bluuebunny/crossref_metadata_2025 huggingface dataset:
Fragmentation of Whole-Transcriptome RNA Using E. coli RNase III
Authors: Ares Manuel
Published: May 2013

High-throughput sequencing (HTS) methods can provide short sequence reads for many millions of individual molecules in a sample, allowing the use of sequencing to measure the abundance of RNA molecules. To quantify the amount of a particular sequence in a sample of large RNAs (e.g., mRNAs), it is important to fragment the RNA into short pieces that can be ligated to oligonucleotides that allow polymerase chain reaction (PCR) amplification and sequencing. The most desired end structure of RNA for such ligation steps is a 5′ phosphate and a 3′ OH. Thus, enzymes that leave these groups after cleavage are of particular utility, avoiding the need to dephosphorylate the 3′ end with phosphatases or phosphorylate the 5′ end with kinase before proceeding. One such enzyme, RNase III, is widely available. Although it primarily cuts duplex RNA, this specificity is salt- and concentration-dependent, and many RNAs that lack strong extended duplexes are nonetheless susceptible to cleavage at many spots. RNA fragmentation by RNase III does not seem to grossly affect the distribution of RNA sequencing reads. Thus, it has become a standard method for creating nominally representative pools of transcriptome sequences with 5′ phosphates and 3′ OH for library construction. Three steps in preparing fragmented transcriptome RNA for sequencing library construction are described here: (1) fragmenting the RNA with RNase III to the extent that ∼60–100-nucleotide fragments are created, (2) purifying the RNA from the RNase III reaction, and (3) analyzing the digestion products for their suitability in library production.
Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs
Authors: Kicheva Anna , Holtzer Laurent , Wartlick Ortrud , Schmidt Thomas , González-Gaitán Marcos
Published: May 2013

Cells at different positions in a developing tissue receive different concentrations of signaling molecules, called morphogens, and this influences their cell fate. Morphogen concentration gradients have been proposed to control patterning as well as growth in many developing tissues. Some outstanding questions about tissue patterning by morphogen gradients are the following: What are the mechanisms that regulate gradient formation and shape? Is the positional information encoded in the gradient sufficiently precise to determine the positions of target gene domain boundaries? What are the temporal dynamics of gradients and how do they relate to patterning and growth? These questions are inherently quantitative in nature and addressing them requires measuring morphogen concentrations in cells, levels of downstream signaling activity, and kinetics of morphogen transport. Here we first present methods for quantifying morphogen gradient shape in which the measurements can be calibrated to reflect actual morphogen concentrations. We then discuss using fluorescence recovery after photobleaching to study the kinetics of morphogen transport at the tissue level. Finally, we present particle tracking as a method to study morphogen intracellular trafficking.
Sporopollenin Biosynthetic Enzymes Interact and Constitute a Metabolon Localized to the Endoplasmic Reticulum of Tapetum Cells
Authors: Lallemand Benjamin , Erhardt Mathieu , Heitz Thierry , Legrand Michel
Published: May 2013

The sporopollenin polymer is the major constituent of exine, the outer pollen wall. Recently fatty acid derivatives have been shown to be the precursors of sporopollenin building units. ACYL-COA SYNTHETASE, POLYKETIDE SYNTHASE A (PKSA) and PKSB, TETRAKETIDE α-PYRONE REDUCTASE1 (TKPR1) and TKPR2 have been demonstrated to be involved in sporopollenin biosynthesis in Arabidopsis (Arabidopsis thaliana). Here all these sporopollenin biosynthetic enzymes but TKPR2 have been immunolocalized to endoplasmic reticulum of anther tapetal cells. Pull-down experiments demonstrated that tagged recombinant proteins interacted to form complexes whose constituents were characterized by immunoblotting. In vivo protein interactions were evidenced by yeast (Saccharomyces cerevisiae) two-hybrid analysis and by fluorescence lifetime imaging microscopy/Förster resonance energy transfer studies in transgenic Nicotiana benthamiana, which were used to test the possibility that the enzymes interact to form a biosynthetic metabolon. Various pairs of proteins fused to two distinct fluorochromes were coexpressed in N. benthamiana leaf tissues and fluorescence lifetime imaging microscopy/Förster resonance energy transfer measurements demonstrated that proteins interacted pairwise in planta. Taken together, these results suggest the existence of a sporopollenin metabolon.
Restitutionary Remedies in the Contractual Context
Authors: Jaffey Peter
Published: May 2013

Contracting parties sometimes have a claim to recover money paid in advance, or for reasonable payment for work done under the contract, commonly described as restitutionary remedies. This claim arising out of a contract is nowadays generally regarded as a non‐contractual, unjust enrichment claim governed by the modern law of unjust enrichment, by contrast with a contractual claim for damages or specific performance. The article argues that the claim is contractual, and that this is relevant to determining when it should be available and what the measure of recovery should be. In particular, it is argued that this follows from the proper understanding of the form of agreement made by contracting parties. The argument involves discussion of doctrinal categories such as contract and unjust enrichment, the relationship between primary and remedial rights in contract, the nature of contractual agreement, and the protection of reliance in contract.
Relatively Absolute? The Undermining of Article 3 ECHR in Ahmad v UK
Authors: Mavronicola Natasa , Messineo Francesco
Published: May 2013

