bluuebunny/crossref_metadata_2025 huggingface dataset:
B Cells Modulate Systemic Responses to Pneumocystis murina Lung Infection and Protect On-Demand Hematopoiesis via T Cell-Independent Innate Mechanisms when Type I Interferon Signaling Is Absent
Authors: Hoyt Teri R. , Dobrinen Erin , Kochetkova Irina , Meissner Nicole
Published: December 2014

HIV infection results in a complex immunodeficiency due to loss of CD4
+
T cells, impaired type I interferon (IFN) responses, and B cell dysfunctions causing susceptibility to opportunistic infections such as
Pneumocystis murina
pneumonia and unexplained comorbidities, including bone marrow dysfunctions. Type I IFNs and B cells critically contribute to immunity to
Pneumocystis
lung infection. We recently also identified B cells as supporters of on-demand hematopoiesis following
Pneumocystis
infection that would otherwise be hampered due to systemic immune effects initiated in the context of a defective type I IFN system. While studying the role of type I IFNs in immunity to
Pneumocystis
infection, we discovered that mice lacking both lymphocytes and type I IFN receptor (IFrag
−/−
) developed progressive bone marrow failure following infection, while lymphocyte-competent type I IFN receptor-deficient mice (IFNAR
−/−
) showed transient bone marrow depression and extramedullary hematopoiesis. Lymphocyte reconstitution of lymphocyte-deficient IFrag
−/−
mice pointed to B cells as a key player in bone marrow protection. Here we define how B cells protect on-demand hematopoiesis following
Pneumocysti
s lung infection in our model. We demonstrate that adoptive transfer of B cells into IFrag
−/−
mice protects early hematopoietic progenitor activity during systemic responses to
Pneumocystis
infection, thus promoting replenishment of depleted bone marrow cells. This activity is independent of CD4
+
T cell help and B cell receptor specificity and does not require B cell migration to bone marrow. Furthermore, we show that B cells protect on-demand hematopoiesis in part by induction of interleukin-10 (IL-10)- and IL-27-mediated mechanisms. Thus, our data demonstrate an important immune modulatory role of B cells during
Pneumocystis
lung infection that complement the modulatory role of type I IFNs to prevent systemic complications.
One-Carbon Metabolic Pathway Rewiring in Escherichia coli Reveals an Evolutionary Advantage of 10-Formyltetrahydrofolate Synthetase (Fhs) in Survival under Hypoxia
Authors: Sah Shivjee , Aluri Srinivas , Rex Kervin , Varshney Umesh
Published: December 2014

In cells,N10-formyltetrahydrofolate (N10-fTHF) is required for formylation of eubacterial/organellar initiator tRNA and purine nucleotide biosynthesis. Biosynthesis ofN10-fTHF is catalyzed by 5,10-methylene-tetrahydrofolate dehydrogenase/cyclohydrolase (FolD) and/or 10-formyltetrahydrofolate synthetase (Fhs). All eubacteria possess FolD, but some possess both FolD and Fhs. However, the reasons for possessing Fhs in addition to FolD have remained unclear. We usedEscherichia coli, which naturally lacksfhs, as our model. We show that inE. coli, the essential function offolDcould be replaced byClostridium perfringensfhswhen it was provided on a medium-copy-number plasmid or integrated as a single-copy gene in the chromosome. Thefhs-supportedfolDdeletion (ΔfolD) strains grow well in a complex medium. However, these strains require purines and glycine as supplements for growth in M9 minimal medium. Thein vivolevels ofN10-fTHF in the ΔfolDstrain (supported by plasmid-bornefhs) were limiting despite the high capacity of the available Fhs to synthesizeN10-fTHFin vitro. Auxotrophy for purines could be alleviated by supplementing formate to the medium, and that for glycine was alleviated by engineering THF import into the cells. The ΔfolDstrain (harboringfhson the chromosome) showed a high NADP+-to-NADPH ratio and hypersensitivity to trimethoprim. The presence offhsinE. coliwas disadvantageous for its aerobic growth. However, under hypoxia,E. colistrains harboringfhsoutcompeted those lacking it. The computational analysis revealed a predominant natural occurrence offhsin anaerobic and facultative anaerobic bacteria.
Congenital abnormalities of the urogenital tract: the clue is in the cord?
Authors: Daoub Ahmed , Drake Thomas M
Published: December 2014

Congenital abnormalities of the female urogenital tract are not uncommon, with an estimated incidence of 2–4% across the female population. Within this population, up to 40% will have associated renal tract abnormalities. A previously well 12-year-old girl presented to the emergency department with abdominal pain, vomiting and a palpable pelvic mass. Ultrasound and MR scans were performed. The imaging revealed a didelphys uterus, an obstructed hemivagina and ipsilateral renal agenesis, characteristic of Herlyn-Werner-Wunderlich syndrome. The patient was noted at birth to have a single umbilical artery, which is associated with an increased risk of congenital abnormalities and useful information for the early identification of abnormalities that have implications for renal function and future fertility.
Examining the reliability and validity of a modified version of the International Physical Activity Questionnaire, long form (IPAQ-LF) in Nigeria: a cross-sectional study
Authors: Oyeyemi Adewale L , Bello Umar M , Philemon Saratu T , Aliyu Habeeb N , Majidadi Rebecca W , Oyeyemi Adetoyeje Y
Published: December 2014

Objectives

To investigate the reliability and an aspect of validity of a modified version of the long International Physical Activity Questionnaire (Hausa IPAQ-LF) in Nigeria.

