Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Kinase A-mediated Phosphorylation of Pah1p Phosphatidate Phosphatase Functions in Conjunction with the Pho85p-Pho80p and Cdc28p-Cyclin B Kinases to Regulate Lipid Synthesis in Yeast*

Background: Pah1p, a phosphatidate phosphatase in yeast, produces diacylglycerol for lipid synthesis. Results: Phosphorylation of Pah1p by protein kinase A inhibited membrane association, phosphatidate phosphatase activity, and triacylglycerol synthesis. Conclusion: Protein kinase A functioned in conjunction with Pho85p-Pho80p and Cdc28p-cyclin B kinases to regulate Pah1p. Significance: Lipid synthesis is regulated through multiple phosphorylations of Pah1p phosphatidate phosphatase. Pah1p, which functions as phosphatidate phosphatase (PAP) in the yeast Saccharomyces cerevisiae, plays a crucial role in lipid homeostasis by controlling the relative proportions of its substrate phosphatidate and its product diacylglycerol. The diacylglycerol produced by PAP is used for the synthesis of triacylglycerol as well as for the synthesis of phospholipids via the Kennedy pathway. Pah1p is a highly phosphorylated protein in vivo and has been previously shown to be phosphorylated by the protein kinases Pho85p-Pho80p and Cdc28p-cyclin B. In this work, we showed that Pah1p was a bona fide substrate for protein kinase A, and we identified by mass spectrometry and mutagenesis that Ser-10, Ser-677, Ser-773, Ser-774, and Ser-788 were the target sites of phosphorylation. Protein kinase A-mediated phosphorylation of Pah1p inhibited its PAP activity by decreasing catalytic efficiency, and the inhibitory effect was primarily conferred by phosphorylation at Ser-10. Analysis of the S10A and S10D mutations (mimicking dephosphorylation and phosphorylation, respectively), alone or in combination with the seven alanine (7A) mutations of the sites phosphorylated by Pho85p-Pho80p and Cdc28p-cyclin B, indicated that phosphorylation at Ser-10 stabilized Pah1p abundance and inhibited its association with membranes, PAP activity, and triacylglycerol synthesis. The S10A mutation enhanced the physiological effects imparted by the 7A mutations, whereas the S10D mutations attenuated the effects of the 7A mutations. These data indicated that the protein kinase A-mediated phosphorylation of Ser-10 functions in conjunction with the phosphorylations mediated by Pho85p-Pho80p and Cdc28p-cyclin B and that phospho-Ser-10 should be dephosphorylated for proper PAP function.
Raptor Codes for Infrastructure-to-Vehicular Broadcast Services

One of the important applications to be available in vehicular ad-hoc networks are value-added or infotainment services. However, vehicular communication suffers from high packet loss due to challenging channel characteristics such as huge Doppler spread and multipath fading. This makes current IEEE 802.11p standard for vehicular network based on the ARQ scheme inefficient. Therefore, the highly scalable and fault-tolerant properties offered by rateless code makes this a promising area of research. This paper investigates the implementation of a systematic Raptor codes for a broadcast service in infrastructure-to-vehicular communications. The code performance in terms of the decoding probability of success, mean decoding time and mean aggregate throughput are presented.
Evaluation of Human Breast Adenocarcinoma (MCF-7) Cells Proliferation in Co-Culture with Human Adipocytes in Three Dimensional Collagen Gel Matrix: Norepinephrine as a Lipolytic Factor