The recent decision of the European Court of Human Rights in Ahmad v UK dangerously undermines the well‐established case law of the Court on counter‐terrorism and non‐refoulement towards torture, inhuman and degrading treatment or punishment. Although ostensibly rejecting the ‘relativist’ approach to Article 3 ECHR adopted by the House of Lords in Wellington v Secretary of State for the Home Department, the Court appeared to accept that what is a breach of Article 3 in a domestic context may not be a breach in an extradition or expulsion context. This statement is difficult to reconcile with the jurisprudence constante of the Court in the last fifteen years, according to which Article 3 ECHR is an absolute right in all its applications, including non‐refoulement, regardless of who the potential victim of torture, inhuman or degrading treatment is, what she may have done, or where the treatment at issue would occur.
What Is Wrong With Turnover Research? Commentary on Russell's Critique
Authors: Hom Peter W. , Griffeth Rodger W.
Published: May 2013

Dr. Russell (2013) provocatively critiqued turnover research, expressing a sentiment that we share—namely, the lamentable modest predictability of turnover. All the same, we disagree with certain criticisms of turnover theory, methodology, and practicality. We organize our reactions into sections: predictive validity for the standard turnover criterion; other criteria for model evaluation; incremental validity controlling quit intentions; Russell's proposed methodology, the potential biases of the Russell and Van Sell (2012) test; and an alternate approach by Hom, Mitchell, Lee, and Griffeth (2012).
Theory, Schmeory. Let's Keep Our Models Simple and Strong
Authors: Kraut Allen I.
Published: May 2013

Craig Russell has done us all a service in his review of current turnover research (2013), but I think he is too severe in his judgment of the validities and relevance of our field's research, and he encourages us to go down some questionable research paths in the future. Despite his expertise in the field, there are several points where I believe other views are more attractive.

We can recognize the usefulness of assessing so many studies and meta-analyses done in recent decades, as summarized in his Table 1 (drawn from Griffeth, Hom, & Gaertner, 2000). But let us also note that Russell would have done readers a bigger favor if the results were presented in some logical order. Right now, not even an alphabetic order among the variables is evident. This is a flaw that obscures key understandings. Looking at the data another way can make one more optimistic about its predictive validity and relevance.
Hydrogen isotopic substitution of solid methylamine through atomic surface reactions at low temperatures: A potential contribution to the D/H ratio of methylamine in molecular clouds
Authors: Oba Yasuhiro , Chigai Takeshi , Osamura Yoshihiro , Watanabe Naoki , Kouchi Akira
Published: May 2013

We experimentally studied hydrogen (H)–deuterium (D) substitution reactions of solid methylamine (CH3NH2) under astrophysically relevant conditions. We also calculated the potential energy surface for the H–D substitution reactions of methylamine isotopologues using quantum chemical methods. Despite the relatively large energy barrier of more than 18 kJ mol−1, CH3NH2 reacted with D atoms to yield deuterated methylamines at 10 K, suggesting that the H–D substitution reaction proceeds through quantum tunneling. Deuterated methylamines reacted with H atoms as well. On the basis of present results, we propose that methylamine has potential for D enrichment through atomic surface reactions on interstellar grains at very low temperatures in molecular clouds. D enrichment would occur in particular in the methyl group of methylamine.
Cryo‐Immunoelectron Microscopy of Adherent Cells Improved by the Use of Electrospun Cell Culture Substrates
Authors: Schmiedinger Thomas , Vogel Georg F. , Eiter Oliver , Pfaller Kristian , Kaufmann Walter A. , Flörl Angelika , Gutleben Karin , Schönherr Sabine , Witting Barbara , Lechleitner Thomas W. , Ebner Hannes‐L. , Seppi Thomas , Hess Michael W.
Published: May 2013

Electrospun nanofibres are an excellent cell culture substrate, enabling the fast and non‐disruptive harvest and transfer of adherent cells for microscopical and biochemical analyses. Metabolic activity and cellular structures are maintained during the only half a minute‐long harvest and transfer process. We show here that such samples can be optimally processed by means of cryofixation combined either with freeze‐substitution, sample rehydration and cryosection‐immunolabelling or with freeze‐fracture replica‐immunolabelling. Moreover, electrospun fibre substrates are equally suitable for complementary approaches, such as biochemistry, fluorescence microscopy and cytochemistry.
Cohomological and projective dimensions
Authors: Varbaro Matteo
Published: May 2013

