bluuebunny/crossref_metadata_2025 huggingface dataset:
Outcomes and factors affecting them in patients with rhino-orbito-cerebral mucormycosis
Authors: Kashkouli Mohsen Bahmani , Abdolalizadeh Parya , Oghazian Mitra , Hadi Yasaman , Karimi Nasser , Ghazizadeh Mahya
Published: December 2018

Aim

To report the frequency and factors affecting patients’, globe and vision survivals in rhino-orbito-cerebral mucormycosis (ROCM).

Methods

This is a retrospective study of 63 patients (79 eyes) with biopsy-proven ROCM at a university hospital 2008–2016. Systemic and ophthalmic manifestations, imaging, management and final outcomes were recorded. Globe survival was defined as no exenteration and vision survival as final visual acuity of light perception and more.

Results

Mean age was 55.5 (SD 12.9) years with no gender preference. Diabetes was the most common underlying disease (68.3%). Patient survival was observed in 57.1 % (36/63). Presence of frozen eye (OR 4.6), nasal mucosal involvement (OR 7.3) and shorter duration of antifungal therapy (OR 1.03) were significantly associated with lower patient survival. Exenteration did not significantly change the survival. Globe survival was detected in 43% (34/79). Higher white blood cell (WBC) count was associated with a lower globe survival (p=0.02). Vision survival was observed in 25.3% (20/79) in whom younger age was significantly associated with a worse vision survival.

Conclusion

Patient, globe and vision survivals were 57%, 43% and 25%, respectively. Exenteration did not affect the patients’ survival. While frozen eye and nasal mucosal involvement were significantly associated with a lower survival, higher WBC count significantly increased the risk of exenteration.
Vitamin K status, supplementation and vascular disease: a systematic review and meta-analysis
Authors: Lees Jennifer Susan , Chapman Fiona A , Witham Miles D , Jardine Alan G , Mark Patrick B
Published: December 2018

Objectives

Vascular stiffness (VS) and vascular calcification (VC) are surrogate markers of vascular health associated with cardiovascular events. Vitamin K-dependent proteins (VKDP) are associated with VS and VC and require vitamin K for activity. We conducted a systematic review and meta-analysis of: (1) the effect of vitamin K supplementation on VS and VC and (2) association of inactive VKDP levels with incident cardiovascular disease and mortality.

Methods

Two authors searched MEDLINE and Embase databases and Cochrane and ISRCTN registries for studies of vitamin K clinical trials that measured effects on VC, VS or VKDP and longitudinal studies assessing effect of VKDP on incident CVD or mortality. Random effects meta-analyses were performed.

Results

Thirteen controlled clinical trials (n=2162) and 14 longitudinal studies (n=10 726) met prespecified inclusion criteria. Vitamin K supplementation was associated with significant reduction in VC (−9.1% (95% CI −17.7 to −0.5); p=0.04) and VKDP (desphospho-uncarboxylated matrix Gla protein; −44.7% (95% CI −65.1 to −24.3), p<0.0001) and uncarboxylated osteocalcin; −12.0% (95% CI −16.7 to −7.2), p<0.0001) compared with control, with a non-significant improvement in VS. In longitudinal studies with median follow-up of 7.8 (IQR 4.9–11.3) years, VKDP levels were associated with a combined endpoint of CVD or mortality (HR 0.45 (95% CI 0.07 to 0.83), p=0.02).

Conclusions

Supplementation with vitamin K significantly reduced VC, but not VS, compared with control. The conclusions drawn are limited by small numbers of studies with substantial heterogeneity. VKDP was associated with combined endpoint of CVD or mortality. Larger clinical trials of effect of vitamin K supplementation to improve VC, VS and long-term cardiovascular health are warranted.

Trial registration number

CRD42017060344.
Meiotic chromatid recombination and segregation assessed with human single cell genome sequencing data
Authors: Ma Jun-Yu , Yan Li-Ying , Wang Zhen-Bo , Luo Shi-Ming , Yeung William S B , Ou Xiang-Hong , Sun Qing-Yuan , Qiao Jie
Published: December 2018

Background

The human oocyte transmits one set of haploid genome into female pronucleus (FPN) while discards the remaining genome into the first polar body (PB1) and the second polar body (PB2). The FPN genome carries an assembly of maternal and paternal genome that resulted from homologous recombination during the prophase of the first meiosis. However, how parental genome has been shuffled and transmitted is difficult to assess by analysing only the progeny’s genome.

Objective

To assess meiotic chromatid recombination and segregation in human oocytes.

Methods

Single cell genome sequencing data of PB1, PB2 and FPN that originated from the same oocyte were used to analyse the human oocyte homologous chromosome interaction and segregation. To analyse whether chromosomes were non-randomly segregated into polar bodies or pronucleus, we analysed the ratio of crossover in PB2 and FPN, and constructed a model to detect the randomness of oocyte chromosome segregation.

