bluuebunny/crossref_metadata_2025 huggingface dataset:
Endothelial dysfunction is associated with activation of the type I interferon system and platelets in patients with systemic lupus erythematosus
Authors: Tydén Helena , Lood Christian , Gullstrand Birgitta , Nielsen Christoffer Tandrup , Heegaard Niels H H , Kahn Robin , Jönsen Andreas , Bengtsson Anders A
Published: October 2017

Objectives

Endothelial dysfunction may be connected to cardiovascular disease (CVD) in systemic lupus erythematosus (SLE). Type I interferons (IFNs) are central in SLE pathogenesis and are suggested to induce both endothelial dysfunction and platelet activation. In this study, we investigated the interplay between endothelial dysfunction, platelets and type I IFN in SLE.

Methods

We enrolled 148 patients with SLE and 79 sex-matched and age-matched healthy controls (HCs). Type I IFN activity was assessed with a reporter cell assay and platelet activation by flow cytometry. Endothelial dysfunction was assessed using surrogate markers of endothelial activation, soluble vascular cell adhesion molecule-1 (sVCAM-1) and endothelial microparticles (EMPs), and finger plethysmograph to determine Reactive Hyperaemia Index (RHI).

Results

In patients with SLE, type I IFN activity was associated with endothelial activation, measured by high sVCAM-1 (OR 1.68, p<0.01) and elevated EMPs (OR 1.40, p=0.03). Patients with SLE with high type I IFN activity had lower RHI than HCs (OR 2.61, p=0.04), indicating endothelial dysfunction.

Deposition of complement factors on platelets, a measure of platelet activation, was seen in patients with endothelial dysfunction. High levels of sVCAM-1 were associated with increased deposition of C4d (OR 4.57, p<0.01) and C1q (OR 4.10, p=0.04) on platelets. High levels of EMPs were associated with C4d deposition on platelets (OR 3.64, p=0.03).

Conclusions

Endothelial dysfunction was associated with activation of platelets and the type I IFN system. We suggest that an interplay between the type I IFN system, injured endothelium and activated platelets may contribute to development of CVD in SLE.
Neutrophils drive alveolar macrophage IL-1β release during respiratory viral infection
Authors: Peiró Teresa , Patel Dhiren F , Akthar Samia , Gregory Lisa G , Pyle Chloe J , Harker James A , Birrell Mark A , Lloyd Clare M , Snelgrove Robert J
Published: October 2017

Background

Alveolar macrophages are sentinels of the airways that must exhibit immune restraint to innocuous antigens but elicit a robust inflammatory response to pathogenic threats. How distinction between these dichotomous functions is controlled is poorly defined.

Neutrophils are the first responders to infection, and we hypothesised that they may free alveolar macrophages from their hyporesponsive state, promoting their activation. Activation of the inflammasome and interleukin (IL)-1β release is a key early inflammatory event that must be tightly regulated. Thus, the role of neutrophils in defining inflammasome activation in the alveolar macrophage was assessed.

Methods

Mice were infected with the X31 strain of influenza virus and the role of neutrophils in alveolar macrophage activation established through administration of a neutrophil-depleting (1A8) antibody.

Results

Influenza elicited a robust IL-1β release that correlated (r=0.6849; p<0.001) with neutrophil infiltrate and was ablated by neutrophil depletion. Alveolar macrophages were shown to be the prominent source of IL-1β during influenza infection, and virus triggered the expression of Nod-like receptor protein 3 (NLRP3) inflammasome and pro-IL-1β in these cells. However, subsequent activation of the inflammasome complex and release of mature IL-1β from alveolar macrophages were critically dependent on the provision of a secondary signal, in the form of antimicrobial peptide mCRAMP, from infiltrating neutrophils.

Conclusions

Neutrophils are critical for the activation of the NLRP3 inflammasome in alveolar macrophages during respiratory viral infection. Accordingly, we rationalise that neutrophils are recruited to the lung to confront a viable pathogenic threat and subsequently commit alveolar macrophages to a pro-inflammatory phenotype to combat infection.
Economic cost of tobacco-related cancers in Sri Lanka
Authors: Amarasinghe Hemantha , Ranaweera Sajeeva , Ranasinghe Thushara , Chandraratne Nadeeka , Kumara Dinesh Ruwan , Thavorncharoensap Montarat , Abeykoon Palitha , de Silva Amala
Published: October 2017

Introduction

Cancer has a high mortality rate and morbidity burden in Sri Lanka. This study estimated the economic cost of smoking and smokeless tobacco (ST) related to cancers in Sri Lanka in 2015.

Methods

Prevalence-based cost of illness is calculated according to the guidelines of the WHO (2011). The direct costs are costs of curative care (costs of inward patients and outpatient care borne by the state and out of pocket expenditure by households) for tobacco-related cancers, weighted by the attributable fractions for these cancers. Indirect costs are lost earnings due to mortality and morbidity (absenteeism of both patient and carers resulting from seeking care and recuperation).

Data were obtained from the Registrar General’s Department, National Cancer Registry, Department of Census and Statistics and the Central Bank of Sri Lanka. Household and systemic costs and relative risks were extracted from research studies. Oncologists (working in both public and private sectors), other clinical specialists, medical administrators and economists were consulted during the estimation and validation processes.

