bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure-oriented networks of shape collections
Authors: Fish Noa , van Kaick Oliver , Bermano Amit , Cohen-Or Daniel
Published: November 2016

We introduce a co-analysis technique designed for correspondence inference within large shape collections. Such collections are naturally rich in variation, adding ambiguity to the notoriously difficult problem of correspondence computation. We leverage the robustness of correspondences between similar shapes to address the difficulties associated with this problem. In our approach, pairs of similar shapes are extracted from the collection, analyzed and matched in an efficient and reliable manner, culminating in the construction of a network of correspondences that connects the entire collection. The correspondence between any pair of shapes then amounts to a simple propagation along the minimax path between the two shapes in the network. At the heart of our approach is the introduction of a robust, structure-oriented shape matching method. Leveraging the idea of projective analysis, we partition 2D projections of a shape to obtain a set of 1D ordered regions, which are both simple and efficient to match. We lift the matched projections back to the 3D domain to obtain a pairwise shape correspondence. The emphasis given to structural compatibility is a central tool in estimating the reliability and completeness of a computed correspondence, uncovering any non-negligible semantic discrepancies that may exist between shapes. These detected differences are a deciding factor in the establishment of a network aiming to capture local similarities. We demonstrate that the combination of the presented observations into a co-analysis method allows us to establish reliable correspondences among shapes within large collections.
Relationship templates for creating scene variations
Authors: Zhao Xi , Hu Ruizhen , Guerrero Paul , Mitra Niloy , Komura Taku
Published: November 2016

We propose a novel example-based approach to synthesize scenes with complex relations, e.g., when one object is 'hooked', 'surrounded', 'contained' or 'tucked into' another object. Existing relationship descriptors used in automatic scene synthesis methods are based on contacts or relative vectors connecting the object centers. Such descriptors do not fully capture the geometry of spatial interactions, and therefore cannot describe complex relationships. Our idea is to enrich the description of spatial relations between object surfaces by encoding the geometry of the open space around objects, and use this as a template for fitting novel objects. To this end, we introduce
relationship templates
as descriptors of complex relationships; they are computed from an example scene and combine the interaction bisector surface (IBS) with a novel feature called the space coverage feature (SCF), which encodes the open space in the frequency domain. New variations of a scene can be synthesized efficiently by fitting novel objects to the template. Our method greatly enhances existing automatic scene synthesis approaches by allowing them to handle complex relationships, as validated by our user studies. The proposed method generalizes well, as it can form complex relationships with objects that have a topology and geometry very different from the example scene.
Blocking harmful blue light while preserving image color appearance
Authors: Shih Kuang-Tsu , Liu Jen-Shuo , Shyu Frank , Yeh Su-Ling , Chen Homer H.
Published: November 2016

Recent study in vision science has shown that blue light in a certain frequency band affects human circadian rhythm and impairs our health. Although applying a light blocker to an image display can block the harmful blue light, it inevitably makes an image look like an aged photo. In this paper, we show that it is possible to reduce harmful blue light while preserving the blue appearance of an image. Moreover, we optimize the spectral transmittance profile of blue light blocker based on psychophysical data and develop a color compensation algorithm to minimize color distortion. A prototype using notch filters is built as a proof of concept.
Emptying, refurnishing, and relighting indoor spaces
Authors: Zhang Edward , Cohen Michael F. , Curless Brian
Published: November 2016

Visualizing changes to indoor scenes is important for many applications. When looking for a new place to live, we want to see how the interior looks not with the current inhabitant's belongings, but with our own furniture. Before purchasing a new sofa, we want to visualize how it would look in our living room. In this paper, we present a system that takes an RGBD scan of an indoor scene and produces a scene model of the empty room, including light emitters, materials, and the geometry of the non-cluttered room. Our system enables realistic rendering not only of the empty room under the original lighting conditions, but also with various scene edits, including adding furniture, changing the material properties of the walls, and relighting. These types of scene edits enable many mixed reality applications in areas such as real estate, furniture retail, and interior design. Our system contains two novel technical contributions: a 3D radiometric calibration process that recovers the appearance of the scene in high dynamic range, and a global-illumination-aware inverse rendering framework that simultaneously recovers reflectance properties of scene surfaces and lighting properties for several light source types, including generalized point and line lights.
Fast and reliable example-based mesh IK for stylized deformations
Authors: Wampler Kevin
Published: November 2016

Example-based shape deformation allows a mesh to be easily manipulated or animated with simple inputs. As the user pulls parts of the shape, the rest of the mesh automatically changes in an intuitive way by drawing from a set of exemplars. This provides a way for virtual shapes or characters to be easily authored and manipulated, or for a set of drawings to be animated with simple inputs. We describe a new approach for example-based inverse kinematic mesh manipulation which generates high quality deformations for a wide range of inputs, and in particular works well even when provided stylized or "cartoony" examples. This approach is fast enough to run in real time, reliably uses the artist's input shapes in an intuitive way even for highly nonphysical deformations, and provides added expressiveness by allowing the input shapes to be utilized in a way which spatially varies smoothly across the resulting deformed mesh. This allows for rich and detailed deformations to be created from a small set of input shapes, and gives an easy way for a set of sketches to be brought alive with simple click-and-drag inputs.
Stochastic structural analysis for context-aware design and fabrication
Authors: Langlois Timothy , Shamir Ariel , Dror Daniel , Matusik Wojciech , Levin David I. W.
Published: November 2016

