bluuebunny/crossref_metadata_2025_split huggingface dataset:
REDEFINE
Authors: Alle Mythri , Varadarajan Keshavan , Fell Alexander , C. Ramesh Reddy , Joseph Nimmy , Das Saptarsi , Biswas Prasenjit , Chetia Jugantor , Rao Adarsh , Nandy S. K. , Narayan Ranjani 
Published: October 2009

Emerging embedded applications are based on evolving standards (e.g., MPEG2/4, H.264/265, IEEE802.11a/b/g/n). Since most of these applications run on handheld devices, there is an increasing need for a single chip solution that can dynamically interoperate between different standards and their derivatives. In order to achieve high resource utilization and low power dissipation, we propose REDEFINE, a polymorphic ASIC in which specialized hardware units are replaced with basic hardware units that can create the same functionality by runtime
re
-composition. It is a “future-proof” custom hardware solution for multiple applications and their derivatives in a domain. In this article, we describe a compiler framework and supporting hardware comprising compute, storage, and communication resources.

Applications described in high-level language (e.g., C) are compiled into application substructures. For each application substructure, a set of compute elements on the hardware are interconnected during runtime to form a pattern that closely matches the communication pattern of that particular application. The advantage is that the bounded CEs are neither processor cores nor logic elements as in FPGAs. Hence, REDEFINE offers the power and performance advantage of an ASIC and the hardware reconfigurability and programmability of that of an FPGA/instruction set processor.
In addition, the hardware supports custom instruction pipelining. Existing instruction-set extensible processors determine a sequence of instructions that repeatedly occur within the application to create custom instructions at design time to speed up the execution of this sequence. We extend this scheme further, where a kernel is compiled into custom instructions that bear strong producer-consumer relationship (and not limited to frequently occurring sequences of instructions). Custom instructions, realized as hardware compositions effected at runtime, allow several instances of the same to be active in parallel. A key distinguishing factor in majority of the emerging embedded applications is stream processing. To reduce the overheads of data transfer between custom instructions, direct communication paths are employed among custom instructions.
In this article, we present the overview of the hardware-aware compiler framework, which determines the NoC-aware schedule of transports of the data exchanged between the custom instructions on the interconnect. The results for the FFT kernel indicate a 25% reduction in the number of loads/stores, and throughput improves by log(n) for n-point FFT when compared to sequential implementation. Overall, REDEFINE offers flexibility and a runtime reconfigurability at the expense of 1.16× in power and 8× in area when compared to an ASIC. REDEFINE implementation consumes 0.1× the power of an FPGA implementation. In addition, the configuration overhead of the FPGA implementation is 1,000× more than that of REDEFINE.
Grace
Authors: Berger Emery D. , Yang Ting , Liu Tongping , Novark Gene 
Published: October 2009

The shift from single to multiple core architectures means that programmers must write concurrent, multithreaded programs in order to increase application performance. Unfortunately, multithreaded applications are susceptible to numerous errors, including deadlocks, race conditions, atomicity violations, and order violations. These errors are notoriously difficult for programmers to debug.
This paper presents Grace, a software-only runtime system that eliminates concurrency errors for a class of multithreaded programs: those based on fork-join parallelism. By turning threads into processes, leveraging virtual memory protection, and imposing a sequential commit protocol, Grace provides programmers with the appearance of deterministic, sequential execution, while taking advantage of available processing cores to run code concurrently and efficiently. Experimental results demonstrate Grace's effectiveness: with modest code changes across a suite of computationally-intensive benchmarks (1-16 lines), Grace can achieve high scalability and performance while preventing concurrency errors.
Profile-guided static typing for dynamic scripting languages
Authors: Furr Michael , An Jong-hoon (David) , Foster Jeffrey S. 
Published: October 2009