Design

Cross-sectional study, examining the reliability and construct validity of the Hausa IPAQ-LF compared with anthropometric and biological variables.

Setting

Metropolitan Maiduguri, the capital city of Borno State in Nigeria.

Participants

180 Nigerian adults (50% women) with a mean age of 35.6 (SD=10.3) years, recruited from neighbourhoods with diverse socioeconomic status and walkability.

Outcome measures

Domains (domestic physical activity (PA), occupational PA, leisure-time PA, active transportation and sitting time) and intensities of PA (vigorous, moderate and walking) were measured with the Hausa IPAQ-LF on two different occasions, 8 days apart. Outcomes for construct validity were measured body mass index (BMI), systolic blood pressure (SBP) and diastolic blood pressure (DBP).

Results

The Hausa IPAQ-LF demonstrated good test–retest reliability (intraclass correlation coefficient, ICC>75) for total PA (ICC=0.79, 95% CI 0.65 to 0.82), occupational PA (ICC=0.77, 95% CI 0.68 to 0.82), active transportation (ICC=0.82, 95% CI 0.75 to 0.87) and vigorous intensity activities (ICC=0.82, 95% CI 0.76 to 0.87). Reliability was substantially higher for total PA (ICC=0.80), occupational PA (ICC=0.78), leisure-time PA (ICC=0.75) and active transportation (ICC=0.80) in men than in women, but domestic PA (ICC=0.38) and sitting time (ICC=0.71) demonstrated more substantial reliability coefficients in women than in men. For the construct validity, domestic PA was significantly related mainly with SBP (r=−0.27) and DBP (r=−0.17), and leisure-time PA and total PA were significantly related only with SBP (r=−0.16) and BMI (r=−0.29), respectively. Similarly, moderate-intensity PA was mainly related with SBP (r=−0.16, p<0.05) and DBP (r=−0.21, p<0.01), but vigorous-intensity PA was only related with BMI (r=−0.11, p<0.05).

Conclusions

The modified Hausa IPAQ-LF demonstrated sufficient evidence of test–retest reliability and may be valid for assessing context specific PA behaviours of adults in Nigeria.
An evaluation of factors associated with completion and benefit from pulmonary rehabilitation in COPD
Authors: Boutou Afroditi K , Tanner Rebecca J , Lord Victoria M , Hogg Lauren , Nolan Jane , Jefford Helen , Corner Evelyn J , Falzon Christine , Lee Cassandra , Garrod Rachel , Polkey Michael I , Hopkinson Nicholas S
Published: December 2014

Background

Pulmonary Rehabilitation (PR) is an important treatment for patients with chronic obstructive pulmonary disease (COPD) but it is not established whether any baseline parameter can predict response or compliance.

Aim

To identify whether baseline measures can predict who will complete the programme and who will achieve a clinically significant benefit from a Minimum Clinical Important Difference (MCID) in terms of exercise capacity and health-related quality of life (HRQoL).

Methods

Data were collected prospectively from patients with COPD at their baseline assessment for an outpatient PR programme in one of eight centres across London. ‘Completion’ was defined as attending at least 75% of the designated PR visits and return for the follow-up evaluation. The MCID for outcome measures was based on published data.

Results

787 outpatients with COPD (68.1±10.5 years old; 49.6% males) were included. Patients who completed PR (n=449, 57.1%) were significantly older with less severe airflow obstruction, lower anxiety and depression scores, less dyspnoea and better HRQoL. Only baseline CAT score (OR=0.925; 95% CI 0.879 to 0.974; p=0.003) was retained in multivariate analysis. Patients with the lowest baseline walking distance were most likely to achieve the MCID for exercise capacity. No baseline variable could independently predict achievement of an MCID in HRQoL.

Conclusions

Patients with better HRQoL are more likely to complete PR while worse baseline exercise performance makes the achievement of a positive MCID in exercise capacity more likely. However, no baseline parameter could predict who would benefit the most in terms of HRQoL.
Equipping veterinary graduates with the skills for partnership
Authors: Moffatt Colin
Published: December 2014

Companion Care's graduate programme aims to develop the business and clinical skills of vets, equipping them to become future partners, explains the group's training and development manager, Colin Moffatt
How to succeed at vet school
Authors: Davis Rachel
Published: December 2014

Rachel Davis, learning development manager at the Royal Veterinary College, describes how small changes in time management, methods of study and motivation can help to improve exam performance
On course
Authors: Wood Alex
Published: December 2014

Having recently completed the certificate in equine internal medicine, Alex Wood attended BEVA's gastroscopy CPD training day held at B&W Equine because she wanted to improve her practical skills. This is what she thought of it.
Ten‐minute chat
Authors: Bowling Peter
Published: December 2014