Let $\mathfrak{a}$ be a homogeneous ideal of a polynomial ring $R$ in $n$ variables over a field $\mathbb{k}$. Assume that $\mathrm{depth} (R/ \mathfrak{a})\geq t$, where $t$ is some number in $\{ 0, \ldots , n\} $. A result of Peskine and Szpiro says that if $\mathrm{char} (\mathbb{k})\gt 0$, then the local cohomology modules ${ H}_{\mathfrak{a}}^{i} (M)$ vanish for all $i\gt n- t$ and all $R$-modules $M$. In characteristic $0$, there are counterexamples to this for all $t\geq 4$. On the other hand, when $t\leq 2$, by exploiting classical results of Grothendieck, Lichtenbaum, Hartshorne and Ogus it is not difficult to extend the result to any characteristic. In this paper we settle the remaining case; specifically, we show that if $\mathrm{depth} (R/ \mathfrak{a})\geq 3$, then the local cohomology modules ${ H}_{\mathfrak{a}}^{i} (M)$ vanish for all $i\gt n- 3$ and all $R$-modules $M$, whatever the characteristic of $\mathbb{k}$ is.
Casein Kinase Iδ Mutations in Familial Migraine and Advanced Sleep Phase
Authors: Brennan K. C. , Bates Emily A. , Shapiro Robert E. , Zyuzin Jekaterina , Hallows William C. , Huang Yong , Lee Hsien-Yang , Jones Christopher R. , Fu Ying-Hui , Charles Andrew C. , Ptáček Louis J.
Published: May 2013

Mutations in casein kinase Iδ that are associated with migraine in patients cause changes in enzymatic function, pain behavior, cortical excitability, and astrocyte signaling in mice.
Staying Smart on Statins
Authors: Mack William J.
Published: May 2013

Asymptomatic carotid artery stenosis patients given statins have a lower incidence of stroke and cognitive dysfunction after surgery.
Stimulating the Prefrontal Cortex to Undo Stimulant Addiction
Authors: Sohal Vikaas S.
Published: May 2013

Chronic cocaine exposure may decrease the excitability of prefrontal neurons; acute changes in prefrontal activity alter cocaine-seeking behavior in rats.
Fungal Virulence in a Lepidopteran Model Is an Emergent Property with Deterministic Features
Authors: Garcia-Solache Monica A. , Izquierdo-Garcia David , Smith Cameron , Bergman Aviv , Casadevall Arturo
Published: May 2013

Virulence has been proposed to be an emergent property, which by definition implies that it is not reducible to its components, but this application of a philosophical concept to the host-microbe interaction has not been experimentally tested. The goals of our study were to analyze the correlation of the phenotype with the ability to cause disease and to determine the dynamics of an experimental cryptococcal infection inGalleria mellonellaandAcanthamoeba castellanii. By studying the outcome of infection as host death, we showed that the dynamics of virulence in theG. mellonella/Cryptococcus neoformansinteraction follow a predictable pattern. We also found that the experimental temperature and not the presence of virulence factors was a critical parameter defining the pathogenic potential of cryptococcal species. Our results established that cryptococcal species not considered pathogenic could be pathogens given suitable conditions. Our results support the idea that virulence is an emergent property that cannot be easily predicted by a reductionist approach and yet it behaves as a deterministic system in a lepidopteran cryptococcal infection. These findings provide a road map for evaluating whether host-microbe interactions in other systems are chaotic, deterministic, or stochastic, including those with public health importance.

IMPORTANCEVirulence is a complex phenotype that cannot be easily studied by analyzing its individual components in isolation. By studying the outcome of infection as the death of the host, we found that a given microbial phenotype does not necessarily correlate with its ability to cause disease and that the presence of so-called virulence factors does not predict pathogenicity, consistent with the notion that virulence is an emergent property. This paper reports that the dynamics of virulence inGalleria mellonellalarvae infected with the fungusCryptococcus neoformansfollows a predictable pattern. Establishing that virulence is an emergent property is important because it implies that it is not reducible to its components, and consequently, this phenomenon needs to be studied by a holistic approach.
Real-world outcomes of US employees with type 2 diabetes mellitus treated with insulin glargine or neutral protamine Hagedorn insulin: a comparative retrospective database study
Authors: Wang Li , Wei Wenhui , Miao Raymond , Xie Lin , Baser Onur
Published: May 2013

Objectives

To compare real-world outcomes of initiating insulin glargine (GLA) versus neutral protamine Hagedorn (NPH) insulin among employees with type 2 diabetes mellitus (T2DM) who had both employer-sponsored health insurance and short-tem-disability coverages.

Design

Retrospective cohort study.

Setting

MarketScan Commercial Claims and Encounters/Health and Productivity Management Databases 2003–2009.

Participants

Adult employees with T2DM who were previously treated with oral antidiabetic drugs and/or glucagon-like-peptide 1 receptor agonists and initiated GLA or NPH were included if they were continuously enrolled in healthcare and short-term-disability coverages for 3 months before (baseline) and 1 year after (follow-up) initiation. Treatment selection bias was addressed by 2:1 propensity score matching. Sensitivity analyses were conducted using different matching ratios.

Primary and secondary outcome measures

Outcomes during 1-year follow-up were measured and compared: insulin treatment persistence and adherence; hypoglycaemia rates and daily average consumption of insulin; total and diabetes-specific healthcare resource utilisation and costs and loss in productivity, as measured by short-term disability, and the associated costs.

