bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient and scalable multiprocessor fair scheduling using distributed weighted round-robin
Authors: Li Tong , Baumberger Dan , Hahn Scott
Published: August 2009

Fairness is an essential requirement of any operating system scheduler. Unfortunately, existing fair scheduling algorithms are either inaccurate or inefficient and non-scalable for multiprocessors. This problem is becoming increasingly severe as the hardware industry continues to produce larger scale multi-core processors. This paper presents
Distributed Weighted Round-Robin
(DWRR), a new scheduling algorithm that solves this problem. With distributed thread queues and small additional overhead to the underlying scheduler, DWRR achieves high efficiency and scalability. Besides conventional priorities, DWRR enables users to specify weights to threads and achieve accurate proportional CPU sharing with constant error bounds. DWRR operates in concert with existing scheduler policies targeting other system attributes, such as latency and throughput. As a result, it provides a practical solution for various production OSes. To demonstrate the versatility of DWRR,we have implemented it in Linux kernels 2.6.22.15 and 2.6.24, which represent two vastly different scheduler designs. Our evaluation shows that DWRR achieves accurate proportional fairness and high performance for a diverse set of workloads.
Opportunities beyond single-core microprocessors
Authors: Hill Mark D.
Published: August 2009

Designers of future hardware and software face many challenges. Performance scaling of sequential cores is not what it once was. The best architectures for many cores, or equivalents, are not clear. Software, especially on clients, does not make abundant parallelism clear. Computer use and disposal is not so green. Smarter phones must not burn your pocket. Transistors and wires are getting less reliable. CMOS may run out of steam for technical or economic reasons. And the list goes on.

But in challenges, optimists find opportunities. This panel will be about opportunities. I have invited experts with experience in academia, industry, and government to discuss the great possibilities ahead. I have asked them to identify two or three topics, where, at most, one is part of their current work. Then we will have a discussion.
Solving dense linear systems on platforms with multiple hardware accelerators
Authors: Quintana-Ortí Gregorio , Igual Francisco D. , Quintana-Ortí Enrique S. , van de Geijn Robert A.
Published: August 2009

In a previous PPoPP paper we showed how the FLAME methodology, combined with the SuperMatrix runtime system, yields a simple yet powerful solution for programming dense linear algebra operations on multicore platforms. In this paper we provide further evidence that this approach solves the programmability problem for this domain by targeting a more complex architecture, composed of a multicore processor and multiple hardware accelerators (GPUs, Cell B.E., etc.), each with its own local memory, resulting in a platform more reminiscent of a heterogeneous distributed-memory system. In particular, we show that the FLAME programming model accommodates this new situation effortlessly so that no significant change needs to be made to the codebase. All complexity is hidden inside the SuperMatrix runtime scheduling mechanism, which incorporates software implementations of standard cache/memory coherence techniques in computer architecture to improve the performance. Our experimental evaluation on a Intel Xeon 8-core host linked to an NVIDIA Tesla S870 platform with four GPUs delivers peak performances around 550 and 450 (single-precision) GFLOPS for the matrix-matrix product and the Cholesky factorization, respectively, which we believe to be the best performance numbers posted on this new architecture for such operations.
A comprehensive strategy for contention management in software transactional memory
Authors: Spear Michael F. , Dalessandro Luke , Marathe Virendra J. , Scott Michael L.
Published: August 2009

In Software Transactional Memory (STM),
contention management
refers to the mechanisms used to ensure forward progress--to avoid livelock and starvation, and to promote throughput and fairness. Unfortunately, most past approaches to contention management were designed for obstruction-free STM frameworks, and impose significant constant-time overheads. Priority-based approaches in particular typically require that reads be visible to all transactions, an expensive property that is not easy to support in most STM systems.

In this paper we present a comprehensive strategy for contention management via fair resolution of conflicts in an STM with invisible reads. Our strategy depends on (1) lazy acquisition of ownership, (2) extendable timestamps, and (3) an efficient way to capture both priority and conflicts. We introduce two mechanisms--one using Bloom filters, the other using
visible read bits
--that implement point (3). These mechanisms unify the notions of conflict resolution,
inevitability
, and
transaction retry
. They are orthogonal to the rest of the contention management strategy, and could be used in a wide variety of hardware and software TM systems. Experimental evaluation demonstrates that the overhead of the mechanisms is low, particularly when conflicts are rare, and that our strategy as a whole provides good throughput and fairness, including livelock and starvation freedom, even for challenging workloads.
Safe open-nested transactions through ownership
Authors: Agrawal Kunal , Lee I-Ting Angelina , Sukha Jim
Published: August 2009

Researchers in transactional memory (TM) have proposed open nesting as a methodology for increasing the concurrency of transactional programs. The idea is to ignore ``low-level'' memory operations of an open-nested transaction when detecting conflicts for its parent transaction, and instead perform abstract concurrency control for the ``high-level'' operation that the nested transaction represents. To support this methodology, TM systems use an open-nested commit mechanism that commits all changes performed by an open-nested transaction directly to memory, thereby avoiding low-level conflicts. Unfortunately, because the TM runtime is unaware of the different levels of memory, unconstrained use of open-nested commits can lead to anomalous program behavior.