Results

We found that during oocyte meiosis, in addition to homologous chromosome recombination, there was also a genome conversion phenomenon which generated a non-reciprocal genetic information transmission between homologous chromosomes. We also inferred that during meiosis, DNA breaks and repairs frequently occurred at centromere-adjacent regions. From our data we did not find obvious evidence supporting the crossover number-based or SNP-based meiotic drive in oocytes.

Conclusion

In addition to the crossover-based recombination, during human oocyte meiosis, a direct genome conversion between homologous chromosomes is used in some oocytes. Our findings are helpful in understanding the specific features of meiotic chromatid recombination and segregation in human oocytes.
Mortality of US astronauts: comparisons with professional athletes
Authors: Reynolds Robert J , Day Steven M
Published: December 2018

Objective

Studies of mortality among US astronauts are complicated by the healthy worker effect, which predicts lower mortality for astronauts than the general population based solely on the ability to become and remain an astronaut. We attempt to evaluate astronaut mortality risk while accounting for the healthy worker effect.

Methods

We compare mortality rates of male US astronauts with those of professional athletes from Major League Baseball and the National Basketball Association between January 1, 1960 and May 31, 2018.

Results

Both athlete cohorts and astronauts had significantly lower-than-expected mortality in comparison with the general population. For the overall study period, there were no significant differences in all-cause mortality rates between astronauts and athletes. Astronauts were at greater risk of death from external causes (SMR=583; 95% CI 377 to 860) and reduced risk of death from cardiovascular disease (SMR=39; 95% CI 18 to 73) and all natural causes (SMR=67; 95% CI 47 to 93).

Conclusions

The data presented here do not support increased mortality for astronauts due to unique exposures received in space. The mortality experience of astronauts as compared with professional baseball and basketball players should be re-examined periodically as part of the ongoing surveillance of astronaut mortality in years to come.
Cold temperature tolerance of albino rainbow shark (Epalzeorhynchos frenatum), a tropical fish with transgenic application in the ornamental aquarium trade
Authors: Leggatt R.A.
Published: December 2018

Application of fluorescent protein transgenesis has commercial use for the ornamental aquarium trade by creating new colour phenotypes in various species. To determine the potential for transgenic ornamental aquarium fish to overwinter in Canada, the minimum temperature tolerance of albino rainbow shark (Epalzeorhynchos frenatum (Fowler, 1934)) was estimated to complement a previous study examining cold tolerance of zebrafish (Danio rerio (Hamilton, 1822)), black tetra (Gymnocorymbus ternetzi (Boulenger, 1895)), and tiger barb (Puntius tetrazona (Bleeker, 1855)). Rainbow shark had higher low temperature tolerance limits (LD50 = 10.7 ± 0.1 °C) than surveyed winter water temperatures in Canada. There was a significant negative correlation between condition factor and temperature at loss of equilibrium, suggesting fish with lower social status may be more susceptible to cold temperature than dominant fish. These results indicate transgenic E. frenatum are not expected to persist over winter in Canadian waters.
Defect formation of CuI-doped by group-IIB elements
Authors: Chen Hui , Gu Mu
Published: December 2018

First-principles calculations have been performed to investigate the doping defects in CuI with group-IIB elements such as Zn, Cd and Hg. The calculated transition energies for substitutional Zn, Cd and Hg are 1.32, 1.28 and 0.60 eV, respectively. These group-IIB elements at the substitutional sites complex with a copper vacancy [Formula: see text] have the lower formation energies as compared to dopants located at the substitutional sites or interstitial sites, respectively. Among all the complex defects considered, [Formula: see text] has the lowest formation energy and it induces the acceptor level [Formula: see text] eV above the valence-band maximum (VBM), which is close to the acceptor level [Formula: see text] eV of [Formula: see text], suggesting that Hg may be a good dopant for CuI to improve its p-type conductivity.
IoT Data Prefetching in Indoor Navigation SOAs
Authors: Konstantinidis Andreas , Irakleous Panagiotis , Georgiou Zacharias , Zeinalipour-Yazti Demetrios , Chrysanthis Panos K.
Published: December 2018

Internet-based Indoor Navigation Service-Oriented Architectures (IIN-SOA)
organize signals collected by IoT-based devices to enable a wide range of novel applications indoors, where people spend 80--90% of their time. In this article, we study the problem of
prefetching (or hoarding) the most important IoT data from an IIN-SOA to a mobile device, without knowing its user’s destination during navigation
. Our proposed
Grap (Graph Prefetching)
framework structurally analyzes building topologies to identify important areas that become virtual targets to an online heuristic search algorithm we developed. We tested Grap with datasets from a real IIN-SOA and found it to be impressively accurate.
FlashNet
Authors: Trivedi Animesh , Ioannou Nikolas , Metzler Bernard , Stuedi Patrick , Pfefferle Jonas , Kourtis Kornilios , Koltsidas Ioannis , Gross Thomas R.
Published: December 2018

During the past decade, network and storage devices have undergone rapid performance improvements, delivering ultra-low latency and several Gbps of bandwidth. Nevertheless, current network and storage stacks fail to deliver this hardware performance to the applications, often due to the loss of I/O efficiency from stalled CPU performance. While many efforts attempt to address this issue solely on either the network or the storage stack, achieving high-performance for networked-storage applications requires a holistic approach that considers both.