Many popular scripting languages such as Ruby, Python, and Perl include highly dynamic language constructs, such as an eval method that evaluates a string as program text. While these constructs allow terse and expressive code, they have traditionally obstructed static analysis. In this paper we present PRuby, an extension to Diamondback Ruby (DRuby), a static type inference system for Ruby. PRuby augments DRuby with a novel dynamic analysis and transformation that allows us to precisely type uses of highly dynamic constructs. PRuby's analysis proceeds in three steps. First, we use run-time instrumentation to gather per-application profiles of dynamic feature usage. Next, we replace dynamic features with statically analyzable alternatives based on the profile. We also add instrumentation to safely handle cases when subsequent runs do not match the profile. Finally, we run DRuby's static type inference on the transformed code to enforce type safety.
We used PRuby to gather profiles for a benchmark suite of sample Ruby programs. We found that dynamic features are pervasive throughout the benchmarks and the libraries they include, but that most uses of these features are highly constrained and hence can be effectively profiled. Using the profiles to guide type inference, we found that DRuby can generally statically type our benchmarks modulo some refactoring, and we discovered several previously unknown type errors. These results suggest that profiling and transformation is a lightweight but highly effective approach to bring static typing to highly dynamic languages.
Static extraction and conformance analysis of hierarchical runtime architectural structure using annotations
Authors: Abi-Antoun Marwan , Aldrich Jonathan 
Published: October 2009

An object diagram makes explicit the object structures that are only implicit in a class diagram. An object diagram may be missing and must extracted from the code. Alternatively, an existing diagram may be inconsistent with the code, and must be analyzed for conformance with the implementation. One can generalize the
global
object diagram of a system into a runtime architecture which abstracts objects into components, represents how those components interact, and can decompose a component into a nested sub-architecture.

A static object diagram represents all objects and inter-object relations possibly created, and is recovered by static analysis of a program. Existing analyses extract static object diagrams that are non-hierarchical, do not scale, and do not provide meaningful architectural abstraction. Indeed, architectural hierarchy is not readily observable in arbitrary code. Previous approaches used breaking language extensions to specify hierarchy and instances in code, or used dynamic analyses to extract dynamic object diagrams that show objects and relations for a few program runs.
Typecheckable ownership domain annotations use existing language support for annotations and specify in code object encapsulation, logical containment and architectural tiers. These annotations enable a points-to static analysis to extract a sound global object graph that provides architectural abstraction by ownership hierarchy and by types, where architecturally significant objects appear near the top of the hierarchy and data structures are further down.
Another analysis can abstract an object graph into a built runtime architecture. Then, a third analysis can compare the built architecture to a target, analyze and measure their structural conformance, establish traceability between the two and identify interesting differences.
LASE Measurements of Water Vapor, Aerosol, and Cloud Distributions in Saharan Air Layers and Tropical Disturbances
Authors: Ismail Syed , Ferrare Richard A. , Browell Edward V. , Chen Gao , Anderson Bruce , Kooi Susan A. , Notari Anthony , Butler Carolyn F. , Burton Sharon , Fenn Marta , Dunion Jason P. , Heymsfield Gerry , Krishnamurti T. N. , Biswas Mrinal K. 
Published: October 2009