We describe the framework of

ownership-aware transactional memory

which incorporates the notion of modules into the TM system and requires that transactions and data be associated with specific

transactional modules

or Xmodules. We propose a new

ownership-aware commit mechanism

, a hybrid between an open-nested and closed-nested commit which commits a piece of data differently depending on which Xmodule owns the data. Moreover, we provide a set of precise constraints on interactions and sharing of data among the Xmodules based on familiar notions of abstraction. The ownership-aware commit mechanism and these restrictions on Xmodules allow us to prove that ownership-aware TM has clean memory-level semantics. In particular, it guarantees

serializability by modules

, an adaptation of the definition of multilevel serializability from database systems. In addition, we describe how a programmer can specify Xmodules and ownership in a Java-like language. Our type system can enforce most of the constraints required by ownership-aware TM statically, and can enforce the remaining constraints dynamically. Finally, we prove that if transactions in the process of aborting obey restrictions on their memory footprint, then ownership-aware TM is free from

semantic deadlock

.
Techniques for efficient placement of synchronization primitives
Authors: Nicolau Alexandru , Li Guangqiang , Kejariwal Arun
Published: August 2009

Harnessing the hardware parallelism of the emerging multi-cores systems necessitates concurrent software. Unfortunately, most of the existing mainstream software is sequential in nature. Although one could auto-parallelize a given program, the efficacy of this is largely limited to floating-point codes. One of the ways to alleviate the above limitation is to parallelize programs, which cannot be auto-parallelized, via explicit synchronization. In this regard, efficient placement of the synchronization primitives - say, post, wait - plays a key role in achieving high degree of thread-level parallelism (
TLP
). In this paper, we propose novel compiler techniques for the above. Specifically, given a control flow graph (
CFG
), the proposed techniques place a post as early as possible and place a wait as late as possible in the CFG, subject to dependences. We demonstrate the efficacy of our techniques, on a real machine, using real codes, specifically, from the industry-standard SPEC CPU benchmarks, the Linux kernel and other widely used open source codes. Our results show that the proposed techniques yield significantly higher levels of TLP than the state-of-the-art.
A compiler-directed data prefetching scheme for chip multiprocessors
Authors: Son Seung Woo , Kandemir Mahmut , Karakoy Mustafa , Chakrabarti Dhruva
Published: August 2009

Data prefetching has been widely used in the past as a technique for hiding memory access latencies. However, data prefetching in multi-threaded applications running on chip multiprocessors (CMPs) can be problematic when multiple cores compete for a shared on-chip cache (L2 or L3). In this paper, we (i) quantify the impact of conventional data prefetching on shared caches in CMPs. The experimental data collected using multi-threaded applications indicates that, while data prefetching improves performance in small number of cores, its benefits reduce significantly as the number of cores is increased, that is, it is not scalable; (ii) identify harmful prefetches as one of the main contributors for degraded performance with a large number of cores; and (iii) propose and evaluate a compiler-directed data prefetching scheme for shared on-chip cache based CMPs. The proposed scheme first identifies program phases using static compiler analysis, and then divides the threads into groups within each phase and assigns a customized prefetcher thread (helper thread) to each group of threads. This helps to reduce the total number of prefetches issued, prefetch overheads, and negative interactions on the shared cache space due to data prefetches, and more importantly, makes compiler-directed prefetching a scalable optimization for CMPs. Our experiments with the applications from the SPEC OMP benchmark suite indicate that the proposed scheme improves overall parallel execution latency by 18.3% over the no-prefetch case and 6.4% over the conventional data prefetching scheme (where each core prefetches its data independently), on average, when 12 cores are used. The corresponding average performance improvements with 24 cores are 16.4% (over the no-prefetch case) and 11.7% (over the conventional prefetching case). We also demonstrate that the proposed scheme is robust under a wide range of values of our major simulation parameters, and the improvements it achieves come very close to those that can be achieved using an optimal scheme.
Effective performance measurement and analysis of multithreaded applications
Authors: Tallent Nathan R. , Mellor-Crummey John M.
Published: August 2009