Peter Bowling, clinical director of the Philip Leverhulme Equine Hospital at the University of Liverpool, is an equine vet who since 2009 has been acting as an adviser to the London Organising Committee of the Olympic Games (LOCOG) in preparation for the London 2012 Olympic equestrian competitions. He has been actively involved in organising the onsite veterinary facilities and services.
New graduate's diary
Authors: Hall Jen
Published: December 2014

Jennifer Hall makes a start on her professional development phase (PDP) record and finds that some skills are dependent on the cases that are presented.
Ten‐minute chat
Authors: Parkes Rebecca
Published: December 2014

Rebecca Parkes has just returned from spending six months volunteering at Animal Care in Egypt (ACE) in Luxor. She recently ran the 19th Egyptian Half Marathon in Luxor to raise funds for an isolation facility for the charity.
Fifty years working with sheep
Authors: Lewis Chris
Published: December 2014

Chris Lewis is a private sheep veterinary adviser whose involvement with sheep began as a boy living in Kent. He is a past‐president and secretary of the Sheep Veterinary Society, and owns and runs a small flock of 35 breeding ewes producing quality lamb. Here, he reflects on his career
New graduate's diary
Authors: Hall Jen
Published: December 2014

Jen Hall recently spent a day with Jules Hudson for BBC Radio 4′s Open Country programme. She describes how it gave her the opportunity to demonstrate the importance of vets' relationships with farmers in protecting animals and the countryside.
Shear behaviour of sandy silt treated with lignosulfonate
Authors: Chen Qingsheng , Indraratna Buddhima
Published: December 2014

Chemical stabilizers (e.g., cement, lime, gypsum, and other alkaline admixtures) have been widely used to enhance the strength and compressibility properties of subgrade soils. However, traditional chemical stabilizers are not always acceptable in Australia because they often pose a threat to the surrounding environment. Moreover, traditionally treated soils usually exhibit excessive brittle behaviour, which is often undesirable for transport infrastructure such as rail embankments and airport runways. To establish an alternative stabilizer that could overcome the above problems, this note presents a series of experimental results on the use of lignosulfonate (by-product of timber and paper industry), an environmentally friendly soil stabilizer effective for treating fine sandy silt that formed the bulk of an embankment fill at Penrith, Australia. The effects of lignosulfonate treatment on the shear behaviour of treated soil, including the stress–strain relationships, and the corresponding development of excess pore pressure and volumetric responses under monotonic triaxial testing are discussed.
Decrease in lactobacilli in the intestinal microbiota of celiac children with a gluten-free diet, and selection of potentially probiotic strains
Authors: Lorenzo Pisarello María J. , Vintiñi Elisa O. , González Silvia N. , Pagani Florencia , Medina Marcela S.
Published: December 2014

The intestinal microbiota would be implicated in pathology associated with celiac disease caused by an abnormal immune system reaction against gluten present in cereal grains. The objectives of this work were to detect through basic methods the changes in the composition of the most common genera of bacteria from the intestinal microbiota of symptom-free celiac disease children with a gluten-free diet compared with healthy children from Tucumán and to select lactobacilli (Lb) strains with probiotic potential from the feces of healthy children. Results demonstrated that the feces of celiac children with a gluten-free diet showed significantly lower counts of Lb (P < 0.05) compared with healthy children, while enterobacteria tended to increase in celiac children. On the basis of these results, isolation of some Lb from the feces of healthy children was carried out. Thus, 5 Lb strains were selected because of their high resistance percentages to gastrointestinal tract conditions. In addition, their autoaggregation and hydrophobicity properties were evaluated: Lactobacillus rhamnosus (LC4) showed the highest percentage of autoaggregation while Lactobacillus paracasei (LC9) showed high hydrophobicity. Based on these results, LC4 and LC9 were selected, and their use as potential probiotic strains to improve signs and symptoms associated with celiac disease is discussed. This is the first study performed in Argentina concerning the relationship between intestinal microbiota and celiac disease in celiac children with a gluten-free diet. In addition, the development of a probiotic food addressed towards celiac patients and designed with Lb isolated from the feces of healthy children from our province represents a promising alternative to improve the quality of life of celiac patients.
Meeting student and teacher needs in computing education
Authors: Guzdial Mark
Published: December 2014

The
Communications
Web site, http://cacm.acm.org, features more than a dozen bloggers in the BLOG@CACM community. In each issue of
Communications
, we'll publish selected posts or excerpts.

twitter

Follow us on Twitter at http://twitter.com/blogCACM

http://cacm.acm.org/blogs/blog-cacm

Mark Guzdial reports on the 2014 meeting of the ACM Education Council, where updates from its global representatives led to action plans.
Hindley-milner elaboration in applicative style
Authors: Pottier François
Published: December 2014

Type inference - the problem of determining whether a program is well-typed - is well-understood. In contrast, elaboration - the task of constructing an explicitly-typed representation of the program - seems to have received relatively little attention, even though, in a non-local type inference system, it is non-trivial. We show that the constraint-based presentation of Hindley-Milner type inference can be extended to deal with elaboration, while preserving its elegance. This involves introducing a new notion of "constraint with a value", which forms an applicative functor.
X10 and APGAS at Petascale
Authors: Tardieu Olivier , Herta Benjamin , Cunningham David , Grove David , Kambadur Prabhanjan , Saraswat Vijay , Shinnar Avraham , Takeuchi Mikio , Vaziri Mandana
Published: December 2014

X10 is a high-performance, high-productivity programming language aimed at large-scale distributed and shared-memory parallel applications. It is based on the Asynchronous Partitioned Global Address Space (APGAS) programming model, supporting the same fine-grained concurrency mechanisms within and across shared-memory nodes.