In this paper we propose failure probabilities as a semantically and mechanically meaningful measure of object fragility. We present a stochastic finite element method which exploits fast rigid body simulation and reduced-space approaches to compute spatially varying failure probabilities. We use an explicit rigid body simulation to emulate the real-world loading conditions an object might experience, including persistent and transient frictional contact, while allowing us to combine several such scenarios together. Thus, our estimates better reflect real-world failure modes than previous methods. We validate our results using a series of real-world tests. Finally, we show how to embed failure probabilities into a stress constrained topology optimization which we use to design objects such as weight bearing brackets and robust 3D printable objects.
GST
Authors: Krajcevski Pavel , Pratapa Srihari , Manocha Dinesh
Published: November 2016

Modern GPUs supporting compressed textures allow interactive application developers to save scarce GPU resources such as VRAM and bandwidth. Compressed textures use fixed compression ratios whose lossy representations are significantly poorer quality than traditional image compression formats such as JPEG. We present a new method in the class of
supercompressed
textures that provides an additional layer of compression to already compressed textures. Our texture representation is designed for endpoint compressed formats such as DXT and PVRTC and decoding on commodity GPUs. We apply our algorithm to commonly used formats by separating their representation into two parts that are processed independently and then entropy encoded. Our method preserves the CPU-GPU bandwidth during the decoding phase and exploits the parallelism of GPUs to provide up to 3X faster decode compared to prior texture supercompression algorithms. Along with the gains in decoding speed, our method maintains both the compression size and quality of current state of the art texture representations.
WarpDriver
Authors: Wolinski David , Lin Ming C. , Pettré Julien
Published: November 2016

Microscopic crowd simulators rely on models of local interaction (e.g. collision avoidance) to synthesize the individual motion of each virtual agent. The quality of the resulting motions heavily depends on this component, which has significantly improved in the past few years. Recent advances have been in particular due to the introduction of a short-horizon motion prediction strategy that enables anticipated motion adaptation during local interactions among agents. However, the simplicity of prediction techniques of existing models somewhat limits their domain of validity. In this paper, our key objective is to significantly improve the quality of simulations by expanding the applicable range of motion predictions. To this end, we present a novel local interaction algorithm with a new context-aware, probabilistic motion prediction model. By context-aware, we mean that this approach allows crowd simulators to account for many factors, such as the influence of environment layouts or in-progress interactions among agents, and has the ability to simultaneously maintain several possible alternate scenarios for future motions and to cope with uncertainties on sensing and other agent's motions. Technically, this model introduces "collision probability fields" between agents, efficiently computed through the cumulative application of
Warp Operators
on a source
Intrinsic Field.
We demonstrate how this model significantly improves the quality of simulated motions in challenging scenarios, such as dense crowds and complex environments.
Exploiting accelerators for efficient high dimensional similarity search
Authors: Agrawal Sandeep R. , Dee Christopher M. , Lebeck Alvin R.
Published: November 2016

Similarity search finds the most similar matches in an object collection for a given query; making it an important problem across a wide range of disciplines such as web search, image recognition and protein sequencing. Practical implementations of High Dimensional Similarity Search (HDSS) search across billions of possible solutions for multiple queries in real time, making its performance and efficiency a significant challenge. Existing clusters and datacenters use commercial multicore hardware to perform search, which may not provide the optimal performance and performance per Watt.

This work explores the performance, power and cost benefits of using throughput accelerators like GPUs to perform similarity search for query cohorts even under tight deadlines. We propose optimized implementations of similarity search for both the host and the accelerator. Augmenting existing Xeon servers with accelerators results in a 3× improvement in throughput per machine, resulting in a more than 2.5× reduction in cost of ownership, even for discounted Xeon servers. Replacing a Xeon based cluster with an accelerator based cluster for similarity search reduces the total cost of ownership by more than 6× to 16× while consuming significantly less power than an ARM based cluster.
Declarative coordination of graph-based parallel programs
Authors: Cruz Flavio , Rocha Ricardo , Goldstein Seth Copen
Published: November 2016

Declarative programming has been hailed as a promising approach to parallel programming since it makes it easier to reason about programs while hiding the implementation details of parallelism from the programmer. However, its advantage is also its disadvantage as it leaves the programmer with no straightforward way to optimize programs for performance. In this paper, we introduce Coordinated Linear Meld (CLM), a concurrent forward-chaining linear logic programming language, with a declarative way to coordinate the execution of parallel programs allowing the programmer to specify arbitrary scheduling and data partitioning policies. Our approach allows the programmer to write graph-based declarative programs and then optionally to use coordination to fine-tune parallel performance. In this paper we specify the set of coordination facts, discuss their implementation in a parallel virtual machine, and show---through example---how they can be used to optimize parallel execution. We compare the performance of CLM programs against the original uncoordinated Linear Meld and several other frameworks.
Articulation points guided redundancy elimination for betweenness centrality
Authors: Wang Lei , Yang Fan , Zhuang Liangji , Cui Huimin , Lv Fang , Feng Xiaobing
Published: November 2016