Results

The total economic cost of tobacco-related cancers for Sri Lanka in 2015 was estimated to be US$121.2 million. The direct cost of smoking and ST-related cancers was US$42.1 million, which was 35% of the total cost, while the indirect cost was US$79.1 million, which was 65% of the total cost.

Conclusion

Burden of tobacco smoking and ST-related cancers as reflected in these economic costs is enormous: affecting the healthcare system and country’s economy. Policymakers should take note of this burden and address tobacco consumption control as a priority.
Frequency of ice-jam flooding of Peace-Athabasca Delta
Authors: Beltaos Spyros
Published: October 2017

Major ice jams that occasionally form in lower Peace River generate extensive flooding, which helps replenish the perched basins of Peace-Athabasca Delta, a Ramsar wetland of international importance and a UNESCO World Heritage Site. This complex and dynamic ecosystem has experienced prolonged dry periods since the late 1960s, coincident with the construction of the W.A.C. Bennett hydroelectric dam in British Columbia. Physically-based and paleolimnological studies differ with respect to the impact of regulation on flood frequency. This issue is examined herein, based entirely on the historical record of observed ice-jam flood events.
Blue marlin (Makaira nigricans) longevity estimates confirmed with bomb radiocarbon dating
Authors: Andrews Allen H. , Humphreys Robert L. , Sampaga Jeffery D.
Published: October 2017

The longevity of blue marlin (Makaira nigricans) remains unresolved. The use of fin spines and sagittal otoliths for age reading has led to unconfirmed longevity estimates near 20–30 years. Age validation has been elusive because large individuals are uncommonly caught, and a technique that can be applied to structures that provide estimates of age was absent. The use of otolith chemical signatures has been limited by sagittal otoliths that are very small — whole otolith mass of adult blue marlin rarely exceeds 10 mg for the largest fish. Recent advances in the detection limits of radiocarbon (14C) with accelerator mass spectrometry — coupled with recently acquired knowledge of marine bomb 14C signals spanning the tropical Pacific Ocean — have led to an opportunity to age blue marlin from small amounts of otolith material. In this study, otoliths from a recently collected 1245 lb (565 kg) female blue marlin at a measured 146-inch (371 cm) lower jaw fork length were analyzed for 14C. Estimated longevity was either 12–21 or 32–44 years on the basis of bomb 14C dating. Using multiple lines of evidence, it was determined that the young age scenario was most likely, with evidence for an age close to 20 years using a series of deductions in the bomb 14C dating method.
Rare unclassified 16S rRNA operational taxonomic units from the uncharted Engaño Bay (Argentinean Patagonia)
Authors: Calvo Andrea Y. , Manrique Julieta M. , Jones Leandro R.
Published: October 2017

Rare microbes make up most of the diversity of marine microbiomes, and recent works have highlighted their importance for microbial community dynamics and in fragmented habitats. Rare taxa have been infrequently studied in comparison with abundant groups, and rare unclassified sequences are common in culture-independent studies. Here, we describe a detailed analysis of nonclassifiable sequences from the Chubut river estuary at the Argentinean Patagonia. Standard taxonomic assignments of environmental 16S rRNA sequences resulted in about 13% unclassified operational taxonomic units (OTUs). The potential affiliations of these OTUs could be narrowed by mapping the classification software assignments on a phylogeny obtained directly from our environmental sequence data. Customized BLAST analyses were remarkably consistent with these phylogenetic assignments, especially when the unclassified OTUs were blasted against sequences from cultured and type microorganisms. In addition, our BLAST analyses revealed significant similarities between several unclassified OTUs and a plethora of unclassified sequences from around the world. Further phylogenetic comparisons with 6194 carefully selected reference sequences showed that these unclassified sequences may correspond to 5 unnamed groups, possibly encompassing ranks from subclass to family inside the Alphaproteobacteria, and to an unknown Gracilibacteria lineage. Overall, these results demonstrate the value of straight phylogenetic analysis, customized BLAST searches, and comparisons with sequences from type material, for the systematic study of rare unclassified sequences.
Infrared Scanning Cloud Monitor for the Indian Astronomical Observatory, Hanle
Authors: Sharma Tarun Kumar , Parihar Padmakar , Banyal Ravinder Kumar , Kemkar Madan Mohan , Stanzin Urgain , Anupam G. C.
Published: October 2017

A large number of clear nights at a given location is one of the key prerequisites for establishing an astronomical observatory. This parameter needs to be reliably determined before the site location is finalized. For an already exiting observatory site, monitoring of clouds on real-time basis helps automating many observing procedures, thus optimizing the scientific returns from the facility. We have developed an infrared (IR) scanning cloud monitor which generates a local sky-map and provides reliable information about the changing sky conditions. Our device measures the IR sky brightness temperature using a circular array of thermopile sensors mounted on a rotating system. In this paper, we give a detailed description of the instrument hardware, laboratory and on-site calibration procedures and further tests carried out to check the reliability of the device. The cloud monitor has been in regular use since its installation at the Indian Astronomical Observation (IAO), Hanle, Ladakh in 2015 December. We also present the analysis of a year long sky data to demonstrate the usefulness of the device.
Coupling of fluid flow to permeability development in mid- to upper crustal environments: a tale of three pressures
Authors: Hobbs Bruce E. , Ord Alison
Published: October 2017