In this article, we present FlashNet, a software I/O stack that unifies high-performance network properties with flash storage access and management. FlashNet builds on RDMA principles and abstractions to provide a direct, asynchronous, end-to-end data path between a client and remote flash storage. The key insight behind FlashNet is to
co-design
the stack’s components (an RDMA controller, a flash controller, and a file system) to enable cross-stack optimizations and maximize I/O efficiency. In micro-benchmarks, FlashNet improves 4kB network I/O operations per second (IOPS by 38.6% to 1.22M, decreases access latency by 43.5% to 50.4μs, and prolongs the flash lifetime by 1.6-5.9× for writes. We illustrate the capabilities of FlashNet by building a Key-Value store and porting a distributed data store that uses RDMA on it. The use of FlashNet’s RDMA API improves the performance of KV store by 2× and requires minimum changes for the ported data store to access remote flash devices.
Hardware Multithreaded Transactions
Authors: Fix Jordan , Nagendra Nayana P. , Apostolakis Sotiris , Zhang Hansen , Qiu Sophie , August David I.
Published: December 2018

Speculation with transactional memory systems helps pro- grammers and compilers produce profitable thread-level parallel programs. Prior work shows that supporting transactions that can span multiple threads, rather than requiring transactions be contained within a single thread, enables new types of speculative parallelization techniques for both programmers and parallelizing compilers. Unfortunately, software support for multi-threaded transactions (MTXs) comes with significant additional inter-thread communication overhead for speculation validation. This overhead can make otherwise good parallelization unprofitable for programs with sizeable read and write sets. Some programs using these prior software MTXs overcame this problem through significant efforts by expert programmers to minimize these sets and optimize communication, capabilities which compiler technology has been unable to equivalently achieve. Instead, this paper makes speculative parallelization less laborious and more feasible through low-overhead speculation validation, presenting the first complete design, implementation, and evaluation of hardware MTXs. Even with maximal speculation validation of every load and store inside transactions of tens to hundreds of millions of instructions, profitable parallelization of complex programs can be achieved. Across 8 benchmarks, this system achieves a geomean speedup of 99% over sequential execution on a multicore machine with 4 cores.
Exploiting Dynamic Thermal Energy Harvesting for Reusing in Smartphone with Mobile Applications
Authors: Dai Yuting , Li Tao , Liu Benyong , Song Mingcong , Chen Huixiang
Published: December 2018

Recently, mobile applications have gradually become performance- and resource- intensive, which results in a massive battery power drain and high surface temperature, and further degrades the user experience. Thus, high power consumption and surface over-heating have been considered as a severe challenge to smartphone design. In this paper, we propose DTEHR, a mobile Dynamic Thermal Energy Harvesting Reusing framework to tackle this challenge. The approach is sustainable in that it generates energy using dynamic Thermoelectric Generators (TEGs). The generated energy not only powers Thermoelectric Coolers (TECs) for cooling down hot-spots, but also recharges micro-supercapacitors (MSCs) for extended smartphone usage. To analyze thermal characteristics and evaluate DTEHR across real-world applications, we build MPPTAT (Multi-comPonent Power and Thermal Analysis Tool), a power and thermal analyzing tool for Android. The result shows that DTEHR reduces the temperature differences between hot areas and cold areas up to 15.4°C (internal) and 7°C (surface). With TEC-based hot-spots cooling, DTEHR reduces the temperature of the surface and internal hot-spots by an average of 8° and 12.8mW respectively. With dynamic TEGs, DTEHR generates 2.7-15mW power, more than hundreds of times of power that TECs need to cool down hot-spots. Thus, extra-generated power can be stored into MSCs to prolong battery life.
SmoothOperator
Authors: Hsu Chang-Hong , Deng Qingyuan , Mars Jason , Tang Lingjia
Published: December 2018

With the ever growing popularity of cloud computing and web services, Internet companies are in need of increased computing capacity to serve the demand. However, power has become a major limiting factor prohibiting the growth in industry: it is often the case that no more servers can be added to datacenters without surpassing the capacity of the existing power infrastructure. In this work, we first investigate the power utilization in Facebook datacenters. We observe that the combination of provisioning for peak power usage, highly fluctuating traffic, and multi-level power delivery infrastructure leads to significant
power budget fragmentation
problem and inefficiently low power utilization. To address this issue, our insight is that heterogeneity of power consumption patterns among different services provides opportunities to re-shape the power profile of each power node by re-distributing services. By grouping services with asynchronous peak times under the same power node, we can reduce the peak power of each node and thus creating more power head-rooms to allow more servers hosted, achieving higher throughput. Based on this insight, we develop a
workload-aware service placement
framework to systematically spread the service instances with synchronous power patterns evenly under the power supply tree, greatly reducing the peak power draw at power nodes. We then leverage
dynamic power profile reshaping
to maximally utilize the headroom unlocked by our placement framework. Our experiments based on real production workload and power traces show that we are able to host up to 13% more machines in production, without changing the underlying power infrastructure. Utilizing the unleashed power headroom with dynamic reshaping, we achieve up to an estimated total of 15% and 11% throughput improvement for latency-critical service and batch service respectively at the same time, with up to 44% of energy slack reduction.
Darwin
Authors: Turakhia Yatish , Bejerano Gill , Dally William J.
Published: December 2018