Betweenness centrality (BC) is an important metrics in graph analysis which indicates critical vertices in large-scale networks based on shortest path enumeration. Typically, a BC algorithm constructs a shortest-path DAG for each vertex to calculate its BC score. However, for emerging real-world graphs, even the state-of-the-art BC algorithm will introduce a number of redundancies, as suggested by the existence of articulation points. Articulation points imply some common sub-DAGs in the DAGs for different vertices, but existing algorithms do not leverage such information and miss the optimization opportunity.

We propose a redundancy elimination approach, which identifies the common sub-DAGs shared between the DAGs for different vertices. Our approach leverages the articulation points and reuses the results of the common sub-DAGs in calculating the BC scores, which eliminates redundant computations. We implemented the approach as an algorithm with two-level parallelism and evaluated it on a multicore platform. Compared to the state-of-the-art implementation using shared memory, our approach achieves an average speedup of 4.6x across a variety of real-world graphs, with the traversal rates up to 45 ~ 2400 MTEPS (Millions of Traversed Edges per Second).
Coarse grain parallelization of deep neural networks
Authors: Tallada Marc Gonzalez
Published: November 2016

Deep neural networks (DNN) have recently achieved extraordinary results in domains like computer vision and speech recognition. An essential element for this success has been the introduction of high performance computing (HPC) techniques in the critical step of training the neural network. This paper describes the implementation and analysis of a network-agnostic and convergence-invariant coarse-grain parallelization of the DNN training algorithm. The coarse-grain parallelization is achieved through the exploitation of the batch-level parallelism. This strategy is independent from the support of specialized and optimized libraries. Therefore, the optimization is immediately available for accelerating the DNN training. The proposal is compatible with multi-GPU execution without altering the algorithm convergence rate. The parallelization has been implemented in Caffe, a state-of-the-art DNN framework. The paper describes the code transformations for the parallelization and we also identify the limiting performance factors of the approach. We show competitive performance results for two state-of-the-art computer vision datasets, MNIST and CIFAR-10. In particular, on a 16-core Xeon E5-2667v2 at 3.30GHz we observe speedups of 8× over the sequential execution, at similar performance levels of those obtained by the GPU optimized Caffe version in a NVIDIA K40 GPU.
ESTIMA
Authors: Chatzopoulos Georgios , Dragojević Aleksandar , Guerraoui Rachid
Published: November 2016

This paper presents ESTIMA, an easy-to-use tool for extrapolating the scalability of in-memory applications. ESTIMA is designed to perform a simple, yet important task: given the performance of an application on a small machine with a handful of cores, ESTIMA extrapolates its scalability to a larger machine with more cores, while requiring minimum input from the user. The key idea underlying ESTIMA is the use of stalled cycles (e.g. cycles that the processor spends waiting for various events, such as cache misses or waiting on a lock). ESTIMA measures stalled cycles on a few cores and extrapolates them to more cores, estimating the amount of
waiting
in the system. ESTIMA can be effectively used to predict the scalability of in-memory applications. For instance, using measurements of memcached and SQLite on a desktop machine, we obtain accurate predictions of their scalability on a server. Our extensive evaluation on a large number of in-memory benchmarks shows that ESTIMA has generally low prediction errors.
Refined transactional lock elision
Authors: Dice Dave , Kogan Alex , Lev Yossi
Published: November 2016

Transactional lock elision (TLE) is a well-known technique that exploits hardware transactional memory (HTM) to introduce concurrency into lock-based software. It achieves that by attempting to execute a critical section protected by a lock in an atomic hardware transaction, reverting to the lock if these attempts fail. One significant drawback of TLE is that it disables hardware speculation once there is a thread running under lock. In this paper we present two algorithms that rely on existing compiler support for transactional programs and allow threads to speculate concurrently on HTM along with a thread holding the lock. We demonstrate the benefit of our algorithms over TLE and other related approaches with an in-depth analysis of a number of benchmarks and a wide range of workloads, including an AVL tree-based micro-benchmark and ccTSA, a real sequence assembler application.
High performance model based image reconstruction
Authors: Wang Xiao , Sabne Amit , Kisner Sherman , Raghunathan Anand , Bouman Charles , Midkiff Samuel
Published: November 2016

Computed Tomography (CT) Image Reconstruction is an important technique used in a wide range of applications, ranging from explosive detection, medical imaging to scientific imaging. Among available reconstruction methods, Model Based Iterative Reconstruction (MBIR) produces higher quality images and allows for the use of more general CT scanner geometries than is possible with more commonly used methods. The high computational cost of MBIR, however, often makes it impractical in applications for which it would otherwise be ideal. This paper describes a new MBIR implementation that significantly reduces the computational cost of MBIR while retaining its benefits. It describes a novel organization of the scanner data into
super-voxels
(SV) that, combined with a
super-voxel buffer
(SVB), dramatically increase locality and prefetching, enable parallelism across SVs and lead to an average speedup of 187 on 20 cores.
The virtues of conflict
Authors: Narayanaswamy Ganesh , Joshi Saurabh , Kroening Daniel
Published: November 2016

