bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey of intelligent assistants for data analysis
Authors: Serban Floarea , Vanschoren Joaquin , Kietz Jörg-Uwe , Bernstein Abraham 
Published: July 2013

Research and industry increasingly make use of large amounts of data to guide decision-making. To do this, however, data needs to be analyzed in typically nontrivial refinement processes, which require technical expertise about methods and algorithms, experience with how a precise analysis should proceed, and knowledge about an exploding number of analytic approaches. To alleviate these problems, a plethora of different systems have been proposed that “intelligently” help users to analyze their data.This article provides a first survey to almost 30 years of research on intelligent discovery assistants (IDAs). It explicates the types of help IDAs can provide to users and the kinds of (background) knowledge they leverage to provide this help. Furthermore, it provides an overview of the systems developed over the past years, identifies their most important features, and sketches an ideal future IDA as well as the challenges on the road ahead.
OWL
Authors: Jog Adwait , Kayiran Onur , Chidambaram Nachiappan Nachiappan , Mishra Asit K. , Kandemir Mahmut T. , Mutlu Onur , Iyer Ravishankar , Das Chita R. 
Published: July 2013

Emerging GPGPU architectures, along with programming models like CUDA and OpenCL, offer a cost-effective platform for many applications by providing high thread level parallelism at lower energy budgets. Unfortunately, for many general-purpose applications, available hardware resources of a GPGPU are not efficiently utilized, leading to lost opportunity in improving performance. A major cause of this is the inefficiency of current warp scheduling policies in tolerating long memory latencies.
In this paper, we identify that the scheduling decisions made by such policies are agnostic to thread-block, or cooperative thread array (CTA), behavior, and as a result inefficient. We present a coordinated CTA-aware scheduling policy that utilizes four schemes to minimize the impact of long memory latencies. The first two schemes, CTA-aware two-level warp scheduling and locality aware warp scheduling, enhance per-core performance by effectively reducing cache contention and improving latency hiding capability. The third scheme, bank-level parallelism aware warp scheduling, improves overall GPGPU performance by enhancing DRAM bank-level parallelism. The fourth scheme employs opportunistic memory-side prefetching to further enhance performance by taking advantage of open DRAM rows. Evaluations on a 28-core GPGPU platform with highly memory-intensive applications indicate that our proposed mechanism can provide 33% average performance improvement compared to the commonly-employed round-robin warp scheduling policy.
Buffer minimization in earliest-deadline first scheduling of dataflow graphs
Authors: Bouakaz Adnan , Talpin Jean-Pierre 
Published: July 2013

Symbolic schedulability analysis of dataflow graphs is the process of synthesizing the timing parameters (i.e. periods, phases, and deadlines) of actors so that the task system is schedulable and achieves a high throughput when using a specific scheduling policy. Furthermore, the resulted schedule must ensure that communication buffers are underflow- and overflow-free. This paper describes a (partitioned) earliest-deadline first symbolic schedulability analysis of dataflow graphs that minimizes the buffering requirements.
Our scheduling analysis consists of three major steps. (1) The construction of an abstract affine schedule of the graph that excludes overflow and underflow exceptions and minimizes the buffering requirements assuming some precedences between jobs. (2) Symbolic deadlines adjustment that guarantees precedences without the need for lock-based synchronizations. (3) The concretization of the affine schedule using a symbolic, fast-converging, processor-demand analysis for both uniprocessor and multiprocessor systems. Experimental results show that our technique improves the buffering requirements in many cases.
Concurrent libraries with foresight
Authors: Golan-Gueta Guy , Ramalingam G. , Sagiv Mooly , Yahav Eran 
Published: July 2013

Linearizable libraries provide operations that appear to execute atomically. Clients, however, may need to execute a sequence of operations (a composite operation) atomically. We consider the problem of extending a linearizable library to support arbitrary atomic composite operations by clients. We introduce a novel approach in which the concurrent library ensures atomicity of composite operations by exploiting information (foresight) provided by its clients. We use a correctness condition, based on a notion of dynamic right-movers, that guarantees that composite operations execute atomically without deadlocks, and without using rollbacks.
We present a static analysis to infer the foresight information required by our approach, allowing a compiler to automatically insert the foresight information into the client. This relieves the client programmer of this burden and simplifies writing client code.
We present a generic technique for extending the library implementation to realize foresight-based synchronization. This technique is used to implement a general-purpose Java library for Map data structures -- the library permits composite operations to simultaneously work with multiple instances of Map data structures.
We use the Maps library and the static analysis to enforce atomicity of a wide selection of real-life Java composite operations. Our experiments indicate that our approach enables realizing efficient and scalable synchronization for real-life composite operations.
How to combine widening and narrowing for non-monotonic systems of equations
Authors: Apinis Kalmer , Seidl Helmut , Vojdani Vesal 
Published: July 2013