Orogenic gold systems are open, flow-controlled thermodynamic systems and generally occur in mid- to upper crustal environments where there is strong coupling between fluid flow and dilatant plastic deformation. This paper considers the principles involved in such coupling, with an emphasis on the elastic and plastic volume changes and their influence on the fluid, mechanical and thermodynamic pressures. Some misconceptions regarding the magnitudes of these three distinctly different pressures and their influences on fluid flow and chemical equilibrium are addressed, with examples at both the tens of metres scale and the crustal scale. We show that the mean stress is less than twice the lithostatic stress for Mohr–Coulomb materials with cohesion and the thermodynamic pressure only has meaning under isentropic conditions and hence is less than many previously published estimates based on high mean stresses. At the crustal scale, we also include the role of critical behaviour in influencing the geometry and magnitudes of fluid pressure gradients and fluid flow velocities in open, flow-controlled systems.
Blazes
Authors: Alvaro Peter , Conway Neil , Hellerstein Joseph M. , Maier David
Published: October 2017

Distributed consistency is perhaps the most-discussed topic in distributed systems today. Coordination protocols can ensure consistency, but in practice they cause undesirable performance unless used judiciously. Scalable distributed architectures avoid coordination whenever possible, but under-coordinated systems can exhibit behavioral anomalies under fault, which are often extremely difficult to debug. This raises significant challenges for distributed system architects and developers.

In this article, we present B
lazes
, a cross-platform program analysis framework that (a) identifies program locations that require coordination to ensure consistent executions, and (b) automatically synthesizes application-specific coordination code that can significantly outperform general-purpose techniques. We present two case studies, one using annotated programs in the Twitter Storm system and another using the Bloom declarative language.
Green Simulation
Authors: Feng Mingbin , Staum Jeremy
Published: October 2017

We introduce a new paradigm in simulation experiment design and analysis, called “green simulation,” for the setting in which experiments are performed repeatedly with the same simulation model. Green simulation means reusing outputs from previous experiments to answer the question currently being asked of the simulation model. As one method for green simulation, we propose estimators that reuse outputs from previous experiments by weighting them with likelihood ratios, when parameters of distributions in the simulation model differ across experiments. We analyze convergence of these estimators as more experiments are repeated, while a stochastic process changes the parameters used in each experiment. As another method for green simulation, we propose an estimator based on stochastic kriging. We find that green simulation can reduce mean squared error by more than an order of magnitude in examples involving catastrophe bond pricing and credit risk evaluation.
EmptyHeaded
Authors: Aberger Christopher R. , Lamb Andrew , Tu Susan , Nötzli Andres , Olukotun Kunle , Ré Christopher
Published: October 2017

There are two types of high-performance graph processing engines: low- and high-level engines. Low-level engines (Galois, PowerGraph, Snap) provide optimized data structures and computation models but require users to write low-level imperative code, hence ensuring that efficiency is the burden of the user. In high-level engines, users write in query languages like datalog (SociaLite) or SQL (Grail). High-level engines are easier to use but are orders of magnitude slower than the low-level graph engines. We present EmptyHeaded, a high-level engine that supports a rich datalog-like query language and achieves performance comparable to that of low-level engines. At the core of EmptyHeaded’s design is a new class of join algorithms that satisfy strong theoretical guarantees, but have thus far not achieved performance comparable to that of specialized graph processing engines. To achieve high performance, EmptyHeaded introduces a new join engine architecture, including a novel query optimizer and execution engine that leverage single-instruction multiple data (SIMD) parallelism. With this architecture, EmptyHeaded outperforms high-level approaches by up to three orders of magnitude on graph pattern queries, PageRank, and Single-Source Shortest Paths (SSSP) and is an order of magnitude faster than many low-level baselines. We validate that EmptyHeaded competes with the best-of-breed low-level engine (Galois), achieving comparable performance on PageRank and at most 3× worse performance on SSSP. Finally, we show that the EmptyHeaded design can easily be extended to accommodate a standard resource description framework (RDF) workload, the LUBM benchmark. On the LUBM benchmark, we show that EmptyHeaded can compete with and sometimes outperform two high-level, but specialized RDF baselines (TripleBit and RDF-3X), while outperforming MonetDB by up to three orders of magnitude and LogicBlox by up to two orders of magnitude.
Designing a Query Language for RDF
Authors: Arenas Marcelo , Ugarte Martin
Published: October 2017

When querying an Resource Description Framework (RDF) graph, a prominent feature is the possibility of extending the answer to a query with optional information. However, the definition of this feature in SPARQL—the standard RDF query language—has raised some important issues. Most notably, the use of this feature increases the complexity of the evaluation problem, and its closed-world semantics is in conflict with the underlying open-world semantics of RDF. Many approaches for fixing such problems have been proposed, the most prominent being the introduction of the semantic notion of weakly monotone SPARQL query. Weakly monotone SPARQL queries have shaped the class of queries that conform to the open-world semantics of RDF. Unfortunately, finding an effective way of restricting SPARQL to the fragment of weakly monotone queries has proven to be an elusive problem. In practice, the most widely adopted fragment for writing SPARQL queries is based on the syntactic notion of well designedness. This notion has proven to be a good approach for writing SPARQL queries, but its expressive power has yet to be fully understood.