Modern shared memory multiprocessors permit reordering of memory operations for performance reasons. These reorderings are often a source of subtle bugs in programs written for such architectures. Traditional approaches to verify weak memory programs often rely on interleaving semantics, which is prone to state space explosion, and thus severely limits the scalability of the analysis. In recent times, there has been a renewed interest in modelling dynamic executions of weak memory programs using partial orders. However, such an approach typically requires ad-hoc mechanisms to correctly capture the data and control-flow choices/conflicts present in real-world programs. In this work, we propose a novel, conflict-aware, composable, truly concurrent semantics for programs written using C/C++ for modern weak memory architectures. We exploit our symbolic semantics based on general event structures to build an efficient decision procedure that detects assertion violations in bounded multi-threaded programs. Using a large, representative set of benchmarks, we show that our conflict-aware semantics outperforms the state-of-the-art partial-order based approaches.
A wait-free queue as fast as fetch-and-add
Authors: Yang Chaoran , Mellor-Crummey John
Published: November 2016

Concurrent data structures that have fast and predictable performance are of critical importance for harnessing the power of multicore processors, which are now ubiquitous. Although wait-free objects, whose operations complete in a bounded number of steps, were devised more than two decades ago, wait-free objects that can deliver scalable high performance are still rare.

In this paper, we present the first wait-free FIFO queue based on fetch-and-add (FAA). While compare-and-swap (CAS) based non-blocking algorithms may perform poorly due to work wasted by CAS failures, algorithms that coordinate using FAA, which is guaranteed to succeed, can in principle perform better under high contention. Along with FAA, our queue uses a custom epoch-based scheme to reclaim memory; on x86 architectures, it requires no extra memory fences on our algorithm's typical execution path. An empirical study of our new FAA-based wait-free FIFO queue under high contention on four different architectures with many hardware threads shows that it outperforms prior queue designs that lack a wait-free progress guarantee. Surprisingly, at the highest level of contention, the throughput of our queue is often as high as that of a microbenchmark that only performs FAA. As a result, our fast wait-free queue implementation is useful in practice on most multi-core systems today. We believe that our design can serve as an example of how to construct other fast wait-free objects.
Causal consistency
Authors: Perrin Matthieu , Mostefaoui Achour , Jard Claude
Published: November 2016

In distributed systems where strong consistency is costly when not impossible, causal consistency provides a valuable abstraction to represent program executions as partial orders. In addition to the sequential program order of each computing entity, causal order also contains the semantic links between the events that affect the shared objects -- messages emission and reception in a communication channel, reads and writes on a shared register. Usual approaches based on semantic links are very difficult to adapt to other data types such as queues or counters because they require a specific analysis of causal dependencies for each data type. This paper presents a new approach to define causal consistency for any abstract data type based on sequential specifications. It explores, formalizes and studies the differences between three variations of causal consistency and highlights them in the light of PRAM, eventual consistency and sequential consistency: weak causal consistency, that captures the notion of causality preservation when focusing on convergence; causal convergence that mixes weak causal consistency and convergence; and causal consistency, that coincides with causal memory when applied to shared memory.
Unifying fixed code and fixed data mapping of load-imbalanced pipelined loops
Authors: Mastoras Aristeidis , Gross Thomas R.
Published: November 2016

Some loops with cross-iteration dependences can execute in parallel by pipelining. The loop body is partitioned into stages such that the data dependences are not violated and then the stages are mapped onto threads. Two well-known mapping techniques are
fixed code
and
fixed data
; they achieve high performance for load-balanced loops, but they fail to perform well for load-imbalanced loops. In this article, we present a novel hybrid mapping that eliminates drawbacks of both prior mapping techniques and enables dynamic scheduling of stages.
Improving efficacy of internal binary search trees using local recovery
Authors: Ramachandran Arunmoezhi , Mittal Neeraj
Published: November 2016

Binary Search Tree (BST) is an important data structure for managing ordered data. Many algorithms---blocking as well as non-blocking---have been proposed for concurrent manipulation of a binary search tree in an asynchronous shared memory system that supports search, insert and delete operations based on both external and internal representations of a search tree.

An important step in executing an operation on a tree is to traverse the tree from top-to-down in order to locate the operation's window. A process may need to perform this traversal several times to handle any failures occurring due to other processes performing conflicting actions on the tree. Most concurrent algorithms that have proposed so far use a naïve approach and simply restart the traversal from the root of the tree.

In this work, we present a new approach to recover from such failures more efficiently in a concurrent binary search tree based on internal representation using
local recovery
by restarting the traversal from the "middle" of the tree in order to locate an operation's window. Our approach is sufficiently general in the sense that it can be applied to a variety of concurrent binary search trees based on both blocking and non-blocking approaches.

