Communication Pipeline Research Articles

The American Society for Preventive Cardiology.

The American Society for Preventive Cardiology (ASPC) has started 2018 with noteworthy initiatives. A recap of just a few will be beneficial for members, as well as nonmembers, who will hopefully be inspired to join our burgeoning society. First, we have continued and augmented our Town Hall Series exploring and solving medication access problems in the United States. The 2016 and 2017 meetings were an extraordinary success as we led the nation in the mission to help appropriate patients gain access to PCSK9i, while simultaneously creating methods to ease the massive burdens on our offices. Continuing such advocacy efforts, the ASPC organized 5 programs in 2018 to convene at the American College of Cardiology (ACC), PriMed California, ASPC, Cardiometabolic Health Congress, and the American Heart Association meetings. We hope to see many of you there, so you can share your opinions and also learn to use the tools we have recently developed to help you and your patients. Second, eager to tear down silos separating diverse medical disciplines, the ASPC founded the American Society for Preventive Cardiology Collaborative Action Group (ACAG). Our inaugural meeting was held at the 2018 ACC meeting, where 20+ groups met to discuss issues seemingly specific to their fields, yet actually sharing a commonality with others. The ACAG mission is to facilitate collaboration among varied groups, helping one another amplify their respective missions. ACAG will not launch its own initiatives; it exists solely as a facilitative pipeline of communication and amplification. Third, ASPC created a robust mobile app designed to help clinicians navigate the complex insurance world, thereby ensuring that your patients receive the medications you have prescribed. We began with the PCSK9i, as these medicines have seen unprecedented insurance barriers, making access to them often impossible. The app contains invaluable resources such as a 10-step guide to success, single-page prior authorization and appeal letters, contact information for all state insurance commissioners, links to other helpful resources, and much more. We will soon add similar solutions for heart failure and diabetes medications. Please know that we always welcome suggestions to improve—or add additional functionality to—the app. I would encourage everyone to download the app and then “join” it. You will find it at the Apple App Store: https://itunes.apple.com/app/id1357143692, and the Google Play Store: https://play.google.com/store/apps/details?id=com.aspc.conf4cvaob. In closing, I invite everyone to view the agenda for the 2018 ASPC Congress at the Tamaya Resort, Santa Ana Pueblo, New Mexico (https://www.aspconline.org/congress2018). The Congress will host some of the world's leading authorities in their respective fields. It will provide an unparalleled educational experience in a relaxing setting, which is the ultimate aim of all our annual meetings. Please join us; you will not be disappointed. Wishing you well,

Resident Fuel Levels: Reframing, Assessing, and Addressing Well-Being.

To optimize resident learning, programs need to readily assess resident well-being. There is a lack of easy-to-use, acceptable instruments for this task. We created a well-being "fuel gauge," and assessed the acceptability and feasibility of this weekly electronic communication pipeline for residents to report and discuss their well-being. A well-being fuel gauge assessment was administered weekly over the course of 1 academic year (July 2016 to June 2017) in a large internal medicine residency program. The well-being gauge asked residents to report their fuel levels using a 1 to 5 Likert-type scale (1, empty; 3, half tank; and 5, full tank). Residents who provided low scores (1 or 2) were contacted by program leadership, and the program director sent weekly e-mail updates that addressed residents' comments on their well-being fuel gauge. Of 163 residents, 149 (91%) provided data on their well-being fuel gauge, with a 53% average weekly response rate. Fifty-four percent of residents (80 of 149) reported a low score over the course of the year, and 4 residents only used the assessment to report a low score. Comments on average consisted of 280 characters (SD = 357) and were lengthier and more prevalent with lower fuel gauge scores. We analyzed the relationship between scores and comments. The well-being fuel gauge was well accepted by most residents and was easy to administer and to oversee by program directors. It facilitated ongoing monitoring of well-being and follow-up to address factors contributing to low well-being.

A Survey on Text Information Extraction from Born-Digital and Scene Text Images

Text information extraction (TIE) from images is an open research area because of its unsolved challenges with respect to the heterogeneity in image types, mode of image capture, position of text and the clarity of text information. Currently, the number of images captured using mobile phones is voluminous. The information from such images is capable of providing valuable input to the user as well to applications that depend on the image text information. Text is the pipeline of human communication and images containing text can aid the semantic understanding of the image. Types of image text are explored along with an introduction to TIE and its applications. Text detection is emphasized and an attempt to categorize the features used by text detection is made. With a brief discussion on the onset research works, the available datasets and performance metrics are listed out. A broad summary regarding the types of text detection methods and systems under them is presented. The paper concludes with existing challenges that pave the way for more active research.

BFCO: A BPSO-Based Fine-Grained Communication Optimization Method for MPSoC

Fine-grained multithreaded models can provide more opportunities for system performance improvements, but they face large amount of communication overhead. To reduce the communication overhead to improve performance, message aggregation and communication pipeline have been proposed and their advantages have been discussed in previous works. However, when exploiting them in real-life applications, it is challenging to maximize their advantages due to their unrevealed problems. This paper investigates the two communication optimization techniques from the view of their problems to fulfill the studies. We have found that when applying the techniques, message aggregation may have the deadlock problem and latency problem, and communication pipeline may face the ineffective problem and prolog and epilog problem. Based on the basic requirement of allocating the two techniques on an initial schedule, we then present general solutions to avoid or handle the problems. To obtain a minimum schedule length for an initial schedule, we further develop a binary particle swarm optimization-based fine-grained communication optimization method to allocate message aggregation and communication pipeline for best performance. The method is also integrated into light and efficient simulink compiler for embedded application multithreaded code generator to generate high quality codes. Experimental results on both synthetic and real-life applications demonstrate the efficiency of the proposed method.