The starting point of this article is to understand the relation between well-designed queries and the semantic notion of weak monotonicity. It is known that every well-designed SPARQL query is weakly monotone; as our first contribution we prove that the converse does not hold, even if an extension of this notion based on the use of disjunction is considered. Given this negative result, we embark on the task of defining syntactic fragments that are weakly monotone and have higher expressive power than the fragment of well-designed queries. To this end, we move to a more general scenario where infinite RDF graphs are also allowed, so interpolation techniques studied for first-order logic can be applied. With the use of these techniques, we are able to define a new operator for SPARQL that gives rise to a query language with the desired properties (over finite and infinite RDF graphs). It should be noticed that every query in this fragment is weakly monotone if we restrict the semantics to finite RDF graphs. Moreover, we use this result to provide a simple characterization of the class of monotone CONSTRUCT queries, that is, the class of SPARQL queries that produce RDF graphs as output. Finally, we pinpoint the complexity of the evaluation problem for the query languages identified in the article.
PrivBayes
Authors: Zhang Jun , Cormode Graham , Procopiuc Cecilia M. , Srivastava Divesh , Xiao Xiaokui
Published: October 2017

Privacy-preserving data publishing is an important problem that has been the focus of extensive study. The state-of-the-art solution for this problem is differential privacy, which offers a strong degree of privacy protection without making restrictive assumptions about the adversary. Existing techniques using differential privacy, however, cannot effectively handle the publication of high-dimensional data. In particular, when the input dataset contains a large number of attributes, existing methods require injecting a prohibitive amount of noise compared to the signal in the data, which renders the published data next to useless.

To address the deficiency of the existing methods, this paper presents P
riv
B
ayes
, a differentially private method for releasing high-dimensional data. Given a dataset
D
, P
riv
B
ayes
first constructs a Bayesian network
N
, which (i) provides a succinct model of the correlations among the attributes in
D
and (ii) allows us to approximate the distribution of data in
D
using a set
P
of low-dimensional marginals of
D
. After that, P
riv
B
ayes
injects noise into each marginal in
P
to ensure differential privacy and then uses the noisy marginals and the Bayesian network to construct an approximation of the data distribution in
D
. Finally, P
riv
B
ayes
samples tuples from the approximate distribution to construct a synthetic dataset, and then releases the synthetic data. Intuitively, P
riv
B
ayes
circumvents the curse of dimensionality, as it injects noise into the low-dimensional marginals in
P
instead of the high-dimensional dataset
D
. Private construction of Bayesian networks turns out to be significantly challenging, and we introduce a novel approach that uses a surrogate function for mutual information to build the model more accurately. We experimentally evaluate P
riv
B
ayes
on real data and demonstrate that it significantly outperforms existing solutions in terms of accuracy.
Synchronized-by-Default Concurrency for Shared-Memory Systems
Authors: Bättig Martin , Gross Thomas R.
Published: October 2017

We explore a programming approach for concurrency that synchronizes all accesses to shared memory by default. Synchronization takes place by ensuring that all program code runs inside atomic sections even if the program code has external side effects. Threads are mapped to atomic sections that a programmer must explicitly split to increase concurrency.

A naive implementation of this approach incurs a large amount of overhead. We show how to reduce this overhead to make the approach suitable for realistic application programs on existing hardware. We present an implementation technique based on a special-purpose software transactional memory system. To reduce the overhead, the technique exploits properties of managed, object-oriented programming languages as well as intraprocedural static analyses and uses field-level granularity locking in combination with transactional I/O to provide good scaling properties.

We implemented the synchronized-by-default (SBD) approach for the Java language and evaluate its performance for six programs from the DaCapo benchmark suite. The evaluation shows that, compared to explicit synchronization, the SBD approach has an overhead between 0.4% and 102% depending on the benchmark and the number of threads, with a mean (geom.) of 23.9%.
Function Call Re-Vectorization
Authors: Moreira Rubens E.A. , Collange Caroline , Quintão Pereira Fernando Magno
Published: October 2017

Programming languages such as C for CUDA, OpenCL or ISPC have contributed to increase the programmability of SIMD accelerators and graphics processing units. However, these languages still lack the flexibility offered by low-level SIMD programming on explicit vectors. To close this expressiveness gap while preserving performance, this paper introduces the notion of \ourinvention{} (CREV). CREV allows changing the dimension of vectorization during the execution of a kernel, exposing it as a nested parallel kernel call. CREV affords programmability close to dynamic parallelism, a feature that allows the invocation of kernels from inside kernels, but at much lower cost. In this paper, we present a formal semantics of CREV, and an implementation of it on the ISPC compiler. We have used CREV to implement some classic algorithms, including string matching, depth first search and Bellman-Ford, with minimum effort. These algorithms, once compiled by ISPC to Intel-based vector instructions, are as fast as state-of-the-art implementations, yet much simpler. Thus, CREV gives developers the elegance of dynamic programming, and the performance of explicit SIMD programming.
Using Butterfly-Patterned Partial Sums to Draw from Discrete Distributions
Authors: Steele Guy L. , Tristan Jean-Baptiste
Published: October 2017