Using experimental evaluation, we demonstrate that our local recovery approach can yield significant speed-ups of up to 69% for many concurrent algorithms.
Hybrid CPU-GPU scheduling and execution of tree traversals
Authors: Liu Jianqiao , Hegde Nikhil , Kulkarni Milind
Published: November 2016

GPUs offer the promise of massive, power-efficient parallelism. However, exploiting this parallelism requires code to be carefully structured to deal with the limitations of the SIMT execution model. In recent years, there has been much interest in mapping
irregular
applications to GPUs: applications with unpredictable, data-dependent behaviors. While most of the work in this space has focused on
ad hoc
implementations of specific algorithms, recent work has looked at generic techniques for mapping a large class of
tree traversal
algorithms to GPUs, through careful restructuring of the tree traversal algorithms to make them behave more regularly. Unfortunately, even this general approach for GPU execution of tree traversal algorithms is reliant on
ad hoc
, handwritten, algorithm-specific scheduling (
i.e.
, assignment of threads to warps) to achieve high performance.

The key challenge of scheduling is that it is a highly irregular process, that requires the inspection of thread behavior and then careful sorting of the threads into warps. In this paper, we present a novel scheduling and execution technique for tree traversal algorithms that is both general and automatic. The key novelty is a hybrid approach: the GPU partially executes tasks to inspect thread behavior and transmits information back to the CPU, which uses that information to perform the scheduling itself, before executing the remaining, carefully scheduled, portion of the traversals on the GPU. We applied this framework to five tree traversal algorithms, achieving significant speedups over optimized GPU code that does not perform application-specific scheduling. Further, we show that in many cases, our hybrid approach is able to deliver better performance even than GPU code that uses hand-tuned, application-specific scheduling.
A programming system for future proofing performance critical libraries
Authors: Chang Li-Wen , El Hajj Izzat , Kim Hee-Seok , Gómez-Luna Juan , Dakkak Abdul , Hwu Wen-mei
Published: November 2016

We present Tangram, a programming system for writing performance-portable programs. The language enables programmers to write computation and composition codelets, supported by tuning knobs and primitives for expressing data parallelism and work decomposition. The compiler and runtime use a set of techniques such as hierarchical composition, coarsening, data placement, tuning, and runtime selection based on input characteristics and micro-profiling. The resulting performance is competitive with optimized vendor libraries.
DSMR
Authors: Maleki Saeed , Nguyen Donald , Lenharth Andrew , Garzarán María , Padua David , Pingali Keshav
Published: November 2016

The Single-Source Shortest Path (SSSP) problem is to find the shortest paths from a source vertex to all other vertices in a graph. In this paper, we introduce the Dijkstra Strip-Mined Relaxation (DSMR) algorithm, an efficient parallel SSSP algorithm for shared and distributed memory systems. Our results show that, DSMR is faster than parallel Δ-Stepping by a factor of up-to 1.66.
Samsara parallel
Authors: Chen Yifeng , Huang Kun , Wang Bei , Li Guohui , Cui Xiang
Published: November 2016

Many time-dependent problems like molecular dynamics of protein folding require a large number of time steps. The latencies and overheads of common-purpose clusters with accelerators are too big for high-frequency iteration. We introduce an algorithmic model called Samsara Parallel (or SP) which, unlike BSP, relies on asynchronous communications and can repeatedly return to earlier time steps to refine the precision of computation. This also extends a line of research called Parallel-in-Time in computational chemistry and physics.
Effect of portable fine-grained locality on energy efficiency and performance in concurrent search trees
Authors: Umar Ibrahim , Anshus Otto J. , Ha Phuong H.
Published: November 2016

Recent research has suggested that improving fine-grained data-locality is one of the main approaches to improving energy efficiency and performance. However, no previous research has investigated the effect of the approach on these metrices in the case of concurrent data structures.

This paper investigates how fine-grained data locality influences energy efficiency and performance in concurrent search trees, a crucial data structure that is widely used in several important systems. We conduct a set of experiments on three lock-based concurrent search trees: DeltaTree, a portable fine-grained locality-aware concurrent search tree; CBTree, a coarse-grained locality-aware B+tree; and BST-TK, a locality-oblivious concurrent search tree. We run the experiments on a commodity x86 platform and an embedded ARM platform. The experimental results show that DeltaTree has 13--25% better energy efficiency and 10--22% more operations/second on the x86 and ARM platforms, respectively. The results confirm that portable fine-grained locality can improve energy efficiency and performance in concurrent search trees.
On ordering transaction commit
Authors: Saad Mohamed M. , Palmieri Roberto , Ravindran Binoy
Published: November 2016

In this poster paper, we briefly introduce an effective solution to address the problem of committing transactions enforcing a predefined order. To do that, we overview the design of two algorithms that deploy a cooperative transaction execution that circumvents the transaction isolation constraint in favor of propagating written values among conflicting transactions. A preliminary implementation shows that even in the presence of data conflicts, the proposed algorithms outperform other competitors, significantly.
Verification of MPI Java programs using software model checking
Authors: Rehman Waqas Ur , Ayub Muhammad Sohaib , Siddiqui Junaid Haroon
Published: November 2016