Understanding why the performance of a multithreaded program does not improve linearly with the number of cores in a shared-memory node populated with one or more multicore processors is a problem of growing practical importance. This paper makes three contributions to performance analysis of multithreaded programs. First, we describe how to measure and attribute
parallel idleness
, namely, where threads are stalled and unable to work. This technique applies broadly to programming models ranging from explicit threading (
e.g.
, Pthreads) to higher-level models such as Cilk and OpenMP. Second, we describe how to measure and attribute
parallel overhead
-- when a thread is performing miscellaneous work other than executing the user's computation. By employing a combination of compiler support and post-mortem analysis, we incur no measurement cost beyond normal profiling to glean this information. Using
idleness
and
overhead
metrics enables one to pinpoint areas of an application where concurrency should be increased (to reduce idleness), decreased (to reduce overhead), or where the present parallelization is hopeless (where idleness and overhead are both high). Third, we describe how to measure and attribute arbitrary performance metrics for high-level multithreaded programming models, such as Cilk. This requires bridging the gap between the expression of logical concurrency in programs and its realization at run-time as it is adaptively partitioned and scheduled onto a pool of threads. We have prototyped these ideas in the context of Rice University's HPCToolkit performance tools. We describe our approach, implementation, and experiences applying this approach to measure and attribute work, idleness, and overhead in executions of Cilk programs.
Petascale computing with accelerators
Authors: Kistler Michael , Gunnels John , Brokenshire Daniel , Benton Brad
Published: August 2009

A trend is developing in high performance computing in which commodity processors are coupled to various types of computational accelerators. Such systems are commonly called hybrid systems. In this paper, we describe our experience developing an implementation of the Linpack benchmark for a petascale hybrid system, the LANL Roadrunner cluster built by IBM for Los Alamos National Laboratory. This system combines traditional x86-64 host processors with IBM PowerXCell™" 8i1 accelerator processors. The implementation of Linpack we developed was the first to achieve a performance result in excess of 1.0 PFLOPS, and made Roadrunner the #1 system on the Top500 list in June 2008. We describe the design and implementation of hybrid Linpack, including the special optimizations we developed for this hybrid architecture. We then present actual results for single node and multi-node executions. From this work, we conclude that it is possible to achieve high performance for certain applications on hybrid architectures when careful attention is given to efficient use of memory bandwidth, scheduling of data movement between the host and accelerator memories, and proper distribution of work between the host and accelerator processors.
Efficient, portable implementation of asynchronous multi-place programs
Authors: Bikshandi Ganesh , Castanos Jose G. , Kodali Sreedhar B. , Nandivada V. Krishna , Peshansky Igor , Saraswat Vijay A. , Sur Sayantan , Varma Pradeep , Wen Tong
Published: August 2009

The X10 programming language is organized around the notion of places (an encapsulation of data and activities operating on the data), partitioned global address space (PGAS), and asynchronous computation and communication.

This paper introduces an expressive subset of X10, Flat X10, designed to permit efficient execution across multiple single-threaded places with a simple runtime and without compromising on the productivity of X10. We present the design, implementation and evaluation of a compiler and runtime system for Flat X10. The Flat X10 compiler translates programs into C++ SPMD programs communicating using an active messaging infrastructure. It uses novel techniques to transform explicitly parallel programs into SPMD programs. The runtime system is based on IBM's LAPI (Low-level API) and is easily portable to other libraries such as GASNet and ARMCI.

Our implementation realizes performance comparable to hand-written MPI programs for well-known HPC benchmarks such as Random Access, Stream, and FFT, on a Federation-based cluster of Power5 SMPs (with hundreds of processors) and the Blue Gene (with thousands of processors). Submissions based on the work presented in this paper were co-winners of the 2007 and 2008 HPC Challenge Type II Awards.
A compiler and runtime system for enabling data mining applications on gpus
Authors: Ma Wenjing , Agrawal Gagan
Published: August 2009

With increasing need for accelerating data mining and scientific data analysis on large data sets, and less chance to improve processor performance by simply increasing clock frequencies, multi-core architectures and accelerators like FPGAs and GPUs have become popular. A recent development in using GPU for general computing has been the release of CUDA (Compute Unified Device Architecture) by NVIDIA. CUDA allows GPU programming with Clanguage-like features, thus easing the development of non-graphics applications on a GPU. However, several challenges still remain in programming the GPUs with CUDA, because CUDA involves explicit parallel programming and management of its complex memory hierarchy, as well as allocating device memory, moving data between CPU anddevice memory, and specification of thread grid configurations.

In this paper, we offer a solution for the programmers to generate CUDA code by specifying the sequential reduction loop(s) with some information about the parameters. With program analysis and code generation, the applications are mapped to a GPU. Several additional optimizations are also performed by the middleware.

We have evaluated our system using three popular data miningapplications, k-means clustering, EM clustering, and Principal Component Analysis (PCA). The speedup that each of these applications achieve over a sequential CPU version ranges between 20 and 50.
A tunable holistic resiliency approach for high-performance computing systems
Authors: Scott Stephen L. , Engelmann Christian , Vallée Geoffroy R. , Naughton Thomas , Tikotekar Anand , Ostrouchov George , Leangsuksun Chokchai , Naksinehaboon Nichamon , Nassar Raja , Paun Mihaela , Mueller Frank , Wang Chao , Nagarajan Arun B. , Varma Jyothish
Published: August 2009