Abstract
The Lidar Atmospheric Sensing Experiment (LASE) on board the NASA DC-8 measured high-resolution profiles of water vapor and aerosols, and cloud distributions in 14 flights over the eastern North Atlantic during the NASA African Monsoon Multidisciplinary Analyses (NAMMA) field experiment. These measurements were used to study African easterly waves (AEWs), tropical cyclones (TCs), and the Saharan air layer (SAL). These LASE measurements represent the first simultaneous water vapor and aerosol lidar measurements to study the SAL and its interactions with AEWs and TCs. Three case studies were selected for detailed analysis: (i) a stratified SAL, with fine structure and layering (unlike a well-mixed SAL), (ii) a SAL with high relative humidity (RH), and (iii) an AEW surrounded by SAL dry air intrusions. Profile measurements of aerosol scattering ratios, aerosol extinction coefficients, aerosol optical thickness, water vapor mixing ratios, RH, and temperature are presented to illustrate their characteristics in the SAL, convection, and clear air regions. LASE extinction-to-backscatter ratios for the dust layers varied from 35 ± 5 to 45 ± 5 sr, well within the range of values determined by other lidar systems. LASE aerosol extinction and water vapor profiles are validated by comparison with onboard in situ aerosol measurements and GPS dropsonde water vapor soundings, respectively. An analysis of LASE data suggests that the SAL suppresses low-altitude convection. Midlevel convection associated with the AEW and transport are likely responsible for high water vapor content observed in the southern regions of the SAL on 20 August 2008. This interaction is responsible for the transfer of about 7 × 1015 J (or 8 × 103 J m−2) latent heat energy within a day to the SAL. Initial modeling studies that used LASE water vapor profiles show sensitivity to and improvements in model forecasts of an AEW.
The Linear Stability of Time-Dependent Baroclinic Shear
Authors: Poulin F. J. 
Published: October 2009

Abstract
This article aims to advance the understanding of inherent randomness in geophysical fluids by considering the particular example of baroclinic shear flows that are spatially uniform in the horizontal directions and aperiodic in time. The time variability of the shear is chosen to be the Kubo oscillator, which is a family of time-dependent bounded noise that is oscillatory in nature with various degrees of stochasticity.
The author analyzed the linear stability of a wide range of temporally periodic and aperiodic shears with a zero and nonzero mean to get a more complete understanding of the effect of oscillations in shear flows in the context of the two-layer quasigeostrophic Phillips model. It is determined that the parametric mode, which exists in the periodic limit, also exists in the range of small and moderate stochasticities but vanishes in highly erratic flows. Moreover, random variations weaken the effects of periodicity and yield growth rates more similar to that of the time-averaged steady-state analog. This signifies that the periodic shear flows possess the most extreme case of stabilization and destabilization and are thus anomalous. In the limit of an f plane, the linear stability problem is solved exactly to reveal that individual solutions to the linear dynamics with time-dependent baroclinic shear have growth rates that are equal to that of the time-averaged steady state. This implies that baroclinic shear flows with zero means are linearly stable in that they do not grow exponentially in time. This means that the stochastic mode that was found to exist in the Mathieu equation does not arise in this model. However, because the perturbations grow algebraically, the aperiodic baroclinic shear on an f plane can give rise to nonlinear instabilities.
Equitability Revisited: Why the “Equitable Threat Score” Is Not Equitable
Authors: Hogan Robin J. , Ferro Christopher A. T. , Jolliffe Ian T. , Stephenson David B. 
Published: October 2009

Abstract
In the forecasting of binary events, verification measures that are “equitable” were defined by Gandin and Murphy to satisfy two requirements: 1) they award all random forecasting systems, including those that always issue the same forecast, the same expected score (typically zero), and 2) they are expressible as the linear weighted sum of the elements of the contingency table, where the weights are independent of the entries in the table, apart from the base rate. The authors demonstrate that the widely used “equitable threat score” (ETS), as well as numerous others, satisfies neither of these requirements and only satisfies the first requirement in the limit of an infinite sample size. Such measures are referred to as “asymptotically equitable.” In the case of ETS, the expected score of a random forecasting system is always positive and only falls below 0.01 when the number of samples is greater than around 30. Two other asymptotically equitable measures are the odds ratio skill score and the symmetric extreme dependency score, which are more strongly inequitable than ETS, particularly for rare events; for example, when the base rate is 2% and the sample size is 1000, random but unbiased forecasting systems yield an expected score of around −0.5, reducing in magnitude to −0.01 or smaller only for sample sizes exceeding 25 000. This presents a problem since these nonlinear measures have other desirable properties, in particular being reliable indicators of skill for rare events (provided that the sample size is large enough). A potential way to reconcile these properties with equitability is to recognize that Gandin and Murphy’s two requirements are independent, and the second can be safely discarded without losing the key advantages of equitability that are embodied in the first. This enables inequitable and asymptotically equitable measures to be scaled to make them equitable, while retaining their nonlinearity and other properties such as being reliable indicators of skill for rare events. It also opens up the possibility of designing new equitable verification measures.
Bayesian modeling of ChIP-chip data using latent variables
Authors: Wu Mingqi , Liang Faming , Tian Yanan 
Published: October 2009