We demonstrate that X10 delivers solid performance at petascale by running (weak scaling) eight application kernels on an IBM Power 775 supercomputer utilizing up to 55,680 Power7 cores (for 1.7 Pflop/s of theoretical peak performance). We detail our advances in distributed termination detection, distributed load balancing, and use of high-performance interconnects that enable X10 to scale out to tens of thousands of cores.

For the four HPC Class 2 Challenge benchmarks, X10 achieves 41% to 87% of the system's potential at scale (as measured by IBM's HPCC Class 1 optimized runs). We also implement K-Means, Smith-Waterman, Betweenness Centrality, and Unbalanced Tree Search (UTS) for geometric trees. Our UTS implementation is the first to scale to petaflop systems.
Towards fair and efficient SMP virtual machine scheduling
Authors: Rao Jia , Zhou Xiaobo
Published: December 2014

As multicore processors become prevalent in modern computer systems, there is a growing need for increasing hardware utilization and exploiting the parallelism of such platforms. With virtualization technology, hardware utilization is improved by encapsulating independent workloads into virtual machines (VMs) and consolidating them onto the same machine. SMP virtual machines have been widely adopted to exploit parallelism. For virtualized systems, such as a public cloud, fairness between tenants and the efficiency of running their applications are keys to success. However, we find that existing virtualization platforms fail to enforce fairness between VMs with different number of virtual CPUs (vCPU) that run on multiple CPUs. We attribute the unfairness to the use of per-CPU schedulers and the load imbalance on these CPUs that incur inaccurate CPU allocations. Unfortunately, existing approaches to reduce unfairness, e.g., dynamic load balancing and CPU capping, introduce significant inefficiencies to parallel workloads.

In this paper, we present Flex, a vCPU scheduling scheme that enforces fairness at VM-level and improves the efficiency of hosted parallel applications. Flex centers on two key designs: (1) dynamically adjusting vCPU weights (FlexW) on multiple CPUs to achieve VM-level fairness and (2) flexibly scheduling vCPUs (FlexS) to minimize wasted busy-waiting time. We have implemented Flex in Xen and performed comprehensive evaluations with various parallel workloads. Results show that Flex is able to achieve CPU allocations with on average no more than 5% error compared to the ideal fair allocation. Further, Flex outperforms Xen's credit scheduler and two representative co-scheduling approaches by as much as 10X for parallel applications using busy-waiting or blocking synchronization methods.
Resilient X10
Authors: Cunningham David , Grove David , Herta Benjamin , Iyengar Arun , Kawachiya Kiyokuni , Murata Hiroki , Saraswat Vijay , Takeuchi Mikio , Tardieu Olivier
Published: December 2014

Scale-out programs run on multiple processes in a cluster. In scale-out systems, processes can fail. Computations using traditional libraries such as MPI fail when any component process fails. The advent of Map Reduce, Resilient Data Sets and MillWheel has shown dramatic improvements in productivity are possible when a high-level programming framework handles scale-out and resilience automatically.

We are concerned with the development of general-purpose languages that support resilient programming. In this paper we show how the X10 language and implementation can be extended to support resilience. In Resilient X10, places may fail asynchronously, causing loss of the data and tasks at the failed place. Failure is exposed through exceptions. We identify a {\em Happens Before Invariance Principle} and require the runtime to automatically repair the global control structure of the program to maintain this principle. We show this reduces much of the burden of resilient programming. The programmer is only responsible for continuing execution with fewer computational resources and the loss of part of the heap, and can do so while taking advantage of domain knowledge.

We build a complete implementation of the language, capable of executing benchmark applications on hundreds of nodes. We describe the algorithms required to make the language runtime resilient. We then give three applications, each with a different approach to fault tolerance (replay, decimation, and domain-level checkpointing). These can be executed at scale and survive node failure. We show that for these programs the overhead of resilience is a small fraction of overall runtime by comparing to equivalent non-resilient X10 programs. On one program we show end-to-end performance of Resilient X10 is ~100x faster than Hadoop.
Leveraging hardware message passing for efficient thread synchronization
Authors: Petrović Darko , Ropars Thomas , Schiper André
Published: December 2014

As the level of parallelism in manycore processors keeps increasing, providing efficient mechanisms for thread synchronization in concurrent programs is becoming a major concern. On cache-coherent shared-memory processors, synchronization efficiency is ultimately limited by the performance of the underlying cache coherence protocol. This paper studies how hardware support for message passing can improve synchronization performance. Considering the ubiquitous problem of mutual exclusion, we adapt two state-of-the-art solutions used on shared-memory processors, namely the server approach and the combining approach, to leverage the potential of hardware message passing. We propose HybComb, a novel combining algorithm that uses both message passing and shared memory features of emerging hybrid processors. We also introduce MP-Server, a straightforward adaptation of the server approach to hardware message passing. Evaluation on Tilera's TILE-Gx processor shows that MP-Server can execute contended critical sections with unprecedented throughput, as stalls related to cache coherence are removed from the critical path. HybComb can achieve comparable performance, while avoiding the need to dedicate server cores. Consequently, our queue and stack implementations, based on MP-Server and HybComb, largely outperform their most efficient pure-shared-memory counterparts.
A decomposition for in-place matrix transposition
Authors: Catanzaro Bryan , Keller Alexander , Garland Michael
Published: December 2014