In order to address anticipated high failure rates, resiliency characteristics have become an urgent priority for next-generation extreme-scale high-performance computing (HPC) systems. This poster describes our past and ongoing efforts in novel fault resilience technologies for HPC. Presented work includes proactive fault resilience techniques, system and application reliability models and analyses, failure prediction, transparent process- and virtual-machine-level migration, and trade-off models for combining preemptive migration with checkpoint/restart. This poster summarizes our work and puts all individual technologies into context with a proposed holistic fault resilience framework.
Turbocharging boosted transactions or
Authors: Kulkarni Chinmay Eishan , Unsal Osman , Cristal Adrián , Ayguadé Eduard , Valero Mateo
Published: August 2009

Boosted transactions offer an attractive method that enables programmers to create larger transactions that scale well and offer deadlock-free guarantees. However, as boosted transactions get larger, they become more susceptible to conflicts and aborts. We describe a linear-time algorithm to detect transactions that cannot make progress,
which
transactions need to be aborted, and
when
. The algorithm guarantees zero false positives with minimal aborts. Our proposals, as implemented in DSTM2, increase the transactional throughput of the system, often by more than 30%.
Mechanism of Auxin-Regulated Gene Expression in Plants
Authors: Chapman Elisabeth J. , Estelle Mark
Published: August 2009

Plant hormones control most aspects of the plant life cycle by regulating genome expression. Expression of auxin-responsive genes involves interactions among auxin-responsive DNA sequence elements, transcription factors and trans-acting transcriptional repressors. Transcriptional output from these auxin signaling complexes is regulated by proteasome-mediated degradation that is triggered by interaction with auxin receptor-E3 ubiquitin ligases such SCFTIR1. Auxin signaling components are conserved throughout land plant evolution and have proliferated and specialized to control specific developmental processes.
Learning and Equilibrium
Authors: Fudenberg Drew , Levine David K.
Published: August 2009

The theory of learning in games explores how, which, and what kind of equilibria might arise as a consequence of a long-run nonequilibrium process of learning, adaptation, and/or imitation. If agents' strategies are completely observed at the end of each round (and agents are randomly matched with a series of anonymous opponents), fairly simple rules perform well in terms of the agent's worst-case payoffs, and also guarantee that any steady state of the system must correspond to an equilibrium. If players do not observe the strategies chosen by their opponents (as in extensive-form games), then learning is consistent with steady states that are not Nash equilibria because players can maintain incorrect beliefs about off-path play. Beliefs can also be incorrect because of cognitive limitations and systematic inferential errors.
Melatonin protects against heart ischemia-reperfusion injury by inhibiting mitochondrial permeability transition pore opening
Authors: Petrosillo Giuseppe , Colantuono Giuseppe , Moro Nicola , Ruggiero Francesca M. , Tiravanti Edy , Di Venosa Nicola , Fiore Tommaso , Paradies Giuseppe
Published: August 2009

Melatonin, a well-known antioxidant, has been shown to protect against ischemia-reperfusion myocardial damage. Mitochondrial permeability transition pore (MPTP) opening is an important event in cardiomyocyte cell death occurring during ischemia-reperfusion and therefore a possible target for cardioprotection. In the present study, we tested the hypothesis that melatonin could protect heart against ischemia-reperfusion injury by inhibiting MPTP opening. Isolated perfused rat hearts were subjected to global ischemia and reperfusion in the presence or absence of melatonin in a Langerdoff apparatus. Melatonin treatment significantly improves the functional recovery of Langerdoff hearts on reperfusion, reduces the infarct size, and decreases necrotic damage as shown by the reduced release of lactate dehydrogenase. Mitochondria isolated from melatonin-treated hearts are less sensitive than mitochondria from reperfused hearts to MPTP opening as demonstrated by their higher resistance to Ca2+. Similar results were obtained following treatment of ischemic-reperfused rat heart with cyclosporine A, a known inhibitor of MPTP opening. In addition, melatonin prevents mitochondrial NAD+release and mitochondrial cytochrome c release and, as previously shown, cardiolipin oxidation associated with ischemia-reperfusion. Together, these results demonstrate that melatonin protects heart from reperfusion injury by inhibiting MPTP opening, probably via prevention of cardiolipin peroxidation.
Partial carotid ligation is a model of acutely induced disturbed flow, leading to rapid endothelial dysfunction and atherosclerosis
Authors: Nam Douglas , Ni Chih-Wen , Rezvan Amir , Suo Jin , Budzyn Klaudia , Llanos Alexander , Harrison David , Giddens Don , Jo Hanjoong
Published: August 2009