Results

A total of 534 patients were matched and analysed (GLA: 356; NPH 178) with no significant differences in baseline characteristics. GLA patients were more persistent and adherent (both p<0.05), had lower rates of hospitalisation (23% vs 31.4%; p=0.036) and endocrinologist visits (19.1% vs 26.9%; p=0.038), similar hypoglycaemia rates (both 4.4%; p=1.0), higher diabetes drug costs ($2031 vs $1522; p<0.001), but similar total healthcare costs ($14 550 vs $16 093; p=0.448) and total diabetes-related healthcare costs ($4686 vs $5604; p=0.416). Short-term disability days and costs were numerically lower in the GLA cohort (16.0 vs 24.5 days; p=0.086 and $2824 vs $4363; p=0.081, respectively). Sensitivity analyses yielded similar findings.

Conclusions

Insulin GLA results in better persistence and adherence, compared with NPH insulin, with no overall cost disadvantages. Better persistence and adherence may lead to long-term health benefits for employees with T2DM.
Influence of societal and practice contexts on health professionals’ clinical reasoning: a scoping study protocol
Authors: Carrier Annie , Levasseur Mélanie , Freeman Andrew , Mullins Gary , Quénec'hdu Suzanne , Lalonde Louise , Gagnon Michaël , Lacasse Francis
Published: May 2013

Introduction

In a context of constrained resources, the efficacy of interventions is a pivotal aim of healthcare systems worldwide. Efficacy of healthcare interventions is highly compromised if clinical reasoning (CR), the process that practitioners use to plan, direct, perform and reflect on client care, is not optimal. The CR process of health professionals is influenced by the institutional dimension (ie, legal, regulatory, administrative and organisational aspects) of their societal and practice contexts. Although several studies have been conducted with respect to the institutional dimension influencing health professionals’ CR, no clear integration of their results is yet available. The aim of this study is to synthesise and disseminate current knowledge on the influence of the institutional dimension of contexts on health professionals’ CR.

Methods and analysis

A scoping study of the scientific literature from January 1980 to March 2013 will be undertaken to summarise and disseminate research findings about the influence of the institutional dimension on CR. Numerous databases (n=18) from three relevant fields (healthcare, health law and politics and management) will be searched. Extended search strategies will include the manual search of bibliographies, health-related websites, public registries and journals of interest. Data will be collected and analysed using a thematic chart and content analysis. A systematic multidisciplinary team approach will allow optimal identification of relevant studies, as well as effective and valid content analysis and dissemination of the results.

Discussion

This scoping study will provide a rigorous, accurate and up-to-date synthesis of existing knowledge regarding: (1) those aspects of the institutional dimension of health professionals’ societal and practice contexts that impact their CR and (2) how these aspects influence health professionals’ CR. Through the synergy of a multidisciplinary research team from a wide range of expertise, clinical pertinence and an exhaustive dissemination of results to knowledge-users will be ensured.
Portrait of rural emergency departments in Quebec and utilisation of the Quebec Emergency Department Management Guide: a study protocol
Authors: Fleet Richard , Archambault Patrick , Légaré France , Chauny Jean-Marc , Lévesque Jean-Frédéric , Ouimet Mathieu , Dupuis Gilles , Haggerty Jeannie , Poitras Julien , Tanguay Alain , Simard-Racine Geneviève , Gauthier Josée
Published: May 2013

Introduction

Emergency departments are important safety nets for people who live in rural areas. Moreover, a serious problem in access to healthcare services has emerged in these regions. The challenges of providing access to quality rural emergency care include recruitment and retention issues, lack of advanced imagery technology, lack of specialist support and the heavy reliance on ambulance transport over great distances. The Quebec Ministry of Health and Social Services published a new version of theEmergency Department Management Guide, a document designed to improve the emergency department management and to humanise emergency department care and services. In particular, theGuiderecommends solutions to problems that plague rural emergency departments. Unfortunately, no studies have evaluated the implementation of the proposed recommendations.

Methods and analysis

To develop a comprehensive portrait of all rural emergency departments in Quebec, data will be gathered from databases at the Quebec Ministry of Health and Social Services, the Quebec Trauma Registry and from emergency departments and ambulance services managers. Statistics Canada data will be used to describe populations and rural regions. To evaluate the use of the 2006Emergency Department Management Guideand the implementation of its various recommendations, an online survey and a phone interview will be administered to emergency department managers. Two online surveys will evaluate quality of work life among physicians and nurses working at rural emergency departments. Quality-of-care indicators will be collected from databases and patient medical files. Data will be analysed using statistical (descriptive and inferential) procedures.