We describe a decomposition for in-place matrix transposition, with applications to Array of Structures memory accesses on SIMD processors. Traditional approaches to in-place matrix transposition involve cycle following, which is difficult to parallelize, and on matrices of dimension m by n require O(mn log mn) work when limited to less than O(mn) auxiliary space. Our decomposition allows the rows and columns to be operated on independently during in-place transposition, reducing work complexity to O(mn), given O(max(m, n)) auxiliary space. This decomposition leads to an efficient and naturally parallel algorithm: we have measured median throughput of 19.5 GB/s on an NVIDIA Tesla K20c processor. An implementation specialized for the skinny matrices that arise when converting Arrays of Structures to Structures of Arrays yields median throughput of 34.3 GB/s, and a maximum throughput of 51 GB/s.

Because of the simple structure of this algorithm, it is particularly suited for implementation using SIMD instructions to transpose the small arrays that arise when SIMD processors load from or store to Arrays of Structures. Using this algorithm to cooperatively perform accesses to Arrays of Structures, we measure 180 GB/s throughput on the K20c, which is up to 45 times faster than compiler-generated Array of Structures accesses.

In this paper, we explain the algorithm, prove its correctness and complexity, and explain how it can be instantiated efficiently for solving various transpose problems on both CPUs and GPUs.
CUDA-NP
Authors: Yang Yi , Zhou Huiyang
Published: December 2014

Parallel programs consist of series of code sections with different thread-level parallelism (TLP). As a result, it is rather common that a thread in a parallel program, such as a GPU kernel in CUDA programs, still contains both se-quential code and parallel loops. In order to leverage such parallel loops, the latest Nvidia Kepler architecture intro-duces dynamic parallelism, which allows a GPU thread to start another GPU kernel, thereby reducing the overhead of launching kernels from a CPU. However, with dynamic parallelism, a parent thread can only communicate with its child threads through global memory and the overhead of launching GPU kernels is non-trivial even within GPUs. In this paper, we first study a set of GPGPU benchmarks that contain parallel loops, and highlight that these bench-marks do not have a very high loop count or high degrees of TLP. Consequently, the benefits of leveraging such par-allel loops using dynamic parallelism are too limited to offset its overhead. We then present our proposed solution to exploit nested parallelism in CUDA, referred to as CUDA-NP. With CUDA-NP, we initially enable a high number of threads when a GPU program starts, and use control flow to activate different numbers of threads for different code sections. We implemented our proposed CUDA-NP framework using a directive-based compiler approach. For a GPU kernel, an application developer only needs to add OpenMP-like pragmas for parallelizable code sections. Then, our CUDA-NP compiler automatically gen-erates the optimized GPU kernels. It supports both the reduction and the scan primitives, explores different ways to distribute parallel loop iterations into threads, and effi-ciently manages on-chip resource. Our experiments show that for a set of GPGPU benchmarks, which have already been optimized and contain nested parallelism, our pro-posed CUDA-NP framework further improves the perfor-mance by up to 6.69 times and 2.18 times on average.
Fast concurrent lock-free binary search trees
Authors: Natarajan Aravind , Mittal Neeraj
Published: December 2014

We present a new
lock-free
algorithm for concurrent manipulation of a binary search tree in an asynchronous shared memory system that supports search, insert and delete operations. In addition to read and write instructions, our algorithm uses (single-word) compare-and-swap (CAS) and bit-test-and-set (SETB) atomic instructions, both of which are commonly supported by many modern processors including Intel~64 and AMD64.

In contrast to existing lock-free algorithms for a binary search tree, our algorithm is based on marking
edges
rather than nodes. As a result, when compared to other lock-free algorithms, modify (insert and delete) operations in our algorithm work on a smaller portion of the tree, thereby reducing conflicts, and execute fewer atomic instructions (one for insert and three for delete). Our experiments indicate that our lock-free algorithm significantly outperforms all other algorithms for a concurrent binary search tree in many cases, especially when contention is high, by as much as 100%.
A practical wait-free simulation for lock-free data structures
Authors: Timnat Shahar , Petrank Erez
Published: December 2014

Lock-free data structures guarantee overall system progress, whereas wait-free data structures guarantee the progress of each and every thread, providing the desirable non-starvation guarantee for concurrent data structures. While practical lock-free implementations are known for various data structures, wait-free data structure designs are rare. Wait-free implementations have been notoriously hard to design and often inefficient. In this work we present a transformation of lock-free algorithms to wait-free ones allowing even a non-expert to transform a lock-free data-structure into a practical wait-free one. The transformation requires that the lock-free data structure is given in a normalized form defined in this work. Using the new method, we have designed and implemented wait-free linked-list, skiplist, and tree and we measured their performance. It turns out that for all these data structures the wait-free implementations are only a few percent slower than their lock-free counterparts, while still guaranteeing non-starvation.
Parallelizing dynamic programming through rank convergence
Authors: Maleki Saeed , Musuvathi Madanlal , Mytkowicz Todd
Published: December 2014