Genomics is transforming medicine and our understanding of life in fundamental ways. Genomics data, however, is far outpacing Moore»s Law. Third-generation sequencing technologies produce 100X longer reads than second generation technologies and reveal a much broader mutation spectrum of disease and evolution. However, these technologies incur prohibitively high computational costs. Over 1,300 CPU hours are required for reference-guided assembly of the human genome, and over 15,600 CPU hours are required for de novo assembly. This paper describes "Darwin" --- a co-processor for genomic sequence alignment that, without sacrificing sensitivity, provides up to $15,000X speedup over the state-of-the-art software for reference-guided assembly of third-generation reads. Darwin achieves this speedup through hardware/algorithm co-design, trading more easily accelerated alignment for less memory-intensive filtering, and by optimizing the memory system for filtering. Darwin combines a hardware-accelerated version of D-SOFT, a novel filtering algorithm, alignment at high speed, and with a hardware-accelerated version of GACT, a novel alignment algorithm. GACT generates near-optimal alignments of arbitrarily long genomic sequences using constant memory for the compute-intensive step. Darwin is adaptable, with tunable speed and sensitivity to match emerging sequencing technologies and to meet the requirements of genomic applications beyond read assembly.
Understanding and Auto-Adjusting Performance-Sensitive Configurations
Authors: Wang Shu , Li Chi , Hoffmann Henry , Lu Shan , Sentosa William , Kistijantoro Achmad Imam
Published: December 2018

Modern software systems are often equipped with hundreds to thousands of configurations, many of which greatly affect performance. Unfortunately, properly setting these configurations is challenging for developers due to the complex and dynamic nature of system workload and environment. In this paper, we first conduct an empirical study to understand performance-sensitive configurations and the challenges of setting them in the real-world. Guided by our study, we design a systematic and general control-theoretic framework, SmartConf, to automatically set and dynamically adjust performance-sensitive configurations to meet required operating constraints while optimizing other performance metrics. Evaluation shows that SmartConf is effective in solving real-world configuration problems, often providing better performance than even the best static configuration developers can choose under existing configuration systems.
DATS - Data Containers for Web Applications
Authors: Hunger Casen , Vilanova Lluis , Papamanthou Charalampos , Etsion Yoav , Tiwari Mohit
Published: December 2018

Data containers enable users to control access to their data while untrusted applications compute on it. However, they require replicating an application inside each container - compromising functionality, programmability, and performance. We propose DATS - a system to run web applications that retains application usability and efficiency through a mix of hardware capability enhanced containers and the introduction of two new primitives modeled after the popular model-view-controller (MVC) pattern. (1) DATS introduces a templating language to create views that compose data across data containers. (2) DATS uses authenticated storage and confinement to enable an untrusted storage service, such as memcached and deduplication, to operate on plain-text data across containers. These two primitives act as robust declassifiers that allow DATS to enforce non-interference across containers, taking large applications out of the trusted computing base (TCB). We showcase eight different web applications including Gitlab and a Slack-like chat, significantly improve the worst-case overheads due to application replication, and demonstrate usable performance for common-case usage.
Demon
Authors: Xu Yu , Yao Jianguo , Dong Yaozu , Tian Kun , Zheng Xiao , Guan Haibing
Published: December 2018

Memory Management Units (MMUs) for on-device address translation are widely used in modern devices. However, conventional solutions for on-device MMU virtualization, such as shadow page table implemented in mediated pass-through, still suffer from high complexity and low performance.

We present Demon, an efficient solution for on-DEvice MMU virtualizatiON in mediated pass-through. The key insight is that Demon takes advantage of IOMMU to construct a two-dimensional address translation and dynamically switches the 2nd-dimensional page table to a proper candidate when the device owner switches. In order to support fine-grained parallelism for the device with multiple engines, we put forward a hardware proposal that separates the address space of each engine and enables simultaneous device address remapping for multiple virtual machines (VMs). We implement Demon with a prototype named gDemon which virtualizes Intel GPU MMU. Nonetheless, Demon is not limited to this particular case. Evaluations show that gDemon provides up to 19.73x better performance in the media transcoding workloads and achieves performance improvement of up to 17.09% and 13.73% in the 2D benchmarks and 3D benchmarks, respectively, compared with gVirt. The current release of gDemon scales up to 6 VMs with moderate performance in our experiments. In addition, gDemon simplifies the implementation of GPU MMU virtualization with 37% code reduction.
Persistency for synchronization-free regions
Authors: Gogte Vaibhav , Diestelhorst Stephan , Wang William , Narayanasamy Satish , Chen Peter M. , Wenisch Thomas F.
Published: December 2018

Nascent persistent memory (PM) technologies promise the performance of DRAM with the durability of disk, but how best to integrate them into programming systems remains an open question. Recent work extends language memory models with a persistency model prescribing semantics for updates to PM. These semantics enable programmers to design data structures in PM that are accessed like memory and yet are recoverable upon crash or failure. Alas, we find the semantics and performance of existing approaches unsatisfying. Existing approaches require high-overhead mechanisms, are restricted to certain synchronization constructs, provide incomplete semantics, and/or may recover to state that cannot arise in fault-free execution.

