Miracle-dz/UniFAR-FTUs huggingface dataset:
Site-specific phosphorylation and microtubule dynamics control Pyrin inflammasome activation

Significance Pyrin, encoded by the MEFV gene, is causative for familial Mediterranean fever (FMF), an autoinflammatory disease. Pyrin responds to bacterial modifications/inactivation of Rho GTPases by assembling an inflammasome complex for activating caspase-1. Pyrin is a unique immune sensor because it senses bacterial virulence rather than recognizing microbial products. We found that Pyrin is phosphorylated on two serine sites which keep Pyrin inactive through binding by 14-3-3 proteins. Toxin stimulation and bacterial infection trigger Pyrin dephosphorylation and 14-3-3 dissociation, allowing Pyrin inflammasome activation. Colchicine, a microtubule-disrupting drug used to treat FMF, inhibits Pyrin activation downstream of dephosphorylation and 14-3-3 dissociation. These findings not only help us understand FMF pathogenesis/treatment but also shed mechanistic insights into cytosolic immunity. Pyrin, encoded by the MEFV gene, is best known for its gain-of-function mutations causing familial Mediterranean fever (FMF), an autoinflammatory disease. Pyrin forms a caspase-1–activating inflammasome in response to inactivating modifications of Rho GTPases by various bacterial toxins or effectors. Pyrin-mediated innate immunity is unique in that it senses bacterial virulence rather than microbial molecules, but its mechanism of activation is unknown. Here we show that Pyrin was phosphorylated in bone marrow-derived macrophages and dendritic cells. We identified Ser-205 and Ser-241 in mouse Pyrin whose phosphorylation resulted in inhibitory binding by cellular 14-3-3 proteins. The two serines underwent dephosphorylation upon toxin stimulation or bacterial infection, triggering 14-3-3 dissociation, which correlated with Pyrin inflammasome activation. We developed antibodies specific for phosphorylated Ser-205 and Ser-241, which confirmed the stimuli-induced dephosphorylation of endogenous Pyrin. Mutational analyses indicated that both phosphorylation and signal-induced dephosphorylation of Ser-205/241 are important for Pyrin activation. Moreover, microtubule drugs, including colchicine, commonly used to treat FMF, effectively blocked activation of the Pyrin inflammasome. These drugs did not affect Pyrin dephosphorylation and 14-3-3 dissociation but inhibited Pyrin-mediated apoptosis-associated Speck-like protein containing CARD (ASC) aggregation. Our study reveals that site-specific (de)phosphorylation and microtubule dynamics critically control Pyrin inflammasome activation, illustrating a fine and complex mechanism in cytosolic immunity.
Glaucoma Increases Retinal Surface Contour Variability as Measured by Optical Coherence Tomography

Purpose We investigated the feasibility of glaucoma detection by measuring retinal surface contour variability (RSCV) using optical coherence tomography (OCT). Methods The peripapillary region in one eye of each participant was scanned over an 8 × 8 mm area with a swept source OCT prototype. The retinal surface contour was sampled at approximately 1.5- to 3.5-mm radius circles centered on the optic nerve head. The RSCV is defined as the average log value within a middle spatial frequency band of the Fourier transform to the elevation profile of the inner retinal surface. The spatial frequency band was optimized to distinguish glaucoma from normal. Nerve fiber layer thickness (NFLT) was sampled around a 1.7-mm radius circle. Glaucoma severity was assessed by automated static perimetry. Results We enrolled 17 glaucomatous eyes and 17 healthy eyes. A great majority of the glaucoma group were in the early stage (visual field mean deviation average −2.48 ± 3.73 dB). Significant differences were found for RSCV between glaucoma and control eyes (P < 0.003) at all radii. The area under the receiver operating characteristic curve (AROC = 0.90) of RSCV was best at the 3.5-mm radius. This was not significantly better than NFLT (AROC = 0.84). With the 99% specificity, the glaucoma detection sensitivity was 53% for RSCV and 29% for NFLT (P = 0.13). Conclusions Retinal surface contour variability was significantly increased in glaucoma patients. The diagnostic accuracy of RSCV was equal to NFLT in early glaucoma. Since the RSCV detects small-scale focal damage and the average NFLT measures global damage, they provide different diagnostic information that may be synergistic.
EAAT2 (GLT-1; slc1a2) Glutamate Transporters Reconstituted in Liposomes Argues against Heteroexchange Being Substantially Faster than Net Uptake