Abstract

Background
The ChIP-chip technology has been used in a wide range of biomedical studies, such as identification of human transcription factor binding sites, investigation of DNA methylation, and investigation of histone modifications in animals and plants. Various methods have been proposed in the literature for analyzing the ChIP-chip data, such as the sliding window methods, the hidden Markov model-based methods, and Bayesian methods. Although, due to the integrated consideration of uncertainty of the models and model parameters, Bayesian methods can potentially work better than the other two classes of methods, the existing Bayesian methods do not perform satisfactorily. They usually require multiple replicates or some extra experimental information to parametrize the model, and long CPU time due to involving of MCMC simulations.

Results
In this paper, we propose a Bayesian latent model for the ChIP-chip data. The new model mainly differs from the existing Bayesian models, such as the joint deconvolution model, the hierarchical gamma mixture model, and the Bayesian hierarchical model, in two respects. Firstly, it works on the difference between the averaged treatment and control samples. This enables the use of a simple model for the data, which avoids the probe-specific effect and the sample (control/treatment) effect. As a consequence, this enables an efficient MCMC simulation of the posterior distribution of the model, and also makes the model more robust to the outliers. Secondly, it models the neighboring dependence of probes by introducing a latent indicator vector. A truncated Poisson prior distribution is assumed for the latent indicator variable, with the rationale being justified at length.

Conclusion
The Bayesian latent method is successfully applied to real and ten simulated datasets, with comparisons with some of the existing Bayesian methods, hidden Markov model methods, and sliding window methods. The numerical results indicate that the Bayesian latent method can outperform other methods, especially when the data contain outliers.
Exploring the molecular basis of insecticide resistance in the dengue vector Aedes aegypti: a case study in Martinique Island (French West Indies)
Authors: Marcombe Sébastien , Poupardin Rodolphe , Darriet Frederic , Reynaud Stéphane , Bonnet Julien , Strode Clare , Brengues Cecile , Yébakima André , Ranson Hilary , Corbel Vincent , David Jean-Philippe 
Published: October 2009

AbstractBackgroundThe yellow fever mosquitoAedes aegyptiis a major vector of dengue and hemorrhagic fevers, causing up to 100 million dengue infections every year. As there is still no medicine and efficient vaccine available, vector control largely based on insecticide treatments remains the only method to reduce dengue virus transmission. Unfortunately, vector control programs are facing operational challenges with mosquitoes becoming resistant to commonly used insecticides. Resistance ofAe. aegyptito chemical insecticides has been reported worldwide and the underlying molecular mechanisms, including the identification of enzymes involved in insecticide detoxification are not completely understood.ResultsThe present paper investigates the molecular basis of insecticide resistance in a population ofAe. aegypticollected in Martinique (French West Indies). Bioassays with insecticides on adults and larvae revealed high levels of resistance to organophosphate and pyrethroid insecticides. Molecular screening for common insecticide target-site mutations showed a high frequency (71%) of the sodium channel 'knock down resistance' (kdr) mutation. Exposing mosquitoes to detoxification enzymes inhibitors prior to bioassays induced a significant increased susceptibility of mosquitoes to insecticides, revealing the presence of metabolic-based resistance mechanisms. This trend was biochemically confirmed by significant elevated activities of cytochrome P450 monooxygenases, glutathione S-transferases and carboxylesterases at both larval and adult stages. Utilization of the microarrayAedes Detox Chipcontaining probes for all members of detoxification and other insecticide resistance-related enzymes revealed the significant constitutive over-transcription of multiple detoxification genes at both larval and adult stages. The over-transcription of detoxification genes in the resistant strain was confirmed by using real-time quantitative RT-PCR.ConclusionThese results suggest that the high level of insecticide resistance found inAe. aegyptimosquitoes from Martinique island is the consequence of both target-site and metabolic based resistance mechanisms. Insecticide resistance levels and associated mechanisms are discussed in relation with the environmental context of Martinique Island. These finding have important implications for dengue vector control in Martinique and emphasizes the need to develop new tools and strategies for maintaining an effective control ofAedesmosquito populations worldwide.
Transcriptome analysis of differentiating trypanosomes reveals the existence of multiple post-transcriptional regulons
Authors: Queiroz Rafael , Benz Corinna , Fellenberg Kurt , Hoheisel Jörg D , Clayton Christine 
Published: October 2009