Background: Norepinephrine plays a trophic role in the control of cell replication and differentiation in target cells that express adrenergic receptors. Methods: In this study, we have tested the influence of infraphysiological, physiological and supraphysiological concentrations (0.0001 nM, 1 nM, 10000 nM) of human norepinephrine on the proliferation of breast cancer cells (human breast adenocarcinoma [MCF-7]) in co-culture with human adipocytes in three-dimensional collagen gel matrix culture. Cell proliferation and lipolysis rate were measured by 3-(4, 5-dimethylthiazolyl)-2, 5-diphenyl-tetrazolium bromide (MTT) and Oil red O colorimetric assay in second, 7 th and 14 th days of culture experiments. Results: Our results showed a direct correlation between lipolysis rate of adipocytes and proliferation rate of MCF-7 cells. Both physiological and supraphysiological concentrations of human norepinephrine significantly (P<0.05) increased the proliferation of MCF-7 cells synchronously with progress of adipocyte lipolysis. The proliferations of MCF-7 cells were significantly decreased after conversion of adipocytes to fibroblast-like cells by supraphysiological concentration of norepinephrine. There was no statistical difference in lipolysis of adipocytes and proliferation of MCF-7 cells in response to infraphysiological concentration of norepinephrine. Conclusion: These findings indicated that norepinephrine stimulated the proliferation of MCF-7 cells in coculture with human adipocytes as a lipolytic factor and that norepinephrine effect was suppressed by conversion of adipocytes to fibroblast-like cells, suggesting adipocytes as another target for prevention and therapy of breast cancer. Iran. Biomed. J. 10 (3): 125-131, 2006
Parallel classification and feature selection in microarray data using SPRINT

The statistical language R is favoured by many biostatisticians for processing microarray data. In recent times, the quantity of data that can be obtained in experiments has risen significantly, making previously fast analyses time consuming or even not possible at all with the existing software infrastructure. High performance computing (HPC) systems offer a solution to these problems but at the expense of increased complexity for the end user. The Simple Parallel R Interface is a library for R that aims to reduce the complexity of using HPC systems by providing biostatisticians with drop‐in parallelised replacements of existing R functions. In this paper we describe parallel implementations of two popular techniques: exploratory clustering analyses using the random forest classifier and feature selection through identification of differentially expressed genes using the rank product method. Copyright © 2012 John Wiley & Sons, Ltd.
Revealing hidden evolutionary capacity to cope with global change

The extent to which global change will impact the long‐term persistence of species depends on their evolutionary potential to adapt to future conditions. While the number of studies that estimate the standing levels of adaptive genetic variation in populations under predicted global change scenarios is growing all the time, few studies have considered multiple environments simultaneously and even fewer have considered evolutionary potential in multivariate context. Because conditions will not be constant, adaptation to climate change is fundamentally a multivariate process so viewing genetic variances and covariances over multivariate space will always be more informative than relying on bivariate genetic correlations between traits. A multivariate approach to understanding the evolutionary capacity to cope with global change is necessary to avoid misestimating adaptive genetic variation in the dimensions in which selection will act. We assessed the evolutionary capacity of the larval stage of the marine polychaete Galeolaria caespitosa to adapt to warmer water temperatures. Galeolaria is an important habitat‐forming species in Australia, and its earlier life‐history stages tend to be more susceptible to stress. We used a powerful quantitative genetics design that assessed the impacts of three temperatures on subsequent survival across over 30 000 embryos across 204 unique families. We found adaptive genetic variation in the two cooler temperatures in our study, but none in the warmest temperature. Based on these results, we would have concluded that this species has very little capacity to evolve to the warmest temperature. However, when we explored genetic variation in multivariate space, we found evidence that larval survival has the potential to evolve even in the warmest temperatures via correlated responses to selection across thermal environments. Future studies should take a multivariate approach to estimating evolutionary capacity to cope with global change lest they misestimate a species’ true adaptive potential.
Social Origins of Rhythm? Synchrony and Temporal Regularity in Human Vocalization

Humans have a capacity to perceive and synchronize with rhythms. This is unusual in that only a minority of other species exhibit similar behavior. Study of synchronizing species (particularly anurans and insects) suggests that simultaneous signal production by different individuals may play a critical role in the development of regular temporal signaling. Accordingly, we investigated the link between simultaneous signal production and temporal regularity in our own species. Specifically, we asked whether inter-individual synchronization of a behavior that is typically irregular in time, speech, could lead to evenly-paced or “isochronous” temporal patterns. Participants read nonsense phrases aloud with and without partners, and we found that synchronous reading resulted in greater regularity of durational intervals between words. Comparison of same-gender pairings showed that males and females were able to synchronize their temporal speech patterns with equal skill. These results demonstrate that the shared goal of synchronization can lead to the development of temporal regularity in vocalizations, suggesting that the origins of musical rhythm may lie in cooperative social interaction rather than in sexual selection.
Multiple scattering in observations of the GPM dual‐frequency precipitation radar: Evidence and impact on retrievals