Ethics and dissemination

This protocol has been approved by the CSSS Alphonse–Desjardins research ethics committee (Project MP-HDL-1213-011). The results will be published in peer-reviewed scientific journals and presented at one or more scientific conferences.
Re-endovascular recanalization for acute middle cerebral artery reocclusion after surgical embolectomy
Authors: Jeon Jin Sue , Sheen Seung Hun , Kim Heung Cheol
Published: May 2013

A 62-year-old woman with atrial fibrillation underwent burr hole trephination for a chronic subdural hematoma. Two days later the patient suddenly presented with motor dysphasia and slightly decreased motor power. Time of flight MR angiography revealed distal M1 occlusion without diffusion restriction. Stent-assisted mechanical thrombectomy was attempted but failed. Post-procedure MRI illustrated a small area of diffusion restriction within the peri-insular and parietal areas. Immediate surgical embolectomy was performed but reocclusion of M1 was documented in the postoperative angiography. Stent-assisted revascularization with a Solitaire stent was conducted and immediate restoration of blood flow was observed. The patient's motor weakness and motor dysphasia recovered fully. Re-endovascular intervention can be beneficial in selected patients for acute middle cerebral artery reocclusion after surgical embolectomy when endovascular thrombectomy fails.
Patterns and trends in Pakistan's heterogeneous HIV epidemic
Authors: Reza Tahira , Melesse Dessalegn Y , Shafer Leigh Anne , Salim Momina , Altaf Arshad , Sonia Altaf , Jayaraman Gayatri C , Emmanuel Faran , Thompson Laura H , Blanchard James F
Published: May 2013

Background

Considerable HIV transmission occurs among injection drug users (IDUs) in Pakistan and recently the HIV prevalence has been increasing among male (MSW),hijra(transgender; HSW) and female (FSW) sex workers. We describe past and estimate future patterns of HIV emergence among these populations in several cities in Pakistan.

Methods

The density of these key populations per 1000 adult men was calculated using 2011 mapping data from Karachi, Lahore, Faisalabad, Larkana, Peshawar and Quetta, and surveillance data were used to assess bridging between these key populations. We used the UNAIDS Estimation and Projection Package model to estimate and project HIV epidemics among these key populations in Karachi, Lahore, Faisalabad and Larkana.

Results

The density and bridging of key populations varied across cities. Lahore had the largest FSW population (11.5/1000 adult men) and the smallest IDU population (1.7/1000 adult men). Quetta had the most sexual and drug injection bridging between sex workers and IDUs (6.7%, 7.0% and 3.8% of FSW, MSW and HSW, respectively, reported injecting drugs). Model evidence suggests that by 2015 HIV prevalence is likely to reach 17–22% among MSWs/HSWs in Karachi, 44–49% among IDUs in Lahore and 46–66% among IDUs in Karachi. Projection suggests the prevalence may reach as high as 65–75% among IDUs in Faisalabad by 2025. HIV prevalence is also estimated to increase among FSWs, particularly in Karachi and Larkana.

Conclusions

There is a need to closely monitor regional and subpopulation epidemic patterns and implement prevention programmes customised to local epidemics.
Modern diagnosis ofTrichomonas vaginalisinfection
Authors: Hobbs Marcia M , Seña Arlene C
Published: May 2013

Recent advances in tests for the sexually transmitted protozoan parasiteTrichomonas vaginalishave increased opportunities for diagnosis and treatment of this important sexually transmitted infection. This review summarises currently available tests, highlighting their performance characteristics, advantages and limitations. The recent development of molecular tests for the detection ofT vaginalis, including rapid antigen detection and nucleic acid amplification tests, has significantly improved the quality of diagnostics for trichomoniasis, particularly in women. In light of the expanded menu of testing options now available, improved recognition and better control of trichomoniasis are in sight, which should enable the eventual reduction of adverse reproductive consequences associated withT vaginalisinfection.
A Transformation Framework for Optimizing Task-Parallel Programs
Authors: Nandivada V. Krishna , Shirako Jun , Zhao Jisheng , Sarkar Vivek
Published: May 2013

Task parallelism has increasingly become a trend with programming models such as OpenMP 3.0, Cilk, Java Concurrency, X10, Chapel and Habanero-Java (HJ) to address the requirements of multicore programmers. While task parallelism increases productivity by allowing the programmer to express multiple levels of parallelism, it can also lead to performance degradation due to increased overheads. In this article, we introduce a transformation framework for optimizing task-parallel programs with a focus on task creation and task termination operations. These operations can appear explicitly in constructs such as async, finish in X10 and HJ, task, taskwait in OpenMP 3.0, and spawn, sync in Cilk, or implicitly in composite code statements such as foreach and ateach loops in X10, forall and foreach loops in HJ, and parallel loop in OpenMP.

Our framework includes a definition of data dependence in task-parallel programs, a happens-before analysis algorithm, and a range of program transformations for optimizing task parallelism. Broadly, our transformations cover three different but interrelated optimizations: (1)
finish-elimination
, (2)
forall-coarsening
, and (3)
loop-chunking
. Finish-elimination removes redundant task termination operations, forall-coarsening replaces expensive task creation and termination operations with more efficient synchronization operations, and loop-chunking extracts useful parallelism from ideal parallelism. All three optimizations are specified in an iterative transformation framework that applies a sequence of relevant transformations until a fixed point is reached. Further, we discuss the impact of exception semantics on the specified transformations, and extend them to handle task-parallel programs with precise exception semantics. Experimental results were obtained for a collection of task-parallel benchmarks on three multicore platforms: a dual-socket 128-thread (16-core) Niagara T2 system, a quad-socket 16-core Intel Xeon SMP, and a quad-socket 32-core Power7 SMP. We have observed that the proposed optimizations interact with each other in a synergistic way, and result in an overall geometric average performance improvement between 6.28× and 10.30×, measured across all three platforms for the benchmarks studied.
TSL
Authors: Lim Junghee , Reps Thomas
Published: May 2013

This article describes the design and implementation of a system, called T
SL
(for Transformer Specification Language), that provides a systematic solution to the problem of creating retargetable tools for analyzing machine code. T
SL
is a tool generator---that is, a metatool---that automatically creates different abstract interpreters for machine-code instruction sets.