We propose persistency semantics that guarantee failure atomicity of synchronization-free regions (SFRs) - program regions delimited by synchronization operations. Our approach provides clear semantics for the PM state recovery code may observe and extends C++11's "sequential consistency for data-race-free" guarantee to post-failure recovery code. We investigate two designs for failure-atomic SFRs that vary in performance and the degree to which commit of persistent state may lag execution. We demonstrate both approaches in LLVM v3.6.0 and compare to a state-of-the-art baseline to show performance improvement up to 87.5% (65.5% avg).
Typed closure conversion for the calculus of constructions
Authors: Bowman William J. , Ahmed Amal
Published: December 2018

Dependently typed languages such as Coq are used to specify and verify the full functional correctness of source programs. Type-preserving compilation can be used to preserve these specifications and proofs of correctness through compilation into the generated target-language programs. Unfortunately, type-preserving compilation of dependent types is hard. In essence, the problem is that dependent type systems are designed around high-level compositional abstractions to decide type checking, but compilation interferes with the type-system rules for reasoning about run-time terms.

We develop a type-preserving closure-conversion translation from the Calculus of Constructions (CC) with strong dependent pairs (Σ types)—a subset of the core language of Coq—to a type-safe, dependently typed compiler intermediate language named CC-CC. The central challenge in this work is how to translate the source type-system rules for reasoning about functions into target type-system rules for reasoning about closures. To justify these rules, we prove soundness of CC-CC by giving a model in CC. In addition to type preservation, we prove correctness of separate compilation.
HHVM JIT: a profile-guided, region-based compiler for PHP and Hack
Authors: Ottoni Guilherme
Published: December 2018

Dynamic languages such as PHP, JavaScript, Python, and Ruby have been gaining popularity over the last two decades. A very popular domain for these languages is web development, including server-side development of large-scale websites. As a result, improving the performance of these languages has become more important. Efficiently compiling programs in these languages is challenging, and many popular dynamic languages still lack efficient production-quality implementations. This paper describes the design of the second generation of the HHVM JIT and how it addresses the challenges to efficiently execute PHP and Hack programs. This new design uses profiling to build an aggressive region-based JIT compiler. We discuss the benefits of this approach compared to the more popular method-based and trace-based approaches to compile dynamic languages. Our evaluation running a very large PHP-based code base, the Facebook website, demonstrates the effectiveness of the new JIT design.
Enhancing computation-to-core assignment with physical location information
Authors: Kislal Orhan , Kotra Jagadish , Tang Xulong , Kandemir Mahmut Taylan , Jung Myoungsoo
Published: December 2018

Going beyond a certain number of cores in modern architectures requires an on-chip network more scalable than conventional buses. However, employing an on-chip network in a manycore system (to improve scalability) makes the latencies of the data accesses issued by a core non-uniform. This non-uniformity can play a significant role in shaping the overall application performance. This work presents a novel compiler strategy which involves exposing architecture information to the compiler to enable an optimized computation-to-core mapping. Specifically, we propose a compiler-guided scheme that takes into account the relative positions of (and distances between) cores, last-level caches (LLCs) and memory controllers (MCs) in a manycore system, and generates a mapping of computations to cores with the goal of minimizing the on-chip network traffic. The experimental data collected using a set of 21 multi-threaded applications reveal that, on an average, our approach reduces the on-chip network latency in a 6×6 manycore system by 38.4% in the case of private LLCs, and 43.8% in the case of shared LLCs. These improvements translate to the corresponding execution time improvements of 10.9% and 12.7% for the private LLC and shared LLC based systems, respectively.
Automated clustering and program repair for introductory programming assignments
Authors: Gulwani Sumit , Radiček Ivan , Zuleger Florian
Published: December 2018

Providing feedback on programming assignments is a tedious task for the instructor, and even impossible in large Massive Open Online Courses with thousands of students. Previous research has suggested that program repair techniques can be used to generate feedback in programming education. In this paper, we present a novel fully automated program repair algorithm for introductory programming assignments. The key idea of the technique, which enables automation and scalability, is to use the existing correct student solutions to repair the incorrect attempts. We evaluate the approach in two experiments: (I) We evaluate the number, size and quality of the generated repairs on 4,293 incorrect student attempts from an existing MOOC. We find that our approach can repair 97% of student attempts, while 81% of those are small repairs of good quality. (II) We conduct a preliminary user study on performance and repair usefulness in an interactive teaching setting. We obtain promising initial results (the average usefulness grade 3.4 on a scale from 1 to 5), and conclude that our approach can be used in an interactive setting.
SWOOP: software-hardware co-design for non-speculative, execute-ahead, in-order cores
Authors: Tran Kim-Anh , Jimborean Alexandra , Carlson Trevor E. , Koukos Konstantinos , Själander Magnus , Kaxiras Stefanos
Published: December 2018

Increasing demands for energy efficiency constrain emerging hardware. These new hardware trends challenge the established assumptions in code generation and force us to rethink existing software optimization techniques. We propose a cross-layer redesign of the way compilers and the underlying microarchitecture are built and interact, to achieve both performance and high energy efficiency.