This paper illustrates how multiple scattering signatures affect Global Precipitation Measuring (GPM) Mission Dual‐Frequency Precipitation Radar (DPR) Ku and Ka band reflectivity measurements and how they are consistent with prelaunch assessments based on theoretical considerations and confirmed by airborne observations. In particular, in the presence of deep convection, certain characteristics of the dual‐wavelength reflectivity profiles cannot be explained with single scattering, whereas they are readily explained by multiple‐scattering theory. Examples of such signatures are the absence of surface reflectivity peaks and anomalously small reflectivity slopes in the lower troposphere. These findings are relevant for DPR‐based rainfall retrievals and stratiform/convective classification algorithms when dealing with deep convective regions. A path to refining the rainfall inversion problem is proposed by adopting a methodology based on a forward operator which accounts for multiple scattering. A retrieval algorithm based on this methodology is applied to a case study over Africa, and it is compared to the standard DPR products obtained with the at‐launch version of the standard algorithms.
Myocardial performance assessment in neonates by one-segment strain and strain rate analysis by tissue Doppler - a quality improvement cohort study

Objectives To investigate one-segment strain and strain rate indices as measures of myocardial performance in asphyxiated term neonates. Design Quality improvement cohort study. Setting Newborns admitted to a neonatal intensive care unit at a Norwegian University Hospital for perinatal asphyxia and non-asphyxiated newborn recruited from the maternity ward at the same hospital. Participants Twenty asphyxiated and 48 non-asphyxiated term neonates. Primary outcome measure Strain and strain rate indices and repeatability measures. One-segment longitudinal strain and strain rate by tissue Doppler were assessed on days 1, 2 and 3 of life in nine heart walls. Repeatability was compared against measurements from two-segment analyses previously performed in the same images. Results The 95% limits of agreement were significantly better for the one-segment than two-segment repeatability analyses, the inter-rater peak systolic strain (PSS) was (−3.1, 3.3) vs (−11.4, 18.3)%, the inter-rater peak systolic strain rate (PSSR) was (−0.38, 0.40) vs (−0.79, 1.15)/s, the intra-rater PSS was (−2.5, 2.6) vs (−8.0, 9.8)% and the intra-rater PSSR was (−0.23, 0.25) vs (−0.75, 0.80)/s (p<0.05). The myocardial performance was lower in the asphyxiated neonates (indices closer to zero) than in the non-asphyxiated neonates, PSS was −17.8 (0.6) (mean (SEM)) vs −21.2 (0.3)%, PSSR −1.43 (0.08) vs −1.61 (0.03)/s, early diastolic strain rate 1.72 (0.11) vs 2.00 (0.11)/s and strain rate during the atrial systole 1.92 (0.17) vs 2.27 (0.10)/s (p<0.05), despite no difference in fractional shortening (29.0 (0.5) vs 29.1 (1.0)%) (p>0.05). Conclusions One-segment strain and strain rate assessed the reduced myocardial performance in asphyxiated neonates with significantly improved reproducibility as compared with two-segment analysis and was therefore more feasible than two-segment analyses for assessment of myocardial performance after perinatal asphyxia.
Fast computation of the fitness function for protein folding prediction in a 2D hydrophilic-hydrophobic model

Protein Folding Prediction (PFP) is essentially an energy minimization problem formalised by the definition of a fitness function. Several PFP models have been proposed including the Hydrophobic-Hydrophilic (HP) model, which is widely used as a test-bed for evaluating new algorithms. The calculation of the fitness is the major computational task in determining the native conformation of a protein in the HP model and this paper presents a new efficient search algorithm (ESA) for deriving the fitness value requiring only O(n) complexity in contrast to the full search approach, which takes O(n2). The improved efficiency of ESA is achieved by exploiting some intrinsic properties of the HP model, with a resulting reduction of more than 50% in the overall time complexity when compared with the previously reported Caching Approach, with the added benefit that the additional space complexity is linear instead of quadratic.
The Ginibre Point Process as a Model for Wireless Networks With Repulsion