The most challenging technical issue that we faced in designing T
SL
was how to automate the generation of the set of
abstract transformers
for a given abstract interpretation of a given instruction set. From a description of the
concrete operational semantics
of an instruction set, together with the datatypes and operations that define an abstract domain, T
SL
automatically creates the set of abstract transformers for the instructions of the instruction set. T
SL
advances the state-of-the-art in program analysis because it provides two dimensions of parameterizability: (i) a given analysis component can be retargeted to different instruction sets; (ii) multiple analysis components can be created automatically from a single specification of the concrete operational semantics of the language to be analyzed.

T
SL
is an
abstract-transformer-generator generator
. The article describes the principles behind T
SL
, and discusses how one uses T
SL
to develop different abstract interpreters.
Paging and list update under bijective analysis
Authors: Angelopoulos Spyros , Schweitzer Pascal
Published: May 2013

It has long been known that for the paging problem in its standard form, competitive analysis cannot adequately distinguish algorithms based on their performance: there exists a vast class of algorithms that achieve the same competitive ratio, ranging from extremely naive and inefficient strategies (such as Flush-When-Full), to strategies of excellent performance in practice (such as Least-Recently-Used and some of its variants). A similar situation arises in the list update problem: in particular, under the cost formulation studied by Martínez and Roura [2000] and Munro [2000] every list update algorithm has, asymptotically, the same competitive ratio. Several refinements of competitive analysis, as well as alternative performance measures have been introduced in the literature, with varying degrees of success in narrowing this disconnect between theoretical analysis and empirical evaluation.

In this article, we study these two fundamental online problems under the framework of
bijective analysis
[Angelopoulos et al. 2007, 2008]. This is an intuitive technique that is based on pairwise comparison of the costs incurred by two algorithms on sets of request sequences of the same size. Coupled with a well-established model of locality of reference due to Albers et al. [2005], we show that Least-Recently-Used and Move-to-Front are the unique optimal algorithms for paging and list update, respectively. Prior to this work, only measures based on average-cost analysis have separated LRU and MTF from all other algorithms. Given that bijective analysis is a fairly stringent measure (and also subsumes average-cost analysis), we prove that in a strong sense LRU and MTF stand out as the best (deterministic) algorithms.
Forbidden information
Authors: Levin Leonid A.
Published: May 2013

Gödel Incompleteness Theorem leaves open a way around it, vaguely perceived for a long time but not clearly identified. (Thus, Gödel believed informal arguments can answer any math question.) Closing this loophole does not seem obvious and involves Kolmogorov complexity. (This is unrelated to, well studied before, complexity quantifications of the usual Gödel effects.) I consider extensions
U
of the universal partial recursive predicate (or, say, Peano Arithmetic). I prove that any
U
either leaves an
n
-bit input (statement) unresolved or contains nearly all information about the
n
-bit prefix of any r.e. real ρ (which is
n
bits for some ρ). I argue that creating significant information about a
specific
math sequence is impossible regardless of the methods used. Similar problems and answers apply to other unsolvability results for tasks allowing multiple solutions, for example, nonrecursive tilings.
Relational transducers for declarative networking
Authors: Ameloot Tom J. , Neven Frank , Van Den Bussche Jan
Published: May 2013

Motivated by a recent conjecture concerning the expressiveness of declarative networking, we propose a formal computation model for “eventually consistent” distributed querying, based on relational transducers. A tight link has been conjectured between coordination-freeness of computations, and monotonicity of the queries expressed by such computations. Indeed, we propose a formal definition of coordination-freeness and confirm that the class of monotone queries is captured by coordination-free transducer networks. Coordination-freeness is a semantic property, but the syntactic class of “oblivious” transducers we define also captures the same class of monotone queries. Transducer networks that are not coordination-free are much more powerful.
High-performance bidiagonal reduction using tile algorithms on homogeneous multicore architectures
Authors: Ltaief Hatem , Luszczek Piotr , Dongarra Jack
Published: May 2013

