Miracle-dz/UniFAR-FTUs huggingface dataset:
Truncation of the carboxy-terminal domain of yeast beta-tubulin causes temperature-sensitive growth and hypersensitivity to antimitotic drugs [published erratum appears in J Cell Biol 1989 Feb;108(2):747]

beta-tubulin of budding yeast Saccharomyces cerevisiae is a polypeptide of 457 amino acids encoded by the unique gene TUB2. We investigated the function of the carboxy-terminal part of yeast beta-tubulin corresponding to the carboxy-terminal variable domain of mammalian and avian beta-tubulins. The GAA codon for Glu-431 of TUB2 was altered to TAA termination codon by using in vitro site-directed mutagenesis so that the 27-amino acid residues of the carboxyl terminus was truncated when expressed. The mutagenized TUB2 gene (tub2(T430)) was introduced into a haploid strain in which the original TUB2 gene had been disrupted. The tub2(T430) haploid strain grows normally less than 30 but not at 37 degrees C. The truncation of the carboxyl terminus caused hypersensitivity to antimitotic drugs and low spore viability at the permissive temperature for vegetative growth. Immunofluorescence labeling with antitubulin antibody and DNA staining with 4',6'- diamidino-2-phenylindole showed that in these cells at 37 degrees C, formation of spindle microtubules and nuclear division was inhibited and cytoplasmic microtubule distribution was aberrant. These results suggest that functions of the carboxy-terminal domain of yeast beta- tubulin are necessary for cells growing under suboptimal growth conditions although it is not essential for growth under the optimal growth conditions. Cells bearing tub2(411), a tub2 gene in which the GAA codon for Glu-412 was altered to TAA were no more viable at any temperature. In addition, a haploid strain carrying two functional beta- tubulin genes is not viable.
Pinning down the superfluid and measuring masses using pulsar glitches

Erratic pulsar behavior hints at new way of measuring the mass of stars. Pulsars are known for their superb timing precision, although glitches can interrupt the regular timing behavior when the stars are young. These glitches are thought to be caused by interactions between normal and superfluid matter in the crust of the star. However, glitching pulsars such as Vela have been shown to require a superfluid reservoir that greatly exceeds that available in the crust. We examine a model in which glitches tap the superfluid in the core. We test a variety of theoretical superfluid models against the most recent glitch data and find that only one model can successfully explain up to 45 years of observational data. We develop a new technique for combining radio and x-ray data to measure pulsar masses, thereby demonstrating how current and future telescopes can probe fundamental physics such as superfluidity near nuclear saturation.
A Service-Oriented Trust Management Framework for E-commerce Systems

While the increasingly e-commerce provides enormous opportunities, it presents potential threats and risks because of lack of trust as well. Various trust management polices are proposed to improve these issues. However, most of these existing approaches only take into account a global attribute. The evaluation granularity is too coarse for customers to make an exact transaction decision. This paper proposes a service-oriented trust management framework for E-commerce systems. It consists of an authentication center, an evaluation controller, a reference controller, an update controller and a history controller. Considering the different services have different quality of service and content, our model evaluates a node under each separate service category, the evaluation result is more exact than some existing approaches and can reduce the risk of transactions. Finally, an example is given to analyze the feasibility and security of the model.
Mangrove tannins in aquatic ecosystems: Their fate and possible influence on dissolved organic carbon and nitrogen cycling