Atherosclerosis is closely associated with disturbed flow characterized by low and oscillatory shear stress, but studies directly linking disturbed flow to atherogenesis is lacking. The major reason for this has been a lack of an animal model in which disturbed flow can be acutely induced and cause atherosclerosis. Here, we characterize partial carotid ligation as a model of disturbed flow with characteristics of low and oscillatory wall shear stress. We also describe a method of isolating intimal RNA in sufficient quantity from mouse carotid arteries. Using this model and method, we found that partial ligation causes upregulation of proatherogenic genes, downregulation of antiatherogenic genes, endothelial dysfunction, and rapid atherosclerosis in 2 wk in a p47phox-dependent manner and advanced lesions by 4 wk. We found that partial ligation results in endothelial dysfunction, rapid atherosclerosis, and advanced lesion development in a physiologically relevant model of disturbed flow. It also allows for easy and rapid intimal RNA isolation. This novel model and method could be used for genome-wide studies to determine molecular mechanisms underlying flow-dependent regulation of vascular biology and diseases.
PI3K, Rho, and ROCK play a key role in hypoxia-induced ATP release and ATP-stimulated angiogenic responses in pulmonary artery vasa vasorum endothelial cells
Authors: Woodward Heather N. , Anwar Adil , Riddle Suzette , Taraseviciene-Stewart Laimute , Fragoso Miguel , Stenmark Kurt R. , Gerasimovskaya Evgenia V.
Published: August 2009

We recently reported that vasa vasorum expansion occurs in the pulmonary artery (PA) adventitia of chronically hypoxic animals and that extracellular ATP is a pro-angiogenic factor for isolated vasa vasorum endothelial cells (VVEC). However, the sources of extracellular ATP in the PA vascular wall, as well as the molecular mechanisms underlying its release, remain elusive. Studies were undertaken to explore whether VVEC release ATP in response to hypoxia and to determine signaling pathways involved in this process. We found that hypoxia (1–3% O2) resulted in time- and O2-dependent ATP release from VVEC. Preincubation with the inhibitors of vesicular transport (monensin, brefeldin A, and N-ethylmaleimide) significantly decreased ATP accumulation in the VVEC conditioned media, suggesting that hypoxia-induced ATP release occurs through vesicular exocytosis. Additionally, both hypoxia and exogenously added ATP resulted in the activation of PI3K and accumulation of GTP-bound RhoA in a time-dependent manner. Pharmacological inhibition of PI3K and ROCK or knockout of RhoA by small interfering RNA significantly abolished hypoxia-induced ATP release from VVEC. Moreover, RhoA and ROCK play a critical role in ATP-induced increases in VVEC DNA synthesis, migration, and tube formation, indicating a functional contribution of PI3K, Rho, and ROCK to both the autocrine mechanism of ATP release and ATP-mediated angiogenic activation of VVEC. Taken together, our findings provide novel evidence for the signaling mechanisms that link hypoxia-induced increases in extracellular ATP and vasa vasorum expansion.
Characteristics of Cl− uptake in rat alveolar type I cells
Authors: Johnson Meshell , Allen Lennell , Dobbs Leland
Published: August 2009

Although Cl− transport in fetal lung is important for fluid secretion and normal lung development, the role of Cl− transport in adult lung is not well understood. In physiological studies, the cystic fibrosis transmembrane regulator (CFTR) plays a role in fluid absorption in the distal air spaces of adult lung, and alveolar type II cells cultured for 5 days have the capacity to transport Cl−. Although both alveolar type I and type II cells express CFTR, it has previously not been known whether type I cells transport Cl−. We studied Cl− uptake in isolated type I cells directly, using either radioisotopic tracers or halide-sensitive fluorescent indicators. By both methods, type I cells take up Cl−. In the presence of β-adrenergic agonist stimulation, Cl− uptake can be inhibited by CFTR antagonists. Type I cells express both the Cl−/HCO3− anion exchanger AE2 and the voltage-gated Cl− channels CLC5 and CLC2. Inhibitors of AE2 also block Cl− uptake in type I cells. Together, these results demonstrate that type I cells are capable of Cl− uptake and suggest that the effects seen in whole lung studies establishing the importance of Cl− movement in alveolar fluid clearance may be, in part, the result of Cl− transport across type I cells.
Characterization of PEBBLEs as a Tool for Real‐Time Measurement of Dictyostelium discoideum Endosomal pH
Authors: Moding Everett , Hellyer Jessica , Rank Kevin , Lostroh Phoebe , Brasuel Murphy
Published: August 2009

The measurement of intracellular ion concentration change is important for understanding the cellular mechanisms for communication. Recently developed nanosensors, (Photonic Explorers for Biomedical use with Biologically Localized Embedding) PEBBLEs, have a number of advantages for measuring ions in cells over established methods using microelectrodes, unbound fluorescent dyes, or NMR. PEBBLE sensors have been shown to work in principle for measuring dynamic ion changes, but few in vivo applications have been demonstrated. We modified the protocol for the fabrication of pH sensing PEBBLEs and developed a protocol for the utilization of these sensors for the monitoring of dynamic pH changes in the endosomes of slime mold Dictyostelium discoideum (D. discoideum). Oregon Green 514‐CdSe Quantum Dot PEBBLEs were used to measure real‐time pH inside D. discoideum endosomes during cAMP stimulation. Endosomal pH was shown to decrease during cAMP signaling, demonstrating a movement of protons into the endosomes of D. discoideum amoebae.
Solitary Fibrous Tumor Arising from the Sphenoid Sinus
Authors: Takasaki Kenji , Watanabe Takeshi , Hayashi Tomayoshi , Kinoshita Naoe , Kumagami Hidetaka , Takahashi Haruo
Published: August 2009