This article presents a new high-performance bidiagonal reduction (BRD) for homogeneous multicore architectures. This article is an extension of the high-performance tridiagonal reduction implemented by the same authors [Luszczek et al., IPDPS 2011] to the BRD case. The BRD is the first step toward computing the singular value decomposition of a matrix, which is one of the most important algorithms in numerical linear algebra due to its broad impact in computational science. The high performance of the BRD described in this article comes from the combination of four important features: (1) tile algorithms with tile data layout, which provide an efficient data representation in main memory; (2) a two-stage reduction approach that allows to cast most of the computation during the first stage (reduction to band form) into calls to Level 3 BLAS and reduces the memory traffic during the second stage (reduction from band to bidiagonal form) by using high-performance kernels optimized for cache reuse; (3) a data dependence translation layer that maps the general algorithm with column-major data layout into the tile data layout; and (4) a dynamic runtime system that efficiently schedules the newly implemented kernels across the processing units and ensures that the data dependencies are not violated. A detailed analysis is provided to understand the critical impact of the tile size on the total execution time, which also corresponds to the matrix bandwidth size after the reduction of the first stage. The performance results show a significant improvement over currently established alternatives. The new high-performance BRD achieves up to a 30-fold speedup on a 16-core Intel Xeon machine with a 12000× 12000 matrix size against the state-of-the-art open source and commercial numerical software packages, namely LAPACK, compiled with optimized and multithreaded BLAS from MKL as well as Intel MKL version 10.2.
An efficient overloaded method for computing derivatives of mathematical functions in MATLAB
Authors: Patterson Michael A. , Weinstein Matthew , Rao Anil V.
Published: May 2013

An object-oriented method is presented that computes without truncation the error derivatives of functions defined by MATLAB computer codes. The method implements forward-mode automatic differentiation via operator overloading in a manner that produces a new MATLAB code that computes the derivatives of the outputs of the original function with respect to the differentiation variables. Because the derivative code has the same input as the original function code, the method can be used recursively to generate derivatives of any order desired. In addition, the approach developed in this article has the feature that the derivatives are generated by simply evaluating the function on an instance of the class, thus making the method straightforward to use while simultaneously enabling differentiation of highly complex functions. A detailed description of the method is presented and the approach is illustrated and shown to be efficient on four examples.
A survey on cloud interoperability
Authors: Zhang Zhizhong , Wu Chuan , Cheung David W.L.
Published: May 2013

Cloud computing is a new computing paradigm that allows users with different computing demands to access a shared pool of configurable computing resources (e.g., servers, network, storage, database, applications and services). Many commercial cloud providers have emerged in the past 6-7 years, and each typically provides its own cloud infrastructure, APIs and application description formats to access the cloud resources, as well as support for service level agreements (SLAs). Such vendor lock-in has seriously limited the flexibility that cloud end users would like to process, when it comes to deploy applications over different infrastructures in different geographic locations, or to migrate a service from one provider's cloud to another. To enable seamless sharing of resources from a pool of cloud providers, efforts have emerged recently to facilitate cloud interoperability, i.e., the ability for multiple cloud providers to work together, from both the industry and academia. In this article, we conduct a comprehensive survey on the state-of-the-art efforts, with a focus on interoperability among different IaaS (infrastructure as a service) cloud platforms. We investigate the existing studies on taxonomies and standardization of cloud interoperability, as well as practical cloud technologies from both the cloud provider's and user's perspectives to enable interoperation. We pose issues and challenges to advance the topic area, and hope to pave a way for the forthcoming research.
On distributed computation rate optimization for deploying cloud computing programming frameworks
Authors: Liu Jia , Xia Cathy H. , Shroff Ness B. , Zhang Xiaodong
Published: May 2013

With the rapidly growing challenges of big data analytics, the need for efficient and distributed algorithms to optimize cloud computing performances is unprecedentedly high. In this paper, we consider how to optimally deploy a cloud computing programming framework (e.g., MapReduce and Dryad) over a given underlying network hardware infrastructure to maximize the end-to-end computation rate and minimize the overall computation and communication costs. The main contributions in this paper are three-fold: i) we develop a new network flow model with a generalized flowconservation law to enable a systematic design of distributed algorithms for computation rate utility maximization problems (CRUM) in cloud computing; ii) based on the network flow model, we reveal key separable properties of the dual functions of Problem CRUM, which further lead to a distributed algorithm design; and iii) we offer important networking insights and meaningful economic interpretations for the proposed algorithm and point out their connections to and distinctions from distributed algorithms design in traditional data communications networks. This paper serves as an important first step towards the development of a theoretical foundation for distributed computation analytics in cloud computing.
Understanding the latency benefits of multi-cloud webservice deployments
Authors: Wu Zhe , Madhyastha Harsha V.
Published: May 2013

To minimize user-perceived latencies, webservices are often deployed across multiple geographically distributed data centers. The premise of our work is that webservices deployed across multiple cloud infrastructure services can serve users from more data centers than that possible when using a single cloud service, and hence, offer lower latencies to users.