In this paper, we address one of the main performance bottlenecks — last-level cache misses — through a software-hardware co-design. Our approach is able to hide memory latency and attain increased memory and instruction level parallelism by orchestrating
a non-speculative, execute-ahead paradigm in software
(SWOOP). While out-of-order (OoO) architectures attempt to hide memory latency by dynamically reordering instructions, they do so through expensive, power-hungry, speculative mechanisms.We aim to shift this complexity into software, and we build upon compilation techniques inherited from VLIW, software pipelining, modulo scheduling, decoupled access-execution, and software prefetching. In contrast to previous approaches we do not rely on either software or hardware speculation that can be detrimental to efficiency. Our SWOOP compiler is enhanced with lightweight architectural support, thus being able to transform applications that include highly complex control-flow and indirect memory accesses.
Inferring type rules for syntactic sugar
Authors: Pombrio Justin , Krishnamurthi Shriram
Published: December 2018

Type systems and syntactic sugar are both valuable to programmers, but sometimes at odds. While sugar is a valuable mechanism for implementing realistic languages, the expansion process obscures program source structure. As a result, type errors can reference terms the programmers did not write (and even constructs they do not know), baffling them. The language developer must also manually construct type rules for the sugars, to give a typed account of the surface language. We address these problems by presenting a process for automatically reconstructing type rules for the surface language using rules for the core. We have implemented this theory, and show several interesting case studies.
Locality analysis through static parallel sampling
Authors: Chen Dong , Liu Fangzhou , Ding Chen , Pai Sreepathi
Published: December 2018

Locality analysis is important since accessing memory is much slower than computing. Compile-time locality analysis can provide detailed program-level feedback for compilers or runtime systems faster than trace-based locality analysis.

In this paper, we describe a new approach to locality analysis based on static parallel sampling. A compiler analyzes loop-based code and generates sampler code which is run to measure locality. Our approach can predict precise cache line granularity miss ratio curves for complex loops with non-linear array references and even branches. The precision and overhead of static sampling are evaluated using PolyBench and a bit-reversal loop. Our result shows that by randomly sampling 2% of loop iterations, a compiler can construct almost exact miss ratio curves as trace based analysis. Sampling 0.5% and 1% iterations can achieve good precision and efficiency with an average 0.6% to 1% the time of tracing respectively. Our analysis can also be parallelized. The analysis may assist program optimization techniques such as tiling, program co-location, cache hint selection and help to analyze write locality and parallel locality.
Verifying that web pages have accessible layout
Authors: Panchekha Pavel , Geller Adam T. , Ernst Michael D. , Tatlock Zachary , Kamil Shoaib
Published: December 2018

Usability and accessibility guidelines aim to make graphical user interfaces accessible to all users, by, say, requiring that text is sufficiently large, interactive controls are visible, and heading size corresponds to importance. These guidelines must hold on the infinitely many possible renderings of a web page generated by differing screen sizes, fonts, and other user preferences. Today, these guidelines are tested by manual inspection of a few renderings, because 1) the guidelines are not expressed in a formal language, 2) the semantics of browser rendering are not well understood, and 3) no tools exist to check all possible renderings of a web page. VizAssert solves these problems. First, it introduces visual logic to precisely specify accessibility properties. Second, it formalizes a large fragment of the browser rendering algorithm using novel finitization reductions. Third, it provides a sound, automated tool for verifying assertions in visual logic.

We encoded 14 assertions drawn from best-practice accessibility and mobile-usability guidelines in visual logic. VizAssert checked them on on 62 professionally designed web pages. It found 64 distinct errors in the web pages, while reporting only 13 false positive warnings.
Probabilistic programming with programmable inference
Authors: Mansinghka Vikash K. , Schaechtle Ulrich , Handa Shivam , Radul Alexey , Chen Yutian , Rinard Martin
Published: December 2018

We introduce inference metaprogramming for probabilistic programming languages, including new language constructs, a formalism, and the rst demonstration of e ectiveness in practice. Instead of relying on rigid black-box inference algorithms hard-coded into the language implementation as in previous probabilistic programming languages, infer- ence metaprogramming enables developers to 1) dynamically decompose inference problems into subproblems, 2) apply in- ference tactics to subproblems, 3) alternate between incorpo- rating new data and performing inference over existing data, and 4) explore multiple execution traces of the probabilis- tic program at once. Implemented tactics include gradient- based optimization, Markov chain Monte Carlo, variational inference, and sequental Monte Carlo techniques. Inference metaprogramming enables the concise expression of proba- bilistic models and inference algorithms across diverse elds, such as computer vision, data science, and robotics, within a single probabilistic programming language.
User-guided program reasoning using Bayesian inference
Authors: Raghothaman Mukund , Kulkarni Sulekha , Heo Kihong , Naik Mayur
Published: December 2018