We describe the fate of mangrove leaf tannins in aquatic ecosystems and their possible influence on dissolved organic nitrogen (DON) cycling. Tannins were extracted and purified from senescent yellow leaves of the red mangrove (Rhizophora mangle) and used for a series of model experiments to investigate their physical and chemical reactivity in natural environments. Physical processes investigated included aggregation, adsorption to organic matter‐rich sediments, and co‐aggregation with DON in natural waters. Chemical reactions included structural change, which was determined by excitation‐emission matrix fluorescence spectra, and the release of proteins from tannin‐protein complexes under solar‐simulated light exposure. A large portion of tannins can be physically eliminated from aquatic environments by precipitation in saline water and also by binding to sediments. A portion of DON in natural water can coprecipitate with tannins, indicating that mangrove swamps can influence DON cycling in estuarine environments. The chemical reactivity of tannins in natural waters was also very high, with a half‐life of less than 1 d. Proteins were released gradually from tannin‐protein complexes incubated under light conditions but not under dark conditions, indicating a potentially buffering role of tannin‐ protein complexes on DON recycling in mangrove estuaries. Although tannins are not detected at a significant level in natural waters, they play an important ecological role by preserving nitrogen and buffering its cycling in estuarine ecosystems through the prevention of rapid DON export/loss from mangrove fringe areas and/or from rapid microbial mineralization.
Trevis: a context tree visualization & analysis framework and its use for classifying performance failure reports

When developers profile their applications to identify performance problems, they normally use profilers producing calling context trees. A calling context tree (CCT) represents the caller-callee relationships of a program. A dynamically collected CCT provides method coverage information. The CCTs produced by profilers also include method hotness information. Trevis, our context tree visualization and analysis framework, allows users to visualize, compare, cluster, and intersect CCTs produced by profilers. We evaluate Trevis in the context of a novel profiling tool called FlyBy. FlyBy runs transparently on an end-user's computer and continuously samples the applications' call stack. When the user perceives the application as sluggish, she presses a "Was Slow! " button to tell FlyBy to file a performance failure report. The report contains the CCT based on the call stack samples FlyBy gathered over the last few seconds before the user pressed the button. We show how Trevis allows us to visualize and classify FlyBy bug reports.
Embedded trapped modes for obstacles in two-dimensional waveguides

In this paper we investigate the existence of embedded trapped modes for symmetric obstacles which are placed on the centreline of a two-dimensional acoustic waveguide. Modes are sought which are antisymmetric about the centreline of the channel but which have frequencies that are above the first cut-off for antisymmetric wave propagation down the guide. In the terminology of spectral theory this means that the eigenvalue associated with the trapped mode is embedded in the continuous spectrum of the relevant operator. A numerical procedure based on a boundary integral technique is developed to search for embedded trapped modes for bodies of general shape. In addition two approximate solutions for trapped modes are found; the first is for long plates on the centreline of the channel and the second is for slender bodies which are perturbations of plates perpendicular to the guide walls. It is found that embedded trapped modes do not exist for arbitrary symmetric bodies but if an obstacle is defined by two geometrical parameters then branches of trapped modes may be obtained by varying both of these parameters simultaneously. One such branch is found for a family of ellipses of varying aspect ratio and size. The thin plates which are parallel and perpendicular to the guide walls are found to correspond to the end points of this branch.
A Simple Necessary and Sufficient Condition for the Double Unicast Problem

We consider a directed acyclic network where there are two source-terminal pairs and the terminals need to receive the symbols generated at the respective sources. Each source independently generates an i.i. d. random process over the same alphabet. Each edge in the network is error-free, delay-free, and can carry one symbol from the alphabet per use. We give a simple necessary and sufficient condition for being able to simultaneously satisfy the unicast requirements of the two source-terminal pairs at rate-pair (1,1) using vector network coding. The condition is also sufficient for doing this using only "XOR" network coding and is much simpler compared to the necessary and sufficient conditions known from previous work. Our condition also yields a simple characterization of the capacity region of a double-unicast network which does not support the rate-pair (1,1).
Loop Pipelining Algorithm for Non-Uniform IncreasingDependency Loops Sissades Tongsima