In this paper, we conduct a comprehensive measurement study to understand the potential latency benefits of deploying webservices across three popular cloud infrastructure services - Amazon EC2, Google Compute Engine (GCE), and Microsoft Azure. We estimate that, as compared to deployments on one of these cloud services, users in up to half the IP address prefixes can have their RTTs reduced by over 20% when a webservice is deployed across the three cloud services. When we dig deeper to understand these latency benefits, we make three significant observations. First, when webservices shift from single-cloud to multi-cloud deployments, a significant fraction of prefixes will see latency benefits simply by being served from a different data center in the same location. This is because routing inefficiencies that exist between a prefix and a nearby data center in one cloud service are absent on the path from the prefix to a nearby data center in a different cloud service. Second, despite the latency improvements that a large fraction of prefixes will perceive, users in several locations (e.g., Argentina and Israel) will continue to incur RTTs greater than 100ms even when webservices span three large-scale cloud services (EC2, GCE, and Azure). Finally, we see that harnessing the latency benefits offered by multi-cloud deployments is likely to be challenging in practice; our measurements show that the data center which offers the lowest latency to a prefix often fluctuates between different cloud services, thus necessitating replication of data.
A first measurement look at the deployment and evolution of thelocator/id separation protocol
Authors: Saucez Damien , Iannone Luigi , Donnet Benoit
Published: May 2013

During the last decade, we have seen the rise of discussions regarding the emergence of a Future Internet. One of the proposed approaches leverages on the separation of the identifier and the locator roles of IP addresses, leading to the LISP (Locator/Identifier Separation Protocol) protocol, currently under development at the IETF (Internet Engineering Task Force). Up to now, researches made on LISP have been rather theoretical, i.e., based on simulations/emulations often using Internet traffic traces. There is no work in the literature attempting to assess the state of its deployment and how this has evolved in recent years. This paper aims at bridging this gap by presenting a first measurement study on the existing worldwide LISP network (lisp4.net). Early results indicate that there is a steady growth of the LISP network but also that network manageability might receive a higher priority than performance in a large scale deployment.
Cognitive radio networks
Authors: Pelechrinis Konstantinos , Krishnamurthy Prashant , Weiss Martin , Znati Taieb
Published: May 2013

A large volume of research has been conducted in the cognitive radio (CR) area the last decade. However, the deployment of a commercial CR network is yet to emerge. A large portion of the existing literature does not build on real world scenarios, hence, neglecting various important aspects of commercial telecommunication networks. For instance, a lot of attention has been paid to spectrum sensing as the front line functionality that needs to be completed in an efficient and accurate manner to enable an opportunistic CR network architecture. While on the one hand it is necessary to detect the existence of spectrum holes, on the other hand, simply sensing (cooperatively or not) the energy emitted from a primary transmitter cannot enable correct dynamic spectrum access. For example, the presence of a primary transmitter's signal does not mean that CR network users cannot access the spectrum since there might not be any primary receiver in the vicinity. Despite the existing solutions to the DSA problem no robust, implementable scheme has emerged. The set of assumptions that these schemes are built upon do not always hold in realistic, wireless environments. Specific settings are assumed, which differ significantly from how existing telecommunication networks work. In this paper, we challenge the basic premises of the proposed schemes. We further argue that addressing the technical challenges we face in deploying robust CR networks can only be achieved if we radically change the way we design their basic functionalities. In support of our argument, we present a set of real-world scenarios, inspired by realistic settings in commercial telecommunications networks, namely TV and cellular, focusing on spectrum sensing as a basic and critical functionality in the deployment of CRs. We use these scenarios to show why existing DSA paradigms are not amenable to realistic deployment in complex wireless environments. The proposed study extends beyond cognitive radio networks, and further highlights the often existing gap between research and commercialization, paving the way to new thinking about how to accelerate commercialization and adoption of new networking technologies and services.
Highlights of consumer electronics show (ces) 2013
Authors: Garcia Calvo Fernando , Lucendo de Gregorio Javier , Soto de Toro Fernando , Munoz Lopez Joaquin , Mayo Muniz Teo , Miranda Jose Maria , Gavilan Ballesteros Oscar
Published: May 2013

The Consumer Electronics Show, which is held every year in Las Vegas in early January, continues to be an important fair in the consumer sector, though increasingly the major manufacturers prefer to announce their new products at their own specific events in order to gain greater impact. Only the leading TV brands unveil their artillery of new models for the coming year. Despite this, it continues to break records: there were over 150,000 visitors (from more than 150 countries), the number of new products announced exceeded 20,000 and the fair occupied over 2 million square meters.
Low Complexity Submatrix Divided MMSE Sparse-SQRD Detection for MIMO-OFDM with ESPAR Antenna Receiver
Authors: Reinoso Chisaguano Diego Javier , Okada Minoru
Published: May 2013

Multiple input multiple output-orthogonal frequency division multiplexing (MIMO-OFDM) with an electronically steerable passive array radiator (ESPAR) antenna receiver can improve the bit error rate performance and obtains additional diversity gain without increasing the number of Radio Frequency (RF) front-end circuits. However, due to the large size of the channel matrix, the computational cost required for the detection process using Vertical-Bell Laboratories Layered Space-Time (V-BLAST) detection is too high to be implemented. Using the minimum mean square error sparse-sorted QR decomposition (MMSE sparse-SQRD) algorithm for the detection process the average computational cost can be considerably reduced but is still higher compared with a conventional MIMOOFDM system without ESPAR antenna receiver. In this paper, we propose to use a low complexity submatrix divided MMSE sparse-SQRD algorithm for the detection process of MIMOOFDM with ESPAR antenna receiver. The computational cost analysis and simulation results show that on average the proposed scheme can further reduce the computational cost and achieve a complexity comparable to the conventional MIMO-OFDM detection schemes.