This paper proposes an efficient parallel algorithm for an important class of dynamic programming problems that includes Viterbi, Needleman-Wunsch, Smith-Waterman, and Longest Common Subsequence. In dynamic programming, the subproblems that do not depend on each other, and thus can be computed in parallel, form stages or wavefronts. The algorithm presented in this paper provides additional parallelism allowing multiple stages to be computed in parallel despite dependences among them. The correctness and the performance of the algorithm relies on rank convergence properties of matrix multiplication in the tropical semiring, formed with plus as the multiplicative operation and max as the additive operation.

This paper demonstrates the efficiency of the parallel algorithm by showing significant speed ups on a variety of important dynamic programming problems. In particular, the parallel Viterbi decoder is up-to 24x faster (with 64 processors) than a highly optimized commercial baseline.
In-place transposition of rectangular matrices on accelerators
Authors: Sung I-Jui , Gómez-Luna Juan , González-Linares José María , Guil Nicolás , Hwu Wen-Mei W.
Published: December 2014

Matrix transposition is an important algorithmic building block for many numeric algorithms such as FFT. It has also been used to convert the storage layout of arrays. With more and more algebra libraries offloaded to GPUs, a high performance in-place transposition becomes necessary. Intuitively, in-place transposition should be a good fit for GPU architectures due to limited available on-board memory capacity and high throughput. However, direct application of CPU in-place transposition algorithms lacks the amount of parallelism and locality required by GPUs to achieve good performance. In this paper we present the first known in-place matrix transposition approach for the GPUs. Our implementation is based on a novel 3-stage transposition algorithm where each stage is performed using an elementary tiled-wise transposition. Additionally, when transposition is done as part of the memory transfer between GPU and host, our staged approach allows hiding transposition overhead by overlap with PCIe transfer. We show that the 3-stage algorithm allows larger tiles and achieves 3X speedup over a traditional 4-stage algorithm, with both algorithms based on our high-performance elementary transpositions on the GPU. We also show our proposed low-level optimizations improve the sustained throughput to more than 20 GB/s. Finally, we propose an asynchronous execution scheme that allows CPU threads to delegate in-place matrix transposition to GPU, achieving a throughput of more than 3.4 GB/s (including data transfers costs), and improving current multithreaded implementations of in-place transposition on CPU.
Infrastructure-free logging and replay of concurrent execution on multiple cores
Authors: Lee Kyu Hyung , Kim Dohyeong , Zhang Xiangyu
Published: December 2014

We develop a logging and replay technique for real concurrent execution on multiple cores. Our technique directly works on binaries and does not require any hardware or complex software infrastructure support. We focus on minimizing logging overhead as it only logs a subset of system calls and thread spawns. Replay is on a single core. During replay, our technique first tries to follow only the event order in the log. However, due to schedule differences, replay may fail. An exploration process is then triggered to search for a schedule that allows the replay to make progress. Exploration is performed within a window preceding the point of replay failure. During exploration, our technique first tries to reorder synchronized blocks. If that does not lead to progress, it further reorders shared variable accesses. The exploration is facilitated by a sophisticated caching mechanism. Our experiments on real world programs and real workload show that the proposed technique has very low logging overhead (2.6% on average) and fast schedule reconstruction.
Concurrency bug localization using shared memory access pairs
Authors: Wang Wenwen , Wu Chenggang , Yew Pen-Chung , Yuan Xiang , Wang Zhenjiang , Li Jianjun , Feng Xiaobing
Published: December 2014

Non-determinism in concurrent programs makes their debugging much more challenging than that in sequential programs. To mitigate such difficulties, we propose a new technique to automatically locate buggy shared memory accesses that triggered concurrency bugs. Compared to existing fault localization techniques that are based on empirical statistical approaches, this technique has two advantages. First, as long as enough successful runs of a concurrent program are collected, the proposed technique can locate buggy memory accesses to the shared data even with only one single failed run captured, as opposed to the need of capturing multiple failed runs in other statistical approaches. Second, the proposed technique is more precise because it considers memory accesses in those failed runs that terminate prematurely.
Task mapping stencil computations for non-contiguous allocations
Authors: Leung Vitus J. , Bunde David P. , Ebbers Jonathan , Feer Stefan P. , Price Nickolas W. , Rhodes Zachary D. , Swank Matthew
Published: December 2014

We examine task mapping algorithms for systems that allocate jobs non-contiguously. Several studies have shown that task placement affects job running time. We focus on jobs with a stencil communication pattern and use experiments on a Cray XE to evaluate novel task mapping algorithms as well as some adapted to this setting. This is done with the miniGhost miniApp which mimics the performance of CTH, a shock physics application. Our strategies improve average and single-run times by as much as 28% and 36% over a baseline strategy, respectively.
Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs
Authors: de O. Sandes Edans F. , Miranda Guillermo , Melo Alba C.M.A. , Martorell Xavier , Ayguade Eduard
Published: December 2014