Development of concurrent software requires the programmer to be aware of non-determinism, data races, and deadlocks. MPI (message passing interface) is a popular standard for writing message oriented distributed applications. Some messages in MPI systems can be processed by one of the many machines and in many possible orders. This non-determinism can affect the result of an MPI application. The alternate results may or may not be correct. To verify MPI applications, we need to check all these possible orderings and use an application specific oracle to decide if these orderings give correct output. MPJ Express is an open source Java implementation of the MPI standard. We developed a Java based model of MPJ Express, where processes are modeled as threads, and which can run unmodified MPI Java programs on a single system. This enabled us to adapt the Java PathFinder explicit state software model checker (JPF) using a custom listener to verify our model running real MPI Java programs. We evaluated our approach using small examples where model checking revealed message orders that would result in incorrect system behavior.
An interval constrained memory allocator for the Givy GAS runtime
Authors: Gindraud François , Rastello Fabrice , Cohen Albert , Broquedis François
Published: November 2016

The
shared memory
model helps parallel programming productivity, but it also has a high hardware cost and imposes scalability constraints. Ultimately, higher performance will use
distributed memories
, which scales better but requires programmers to manually transfer data between local memories, which is a complex task. Distributed memories are also more energy efficient than shared memories, and are used in a family of embedded computing solutions called
multi processor system on chip
(MPSoC).
A scalable lock-free hash table with open addressing
Authors: Nielsen Jesper Puge , Karlsson Sven
Published: November 2016

Concurrent data structures synchronized with locks do not scale well with the number of threads. As more scalable alternatives, concurrent data structures and algorithms based on widely available, however advanced, atomic operations have been proposed. These data structures allow for correct and concurrent operations without any locks. In this paper, we present a new fully lock-free open addressed hash table with a simpler design than prior published work. We split hash table insertions into two atomic phases: first inserting a value ignoring other concurrent operations, then in the second phase resolve any duplicate or conflicting values.

Our hash table has a constant and low memory usage that is less than existing lock-free hash tables at a fill level of 33% and above. The hash table exhibits good cache locality. Compared to prior art, our hash table results in 16% and 15% fewer L1 and L2 cache misses respectively, leading to 21% fewer memory stall cycles. Our experiments show that our hash table scales close to linearly with the number of threads and outperforms, in throughput, other lock-free hash tables by 19%.
Assessment of first-year medical students’ perceptions of teaching and learning through team-based learning sessions
Authors: Obad Adam S. , Peeran Ahmed A. , Shareef Mohammad Abrar , Alsheikh Wissal J. , Kalagi Dana A. , AlAmodi Abdulhadi A. , Khan Tehreem A. , Shaikh Abdul Ahad , Ganguly Paul , Yaqinuddin Ahmed
Published: November 2016

Team-based learning (TBL) is an emerging teaching and learning strategy being employed in medical schools. The College of Medicine at Alfaisal University has adopted a TBL approach as an instructional method for first-year medical students. The aim of the present study was to describe the TBL method employed at Alfaisal University College of Medicine and to assess first-year medical students' perceptions of this learning modality for the anatomy- and physiology-based blocks/courses in organ systems form of curriculum. A five-point Likert scale questionnaire was structured based on Kirkpatrick’s theory and assessed three major domains: reaction, learning, and behavior. Confirmatory factor analysis (CFA) and Cronbach’s α-coefficient tests were used to assess the validity and reliability of the construct, respectively. CFA showed an adequate validity of the survey and Cronbach’s α revealed an acceptable internal uniformity (0.69). A total of 185 respondents rated reaction, learning, and behavior toward introduction of TBL as 3.53 ± 1.01, 3.59 ± 1.12, and 3.57 ± 1.12, respectively. Excellent students rated TBL highly in all major domains compared with borderline students (reaction, behavior, and learning domains with P values of <0.049, <0.035, and <0.031, respectively). Students who had prior teamwork experience rated TBL higher in terms of their learning experience compared with those who were rarely involved in team work. This study demonstrated that Alfaisal University first-year medical students perceived TBL positively as a teaching and learning strategy for functional anatomy, and prior involvement in teamwork and academic performance correlates with higher ratings of TBL.
Reduced nitric oxide bioavailability mediates cerebroarterial dysfunction independent of cerebral amyloid angiopathy in a mouse model of Alzheimer’s disease
Authors: Merlini Mario , Shi Yi , Keller Stephan , Savarese Gianluigi , Akhmedov Alexander , Derungs Rebecca , Spescha Remo D. , Kulic Luka , Nitsch Roger M. , Lüscher Thomas F. , Camici Giovanni G.
Published: November 2016