Using parallel processing systems to execute scientiic applications is one of the most common solutions for achieving more eecient computing performance. However, those applications may contain loops with non-uniform dependencies which may cause a compiler to produce sequential codes. This paper presents a new scheduling methodology for non-uniform dependency loops, considering a limited number of target processors. A loop pipelining technique, called rotation scheduling, is used as the basis for a new algorithm that systematically computes a new schedule table. New mathematical models are derived to handle the diiculties of the non-uniform dependencies.
Raced profiles: efficient selection of competing compiler optimizations

Many problems in embedded compilation require one set of optimizations to be selected over another based on run time performance. Self-tuned libraries, iterative compilation and machine learning techniques all compare multiple compiled program versions. In each, program versions are timed to determine which has the best performance. The program needs to be run multiple times for each version because there is noise inherent in most performance measurements. The number of runs must be enough to compare different versions, despite the noise, but executing more than this will waste time and energy. The compiler writer must either risk taking too few runs, potentially getting incorrect results, or taking too many runs increasing the time for their experiments or reducing the number of program versions evaluated. Prior works choose constant size sampling plans where each compiled version is executed a fixed number of times without regard to the level of noise. In this paper we develop a sequential sampling plan which can automatically adapt to the experiment so that the compiler writer can have both confidence in the results and also be sure that no more runs were taken than were needed. We show that our system is able to correctly determine the best optimization settings with between 76% and 87% fewer runs than needed by a brute force, constant sampling size approach. We also compare our approach to JavaSTATS(10); we needed 77% to 89% fewer runs than it needed.
ORDER SELECTION IN FINITE MIXTURE MODELS

Jiahua Chen, Abbas Khalili Department of Statistics and Actuarial Science University of Waterloo Abstract A fundamental and challenging problem in the application of finite mixture models is to make inference on the order of the model. In this paper, we develop a new penalized likelihood approach to the order selection problem. The new method deviates from the information-based methods such as AIC and BIC by introducing two penalty functions which depend on the mixing proportions and the component parameters. The new method is shown to be consistent and have other good properties. Simulations show that the method has much better performance compared to a number of existing methods. We further demonstrate the new method by analyzing two well known real data sets. Short Title: ORDER SELECTION
An Empirical Study on the Procedure to Derive Software Quality Estimation Models

Software quality assurance has been a heated topic for several decades. If factors that influence software quality can be identified, they may provide more insight for better software development management. More precise quality assurance can be achieved by employing resources according to accurate quality estimation at the early stages of a project. In this paper, a general procedure is proposed to derive software quality estimation models and various techniques are presented to accomplish the tasks in respective steps. Several statistical techniques together with machine learning method are utilized to verify the effectiveness of software metrics. Moreover, a neuro-fuzzy approach is adopted to improve the accuracy of the estimation model. This procedure is carried out based on data from the ISBSG repository to present its empirical value.
A Control Architecture for Massive Adaptive Video Streaming Delivery

The optimization of massive video delivery, with the purpose of improving user engagement by delivering the maximum available quality of experience (QoE) to users, is a hot topic. In this paper we propose a Network Control Plane (NCP) for video streaming aimed at jointly maximizing users QoE and network utilization by reserving bandwidth on a per-flow basis. The NCP is placed on top of the controlled network and cooperates with distributed buffer-based adaptation techniques implemented at the client. It is specifically designed to take into account scalability and adaptivity issues. No communication with external entities involved in the delivery process, such as other networks or the streaming server, is required. We provide a reference implementation and a performance evaluation through simulations.
GaN HEMTs and MMICs for space applications

We report on recent results from our GaN transistor and circuit technology. Epitaxial growth can be performed on either SiC or Si substrates in order to provide high-quality AlGaN/GaN heterostructures. These heterostructures are then utilized in order to realize transistors and integrated circuits ranging from high-voltage transistors for voltage conversion in efficient power switches, L/S-band power bars and X-band MMICs for next-generation communication systems, and finally W-band MMICs for radar applications. The technology is characterized by state-of-the-art performance, good uniformity and high yield as well as excellent long-term stability. In combination with the space compatibility we believe that this technology is ideal for space. X-band MMICs from Fraunhofer IAF are scheduled to have the first in-orbit demonstration of European GaN within the Proba-V mission which is planned to be launched in spring 2013.
Adrenergic Stimulation of DUSP1 Impairs Chemotherapy Response in Ovarian Cancer