This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) algorithm for megabase DNA sequences in heterogeneous multi-GPU platforms. In our strategy, the computation of a single huge SW matrix is spread over multiple GPUs, which communicate border elements to the neighbour, using a circular buffer mechanism that hides the communication overhead. We compared 4 pairs of human-chimpanzee homologous chromosomes using 2 different GPU environments, obtaining a performance of up to 140.36 GCUPS (Billion of cells processed per second) with 3 heterogeneous GPUS.
Provably good scheduling for parallel programs that use data structures through implicit batching
Authors: Agrawal Kunal , Fineman Jeremy T. , Sheridan Brendan , Sukha Jim , Utterback Robert
Published: December 2014

This poster proposes an efficient runtime scheduler that provides provable performance guarantees to parallel programs that use data structures through the use of implicit batching.
Initial study of multi-endpoint runtime for MPI+OpenMP hybrid programming model on multi-core systems
Authors: Luo Miao , Lu Xiaoyi , Hamidouche Khaled , Kandalla Krishna , Panda Dhabaleswar K.
Published: December 2014

State-of-the-art MPI libraries rely on locks to guarantee thread-safety. This discourages application developers from using multiple threads to perform MPI operations. In this paper, we propose a high performance, lock-free multi-endpoint MPI runtime, which can achieve up to 40\% improvement for point-to-point operation and one representative collective operation with minimum or no modifications to the existing applications.
Resolute
Authors: Gacek Andrew , Backes John , Cofer Darren , Slind Konrad , Whalen Mike
Published: December 2014

Arguments about the safety, security, and correctness of a complex system are often made in the form of an assurance case. An assurance case is a structured argument, often represented with a graphical interface, that presents and supports claims about a system's behavior. The argument may combine different kinds of evidence to justify its top level claim. While assurance cases deliver some level of guarantee of a system's correctness, they lack the rigor that proofs from formal methods typically provide. Furthermore, changes in the structure of a model during development may result in inconsistencies between a design and its assurance case. Our solution is a framework for automatically generating assurance cases based on 1) a system model specified in an architectural design language, 2) a set of logical rules expressed in a domain specific language that we have developed, and 3) the results of other formal analyses that have been run on the model. We argue that the rigor of these automatically generated assurance cases exceeds those of traditional assurance case arguments because of their more formal logical foundation and direct connection to the architectural model.
A framework for model checking UDP network programs with Java pathfinder
Authors: Rathje William , Richards Brad
Published: December 2014

Complex asynchronous, distributed systems could benefit significantly from model checking, but model checking programs do not natively support verification of distributed software. Several frameworks have been developed recently that apply model checking to networked software, but none of these frameworks support complete modeling of programs that use the User Datagram Protocol (UDP). This paper presents the first framework to model realistic rather than ideal UDP network operations using Java Pathfinder, and describes its use in verifying a distributed UDP-based application.
Using Intelligent Techniques in Construction Project Cost Estimation: 10-Year Survey
Authors: Elfaki Abdelrahman Osman , Alatawi Saleh , Abushandi Eyad
Published: December 2014

Cost estimation is the most important preliminary process in any construction project. Therefore, construction cost estimation has the lion’s share of the research effort in construction management. In this paper, we have analysed and studied proposals for construction cost estimation for the last 10 years. To implement this survey, we have proposed and applied a methodology that consists of two parts. The first part concerns data collection, for which we have chosen special journals as sources for the surveyed proposals. The second part concerns the analysis of the proposals. To analyse each proposal, the following four questions have been set. Which intelligent technique is used? How have data been collected? How are the results validated? And which construction cost estimation factors have been used? From the results of this survey, two main contributions have been produced. The first contribution is the defining of the research gap in this area, which has not been fully covered by previous proposals of construction cost estimation. The second contribution of this survey is the proposal and highlighting of future directions for forthcoming proposals, aimed ultimately at finding the optimal construction cost estimation. Moreover, we consider the second part of our methodology as one of our contributions in this paper. This methodology has been proposed as a standard benchmark for construction cost estimation proposals.
AC Loss Measurements of a Trapezoidal Shaped HTS Coil Using an Electrical Method
Authors: Messina G. , Morici L. , Besi Vetrella U. , Celentano G. , Marchetti M. , Viola R. , Sabatino P.
Published: December 2014

High temperature superconducting (HTS) coils of different shapes (typically circular or trapezoidal) wound on iron or ironless core are fundamental components of many superconducting electrical power devices. A 150-turn (75 turns/pancake) trapezoidal coil in double pancake configuration has been designed and realized in our laboratory of ENEA Frascati. Various epoxy resins and YBCO tapes have been tested in the temperature range room to liquid nitrogen, leading us to the choice of AmSC (American Superconductor) tape for the winding and araldite resin for the impregnation process. The trapezoidal shape has been chosen because of its suitable geometry for practical applications, the results being complementary to what was previously achieved on round shaped HTS coils. The AC transport current losses have been measured using a compensated electrical method and expressed in terms of a linearly frequency dependent resistance. A linear dependence of the losses resistance from frequency was expected and found in agreement with previous results. The current-voltage curve has been measured in zero externally applied field condition, the results being in good agreement with a numerical simulation. The magnetic field distributions, at different air gaps from coil top and zero externally applied filed condition, have been simulated and reported as well.
Separation of Methylene Blue Dye from Aqueous Solution Using Triton X-114 Surfactant
Authors: Appusamy Arunagiri , Purushothaman Prabisha , Ponnusamy Kalaichelvi , Ramalingam Anantharaj
Published: December 2014