In Alzheimer’s disease (AD), cerebral arteries, in contrast to cerebral microvessels, show both cerebral amyloid angiopathy (CAA) -dependent and -independent vessel wall pathology. However, it remains unclear whether CAA-independent vessel wall pathology affects arterial function, thereby chronically reducing cerebral perfusion, and, if so, which mechanisms mediate this effect. To this end, we assessed the ex vivo vascular function of the basilar artery and a similar-sized peripheral artery (femoral artery) in the Swedish-Arctic (SweArc) transgenic AD mouse model at different disease stages. Furthermore, we used quantitative immunohistochemistry to analyze CAA, endothelial morphology, and molecular pathways pertinent to vascular relaxation. We found that endothelium-dependent, but not smooth muscle-dependent, vasorelaxation was significantly impaired in basilar and femoral arteries of 15-mo-old SweArc mice compared with that of age-matched wild-type and 6-mo-old SweArc mice. This impairment was accompanied by significantly reduced levels of cyclic GMP, indicating a reduced nitric oxide (NO) bioavailability. However, no age- and genotype-related differences in oxidative stress as measured by lipid peroxidation were observed. Although parenchymal capillaries, arterioles, and arteries showed abundant CAA in the 15-mo-old SweArc mice, no CAA or changes in endothelial morphology were detected histologically in the basilar and femoral artery. Thus our results suggest that, in this AD mouse model, dysfunction of large intracranial, extracerebral arteries important for brain perfusion is mediated by reduced NO bioavailability rather than by CAA. This finding supports the growing body of evidence highlighting the therapeutic importance of targeting the cerebrovasculature in AD.

NEW & NOTEWORTHY We show that vasorelaxation of the basilar artery, a large intracranial, extracerebral artery important for cerebral perfusion, is impaired independent of cerebral amyloid angiopathy in a transgenic mouse model of Alzheimer’s disease. Interestingly, this dysfunction is specifically endothelium related and is mediated by impaired nitric oxide–cyclic GMP bioavailability.

Listen to this article’s corresponding podcast at http://ajpheart.podbean.com/e/cerebroarterial-dysfunction-in-swedish-arctic-ad-mice/ .
S100A4 Elevation Empowers Expression of Metastasis Effector Molecules in Human Breast Cancer
Authors: Ismail Thamir M. , Bennett Daimark , Platt-Higgins Angela M. , Al-Medhity Morteta , Barraclough Roger , Rudland Philip S.
Published: November 2016

Many human glandular cancers metastasize along nerve tracts, but the mechanisms involved are generally poorly understood. The calcium-binding protein S100A4 is expressed at elevated levels in human cancers, where it has been linked to increased invasion and metastasis. Here we report genetic studies in a Drosophila model to define S100A4 effector functions that mediate metastatic dissemination of mutant Ras-induced tumors in the developing nervous system. In flies overexpressing mutant RasVal12 and S100A4, there was a significant increase in activation of the stress kinase JNK and production of the matrix metalloproteinase MMP1. Genetic or chemical blockades of JNK and MMP1 suppressed metastatic dissemination associated with S100A4 elevation, defining required signaling pathway(s) for S100A4 in this setting. In clinical specimens of human breast cancer, elevated levels of the mammalian paralogs MMP2, MMP9, and MMP13 are associated with a 4- to 9-fold relative decrease in patient survival. In individual tumors, levels of MMP2 and MMP13 correlated more closely with levels of S100A4, whereas MMP9 levels correlated more closely with the S100 family member S100P. Overall, our results suggest the existence of evolutionarily conserved pathways used by S100A4 to promote metastatic dissemination, with potential prognostic and therapeutic implications for metastasis by cancers that preferentially exploit nerve tract migration routes. Cancer Res; 77(3); 780–9. ©2016 AACR.
Sequencing of Sipuleucel-T and Androgen Deprivation Therapy in Men with Hormone-Sensitive Biochemically Recurrent Prostate Cancer: A Phase II Randomized Trial
Authors: Antonarakis Emmanuel S. , Kibel Adam S. , Yu Evan Y. , Karsh Lawrence I. , Elfiky Aymen , Shore Neal D. , Vogelzang Nicholas J. , Corman John M. , Millard Frederick E. , Maher Johnathan C. , Chang Nancy N. , DeVries Todd , Sheikh Nadeem A. , Drake Charles G.
Published: November 2016

Purpose: STAND, a randomized, phase II, open-label trial (NCT01431391), assessed sequencing of sipuleucel-T (an autologous cellular immunotherapy) with androgen deprivation therapy (ADT) in biochemically recurrent prostate cancer (BRPC) patients at high risk for metastasis.

Experimental Design: Men with BRPC following prostatectomy and/or radiotherapy, a PSA doubling time ≤12 months, and no metastasis were enrolled. Patients were randomized (34/arm) to sipuleucel-T followed by ADT (started 2 weeks after sipuleucel-T completion), or ADT followed by sipuleucel-T (started 12 weeks after ADT initiation); ADT continued for 12 months in both arms. The primary endpoint was PA2024-specific T-cell response [enzyme-linked immunospot (ELISPOT)] over time.

Results: PA2024-specific ELISPOT responses over time were similar between groups, except at week 6, where responses were higher with sipuleucel-T→ADT versus ADT→sipuleucel-T (P = 0.013). PA2024-specific T-cell proliferation responses, averaged across time points, were approximately 2-fold higher with sipuleucel-T→ADT versus ADT→sipuleucel-T (P = 0.001). PA2024-specific cellular and humoral responses and prostatic acid phosphatase–specific humoral responses increased significantly versus baseline (P < 0.001) and were maintained for 24 months (both arms). Median time-to-PSA recurrence was similar between arms (21.8 vs. 22.6 months, P = 0.357). Development of a PA2024-specific humoral response correlated with prolonged time-to-PSA progression (HR, 0.22; 95% CI, 0.08–0.67; P = 0.007). Sipuleucel-T with ADT was generally well tolerated.