Solitary fibrous tumor (SFT) is an uncommon neoplasm that usually arises from the pleura. To our knowledge, only 30 cases of SFTs in the nasal cavity and paranasal sinuses have been reported in the literature. We describe an SFT that arose from the right sphenoid sinus and extended to the nasal cavity and epipharynx. The tumor was completely removed by endoscopic sinus surgery without complication. The patient is taking an uneventful course without any evidence of recurrence of the disease 8 months after surgery now.
Equilibrium and Kinetic Investigations of the Interaction of Model Platinum(II) Complex with DNA Constituents in Reference to the Antitumour Activity: Complex‐Formation Reactions of [Pd(N,N‐diethylethylenediamine)(H2O)2]2+ with Ligands of Biological Significance and Displacement Reactions of DNA Constituents
Authors: Shoukry Eman Mohamed
Published: August 2009

The [Pd(DEEN)Cl2] and [Pt(DEEN)Cl2] complexes were synthesized and characterized where DEEN = N,N‐diethylethylenediamine. The stoichiometry and stability of the complexes formed between various biologically relevant ligands (amino acids, peptides, DNA constituents and dicarboxylic acids) and were investigated at 37∘C and 0.16 M ionic strength. The stability constant of the complexes formed in solution were determined and the binding centres of the ligands were assigned. The concentration distribution diagrams of the complexes were evaluated The equilibrium constants for the displacement of representative coordinated ligands such as inosine, glycine or methionine by cysteine were calculated and the concentration distribution diagrams of the various species were evaluated. The kinetics of base hydrolysis of free and coordinated S‐methylcysteine methyl ester was investigated. The mechanism of hydrolysis was discussed.
(a, k)‐Regularized C‐Resolvent Families: Regularity and Local Properties
Authors: Kostić Marko
Published: August 2009

We introduce the class of (local) (a, k)‐regularized C‐resolvent families and
discuss its basic structural properties. In particular, our analysis covers subjects
like regularity, perturbations, duality, spectral properties and subordination
principles. We apply our results in the study of the backwards fractional
diffusion‐wave equation and provide several illustrative examples of differentiable
(a, k)‐regularized C‐resolvent families.
The 200 Year Continuum
Authors: Kerrigan Christian
Published: August 2009

The 200 Year Continuum is the producer, recorder, and exhibitor in Christian Kerrigan's advancing anthology of narratives. Central to Kerrigan's practice is storytelling and mythmaking as a means of engaging his audience. Kerrigan uses drawing as his primary mode of research into these narratives, which are consequently offered in the form of live internet-feed installations acting as ecological sites, scientific experiments introducing new organic technologies, and digital images of worlds unseen. Each addition acts as a “middle story” within The 200 Year Continuum. In his narrative, The Amber Clock, a ship is grown in the yew forest of Kingley Vale over a period of 200 years. The narrative explores the possibilities of time in relationship to technology and the natural world. In his narrative, artificial and wild systems are choreographed, and the natural production of resin is harvested from the yew trees as a way of measuring time.
MobiSpray: Mobile Phone as Virtual Spray Can for Painting BIG Anytime Anywhere on Anything
Authors: Scheible Jürgen , Ojala Timo
Published: August 2009

This paper presents MobiSpray, a novel interactive art tool for creating ubiquitous ephemeral digital art. The mobile phone is employed as a virtual spray can to spray dabs of digital paint onto the physical environment via large-scale projections. The gesture-based control of the mobile phone provides a natural pointing mechanism for the virtual spray can. Experiences from extensive field use around the world testify in favor of a successful design. Most importantly, MobiSpray liberates and empowers the artist to change the environment via large-scale artistic expressions.
A New System to Appreciate the Visual Characteristics of a Painting
Authors: Miyashita Tsutomu
Published: August 2009

A painting-viewing system is proposed as a tool to help painting appreciation and to improve the museum experience. This system simultaneously highlights certain visual characteristics of multiple paintings, thus informing users of the links between paintings and the semantic elements that may appear superficially different, and also conveying the art-historical explanation of those characteristics. Through this system's evaluation, the approach based on “the awareness of the visual characteristics” may be effective as a method of developing the user's interest in the paintings. When this system is placed in museums and galleries as a mediation tool, it will be useful to a viewer's preparation for the art-viewing experience. This paper presents the concepts behind the system's development and the results of the first survey as a piece of a larger project to explore the improvement of painting appreciation as a museum experience.
Partial Orders of Similarity Differences Invariant Between EEG-Recorded Brain and Perceptual Representations of Language
Authors: Suppes Patrick , Perreau-Guimaraes Marcos , Wong Dik Kin
Published: August 2009