In this study, the interaction energy between Triton X-114 surfactant + methylene blue or water and methylene blue + water was investigated using Hartree-Fock (HF) theory with 6-31G* basis set. The results of structures and interaction energies show that these complexes have good physical and chemical interactions at atom and molecular levels. However, the Triton X-114 surfactant + methylene blue complex shows stronger molecular interaction compared to other complexes systems. The order of the interaction energy is 4303.472023 (Triton X-114 surfactant + water) > -1222.962 (methylene blue + water) > -3573.28 (Triton X-114 surfactant + methylene blue) kJ·mole−1. Subsequently, the cloud point extraction was carried out for 15 ppm of methylene blue in a mixture at 313.15 and 323.15 K over the surfactant concentration range from 0.01 M to 0.1 M. From the measured data, the excess molar volume was calculated for both phases. The results show a positive deviation in the dilute phase and a negative deviation in the surfactant rich phase. It is confirmed that the interaction between Triton X-114 and methylene blue is stronger than other complex systems due to the presence of chemical and structural orientation. The concentration of dyes and surfactant in the feed mixture and temperature effect in both phases has been studied. In addition, the thermodynamics feasibility and efficiency of the process have also been investigated.
A Preliminary Appraisal of the Effect of Pumping on Seawater Intrusion and Upconing in a Small Tropical Island Using 2D Resistivity Technique
Authors: Kura Nura Umar , Ramli Mohammad Firuz , Ibrahim Shaharin , Sulaiman Wan Nor Azmin , Zaudi Muhammad Amar , Aris Ahmad Zaharin
Published: December 2014

The existing knowledge regarding seawater intrusion and particularly upconing, in which both problems are linked to pumping, entirely relies on theoretical assumptions. Therefore, in this paper, an attempt is made to capture the effects of pumping on seawater intrusion and upconing using 2D resistivity measurement. For this work, two positions, one perpendicular and the other parallel to the sea, were chosen as profile line for resistivity measurement in the coastal area near the pumping wells of Kapas Island, Malaysia. Subsequently, water was pumped out of two pumping wells simultaneously for about five straight hours. Then, immediately after the pumping stopped, resistivity measurements were taken along the two stationed profile lines. This was followed by additional measurements after four and eight hours. The results showed an upconing with low resistivity of about 1–10 Ωm just beneath the pumping well along the first profile line that was taken just after the pumping stopped. The resistivity image also shows an intrusion of saline water (water enriched with diluted salt) from the sea coming towards the pumping well with resistivity values ranging between 10 and 25 Ωm. The subsequent measurements show the recovery of freshwater in the aquifer and how the saline water is gradually diluted or pushed out of the aquifer. Similarly the line parallel to the sea (L2) reveals almost the same result as the first line. However, in the second and third measurements, there were some significant variations which were contrary to the expectation that the freshwater may completely flush out the saline water from the aquifer. These two time series lines show that as the areas with the lowest resistivity (1 Ωm) shrink with time, the low resistivity (10 Ωm) tends to take over almost the entire area implying that the freshwater-saltwater equilibrium zone has already been altered. These results have clearly enhanced our current understanding and add more scientific weight to the theoretical assumptions on the effects of pumping on seawater intrusion and upconing.
Relationships of Mean Platelet Volume and Plasma Thrombopoietin with Glycocalicin Levels in Thrombocytopenic Patients
Authors: Khaspekova Svetlana G. , Shustova Olga N. , Golubeva Nina V. , Vasiliev Sergey A. , Mazurov Alexey V.
Published: December 2014

Backgrounds/Aims: Relationships of mean platelet volume (MPV) and thrombopoietin (TPO) with platelet turnover assessed by glycocalicin measurement were evaluated in thrombocytopenic patients. Methods: MPV, glycocalicin and platelet-associated IgG (PA-IgG) were measured in 107 patients with idiopathic thrombocytopenic purpura (ITP) and 19 patients with hypoproductive thrombocytopenia (HPT; aplastic anemia or leukemia), and TPO was measured in 53 ITP and 12 HPT patients. All the included ITP patients had PA-IgG ≥300% and glycocalicin ≥50% of control values, and HPT patients had PA-IgG <300% and glycocalicin <50% of control values. Results and Conclusions: MPV was higher in ITP than in HPT patients: 9.56 ± 1.69 and 7.59 ± 0.90 fl (p < 0.001). In the ITP group a direct correlation was detected between MPV and glycocalicin (r = 0.344, p < 0.001). This interaction was essentially expressed in patients with normal/increased glycocalicin (≥100% of control; r = 0.470, p < 0.001, n = 64). TPO was greatly enhanced in HPT in comparison with ITP patients (958 ± 659 and 11 ± 27 pg/ml, p < 0.001). In the ITP group a reverse correlation was detected between TPO and glycocalicin (r = -0.373, p = 0.006). © 2014 S. Karger AG, Basel