We describe a SIMD technique for drawing values from multiple discrete distributions, such as sampling from the random variables of a mixture model, that avoids computing a complete table of partial sums of the relative probabilities. A table of alternate ("butterfly-patterned") form is faster to compute, making better use of coalesced memory accesses; from this table, complete partial sums are computed on the fly during a binary search. Measurements using CUDA 7.5 on an NVIDIA Titan Black GPU show that this technique makes an entire machine-learning application that uses a Latent Dirichlet Allocation topic model with 1024 topics about about 13% faster (when using single-precision floating-point data) or about 35% faster (when using double-precision floating-point data) than doing a straightforward matrix transposition after using coalesced accesses.
KiWi
Authors: Basin Dmitry , Bortnikov Edward , Braginsky Anastasia , Golan-Gueta Guy , Hillel Eshcar , Keidar Idit , Sulamy Moshe
Published: October 2017

Modern big data processing platforms employ huge in-memory key-value (KV) maps. Their applications simultaneously drive high-rate data ingestion and large-scale analytics. These two scenarios expect KV-map implementations that scale well with both real-time updates and large atomic scans triggered by range queries.

We present KiWi, the first atomic KV-map to efficiently support simultaneous large scans and real-time access. The key to achieving this is treating scans as first class citizens,and organizing the data structure around them. KiWi provides wait-free scans, whereas its put operations are lightweight and lock-free. It optimizes memory management jointly with data structure access.We implement KiWi and compare it to state-of-the-art solutions. Compared to other KV-maps providing atomic scans, KiWi performs either long scans or concurrent puts an order of magnitude faster. Its scans are twice as fast as non-atomic ones implemented via iterators in the Java skiplist.
S-Caffe
Authors: Awan Ammar Ahmad , Hamidouche Khaled , Hashmi Jahanzeb Maqbool , Panda Dhabaleswar K.
Published: October 2017

Availability of large data sets like ImageNet and massively parallel computation support in modern HPC devices like NVIDIA GPUs have fueled a renewed interest in Deep Learning (DL) algorithms. This has triggered the development of DL frameworks like Caffe, Torch, TensorFlow, and CNTK. However, most DL frameworks have been limited to a single node. In order to scale out DL frameworks and bring HPC capabilities to the DL arena, we propose, S-Caffe; a scalable and distributed Caffe adaptation for modern multi-GPU clusters. With an in-depth analysis of new requirements brought forward by the DL frameworks and limitations of current communication runtimes, we present a co-design of the Caffe framework and the MVAPICH2-GDR MPI runtime. Using the co-design methodology, we modify Caffe's workflow to maximize the overlap of computation and communication with multi-stage data propagation and gradient aggregation schemes. We bring DL-Awareness to the MPI runtime by proposing a hierarchical reduction design that benefits from CUDA-Aware features and provides up to a massive 133x speedup over OpenMPI and 2.6x speedup over MVAPICH2 for 160 GPUs. S-Caffe successfully scales up to 160 K-80 GPUs for GoogLeNet (ImageNet) with a speedup of 2.5x over 32 GPUs. To the best of our knowledge, this is the first framework that scales up to 160 GPUs. Furthermore, even for single node training, S-Caffe shows an improvement of 14\% and 9\% over Nvidia's optimized Caffe for 8 and 16 GPUs, respectively. In addition, S-Caffe achieves up to 1395 samples per second for the AlexNet model, which is comparable to the performance of Microsoft CNTK.
Optimizing the Four-Index Integral Transform Using Data Movement Lower Bounds Analysis
Authors: Rajbhandari Samyam , Rastello Fabrice , Kowalski Karol , Krishnamoorthy Sriram , Sadayappan P.
Published: October 2017

The four-index integral transform is a fundamental and computationally demanding calculation used in many computational chemistry suites such as NWChem. It transforms a four-dimensional tensor from one basis to another. This transformation is most efficiently implemented as a sequence of four tensor contractions that each contract a four- dimensional tensor with a two-dimensional transformation matrix. Differing degrees of permutation symmetry in the intermediate and final tensors in the sequence of contractions cause intermediate tensors to be much larger than the final tensor and limit the number of electronic states in the modeled systems.

Loop fusion, in conjunction with tiling, can be very effective in reducing the total space requirement, as well as data movement. However, the large number of possible choices for loop fusion and tiling, and data/computation distribution across a parallel system, make it challenging to develop an optimized parallel implementation for the four-index integral transform. We develop a novel approach to address this problem, using lower bounds modeling of data movement complexity. We establish relationships between available aggregate physical memory in a parallel computer system and ineffective fusion configurations, enabling their pruning and consequent identification of effective choices and a characterization of optimality criteria. This work has resulted in the development of a significantly improved implementation of the four-index transform that enables higher performance and the ability to model larger electronic systems than the current implementation in the NWChem quantum chemistry software suite.
It's Time for a New Old Language
Authors: Steele Guy L.
Published: October 2017

The most popular programming language in computer science has no compiler or interpreter. Its definition is not written down in any one place. It has changed a lot over the decades, and those changes have introduced ambiguities and inconsistencies. Today, dozens of variations are in use, and its complexity has reached the point where it needs to be re-explained, at least in part, every time it is used. Much effort has been spent in hand-translating between this language and other languages that do have compilers. The language is quite amenable to parallel computation, but this fact has gone unexploited.