The idea of a hierarchical structure of language constituents of phonemes, syllables, words, and sentences is robust and widely accepted. Empirical similarity differences at every level of this hierarchy have been analyzed in the form of confusion matrices for many years. By normalizing such data so that differences are represented by conditional probabilities, semiorders of similarity differences can be constructed. The intersection of two such orderings is an invariant partial ordering with respect to the two given orders. These invariant partial orderings, especially between perceptual and brain representations, but also for comparison of brain images of words generated by auditory or visual presentations, are the focus of this letter. Data from four experiments are analyzed, with some success in finding conceptually significant invariants.
Cortical Circuitry Implementing Graphical Models
Authors: Litvak Shai , Ullman Shimon
Published: August 2009

In this letter, we develop and simulate a large-scale network of spiking neurons that approximates the inference computations performed by graphical models. Unlike previous related schemes, which used sum and product operations in either the log or linear domains, the current model uses an inference scheme based on the sum and maximization operations in the log domain. Simulations show that using these operations, a large-scale circuit, which combines populations of spiking neurons as basic building blocks, is capable of finding close approximations to the full mathematical computations performed by graphical models within a few hundred milliseconds. The circuit is general in the sense that it can be wired for any graph structure, it supports multistate variables, and it uses standard leaky integrate-and-fire neuronal units. Following previous work, which proposed relations between graphical models and the large-scale cortical anatomy, we focus on the cortical microcircuitry and propose how anatomical and physiological aspects of the local circuitry may map onto elements of the graphical model implementation. We discuss in particular the roles of three major types of inhibitory neurons (small fast-spiking basket cells, large layer 2/3 basket cells, and double-bouquet neurons), subpopulations of strongly interconnected neurons with their unique connectivity patterns in different cortical layers, and the possible role of minicolumns in the realization of the population-based maximum operation.
Electrical Coupling Promotes Fidelity of Responses in the Networks of Model Neurons
Authors: Medvedev Georgi S.
Published: August 2009

We consider an integrate-and-fire element subject to randomly perturbed synaptic input and an electrically coupled ensemble of such elements. The latter is interpreted as either a model of electrically coupled population of neurons or a multicompartment model of a dendrite. Random fluctuations blur the input signal and cause false responses in the system dynamics. For instance, under the influence of noise, the system may respond with an action potential to a subthreshold stimulus. We show that the responses of the elements within the network are more reliable than the responses of the same elements in isolation. Specifically, we show that the variances of the stochastic processes generated by the coupled model can be made arbitrarily small (i.e., the network responses can be made arbitrarily accurate) by increasing the number of elements in the network and the strength of electrical coupling. Our results suggest that the organization of cells in electrically coupled groups on the network level, or the dendritic morphology on the cellular level, may be involved in the filtering noise and therefore may play an important role in the information processing mechanisms operating on the network or cellular level respectively.
Approximate Learning Algorithm in Boltzmann Machines
Authors: Yasuda Muneki , Tanaka Kazuyuki
Published: August 2009

Boltzmann machines can be regarded as Markov random fields. For binary cases, they are equivalent to the Ising spin model in statistical mechanics. Learning systems in Boltzmann machines are one of the NP-hard problems. Thus, in general we have to use approximate methods to construct practical learning algorithms in this context. In this letter, we propose new and practical learning algorithms for Boltzmann machines by using the belief propagation algorithm and the linear response approximation, which are often referred as advanced mean field methods. Finally, we show the validity of our algorithm using numerical experiments.
Is the Homunculus “Aware” of Sensory Adaptation?
Authors: Seriès Peggy , Stocker Alan A. , Simoncelli Eero P.
Published: August 2009

Neural activity and perception are both affected by sensory history. The work presented here explores the relationship between the physiological effects of adaptation and their perceptual consequences. Perception is modeled as arising from an encoder-decoder cascade, in which the encoder is defined by the probabilistic response of a population of neurons, and the decoder transforms this population activity into a perceptual estimate. Adaptation is assumed to produce changes in the encoder, and we examine the conditions under which the decoder behavior is consistent with observed perceptual effects in terms of both bias and discriminability. We show that for all decoders, discriminability is bounded from below by the inverse Fisher information. Estimation bias, on the other hand, can arise for a variety of different reasons and can range from zero to substantial. We specifically examine biases that arise when the decoder is fixed, “unaware” of the changes in the encoding population (as opposed to “aware” of the adaptation and changing accordingly). We simulate the effects of adaptation on two well-studied sensory attributes, motion direction and contrast, assuming a gain change description of encoder adaptation. Although we cannot uniquely constrain the source of decoder bias, we find for both motion and contrast that an “unaware” decoder that maximizes the likelihood of the percept given by the preadaptation encoder leads to predictions that are consistent with behavioral data. This model implies that adaptation-induced biases arise as a result of temporary suboptimality of the decoder.
The Siege of “Castle Pox”: A Medical Revolution in Marblehead, Massachusetts, 1764–1777
Authors: Wehrman Andrew M.
Published: August 2009