Non-trivial analysis problems require complete lattices with infinite ascending and descending chains. In order to compute reasonably precise post-fixpoints of the resulting systems of equations, Cousot and Cousot have suggested accelerated fixpoint iteration by means of widening and narrowing.
The strict separation into phases, however, may unnecessarily give up precision that cannot be recovered later. While widening is also applicable if equations are non-monotonic, this is no longer the case for narrowing. A narrowing iteration to improve a given post-fixpoint, additionally, must assume that all right-hand sides are monotonic. The latter assumption, though, is not met in presence of widening. It is also not met by equation systems corresponding to context-sensitive interprocedural analysis, possibly combining context-sensitive analysis of local information with flow-insensitive analysis of globals.
As a remedy, we present a novel operator that combines a given widening operator with a given narrowing operator. We present adapted versions of round-robin as well as of worklist iteration, local, and side-effecting solving algorithms for the combined operator and prove that the resulting solvers always return sound results and are guaranteed to terminate for monotonic systems whenever only finitely many unknowns (constraint variables) are encountered.
Fast RMWs for TSO
Authors: Rajaram Bharghava , Nagarajan Vijay , Sarkar Susmit , Elver Marco 
Published: July 2013

Read-Modify-Write (RMW) instructions are widely used as the building blocks of a variety of higher level synchronization constructs, including locks, barriers, and lock-free data structures. Unfortunately, they are expensive in architectures such as x86 and SPARC which enforce (variants of) Total-Store-Order (TSO). A key reason is that RMWs in these architectures are ordered like a memory barrier, incurring the cost of a write-buffer drain in the critical path. Such strong ordering semantics are dictated by the requirements of the strict atomicity definition (type-1) that existing TSO RMWs use. Programmers often do not need such strong semantics. Besides, weakening the atomicity definition of TSO RMWs, would also weaken their ordering -- thereby leading to more efficient hardware implementations.
In this paper we argue for TSO RMWs to use weaker atomicity definitions -- we consider two weaker definitions: type-2 and type-3, with different relaxed ordering differences. We formally specify how such weaker RMWs would be ordered, and show that type-2 RMWs, in particular, can seamlessly replace existing type-1 RMWs in common synchronization idioms -- except in situations where a type-1 RMW is used as a memory barrier. Recent work has shown that the new C/C++11 concurrency model can be realized by generating conventional (type-1) RMWs for C/C++11 SC-atomic-writes and/or SC-atomic-reads. We formally prove that this is equally valid using the proposed type-2 RMWs; type-3 RMWs, on the other hand, could be used for SC-atomic-reads (and optionally SC-atomic-writes). We further propose efficient microarchitectural implementations for type-2 (type-3) RMWs -- simulation results show that our implementation reduces the cost of an RMW by up to 58.9% (64.3%), which translates into an overall performance improvement of up to 9.0% (9.2%) on a set of parallel programs, including those from the SPLASH-2, PARSEC, and STAMP benchmarks.
Fast condensation of the program dependence graph
Authors: Johnson Nick P. , Oh Taewook , Zaks Ayal , August David I. 
Published: July 2013

Aggressive compiler optimizations are formulated around the Program Dependence Graph (PDG). Many techniques, including loop fission and parallelization are concerned primarily with dependence cycles in the PDG. The Directed Acyclic Graph of Strongly Connected Components (DAGSCC) represents these cycles directly. The naive method to construct the DAGSCC first computes the full PDG. This approach limits adoption of aggressive optimizations because the number of analysis queries grows quadratically with program size, making DAGSCC construction expensive. Consequently, compilers optimize small scopes with weaker but faster analyses.
We observe that many PDG edges do not affect the DAGSCC and that ignoring them cannot affect clients of the DAGSCC. Exploiting this insight, we present an algorithm to omit those analysis queries to compute the DAGSCC efficiently. Across 366 hot loops from 20 SPEC2006 benchmarks, this method computes the DAGSCC in half of the time using half as many queries.
Writing More and Less ‘Jewishly’ in Judezmo and Yiddish
Authors: Bunis David M. 
Published: June 2013

Abstract
Max Weinreich used the term yídishlekh to describe the traditional, ‘Jewishly patterned’ style of writing in Yiddish. Weinreich illustrated this style by comparing Mendele Moykher Sforim’s ‘Jewishly-styled’ 1884 Yiddish translation of Leo Pinsker’s Autoemanzipation (Berlin 1882) with the original German-language text. The present article demonstrates that in Judezmo as well as Yiddish, writers have consciously used ‘Jewish styling,’ and its converse, in the diverse literary genres they cultivated from the Middle Ages into the early twentieth century. However, as a result of somewhat divergent social, political, and ideological trends in the Judezmo as opposed to Yiddish speech communities later in the twentieth century, Yiddish writers today prefer to incorporate features of ‘Jewish styling’ in their writing, while Judezmo writers tend to reject them.
Alcohol drinking among college students: college responsibility for personal troubles
Authors: Lorant Vincent , Nicaise Pablo , Soto Victoria Eugenia , d’Hoore William 
Published: June 2013