In this talk we will summarize the history of the language, highlight the variations and some of the problems that have arisen, and propose specific solutions. We suggest that it is high time that this language be given a complete formal specification, and that compilers, IDEs, and proof-checkers be created to support it, so that all the best tools and techniques of our trade may be applied to it also.
POSTER
Authors: Ramalhete Pedro , Correia Andreia
Published: October 2017

RCU is, among other things, a well known mechanism for memory reclamation that is meant to be used in languages without an automatic Garbage Collector, unfortunately, it requires operating system support, which is currently provided only in Linux. An alternative is to use Userspace RCU (URCU) which has two variants that can be deployed on other operating systems, named \emph{Memory Barrier} and \emph{Bullet Proof}.

We present a novel algorithm that implements the three core APIs of RCU: \texttt{rcu\_read\_lock()}, \texttt{rcu\_read\_unlock()}, and \texttt{synchronize\_rcu()}. Our algorithm uses one mutual exclusion lock and two reader-writer locks with \texttt{trylock()} capabilities, which means it does not need a language with a memory model or atomics API, and as such, it can be easily implemented in almost any language, regardless of the underlying CPU architecture, or operating system.
POSTER
Authors: Li Shigang , Zhang Yunquan , Hoefler Torsten
Published: October 2017

In the many-core era, the performance of MPI collectives is more dependent on the intra-node communication component. However, the communication algorithms generally inherit from the inter-node version and ignore the cache complexity. We propose cache-oblivious algorithms for MPI all-to-all operations, in which data blocks are copied into the receive buffers in Morton order to exploit data locality. Experimental results on different many-core architectures show that our cache-oblivious implementations significantly outperform the naive implementations based on shared heap and the highly optimized MPI libraries.
POSTER
Authors: Bhattacharyya Arnamoy , Dai Wang Mike , Burcea Mihai , Ding Yi , Deng Allen , Varikooty Sai , Hossain Shafaaf , Amza Cristiana
Published: October 2017

In this work, we introduce and experimentally evaluate a new hybrid software-hardware Transactional Memory prototype based on Intel's Haswell TSX architecture. Our prototype extends the applicability of the existing hardware support for TM by interposing a hybrid fall-back layer before the sequential, big-lock fall-back path, used by standard TSX-supported solutions in order to guarantee progress. In our experimental evaluation we use SynQuake, a realistic game benchmark modeled after Quake. Our results show that our hybrid transactional system,which we call HythTM, is able to reduce the number of transactions that go to the sequential software layer, hence avoiding hardware transaction aborts and loss of parallelism. HythTM optimizes application throughput and scalability up to 5.05x, when compared to the hardware TM with sequential fall-back path.
POSTER
Authors: Tang Yuan , You Ronghui
Published: October 2017

It's important to hit a space-time balance for a real-world algorithm to achieve high performance on modern shared-memory multi-core or many-core systems. However, a large class of dynamic programs with more than $O(1)$ dependency achieve optimality either in space or time, but not both. In the literature, the problem is known as the fundamental space-time tradeoff. By exploiting properly on the runtime system, we show that our STAR (Space-Time Adaptive and Reductive) technique can help these dynamic programs to achieve sublinear parallel time bounds while still maintaining work-, space-, and cache-optimality in a processor- and cache-oblivious fashion.
POSTER
Authors: Menon Harshitha , Chandrasekar Kavitha , Kale Laxmikant V.
Published: October 2017

Many HPC applications require dynamic load balancing to achieve high performance and system utilization. Different applications have different characteristics and hence require different load balancing strategies. Invocation of a suboptimal load balancing strategy can lead to inefficient execution. We propose Meta-Balancer, a framework to automatically decide the best load balancing strategy. It employs randomized decision forests, a machine learning method, to learn a model for choosing the best load balancing strategy for an application represented by a set of features that capture the application characteristics.
A Genome-Wide Search for Bipolar Disorder Risk Loci Modified by Mitochondrial Genome Variation
Authors: Ryu Euijung , Nassan Malik , Jenkins Gregory D. , Armasu Sebastian M. , Andreazza Ana , McElroy Susan L. , Vawter Marquis P. , Frye Mark A. , Biernacka Joanna M.
Published: October 2017