Abstract

Background
Trypanosome gene expression is regulated almost exclusively at the post-transcriptional level, with mRNA degradation playing a decisive role. When trypanosomes are transferred from the blood of a mammal to the midgut of a Tsetse fly, they transform to procyclic forms: gene expression is reprogrammed, changing the cell surface and switching the mode of energy metabolism. Within the blood, trypanosomes can pre-adapt for Tsetse transmission, becoming growth-arrested stumpy forms. We describe here the transitions in gene expression that occur during differentiation of in-vitro cultured bloodstream forms to procyclic forms.

Results
Some mRNAs showed changes within 30 min of cis- aconitate addition, whereas others responded 12-24 hours later. For the first 12 h after addition of cis-aconitate, cells accumulated at the G1 phase of the cell cycle, and showed decreases in mRNAs required for proliferation, mimicking the changes seen in stumpy forms: many mRNAs needed for ribosomal and flagellar biogenesis showed striking co-regulation. Other mRNAs encoding components of signal transduction pathways and potential regulators were specifically induced only during differentiation. Messenger RNAs encoding proteins required for individual metabolic pathways were often co-regulated.

Conclusion
Trypanosome genes form post-transcriptional regulons in which mRNAs with functions in particular pathways, or encoding components of protein complexes, show almost identical patterns of regulation.
Classification of Myoviridae bacteriophages using protein sequence similarity
Authors: Lavigne Rob , Darius Paul , Summer Elizabeth J , Seto Donald , Mahadevan Padmanabhan , Nilsson Anders S , Ackermann Hans W , Kropinski Andrew M 
Published: October 2009

Abstract

Background
We advocate unifying classical and genomic classification of bacteriophages by integration of proteomic data and physicochemical parameters. Our previous application of this approach to the entirely sequenced members of the Podoviridae fully supported the current phage classification of the International Committee on Taxonomy of Viruses (ICTV). It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages.

Results
CoreGenes/CoreExtractor proteome comparison techniques applied to 102 Myoviridae suggest the establishment of three subfamilies (Peduovirinae, Teequatrovirinae, the Spounavirinae) and eight new independent genera (Bcep781, BcepMu, FelixO1, HAP1, Bzx1, PB1, phiCD119, and phiKZ-like viruses). The Peduovirinae subfamily, derived from the P2-related phages, is composed of two distinct genera: the "P2-like viruses", and the "HP1-like viruses". At present, the more complex Teequatrovirinae subfamily has two genera, the "T4-like" and "KVP40-like viruses". In the genus "T4-like viruses" proper, four groups sharing >70% proteins are distinguished: T4-type, 44RR-type, RB43-type, and RB49-type viruses. The Spounavirinae contain the "SPO1-"and "Twort-like viruses."

Conclusion
The hierarchical clustering of these groupings provide biologically significant subdivisions, which are consistent with our previous analysis of the Podoviridae.