In January 1773 sailors and other members of Marblehead's so-called “Savage Mobility” burned down the new inoculation hospital, nicknamed “Castle Pox.” This article re-creates those explosive events, places them within the history of the American Revolution, and argues that Marblehead's people demanded equal access to medicine as well as to political rights.
“Neither Justice nor Mercy”: Public and Private Executions in Rhode Island, 1832–1833
Authors: Chambers Stephen
Published: August 2009

After the 1831 Snowtown race riots, Rhode Island held its first executions in thirty years, hanging three men within nineteen months. The same tumult of class, race, and conceptions of public space that contributed to these deaths led Rhode Island to become the first state to abolish public execution in 1833.
Catharine Beecher and the American Woman's Puritan Home
Authors: Strazdes Diana
Published: August 2009

Catharine Beecher's publications on household management, published between 1841 and 1869, offered architectural designs with a surprisingly consistent feature: they promoted the long-forgotten center-chimney New England house plan. For Beecher, that remnant of the Puritan era promised a radically new lifestyle, one that profoundly undercut the domestic social rituals of her time.
The Rise and Fall of the Province of Lygonia, 1643–1658
Authors: Farber Hannah
Published: August 2009

During the 1640s, George Cleeve and Thomas Morton carved the province of Lygonia out of Ferdinando Gorges' Maine. Cleeve believed Lygonia's legitimacy was guaranteed by its legal standing and by the authority of its Parliamentarian proprietor, but he could not stop Lygonian towns from opting to join the Massachusetts Bay Colony in 1658.
Wave Driving in the Tropical Lower Stratosphere as Simulated by WACCM. Part II: ENSO-Induced Changes for Northern Winter
Authors: Taguchi Masakazu
Published: August 2009

This study investigates ENSO-induced changes in the tropical lower stratosphere for northern winter as simulated by the Whole Atmosphere Community Climate Model (WACCM). A comparison is made between two 3650-day perpetual January experiments forced with La Niña– and El Niño–like sea surface temperature conditions over the equatorial Pacific. The present analysis includes an extension of the diagnostic framework used for the climatological annual cycle in Part I. A comprehensive description of the ENSO-induced changes, together with their heat and zonal momentum budget diagnoses, demonstrates that the changes are consistently characterized by cooling, locally accelerated Brewer–Dobson circulation (upwelling and poleward flow) and strengthened tropical/subtropical wave driving for the El Niño–like condition. The cooling broadly peaks near the equator with general hemispheric symmetry, and the strengthenings in the poleward flow and wave driving take place in both hemispheres. An important role in the strengthened wave driving is played by changes in tropical/subtropical stationary waves. The changes notably include a dumbbell-shaped height pattern over the Pacific or a modulation of equatorial Rossby waves in response to redistributed convective heating with the ENSO-like perturbation.
The Intra-Americas Springtime Sea Surface Temperature Anomaly Dipole as Fingerprint of Remote Influences
Authors: Muñoz Ernesto , Wang Chunzai , Enfield David
Published: August 2009

The influence of teleconnections on the Intra-Americas Sea (IAS; Gulf of Mexico and Caribbean Sea) has been mostly analyzed from the perspective of El Niño–Southern Oscillation (ENSO) on the Caribbean Sea (the latter being an extension of the tropical North Atlantic). This emphasis has overlooked both 1) the influence of other teleconnections on the IAS and 2) which teleconnections affect the Gulf of Mexico climate variability. In this study the different fingerprints that major teleconnection patterns have on the IAS during boreal spring are analyzed. Indices of teleconnection patterns are regressed and correlated to observations of oceanic temperature and atmospheric data from reanalyses and observational datasets. It is found that the Pacific teleconnection patterns that influence the IAS SSTs do so by affecting the Gulf of Mexico in an opposite manner to the Caribbean Sea. These analyzed Pacific climate patterns are the Pacific–North American (PNA) teleconnection, the Pacific decadal oscillation (PDO), and ENSO. The North Atlantic Oscillation (NAO) is related to a lesser degree with the north–south SST anomaly dipole than are Pacific teleconnection patterns. It is also found that the IAS influence from the midlatitude Pacific mostly affects the Gulf of Mexico, whereas the influence from the tropical Pacific mostly affects the Caribbean Sea. Therefore, the combination of a warm ENSO event and a positive PNA event induces a strong IAS SST anomaly dipole between the Gulf of Mexico and the Caribbean Sea during spring.

By calculating an index that represents the IAS SST anomaly dipole, it is found that the dipole forms mostly in response to changes in the air–sea heat fluxes. In the Gulf of Mexico the dominant mechanisms are the air–sea differences in humidity and temperature. The changes in shortwave radiation also contribute to the dipole of net air–sea heat flux. The changes in shortwave radiation arise, in part, by the cloudiness triggered by the air–sea differences in humidity, and also by the changes in the convection cell that connects the Amazon basin to the IAS. Weaker Amazon convection (e.g., in the event of a warm ENSO event) reduces the subsidence over the IAS, and henceforth the IAS cloudiness increases (and the shortwave radiation decreases). This study contributes to a greater understanding of how the IAS is influenced by different Pacific and Atlantic teleconnections.