Purpose: Chronic adrenergic activation has been shown to associate with adverse clinical outcomes in cancer patients, but the underlying mechanisms are not well understood. The focus of the current study was to determine the functional and biologic effects of adrenergic pathways on response to chemotherapy in the context of ovarian cancer. Experimental Design: Increased DUSP1 production by sympathetic nervous system mediators (e.g., norepinephrine) was analyzed by real-time quantitative RT-PCR and by Western blotting. In vitro chemotherapy-induced cell apoptosis was examined by flow cytometry. For in vivo therapy, a well-characterized model of chronic stress was used. Results: Catecholamines significantly inhibited paclitaxel- and cisplatin-induced apoptosis in ovarian cancer cells. Genomic analyses of cells treated with norepinephrine identified DUSP1 as a potential mediator. DUSP1 overexpression resulted in reduced paclitaxel-induced apoptosis in ovarian cancer cells compared with control; conversely, DUSP1 gene silencing resulted in increased apoptosis compared with control cells. DUSP1 gene silencing in vivo significantly enhanced response to paclitaxel and increased apoptosis. In vitro analyses indicated that norepinephrine-induced DUSP1 gene expression was mediated through ADRB2 activation of cAMP–PLC–PKC–CREB signaling, which inhibits JNK-mediated phosphorylation of c-Jun and protects ovarian cancer cells from apoptosis. Moreover, analysis of The Cancer Genome Atlas data showed that increased DUSP1 expression was associated with decreased overall (P = 0.049) and progression-free (P = 0.0005) survival. Conclusions: These findings provide a new understanding of the mechanisms by which adrenergic pathways can impair response to chemotherapy and have implications for cancer management. Clin Cancer Res; 22(7); 1713–24. ©2015 AACR.
An algorithm for detecting a maneuvering target based on TFR and Viterbi algorithm

An algorithm for radar signal detection method based on a time-frequency representation (TFR) and Viterbi algorithm (VA) is proposed. Two TFR methods are considered, Short-time Fourier Transform (STFT) and S-method (SM). Performance and detection ability of the proposed algorithm was investigated on real radar signals of a single manuvering target with added Gaussian noise and signal-to-noise ratio from −15 dB to −2 dB. The results show that the proposed algorithm works well even in very low SNR values.
Isolation and Characterization of Bacteriophages Infecting Nocardioforms in Wastewater Treatment Plant

Activated sludge plants (ASP) are associated with the stable foaming problem worldwide. Apart from the physical and chemical treatment methods, biological treatment method has been least explored and may prove to be a novel and ecofriendly approach to tackle the problem of stable foam formation. In ASP Nocardia species are commonly found and are one of the major causes for forming sticky and stable foam. This study describes the isolation and characterization of three Nocardia bacteriophages NOC1, NOC2, and NOC3 for the control of Nocardia species. The bacteriophages isolated in this study have shown promising results in controlling foam producing bacterial growth under laboratory conditions, suggesting that it may prove useful in the field as an alternative biocontrol agent to reduce the foaming problem. To the best of our knowledge to date no work has been published from India related to biological approach for the control of foaming.
Mutation of the aspartic acid residues of the GDD sequence motif of poliovirus RNA-dependent RNA polymerase results in enzymes with altered metal ion requirements for activity