The EAAT2 glutamate transporter, accounts for >90% of hippocampal glutamate uptake. Although EAAT2 is predominantly expressed in astrocytes, ∼10% of EAAT2 molecules are found in axon terminals. Despite the lower level of EAAT2 expression in glutamatergic terminals, when hippocampal slices are incubated with low concentration of d-aspartate (an EAAT2 substrate), axon terminals accumulate d-aspartate as quickly as astroglia. This implies an unexplained mismatch between the distribution of EAAT2 protein and of EAAT2-mediated transport activity. One hypothesis is that (1) heteroexchange of internal substrate with external substrate is considerably faster than net uptake and (2) terminals favor heteroexchange because of high levels of internal glutamate. However, it is currently unknown whether heteroexchange and uptake have similar or different rates. To address this issue, we used a reconstituted system to compare the relative rates of the two processes in rat and mice. Net uptake was sensitive to changes in the membrane potential and was stimulated by external permeable anions in agreement with the existence of an uncoupled anion conductance. By using the latter, we also demonstrate that the rate of heteroexchange also depends on the membrane potential. Additionally, our data further suggest the presence of a sodium leak in EAAT2. By incorporating the new findings in our previous model of glutamate uptake by EAAT2, we predict that the voltage sensitivity of exchange is caused by the voltage-dependent third Na+ binding. Further, both our experiments and simulations suggest that the relative rates of net uptake and heteroexchange are comparable in EAAT2.
An unsupervised technical difficulty ranking model based on conceptual terrain in the latent space

Search results of the existing general-purpose search engines usually do not satisfy domain-specific information retrieval tasks as there is a mis-match between the technical expertise of a user and the results returned by the search engine. In this paper, we investigate the problem of ranking domain-specific documents based on the technical difficulty. We propose an unsupervised conceptual terrain model using Latent Semantic Indexing (LSI) for re-ranking search results obtained from a similarity based search system. We connect the sequences of terms under the latent space by the semantic distance between the terms and compute the traversal cost for a document indicating the technical difficulty. Our experiments on a domain-specific corpus demonstrate the efficacy of our method.
Implicit alternative splicing for genetic algorithms

In this paper we present a new nature-inspired variation operator for binary encodings in genetic algorithms (GAs). Our method, called implicit alternative splicing (iAS), is repeatedly applied to the individual encodings in the algorithm's population and inverts randomly chosen segments of decreasing size in a systematic fashion. Its goal is to determine the largest possible segment the inversion of which yields no loss in the encoding's quality. The application of iAS potentially produces a new encoding of equal or greater quality that is maximum possible Hamming distance from its source. This allows iAS to uphold the diversity of the population even if a minimal population size is chosen. This significantly improves the performance of an otherwise standard GA on a representative set of three different optimisation problems. Empirical results are compared and analysed and future work prospects are considered.
Multiagent system solutions for distributed computing, communications, and data integration needs in the power industry

We identify three fundamental issues underlying many problems in power systems today: distributed computing, communications, and data integration. We review the characteristics of intelligent agents and multi-agent systems (MAS) technologies and argue that MAS offer a modular, extensible, flexible, and integrated approach to address all three of these issues and the problems resulting from them. The MAS design methodology is summarized, and an illustrative MAS application scenario in electric power systems is presented.
Using Index in the MapReduce Framework

MapReduce is a programming framework introduced by Google for large-scale data processing. It is usually used in a scan-centric fashion where all the data are split into blocks and Maps are generated for each block to scan and process the data in the block, then Reduces merge outputs from all the Maps. When a query intends to process only a subset of the data selected by a predicate, this brute-force method may cause extra I/O overhead spent on irrelevant data, and the overhead for initiating so many Maps may be non-trivial given that the actually interesting data for the query is comparatively small in volume. We propose an approach to integrate the index into the MapReduce execution in which only an appropriate number of Maps are generated, each of which accesses the data using an index. This approach incurs random I/O and remote access to data, so the overall performance depends on both system parameters and the query characteristics. We build a cost model for both this index access execution and the traditional full scan execution. This cost model can be used to choose between the two execution modes before executing a query. Experiments show that the index access execution can greatly outperform full scan execution when the selectivity of the predicate is low, and the cost model predicts the actual execution cost very well so can be used to determine the execution plan for a query.
Comparison of microwave and thermal cure of an epoxy/amine matrix

An investigation was carried out into the effect of a microwave cure on an epoxy prepolymer with a cycloaliphatic diamine mixture, as compared to a standard thermal cure. The microwave waveguide and process (propagation mode TE 01 ) were adjusted to obtain large homogeneous samples. The extent of reaction, x, was measured during the microwave processing by size exclusion chromatography and differential scanning calorimetry. A good estimate of x was found using a modified DiBenedetto equation correlating x and the glass transition temperature T g . The homogeneity of the samples was checked during the last steps of cure, showing the efficiency of the microwave processing and wavegulde. The influence of the nature of the mold (metallic or dielectric) on the reaction kinetic was also investigated. Samples cured by both thermal and microwave processing were characterized by dynamic and static mechanical properties and then compared with those of fully crosslinked networks, i.e., postcured at a high temperature
The Biggest Loser Thinks Long-Term: Recency as a Predictor of Success in Weight Management

