpret this projection. We are able to derive the data’s properties from their initial representation. The provided methods are valid not only for SDTs, but also for projections based on principal components analysis, addressing a frequent problem when applying this technology. We further show how interactive exploration based on SDTs can be applied to visual cluster analysis as one of its application domains. To address the urgent need to analyze vast and complex amounts of data, we also introduce means for scalable processing and representation. Given the importance and broader relevance of the discussed problem domains, this paper justifies and further motivates the usefulness and wide applicability of SDTs as a novel visualization approach for high-dimensional data.