The spatial structure of transmitters in wireless networks plays a key role in evaluating mutual interference and, hence, performance. Although the Poisson point process (PPP) has been widely used to model the spatial configuration of wireless networks, it is not suitable for networks with repulsion. The Ginibre point process (GPP) is one of the main examples of determinantal point processes that can be used to model random phenomena where repulsion is observed. Considering the accuracy, tractability, and practicability tradeoffs, we introduce and promote the β-GPP, which is an intermediate class between the PPP and the GPP, as a model for wireless networks when the nodes exhibit repulsion. To show that the model leads to analytically tractable results in several cases of interest, we derive the mean and variance of the interference using two different approaches: the Palm measure approach and the reduced second-moment approach, and then provide approximations of the interference distribution by three known probability density functions. In addition, to show that the model is relevant for cellular systems, we derive the coverage probability of a typical user and find that the fitted β-GPP can closely model the deployment of actual base stations in terms of coverage probability and other statistics.
Insecticide Resistance in Eggs and First Instars of the Bed Bug, Cimex lectularius (Hemiptera: Cimicidae)

Two strains of the common bed bug, Cimex lectularius L. , eggs and first instars collected from pyrethroid-resistant adults were evaluated for insecticide resistance and compared to a susceptible strain. Dose-response bioassays were conducted using two insecticide formulations (Temprid: imidacloprid/β-cyfluthrin, and Transport: acetamiprid/bifenthrin). The lethal concentration (LC50) for the two resistant egg strains exposed to imidacloprid/β-cyfluthrin ranged from 3 to 5-fold higher than susceptible strain eggs. Resistant strain eggs dipped into formulations of acetamiprid/bifenthrin had LC50 values which were significantly greater (39 to 1,080-fold) than susceptible strain eggs. Similar to eggs, resistant strain first instars exposed to residual applications of imidacloprid/β-cyfluthrin had LC50 values ranging from 121 to 493-fold greater than susceptible strain first instars. When resistant strain first instars were treated with acetamiprid/bifenthrin, they had LC50 values that were 99 to >1,900-fold greater than susceptible strain first instars. To determine differences between egg and first instar resistance, stage resistance ratios (SRR) were compared between the two stages. There was little difference between the egg and first instar stages, indicated by small SRR values ranging from 1.1 to 10.0. This study suggests that insecticide resistance is expressed early during bed bug development.
L-Selectin ligands in human endometrium: comparison of fertile and infertile subjects

BACKGROUND L-selectin ligands, localized to the luminal epithelium at the time of implantation, may support the early stages of blastocyst attachment. We have assessed the expression of two L-selectin ligands, defined by MECA-79 and HECA-452 monoclonal antibodies, and the sulfotransferase GlcNAc6ST-2, involved in generation of L-selectin ligand epitopes, in the secretory phase of the endometrium from fertile and infertile patients. METHODS Endometrial samples were obtained from 33 fertile, 26 PCOS, 25 endometriosis and 33 patients diagnosed with unexplained infertility. L-selectin ligands and GlcNAc6ST-2 expression was assessed by immunohistochemistry and immunoblotting. RESULTS Immunohistochemical staining of uterine epithelium, from fertile and infertile women, demonstrated differential expression of MECA-79 and HECA-452 epitopes. In fertile women in the secretory phase MECA-79 was more strongly expressed, particularly on the lumen, than in infertile women. HECA-452 staining was significantly stronger in the glands in PCOS and endometriosis patients than in fertile women. GlcNAc6ST-2 expression was reduced in infertile patients, correlating with MECA-79 expression. CONCLUSIONS This study demonstrated significant differences in expression of L-selectin ligands between fertile and infertile women in natural cycles, and could contribute to patient assessment prior to initiating fertility treatment.
Risk of chemotherapy-induced pulmonary fibrosis is associated with polymorphic tumour necrosis factor-a2 gene