Only a minority of participants in behavioral weight management lose weight significantly. The ability to predict who is likely to benefit from weight management can improve the efficiency of obesity treatment. Identifying predictors of weight loss can also reveal potential ways to improve existing treatments. We propose a neuro-psychological model that is focused on recency: the reliance on recent information at the expense of time-distant information. Forty-four weight-management patients completed a decision-making task and their recency level was estimated by a mathematical model. Impulsivity and risk-taking were also measured for comparison. Weight loss was measured in the end of the 16-week intervention. Consistent with our hypothesis, successful dieters (n = 12) had lower recency scores than unsuccessful ones (n = 32; p = 0.006). Successful and unsuccessful dieters were similar in their demographics, intelligence, risk taking, impulsivity, and delay of gratification. We conclude that dieters who process time-distant information in their decision making are more likely to lose weight than those who are high in recency. We argue that having low recency facilitates future-oriented thinking, and thereby contributes to behavior change treatment adherence. Our findings underline the importance of choosing the right treatment for every individual, and outline a way to improve weight-management processes for more patients.
NCTUns network simulation and emulation for wireless resource management

Summary This paper describes NCTUns, an innovative network simulator and emulator for wireless and mobile networks. Effects of various radio resource management and quality of service (QoS) schemes on higher-layer protocols and real-world applications can be easily studied using NCTUns. In this paper, we elaborate on NCTUns simulation methodology, architecture, design, functionalities, performance, and applications. NCTUns simulation for wireless ad hoc, sensor, inter-vehicle communication networks, GPRS cellular networks, and wireless mesh networks are also illustrated. More details about this tool can be found in http://NSL.csie. nctu.edu. tw/nctuns.html. Copyright # 2005 John Wiley & Sons, Ltd.
Clothing Air Gap Layers and Thermal Protective Performance in Single Layer Garment

A three-dimensional body scanning technique is used to measure the air gap layer distribution between different-sized protective garments and the body of a manikin used to evaluate garment thermal protective performance. The influence of fabric material and garment size on the manikin skin-clothing air gap layers existing in single layer thermally protective coveralls is analyzed. Protective performance of these garments is evaluated using the Manikin Thermal Protective Clothing Analysis System. Relationships between the burn patterns, measured on a flash fire manikin and measured manikin-garment air gap layers, are examined. The effects of thermally induced shrinkage as a result of flash fire exposure are discussed in comparisons between single layer protective coverall clothing made with heat resistant fabrics. An established numerical model is used to forecast the dimensions of skin-clothing air gap for optimum thermal protection.
A Survey of Frequent Subgraph Mining algorithms for Uncertain Graph Data

- Mining uncertain graph data is different from exact graph data semantically and is more challenging task in recent days of research. Mining frequent sub graphs from uncertain graph data is the latest topic in research. Few algorithms for finding frequent sub graphs from uncertain graph data are Mining Uncertain Subgraph patterns (MUSE), Weighted MUSE (WMUSE), UGRAP Index(UGRAP), Mining Uncertain Subgraph patterns under Probabilistic semantics (MUSE-P). In these algorithms MUSE is the first algorithm proposed to find the frequent sub graphs from uncertain graph data. All the three algorithms MUSE, WMUSE, UGRAP are proposed under expected semantics where as MUSE-P is the algorithm proposed under probabilistic semantics. In this paper we are presenting a survey of various algorithms for mining frequent sub graphs from uncertain graph data. This survey is to help the user in real world applications of various domains.
Thermal barrier coatings for heat engine components

A comprehensive NASA-Lewis program of coating development for aircraft gas turbine blades and vanes is presented. Improved ceramic layer compositions are investigated, along the MCrAlY bond films and the methods of uniform deposition of the coatings; the thermomechanical and fuel impurity tolerance limits of the coatings are being studied. Materials include the ZrO2-Y2O3/NiCrAlY system; the effects of the bond coat and zirconia composition on coating life and Mach 1 burner rig test results are discussed. It is concluded that Diesel engines can also utilize thermal barrier coatings; they have been used successfully on piston crowns and exhaust valves of shipboard engines to combat lower grade fuel combustion corrosion.
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu. au
Prox1 postmitotically defines dentate gyrus cells by specifying granule cell identity over CA3 pyramidal cell fate in the hippocampus