Mitochondrial DNA mutations have been reported to be associated with bipolar disorder (BD). In this study, we performed genome-wide analyses to assess mitochondrial single-nucleotide polymorphism (mtSNP) effects on BD risk and early-onset BD (EOBD) among BD patients, focusing on interaction effects between nuclear SNPs (nSNPs) and mtSNPs. Common nSNP and mtSNP data from European American BD cases (n = 1,001) and controls (n = 1,034) from the Genetic Association Information Network BD study were analyzed to assess the joint effect of nSNP and nSNP-mtSNP interaction on the risk of BD and EOBD. The effect of nSNP-mtSNP interactions was also assessed. For BD risk, the strongest evidence of an association was obtained for nSNP rs1880924 in MGAM and mtSNP rs3088309 in CytB (pjoint = 8.2 × 10-8, pint = 1.4 × 10-4). Our results also suggest that the minor allele of the nSNP rs583990 in CTNNA2 increases the risk of EOBD among carriers of the mtSNP rs3088309 minor allele, while the nSNP has no effect among those carrying the mtSNP major allele (OR = 4.53 vs. 1.05, pjoint = 2.1 × 10-7, pint = 1.16 × 10-6). While our results are not statistically significant after multiple testing correction and a large-sample replication is required, our exploratory study demonstrates the potential importance of considering the mitochondrial genome for identifying genetic factors associated with BD.
Thiamine Diphosphate Status and Dialysis-Related Losses in End-Stage Kidney Disease Patients Treated with Hemodialysis
Authors: Jankowska Magdalena , Rudnicki-Velasquez Paweł , Storoniak Hanna , Rutkowski Przemysław , Rutkowski Bolesław , Krzymiński Karol , Dębska-Ślizień Alicja
Published: October 2017

Aim: (1) To describe the whole blood content of thiamine diphosphate (TDP), a biologically active form of vitamin B1 in end-stage kidney disease patients treated with hemodialysis (HD); (2) to establish the impact of a single HD procedure on TDP blood concentrations; and (3) to describe potential explanatory variables influencing TDP dialysis related losses, including dialysis prescription, vitamin B1 dietary intake and supplementation. Methods: Single-center, cross-sectional study in 50 clinically stable maintenance HD patients. The assessment of whole blood TDP with the High Performance Liquid Chromatography method, before and after a single, middle-week dialysis session and analysis of clinical and laboratory parameters potentially influencing TDP status Results: We report a significant difference in TDP levels before and after HD sessions - 42.5 (95% CI 38.7-46.2) μg/L and 23.6 (95% CI 18.9-28.2) μg/L, respectively (p = 0.000). The magnitude of intradialytic TDP changes is highly variable among individuals and is negatively associated only with the body weight of the patients (p < 0.013). Vitamin B1 dietary intake and supplementation do not influence whole blood TDP and dialysis-related loss of TDP. Conclusions: TDP, a bioactive compound of vitamin B1, is substantially lost during the HD procedure, and the magnitude of its loss is associated with the patient's body weight but it is not influenced by vitamin B1 dietary intake and standard supplementation dose.
Posttraumatic Intralaminar Hematoma Developing between Cranial Dural Layers: A Case Report
Authors: Bahuleyan Biji , Patel Vineetkumar Thakorbhai , Usurumarthi Prashanth , Madhavan Girish Kuranjiyoor , Thomas Santhosh George
Published: October 2017

We present a case of post-traumatic hematoma developing between the 2 layers of the cranial dura in a 2-year-old child following head injury. This child presented with history of fall from a height in altered sensorium with paucity of movements on the left side. Computerized tomography scan of the brain showed a right parietal linear fracture with an underlying hyperdense biconvex hematoma. Emergency evacuation of the hematoma was done. On elevation of the scalp flap, a fibrous membrane was seen protruding between the fracture lines. Following craniotomy, the hematoma was identified between the 2 layers of the dura and the fibrous membrane that protruded between the fracture lines was identified as the endosteal layer of dura. The hematoma was evacuated after opening the outer endosteal layer. After evacuation of the hematoma, the endosteal and meningeal layers could be identified separately and the point where these 2 layers split to enclose the hematoma was identified at the outer border of the hematoma. The child had no neurological sequel at the time of discharge.
Letramento literário multimodal e intermidiático: a construção do leitor/scriptor de una nova mídia
Authors: Ghirardi Ana Luiza Ramazzina
Published: October 2017

Esse artigo apresenta uma experiência didática realizada com estudantes da graduação de Letras (Português, Português-Francês, Português-Inglês, Português-Espanhol), da Escola de Filosofia, Letras e Ciências Humanas/UNIFESP, campus Guarulhos, durante o segundo semestre de 2015. O objetivo do curso, intitulado “Adaptação Literária e Multimodalidade”, era o de levar o aprendiz a se apropriar dos conceitos fundamentais de multimodalidade e de intermidialidade por meio de análise de adaptações literárias em diversas mídias. A estratégia didática adotada foi a de convidar o aprendiz a tomar o papel de autor/scriptor de uma transposição intermidiática multimodal através do manuseio de uma obra literária pertencente a uma mídia verbal textual (mídia-fon-te) com o objetivo de reconfigurá-la em uma mídia qualificada – filme, HQ, stop-motion etc. (mídia-alvo) a partir de sua apropriação da linguagem literária textual.
Letramento midiático no ensino de português: a formação da contrapalavra crítica
Authors: Barbosa Jacqueline Peixoto , Simões Pedro Henrique de Oliveira
Published: October 2017