In some patients, chemotherapy (CHT) of cancer can result in pulmonary inflammation and fibrosis, eventually leading to respiratory insufficiency. As animal studies have underlined the importance of major histocompatibility complex (MHC) genes in the susceptibility to bleomycin (BLM)-induced pulmonary fibrosis, the authors typed human leukocyte antigen-DR (HLA-DR) and tumor necrosis factor (TNF) genes in patients treated for Hodgkin's disease by a therapy including bleomycin. Patients were divided into pulmonary responders (PR) (n=21) or nonresponders (PNR) (n=20) on the basis of pulmonary alterations detected on chest radiography and the cumulated amount of BLM injected. The incidence of TNFa2, a microsatellite allele in the promoter region of the TNFB gene reported to be associated with increased TNF-α production, was significantly higher in PR than PNR (65% versus 19%). HLA-DRB1*15 showed a weak but nonsignificant association with the PR phenotype (50% versus 14%), as well as HLA-DRB1*03 (30% versus 19%) and TNFA-308*2 (30% versus 14 %). TNFa2 and DR15 were independent risk factors and the occurrence of either genetic marker was 85% versus 29% in the PR and PNR groups respectively. Thus, the polymorphic TNFa2 microsatellite is associated with a risk of chemotherapy-induced pulmonary fibrosis.
Azelastine hydrochloride, a dual-acting anti-inflammatory ophthalmic solution, for treatment of allergic conjunctivitis

Over 50% of patients who seek treatment for allergies present with ocular symptoms. Our current ability to control ocular allergic symptoms is greater than ever before. Newer dual-acting topical eyedrops attack multiple facets of the allergic cascade. Azelastine has antihistaminic effects providing immediate relief, mast cell stabilization providing early-phase intervention, and inhibition of expression and activation of anti-inflammatory mediators which characterize the late phase of the immune reaction. The ophthalmic eyedrop formulation is approved for treatment of allergic conjunctivitis in adults and children aged over 3 years. In clinical trials comparing azelastine with other dual-acting eyedrops, such as levocabastine and olopatadine, azelastine was reported to be slightly less efficacious and to sting briefly upon administration. Even so, many patients experienced the full benefit of symptom relief, and preferred azelastine. As a broad-spectrum drug, azelastine offers many desirable properties for management of ocular allergies. Because it can often produce maximal effect with just twice-daily dosing, azelastine is a particularly good choice for the allergic population in whom minimizing exposure to topical products and preservatives is a key concern.
The Strategy of T Cell Antigen-presenting Cell Encounter in Antigen-draining Lymph Nodes Revealed by Imaging of Initial T Cell Activation

The development of an immune response critically relies on the encounter of rare antigen (Ag)-specific T cells with dendritic cells (DCs) presenting the relevant Ag. How two rare cells find each other in the midst of irrelevant other cells in lymph nodes (LNs) is unknown. Here we show that initial T cell activation clusters are generated near high endothelial venules (HEVs) in the outer paracortex of draining LNs by retention of Ag-specific T cells as they exit from HEVs. We further show that tissue-derived DCs preferentially home in the vicinity of HEVs, thus defining the site of cluster generation. At this location DCs efficiently scan all incoming T cells and selectively retain those specific for the major histocompatibility complex–peptide complexes the DCs present. Such strategic positioning of DCs on the entry route of T cells into the paracortex may foster T cell–DC encounter and thus optimize initial T cell activation in vivo.
Unanticipated benefits of CAM therapies for back pain: an exploration of patient experiences.

OBJECTIVES The goal of this research was to provide insight into the full range of meaningful outcomes experienced by patients who participate in clinical trials of complementary and alternative medicine (CAM) therapies. DESIGN Data for this study were assembled from five randomized trials evaluating six different CAM treatments for back pain. A conventional qualitative content analysis was conducted on responses to open-ended questions asked at the end of telephone interviews assessing treatment outcomes. SUBJECTS A total of 884 study participants who received CAM therapies completed post-treatment interviews. Of these, 327 provided qualitative data used in the analyses. RESULTS Our analysis identified a range of positive outcomes that participants in CAM trials considered important but were not captured by standard quantitative outcome measures. Positive outcome themes included increased options and hope, increased ability to relax, positive changes in emotional states, increased body awareness, changes in thinking that increased the ability to cope with back pain, increased sense of well-being, improvement in physical conditions unrelated to back pain, increased energy, increased patient activation, and dramatic improvements in health or well-being. The first five of these themes were mentioned for all of the CAM treatments, while others tended to be more treatment specific. A small fraction of these effects were considered life transforming. CONCLUSIONS Our findings suggest that standard measures used to assess the outcomes of CAM treatments fail to capture the full range of outcomes that are important to patients. In order to capture the full impact of CAM therapies, future trials should include a broader range of outcomes measures.