Abstract

Background
One young adult in two has entered university education in Western countries. Many of these young students will be exposed, during this transitional period, to substantial changes in living arrangements, socialisation groups, and social activities. This kind of transition is often associated with risky behaviour such as excessive alcohol consumption. So far, however, there is little evidence about the social determinants of alcohol consumption among college students. We set out to explore how college environmental factors shape college students' drinking behaviour.

Methods
In May 2010 a web questionnaire was sent to all bachelor and master students registered with an important Belgian university; 7,015 students participated (participation = 39%). The survey looked at drinking behaviour, social involvement, college environmental factors, drinking norms, and positive drinking consequences.

Results
On average each student had 1.7 drinks a day and 2.8 episodes of abusive drinking a month. We found that the more a student was exposed to college environmental factors, the greater the risk of heavy, frequent, and abusive drinking. Alcohol consumption increased for students living on campus, living in a dormitory with a higher number of room-mates, and having been in the University for a long spell. Most such environmental factors were explained by social involvement, such as participation to the student folklore, pre-partying, and normative expectations.

Conclusions
Educational and college authorities need to acknowledge universities’ responsibility in relation to their students’ drinking behaviour and to commit themselves to support an environment of responsible drinking.
Elastomeric microparticles for acoustic mediated bioseparations
Authors: Johnson Leah M , Gao Lu , Shields IV C Wyatt , Smith Margret , Efimenko Kirill , Cushing Kevin , Genzer Jan , López Gabriel P 
Published: June 2013

Abstract

Background
Acoustophoresis has been utilized successfully in applications including cell trapping, focusing, and purification. One current limitation of acoustophoresis for cell sorting is the reliance on the inherent physical properties of cells (e.g., compressibility, density) instead of selecting cells based upon biologically relevant surface-presenting antigens. Introducing an acoustophoretic cell sorting approach that allows biochemical specificity may overcome this limitation, thus advancing the value of acoustophoresis approaches for both the basic research and clinical fields.

Results
The results presented herein demonstrate the ability for negative acoustic contrast particles (NACPs) to specifically capture and transport positive acoustic contrast particles (PACPs) to the antinode of an ultrasound standing wave. Emulsification and post curing of pre-polymers, either polydimethylsiloxane (PDMS) or polyvinylmethylsiloxane (PVMS), within aqueous surfactant solution results in the formation of stable NACPs that focus onto pressure antinodes. We used either photochemical reactions with biotin-tetrafluorophenyl azide (biotin-TFPA) or end-functionalization of Pluronic F108 surfactant to biofunctionalize NACPs. These biotinylated NACPs bind specifically to streptavidin polystyrene microparticles (as cell surrogates) and transport them to the pressure antinode within an acoustofluidic chip.

Conclusion
To the best of our knowledge, this is the first demonstration of using NACPs as carriers for transport of PACPs in an ultrasound standing wave. By using different silicones (i.e., PDMS, PVMS) and curing chemistries, we demonstrate versatility of silicone materials for NACPs and advance the understanding of useful approaches for preparing NACPs. This bioseparation scheme holds potential for applications requiring rapid, continuous separations such as sorting and analysis of cells and biomolecules.
Some results about functions that share functions with their derivative of higher order
Authors: Qi Jianming , Lü Feng , Yuan Wenjun 
Published: July 2013

Abstract
In this paper, we investigate the growth of some functions that share functions with their derivative of higher order. The first main theorem is an improvement of the result obtained by Lü (Bull. Korean Math. Soc. 48: 951-957, 2011), two examples are given to show that the conclusion is sharp. The second main theorem is of estimating, more exactly, the order of an entire function sharing polynomial, which extends the related result of Lü, Xu and Chen (Arch. Math. 92: 593-601, 2009).