Neste trabalho, tomando como ponto de partida a entrada dos textos jornalísticos no ensino de português, no Brasil, e suas diferentes perspectivas de abordagem nas últimas décadas, situados na perspectiva enunciativo-discursiva de ensino de língua, pretendemos discutir fundamentos do letramento midiático e perspectivas de trabalho com a esfera jornalística, em sala de aula. O acento apreciativo deste texto é o de que esse trabalho deve estar voltado não só para uma apropriação contextualizada dos gêneros jornalísticos, mas também, e principalmente, para a vivência significativa de prática sociais próprias dessa esfera e para a problematização crítica dos usos da língua, no diálogo com outras linguagens, a fim de que se formem sujeitos capazes de construir, nas práticas de leitura e de produção de textos, contrapalavras reflexivas e críticas acerca das questões éticas, estéticas e políticas com as quais se depara em suas práticas de letramentos.
Slams - letramentos literários de reexistência ao/no mundo contemporâneo
Authors: Neves C. A. B.
Published: October 2017

Um novo fenômeno de poesia oral e performática cresce no mundo contemporâneo: são os chamados slams – competições ou batalhas de poesias que dão vez e voz a poetas da periferia, os quais versam sobre as adversidades do seu cotidiano, abordando temas como racismo, violência, drogas, machismo, sexismo, sempre de teor crítico e engajado, que requerem a escuta, a reflexão e a politização do seu público- ouvinte. Os slammers incorporam as “vozes das margens” (HALL, 2003), as “vozes do Sul” (MOITA LOPES, 2006) ou as “vozes do corpo” (DE CERTEAU, 1994) e, nos palcos, atuam como agentes de letramentos de reexistência (SOUZA, 2011) ao declamarem poesias de sua própria autoria para cinco jurados escolhidos da plateia pelos organizadores do slam. Ao vencedor(a), livros!
Personal History, Beyond Narrative: an Embodied Perspective
Authors: Køster Allan
Published: October 2017

Narrative theories currently dominate our understanding of how selfhood is constituted and concretely individuated throughout personal history. Despite this success, the narrative perspective has recently been exposed to a range of critiques. Whilst these critiques have been effective in pointing out the shortcomings of narrative theories of selfhood, they have been less willing and able to suggest alternative ways of understanding personal history. In this article, I assess the criticisms and argue that an adequate phenomenology of personal history must also go beyond narrative. Drawing on a distinction between history and narrative, I outline an account of historical becoming through a process of sedimentation and a rich notion of what I call historical selfhood on an embodied level. Five embodied existentials are suggested, sketching a preliminary understanding of how selves are concretely individuated on a pre-narrative level.
The Phenomenology of Anomalous World Experience in Schizophrenia: A Qualitative Study
Authors: Pienkos Elizabeth , Silverstein Steven , Sass Louis
Published: October 2017

This current study is a pilot project designed to clarify changes in the lived world among people with diagnoses within the schizophrenia spectrum. The Examination of Anomalous World Experience (eawe) was used to interview ten participants with schizophrenia spectrum disorders (sz) and a comparison group of three participants with major depressive disorder (dep). Interviews were analyzed using the descriptive phenomenological method. This analysis revealed two complementary forms of experience unique toszparticipants: Destabilization, the experience that reality and the intersubjective world are less comprehensible, less stable, and generally less real; and Subjectivization, the dominance of one’s internal, subjective experiences in the perception or interpretation of the lived world. Persons with depressive disorders, by contrast, did not experience disruptions of the reality or independence of the world or any significant disruptions of appearance or meaning. These results are consistent with contemporary and classic phenomenological views on anomalous world experience in schizophrenia.
Reflexivity and Rapprochement: Explorations of a ‘Postsecular’ Public Theology
Authors: Graham Elaine
Published: October 2017

Accounts of secularization, decline and marginalization in relation to the public position of religion in western society have failed to account for the continued vitality and relevance of religion in the global public square. It is important, however, to challenge simplistic accounts and think of the new visibility of religion (not least in Europe) in terms of complexity and multi-dimensionality. This article will ask how public theology might contribute constructively to repairing our fractured body politic and promoting new models of citizenship and civic engagement around visions of the common good.
The Administration of International Law in National Courts and the Legitimacy of International Law
Authors: Chigara Benedict Abrahamson
Published: October 2017

Increasingly, national courts find themselves called upon to determine matters where un
lex specialis; regional supranational law; customary international law and domestic law all appear relevant. Lower court judges may be challenged significantly because such matters often lie beyond their day-to-day practice of interpreting and applying national law to local legal issues. This article recommends that to ensure both justice and legitimacy of international law, national courts − especially lower courts, should a priori consider whether the matters before them would be best served by appointing an expert academician ‘friend of the court’ to illuminate the contested applicable international law.
5. The Song of the Calf
Authors: Dechun Li , Roche Gerald
Published: October 2017

The Calf’s Song, meanwhile, tells the story of a calf and her mother. The two animals live as domestic livestock in a valley, and the calf dreams of escaping to freedom in the mountains. The mother discourages the calf, but she nonetheless escapes to the mountains, where she is surrounded by wolves. The mother appears to rescue the calf, who flees and, returning one week later, finds her mother’s remains. She then meditates on death, impermanence, and filial piety before returning to the valley to continue her life there.