Program analyses necessarily make approximations that often lead them to report true alarms interspersed with many false alarms. We propose a new approach to leverage user feedback to guide program analyses towards true alarms and away from false alarms. Our approach associates each alarm with a confidence value by performing Bayesian inference on a probabilistic model derived from the analysis rules. In each iteration, the user inspects the alarm with the highest confidence and labels its ground truth, and the approach recomputes the confidences of the remaining alarms given this feedback. It thereby maximizes the return on the effort by the user in inspecting each alarm. We have implemented our approach in a tool named Bingo for program analyses expressed in Datalog. Experiments with real users and two sophisticated analyses---a static datarace analysis for Java programs and a static taint analysis for Android apps---show significant improvements on a range of metrics, including false alarm rates and number of bugs found.
Bounding data races in space and time
Authors: Dolan Stephen , Sivaramakrishnan KC , Madhavapeddy Anil
Published: December 2018

We propose a new semantics for shared-memory parallel programs that gives strong guarantees even in the presence of data races. Our
local data race freedom
property guarantees that all data-race-free portions of programs exhibit sequential semantics. We provide a straightforward operational semantics and an equivalent axiomatic model, and evaluate an implementation for the OCaml programming language. Our evaluation demonstrates that it is possible to balance a comprehensible memory model with a reasonable (no overhead on x86, ~0.6% on ARM) sequential performance trade-off in a mainstream programming language.
On the System Entropy and Energy Dissipativity of Stochastic Systems and Their Application in Biological Systems
Authors: Chen Bor-Sen , Lin Xiangyun , Zhang Weihai , Zhou Tianshou
Published: December 2018

This study discusses the relationship between the entropy and the dissipativity of stochastic systems under the background of biological systems. First, measurement methods of the system entropy and energy dissipativity of linear stochastic biological systems are introduced. We found that the system entropy is negatively proportional to the energy dissipativity in logarithmic scale. Some opposite effects between system entropy and energy dissipativity are also discussed and compared based on their measured values to get insight into the understanding of the system mechanisms and the system characteristics. We found that the intrinsic random fluctuation and the enhancement of the system robust stability both can increase the system entropy but decrease the system dissipativity. The system entropy and the energy dissipativity of nonlinear stochastic biological systems are also discussed and compared based on a global linearization method. Computation methods are also provided. Finally, two numerical examples are demonstrated to verify theoretical prediction.
Aluminum in Effluents and Sludges from the Preliminary Coagulation in Dairy Factory Aerated Balancing Tanks: An Analytical and Sorption Study
Authors: Sadowski Michał , Anielak Piotr , Wolf Wojciech M.
Published: December 2018

The coagulation process is used as the first step for the chemical treatment of liquid waste. Resulting wet sludge is treated with coagulants or polyelectrolytes to improve dewatering characteristics of its so-called conditioning. The coagulants such as aluminum sulphate or polyaluminum chloride (Al2Cln(OH)6−n) are widely used for dairy wastewater treatment systems. The pretreatment dairy sludge can be applied in agriculture as fertilizer containing valuable nutrients. Hence, a simple, cost effective, and rapid method for the determination of aluminum content in the sludge is essential for calculation of the appropriate coagulant dose at the sludge pretreatment process. In this paper either colorimetric or atomic absorption spectrometric methods as applied for the determination of aluminum concentration in the dairy wastewater are compared. For colorimetric method, the optimum experimental conditions such as pH, reaction time, and concentration of other ions in the sample were determined. The sorption isotherms of aluminum on the activated sludge were determined for diverse aluminum species.
Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein
Authors: Fu Yi , Zhao Ji , Chen Zhiguo
Published: December 2018

Protein-ligand interactions are a necessary prerequisite for signal transduction, immunoreaction, and gene regulation. Protein-ligand interaction studies are important for understanding the mechanisms of biological regulation, and they provide a theoretical basis for the design and discovery of new drug targets. In this study, we analyzed the molecular interactions of protein-ligand which was docked by AutoDock 4.2 software. In AutoDock 4.2 software, we used a new search algorithm, hybrid algorithm of random drift particle swarm optimization and local search (LRDPSO), and the classical Lamarckian genetic algorithm (LGA) as energy optimization algorithms. The best conformations of each docking algorithm were subjected to molecular dynamic (MD) simulations to further analyze the molecular mechanisms of protein-ligand interactions. Here, we analyze the binding energy between protein receptors and ligands, the interactions of salt bridges and hydrogen bonds in the docking region, and the structural changes during complex unfolding. Our comparison of these complexes highlights differences in the protein-ligand interactions between the two docking methods. It also shows that salt bridge and hydrogen bond interactions play a crucial role in protein-ligand stability. The present work focuses on extracting the deterministic characteristics of docking interactions from their dynamic properties, which is important for understanding biological functions and determining which amino acid residues are crucial to docking interactions.
Facilitators and Barriers of Assistive Technology and Learning Environment for Children with Special Needs
Authors: Lersilp Suchitporn , Putthinoi Supawadee , Lersilp Theeratorn
Published: December 2018