MSC:30D35, 30D45.
Integrating multi-platform genomic data using hierarchical Bayesian relevance vector machines
Authors: Srivastava Sanvesh , Wang Wenyi , Manyam Ganiraju , Ordonez Carlos , Baladandayuthapani Veerabhadran 
Published: June 2013

AbstractBackgroundRecent advances in genome technologies and the subsequent collection of genomic information at various molecular resolutions hold promise to accelerate the discovery of new therapeutic targets. A critical step in achieving these goals is to develop efficient clinical prediction models that integrate these diverse sources of high-throughput data. This step is challenging due to the presence of high-dimensionality and complex interactions in the data. For predicting relevant clinical outcomes, we propose a flexible statistical machine learning approach that acknowledges and models the interaction between platform-specific measurements through nonlinear kernel machines and borrows information within and between platforms through a hierarchical Bayesian framework. Our model has parameters with direct interpretations in terms of the effects of platforms and data interactions within and across platforms. The parameter estimation algorithm in our model uses a computationally efficient variational Bayes approach that scales well to large high-throughput datasets.ResultsWe apply our methods of integrating gene/mRNA expression and microRNA profiles for predicting patient survival times to The Cancer Genome Atlas (TCGA) based glioblastoma multiforme (GBM) dataset. In terms of prediction accuracy, we show that our non-linear and interaction-based integrative methods perform better than linear alternatives and non-integrative methods that do not account for interactions between the platforms. We also find several prognostic mRNAs and microRNAs that are related to tumor invasion and are known to drive tumor metastasis and severe inflammatory response in GBM. In addition, our analysis reveals several interesting mRNA and microRNA interactions that have known implications in the etiology of GBM.ConclusionsOur approach gains its flexibility and power by modeling the non-linear interaction structures between and within the platforms. Our framework is a useful tool for biomedical researchers, since clinical prediction using multi-platform genomic information is an important step towards personalized treatment of many cancers. We have a freely available software at:http://odin.mdacc.tmc.edu/~vbaladan.
Inhibition of hepatitis B virus (HBV) gene expression and replication by HBx gene silencing in a hydrodynamic injection mouse model with a new clone of HBV genotype B
Authors: Li Lei , Shen Hong , Li Anyi , Zhang Zhenhua , Wang Baoju , Wang Junzhong , Zheng Xin , Wu Jun , Yang Dongliang , Lu Mengji , Song Jingjiao 
Published: June 2013

AbstractBackgroundIt has been suggested that different hepatitis B virus (HBV) genotypes may have distinct virological characteristics that correlate with clinical outcomes during antiviral therapy and the natural course of infection. Hydrodynamic injection (HI) of HBV in the mouse model is a useful tool for study of HBV replicationin vivo. However, only HBV genotype A has been used for studies with HI.MethodsWe constructed 3 replication-competent clones containing 1.1, 1.2 and 1.3 fold overlength of a HBV genotype B genome and tested them bothin vitroandin vivo. Moreover, A HBV genotype B clone based on the pAAV-MCS vector was constructed with the 1.3 fold HBV genome, resulting in the plasmid pAAV-HBV1.3Band tested by HI in C57BL/6 mice. Application of siRNA againstHBxgene was tested in HBV genotype B HI mouse model.ResultsThe 1.3 fold HBV clone showed higher replication and gene expression than the 1.1 and 1.2 fold HBV clones. Compared with pAAV-HBV1.2 (genotype A), the mice HI with pAAV-HBV1.3Bshowed higher HBsAg and HBeAg expression as well as HBV DNA replication level but a higher clearance rate. Application of two plasmids pSB-HBxi285 and pSR-HBxi285 expressing a small/short interfering RNA (siRNA) to theHBxgene in HBV genotype B HI mouse model, leading to an inhibition of HBV gene expression and replication. However, HBV gene expression may resume in some mice despite an initial delay, suggesting that transient suppression of HBV replication by siRNA may be insufficient to prevent viral spread, particularly if the gene silencing is not highly effective.ConclusionsTaken together, the HI mouse model with a HBV genotype B genome was successfully established and showed different characteristicsin vivocompared with the genotype A genome. The effectiveness of gene silencing againstHBxgene determines whether HBV replication may be sustainably inhibited by siRNAin vivo.
Characterization of Farmington virus, a novel virus from birds that is distantly related to members of the family Rhabdoviridae
Authors: Palacios Gustavo , Forrester Naomi L , Savji Nazir , Travassos da Rosa Amelia P A , Guzman Hilda , DeToy Kelly , Popov Vsevolod L , Walker Peter J , Lipkin W Ian , Vasilakis Nikos , Tesh Robert B 
Published: July 2013

Abstract

Background
Farmington virus (FARV) is a rhabdovirus that was isolated from a wild bird during an outbreak of epizootic eastern equine encephalitis on a pheasant farm in Connecticut, USA.

Findings
Analysis of the nearly complete genome sequence of the prototype CT AN 114 strain indicates that it encodes the five canonical rhabdovirus structural proteins (N, P, M, G and L) with alternative ORFs (> 180 nt) in the N and G genes. Phenotypic and genetic characterization of FARV has confirmed that it is a novel rhabdovirus and probably represents a new species within the family Rhabdoviridae.

Conclusions
In sum, our analysis indicates that FARV represents a new species within the family Rhabdoviridae.