Conclusions: Sipuleucel-T→ADT appears to induce greater antitumor immune responses than the reverse sequence. These results warrant further investigation to determine whether this sequence leads to improved clinical outcomes, as well as the independent contribution of ADT alone in terms of immune activation. Clin Cancer Res; 23(10); 2451–9. ©2016 AACR.
Effect of Iron Chelation Therapy on Glucose Metabolism in Non-Transfusion-Dependent Thalassaemia
Authors: Chuansumrit Ampaiwan , Pengpis Pimprae , Mahachoklertwattana Pat , Sirachainan Nongnuch , Poomthavorn Preamrudee , Sungkarat Witaya , Kadegasem Praguywan , Khlairit Patcharin , Wongwerawattanakoon Pakawan
Published: November 2016

Aims: To compare insulin sensitivity, β-cell function and iron status biomarkers in non-transfusion-dependent thalassaemia (NTDT) with iron excess during pre- and post-iron chelation. Methods: Subjects with NTDT, aged older than 10 years, with serum ferritin >300 ng/ml, were included. Iron chelation with deferasirox (10 mg/kg/day) was prescribed daily for 6 months. Results: Ten patients with a median age of 17.4 years were enrolled. The comparison between pre- and post-chelation demonstrated significantly lower iron load: median serum ferritin (551.4 vs. 486.2 ng/ml, p = 0.047), median TIBC (211.5 vs. 233.5 µg/dl, p = 0.009) and median non-transferrin binding iron (5.5 vs. 1.4 µM, p = 0.005). All patients had a normal oral glucose tolerance test (OGTT) both pre- and post-chelation. However, fasting plasma glucose was significantly reduced after iron chelation (85.0 vs.79.5 mg/dl, p = 0.047). MRI revealed no significant changes of iron accumulation in the heart and liver after chelation, but there was a significantly lower iron load in the pancreas, assessed by higher T2* at post-chelation compared with pre-chelation (41.9 vs. 36.7 ms, p = 0.047). No adverse events were detected. Conclusions: A trend towards improving insulin sensitivity and β-cell function as well as a reduced pancreatic iron load was observed following 6 months of iron chelation (TCTR20160523003).
Constitutional Trisomy 8 Mosaicism with Persistent Macrocytosis
Authors: Altıner Şule , Kutlay Nüket Y. , İlhan Osman
Published: November 2016

Constitutional trisomy 8 mosaicism (CT8M) is a rare chromosomal abnormality. The phenotype varies from normal features to severe malformations. CT8M increases the risk of developing leukemia and myelodysplastic syndrome. As CT8M is very rare, its diagnosis can easily be overlooked, especially in cases with mild phenotypes. Here, we report the diagnostic process of a 40-year-old female patient with CT8M and discuss the importance of follow-up in monitoring for hematological malignancies.
Lung Volume Reduction with Vapor Ablation in the Presence of Incomplete Fissures: 12-Month Results from the STEP-UP Randomized Controlled Study
Authors: Gompelmann Daniela , Eberhardt Ralf , Schuhmann Maren , Valipour Arschang , Shah Pallav L. , Herth Felix J.F. , Kontogianni Konstantina
Published: November 2016

Background: Emphysema patients with collateral ventilation (CV) will not benefit from valve therapy, the most common endoscopic lung volume reduction procedure. A recent randomized controlled trial (STEP-UP) of the alternative bronchoscopic thermal vapor ablation (BTVA) included patients with (CV+) and without interlobar CV (CV-). Objectives: This analysis evaluated the efficacy and safety of the CV+ population following BTVA. Method: A post hoc fissure analysis of the baseline computed tomography of all treatment and control patients was performed with the VIDA Diagnostics Apollo software. A patient was considered to be CV+ if either of the treated upper lobes was adjacent to a fissure that was <90% complete. The primary endpoints, forced expiratory volume in 1 s (FEV1) and St. George's Respiratory Questionnaire (SGRQ-C), were calculated for these CV+ patients following BTVA and safety results summarized. Results: 78% (35/45) of the patients in the treatment arm and 79% (19/24) of the patients in the control arm were found to be CV+. At 12 months, the FEV1 improvement of the treatment arm was 9.2%, as compared with a decrease of 5.4% in the control group, resulting in a mean between-group difference of 14.6% (p = 0.0137). The improvement in SGRQ-C of the treatment arm as compared to the control arm was 8.4 points (p = 0.0712). An increase in respiratory related serious adverse events was observed immediately following treatment, but most resolved with routine care. Conclusion: BTVA can achieve safe and clinically meaningful improvement in pulmonary function and quality of life in patients with CV. These randomized controlled trial subgroup results offer proof of a viable solution for CV+ patients.