The purpose of this research was to study the facilitators and barriers of assistive technology (AT) and the learning environment for children with special needs in special education schools in Chiang Mai, Thailand. The informants were one hundred and sixteen children with special needs, who studied in nursery to Grade 12, or with their caregivers. The instrument was a questionnaire applied by the International Classification of Functioning, Disability and Health (ICF) and examined for content validity by five specialists. The results in terms of AT showed that a majority of children with physical disability needed it for mobility and use of school buildings and those with hearing disability for communication. However, most of the children did not need to use AT for culture, recreation, or sports, while many considered it as a facilitator for education. In terms of the learning environment, most characteristics of the physical environment were facilitators for children with special needs, as were those of the social environment for all groups of such children. The results of this study were useful in providing information for AT and design of a learning environment relating to the varied characteristics of children with special needs in special education schools.
A MEMS-IMU Assisted BDS Triple-Frequency Ambiguity Resolution Method in Complex Environments
Authors: Cheng Junbing , Li Deng-ao , Zhao Jumin
Published: December 2018

Emerging technologies such as smart cities and unmanned vehicles all need Global Navigation Satellite Systems (GNSS) to provide high-precision positioning and navigation services. Fast and reliable carrier phase ambiguity resolution (AR) is a prerequisite for high-precision positioning. The poor satellite geometry and severe multipath effect caused by Beidou Navigation Satellite System (BDS) signal occlusion and reflection in complex environments will degrade the AR performance. In this contribution, a fast triple-frequency AR method combining Microelectromechanical System-Inertial Measurement Unit (MEMS-IMU) and BDS is proposed. First, the Extra-Wide Lane (EWL) ambiguity is fixed with the positioning parameters of MEMS-IMU instead of the pseudorange. Then, the phase noise variance of Narrow Lane (NL) observation is obtained from ambiguity-fixed EWL observation to reduce the total noise level of NL observation, and the NL ambiguity can be reliably fixed, and the BDS positioning result is obtained. Finally, the BDS positioning result is used as the posterior measurement of the extended Kalman filter to update the MEMS-IMU positioning parameters to form the coupling loop of MEMS-IMU and BDS. The data of urban road vehicle experiments were collected to verify the feasibility and effectiveness of the proposed algorithm. Results show that MEMS-IMU can speed up AR, and reduction of total noise level can significantly improve the reliability of AR.
Crisis Spreading Model of the Shareholding Networks of Listed Companies and Their Main Holders and Their Controllability
Authors: Ma Yuanyuan , Li Lingxuan
Published: December 2018

Bankruptcy of listed companies or shareholders delisting usually causes the crisis spreading in stock markets. Based on the systematic analysis of the epidemic diseases and rumors spreading on the complex networks, the SIR model is introduced to research the crisis spreading in shareholding networks of listed companies and their main holders on the basis of the data about ownership structure in Chinese Stock Markets. The characteristics of shareholding networks are studied, and the parameters for the SIR model are obtained by empirical approach. Then, the numerical computation method is successfully used to analyze the crisis spreading in the networks when the networks meet random failures or intentional attacks. We find the networks have good robustness against the random failures. However, the crisis will spread at a high speed and cause catastrophic damage if there are some failures or attacks on hub vertices in the networks. Under this condition, the networks show obvious vulnerability. Last but not least, the controllability of the networks under the condition of intentional attacks and random failures is studied. The results show that if the network is controlled globally, it is more reliable to allow a politically good new or an appropriate exciting economical policy to play the role in orienting markets under the control of public opinions as the crisis occurs. However, under normal circumstances, controlling a small part of driver vertices representing listed companies, applying appropriate control strategies, and using its characteristics of high efficiency of sending information can effectively control the stock market. Our research provides a new reference to further exploration about the transmission mechanism of the crisis based SIR model and further research on the controllability of crisis spreading in financial markets.
Predicting Pedestrian Counts for Crossing Scenario Based on Fused Infrared-Visual Videos
Authors: Huang Shize , Chen Wei , Yu Rongjie , Yang Xiaolu , Dong Decun
Published: December 2018

Estimating the number of pedestrians based upon surveillance videos and images has been a critical task while implementing intelligent signal controls at intersections. However, this has been a difficult task considering the pedestrian waiting area is an outdoor scenario with complex and time-varying surrounding environment. In this study, a method for estimating pedestrian counts based on multisource video data has been proposed. First, the partial least squares regression (PLSR) model is developed to estimate the number of pedestrians from single-source video (either visible light video or infrared video). Meanwhile, the temporal feature of the scenario (daytime or nighttime) is identified based on visible light video. According to the recognized time periods, pedestrian count detection results from the visible light and infrared video data can be obtained with preset corresponding confidence levels. The empirical experiments showed that this fusion method based on environment perception holds the benefits of 24-hour monitoring for outdoor scenarios at the pedestrian waiting area and substantially improved accuracy of pedestrian counting.