The poliovirus RNA-dependent RNA polymerase, 3Dpol, is known to share a region of sequence homology with all RNA polymerases centered at the GDD amino acid motif. The two aspartic acids have been postulated to be involved in the catalytic activity and metal ion coordination of the enzyme. To test this hypothesis, we have utilized oligonucleotide site-directed mutagenesis to generate defined mutations in the aspartic acids of the GDD motif of the 3Dpol gene. The codon for the first aspartate (3D-D-328 [D refers to the single amino acid change, and the number refers to its position in the polymerase]) was changed to that for glutamic acid, histidine, asparagine, or glutamine; the codons for both aspartic acids were simultaneously changed to those for glutamic acids; and the codon for the second aspartic acid (3D-D-329) was changed to that for glutamic acid or asparagine. The mutant enzymes were expressed in Escherichia coli, and the in vitro poly(U) polymerase activity was characterized. All of the mutant 3Dpol enzymes were enzymatically inactive in vitro when tested over a range of Mg2+ concentrations. However, when Mn2+ was substituted for Mg2+ in the in vitro assays, the mutant that substituted the second aspartic acid for asparagine (3D-N-329) was active. To further substantiate this finding, a series of different transition metal ions were substituted for Mg2+ in the poly(U) polymerase assay. The wild-type enzyme was active with all metals except Ca2+, while the 3D-N-329 mutant was active only when FeC6H7O5 was used in the reaction. To determine the effects of the mutations on poliovirus replication, the mutant 3Dpol genes were subcloned into an infectious cDNA of poliovirus. The cDNAs containing the mutant 3Dpol genes did not produce infectious virus when transfected into tissue culture cells under standard conditions. Because of the activity of the 3D-N-329 mutant in the presence of Fe2+ and Mn2+, transfections were also performed in the presence of the different metal ions. Surprisingly, the transfection of the cDNA containing the 3D-N-329 mutation resulted in the production of virus at a low frequency in the presence of FeSO4 or CoCl2. The virus derived from transfection in the presence of FeSO4 grew slowly, while the viruses recovered from transfection in CoCl2 grew at a rate which was similar to that of the wild-type poliovirus. (ABSTRACT TRUNCATED AT 400 WORDS)
Effects of behavior network as a suggestion system to assist BCI users

This work describes the development of an intelligent agent responsible for making relevant action suggestions to a BCI user in the context of an intelligent environment. For the development of this agent, a modified version of a behavior network, embedded into a neuroscience inspired cognitive architecture, has been implemented. A new soft-preconditions list has been introduced in the original model in order for it to be used as an assistant agent. A number of simulated experiments were performed to evaluate if the behavior network was indeed presenting valuable suggestions and performing as expected. Results suggest that the agent was able to take into account predefined goals, scheduled events and topological information about the environment in order to deliberate over the possible behaviors and make relevant suggestions. A discussion is made about the strong points and drawbacks of this approach and future work is suggested.
Transformation Process Priors

Key idea. As a prior over discrete distributions over X , it is common to use a Dirichlet or Dirichlet process [9]. However, because of the neutrality property, these priors cannot capture correlations among the probabilities of “similar” events. We propose obtaining the discrete distribution from a random walk model or transformation model [7], in which each observed event has evolved via a latent sequence of transformations. The transformation model is specified by a collection δ of conditional distributions (the transformations), so placing any prior ∆ over δ yields the desired prior over discrete distributions over X . Two events x1, x2 ∈ X have correlated probabilities in this transformation process prior if they tend to emerge from similar transformation sequences.
Non-negative matrix factorization and term structure of interest rates

Non-Negative Matrix Factorization (NNMF) is a technique for dimensionality reduction with a wide variety of applications from text mining to identification of concentrations in chemistry. NNMF deals with non-negative data and results in non-negative factors and factor loadings. Consequently, it is a natural choice when studying the term structure of interest rates. In this paper, NNMF is applied to obtain factors from the term structure of interest rates and the procedure is compared with other very popular techniques: principal component analysis and Nelson-Siegel model. The NNMF approximation for the term structure of interest rates is better in terms of fitting. From a practitioner point of view, the NNMF factors and factor loadings obtained possess straightforward financial interpretations due to their non-negativeness.