The brain is composed of diverse types of neurons that fulfill distinct roles in neuronal circuits, as manifested by the hippocampus, where pyramidal neurons and granule cells constitute functionally distinct domains: cornu ammonis (CA) and dentate gyrus (DG), respectively. Little is known about how these two types of neuron differentiate during hippocampal development, although a set of transcription factors that is expressed in progenitor cells is known to be required for the survival of granule cells. Here, we demonstrate in mice that Prox1, a transcription factor constitutively expressed in the granule cell lineage, postmitotically functions to specify DG granule cell identity. Postmitotic elimination of Prox1 caused immature DG neurons to lose the granule cell identity and in turn terminally differentiate into the pyramidal cell type manifesting CA3 neuronal identity. By contrast, Prox1 overexpression caused opposing effects on presumptive hippocampal pyramidal cells. These results indicate that the immature DG cell has the potential to become a granule cell or a pyramidal cell, and Prox1 defines the granule cell identity. This bi-potency is lost in mature DG cells, although Prox1 is still required for correct gene expression in DG granule cells. Thus, our data indicate that Prox1 acts as a postmitotic cell fate determinant for DG granule cells over the CA3 pyramidal cell fate and is crucial for maintenance of the granule cell identity throughout the life.
Role of cAMP-phosphodiesterase 1C signaling in regulating growth factor receptor stability, vascular smooth muscle cell growth, migration, and neointimal hyperplasia.

RATIONALE Neointimal hyperplasia characterized by abnormal accumulation of vascular smooth muscle cells (SMCs) is a hallmark of occlusive disorders such as atherosclerosis, postangioplasty restenosis, vein graft stenosis, and allograft vasculopathy. Cyclic nucleotides are vital in SMC proliferation and migration, which are regulated by cyclic nucleotide phosphodiesterases (PDEs). OBJECTIVE Our goal is to understand the regulation and function of PDEs in SMC pathogenesis of vascular diseases. METHODS AND RESULTS We performed screening for genes differentially expressed in normal contractile versus proliferating synthetic SMCs. We observed that PDE1C expression was low in contractile SMCs but drastically elevated in synthetic SMCs in vitro and in various mouse vascular injury models in vivo. In addition, PDE1C was highly induced in neointimal SMCs of human coronary arteries. More importantly, injury-induced neointimal formation was significantly attenuated by PDE1C deficiency or PDE1 inhibition in vivo. PDE1 inhibition suppressed vascular remodeling of human saphenous vein explants ex vivo. In cultured SMCs, PDE1C deficiency or PDE1 inhibition attenuated SMC proliferation and migration. Mechanistic studies revealed that PDE1C plays a critical role in regulating the stability of growth factor receptors, such as PDGF receptor β (PDGFRβ) known to be important in pathological vascular remodeling. PDE1C interacts with low-density lipoprotein receptor-related protein-1 and PDGFRβ, thus regulating PDGFRβ endocytosis and lysosome-dependent degradation in an low-density lipoprotein receptor-related protein-1-dependent manner. A transmembrane adenylyl cyclase cAMP-dependent protein kinase cascade modulated by PDE1C is critical in regulating PDGFRβ degradation. CONCLUSIONS These findings demonstrated that PDE1C is an important regulator of SMC proliferation, migration, and neointimal hyperplasia, in part through modulating endosome/lysosome-dependent PDGFRβ protein degradation via low-density lipoprotein receptor-related protein-1.
Achievable Rates of Compress-and-Forward Cooperative Relaying on Gaussian Vector Channels

The compress-and-forward (C&F) cooperative relaying strategy is known to outperform decode-and-forward (D&F) when the relay is close to the destination. In this paper, we derive achievable rates on Gaussian vector channels with cooperative C&F relaying. In order to extend previous information-theoretic results from the scalar to the vector Gaussian channel, we exploit recent results in distributed source coding. Like in source coding with side information at the decoder, the relay applies a conditional Karhunen Loeve transform (CKLT) to its observed signal, followed by a separate Wyner-Ziv encoding of each output stream with a different rate and under a sum-rate constraint. However, these Wyner-Ziv coding rates are such that the total mutual information between the source and destination is maximized. This differs from the conventional source coding approach in which the rates are selected to minimize the total squared distortion, leading to the well-known reverse-waterfilling algorithm. We show that the maximization of the C&F mutual information is also a convex problem. The optimum Wyner-Ziv coding rates have a simple analytical expression, and can be obtained by a waterfilling algorithm. Finally, we illustrate these results by simulations of MIMO-OFDM relaying in a system similar to IEEE802.16.