Offloading Collective Operations to Programmable Logic

The authors describe their architecture and implementation for offloading collective operations to programmable logic in the communication substrate. Collective operations are widely used in parallel processing. Their design and implementation strategies affect the performance of many high-performance computing applications that utilize them. Collectives are central to the message passing interface (MPI) programming model. The programmable logic provided by field-programmable gate arrays (FPGAs) is a powerful option for creating task-specific logic to aid applications. The authors' approach is applicable in scenarios where there is programmable logic in the communication pipeline and can be used to accelerate various network-based operations. In this article, the authors present a general collective offloading framework for use in applications using MPI. They evaluate their approach on the Xilinx Zynq system on a chip and an FPGA-based network interface card called the NetFPGA. Results are presented both from microbenchmarks and a benchmark scientific application using MPI.

Conserved Mechanism of Conformational Stability and Dynamics in G-Protein-Coupled Receptors

G-protein-coupled receptors (GPCRs) are transmembrane receptors involved in diverse biological functions. Despite the diversity in their amino acid sequences, class A GPCRs exhibit a conserved structural topology and possibly a common mechanism of receptor activation. To understand how this high sequence diversity translates to a conserved functional mechanism, we have compared the dynamic behavior of eight class A GPCRs comprised of six biogenic amine receptors, adenosine A2A, and the peptide receptor protease-activated receptor 1. Starting from the crystal structures of the inactive state of these receptors bound to inverse agonists or antagonists, we have performed multiple all-atom MD simulations adding up to several microseconds of simulation. We elucidated the similarities and differences in the dynamic behavior and the conformational ensembles sampled by these eight class A GPCRs. Among the six biogenic amine receptors studied here, β2-adrenergic receptor shows the highest level of fluctuation in the sixth and seventh transmembrane helices, possibly explaining its high basal activity. In contrast, the muscarinic acetylcholine receptors show the lowest fluctuations as well as tight packing and low hydration of the transmembrane domain. All eight GPCRs show several conserved allosteric communication pipelines from the residues in the agonist binding site with the G-protein interface. Positions of the residues along these pipelines that serve as major hubs of allosteric communication are conserved in their respective structures. These findings have important implications in understanding the dynamics and allosteric mechanism of communication in class A GPCRs and hence are useful for designing conformation-specific drugs.

Augmented immersion: video cutout and gesture-guided embedding for gaming applications

This paper introduces a novel framework, Gesture and Appearance Cutout Embedding (GACE), that supports real-time integration of human appearance and gesture-guided control within a game. It aims to enhance immersion since it allows game users to see their personal appearance in a real-time manner. In addition, we exploit the gesture-based control to allow user interaction with other in-game characters. With the goal to make implementation easier, we address the challenges in the whole pipeline of video processing, gesture recognition, and communication. The system is successfully integrated into both entertainment and serious games. Extensive experiments show that the proposed system runs reliably and comfortably with a commodity setting. Meanwhile, the user impression study indicates our system is favored by end users.

Unix Philosophy and the Real World: Control Software for Humanoid Robots

Robot software combines the challenges of general purpose and real-time software, requiring complex logic and bounded resource use. Physical safety, particularly for dynamic systems such as humanoid robots, depends on correct software. General purpose computation has converged on unix-like operating systems -- standardized as POSIX, the Portable Operating System Interface -- for devices from cellular phones to supercomputers. The modular, multi-process design typical of POSIX applications is effective for building complex and reliable software. Absent from POSIX, however, is an interproccess communication mechanism that prioritizes newer data as typically desired for control of physical systems. We address this need in the Ach communication library which provides suitable semantics and performance for real-time robot control. Although initially designed for humanoid robots, Ach has broader applicability to complex mechatronic devices -- humanoid and otherwise -- that require real-time coupling of sensors, control, planning, and actuation. The initial user space implementation of Ach was limited in the ability to receive data from multiple sources. We remove this limitation by implementing Ach as a Linux kernel module, enabling Ach's high-performance and latest-message-favored semantics within conventional POSIX communication pipelines. We discuss how these POSIX interfaces and design principles apply to robot software, and we present a case study using the Ach kernel module for communication on the Baxter robot.

Forensic 3D surface documentation at the Institute of Forensic Medicine in Zurich – Workflow and communication pipeline

Abstract This educational article is an introduction for forensic pathologists to the use of structured light scanners for the documentation of bodies, living persons and objects. We discuss the general layout of the relevant parts for Virtual Autopsy at the Institute of Forensic Medicine in Zurich, the communication organization and the embedding of scanning into the general workflow. A brief introduction on the processing of compiled data for use in incident reconstruction is also provided.

Communication Optimizations for Multithreaded Code Generation from Simulink Models

Communication frequency is increasing with the growing complexity of emerging embedded applications and the number of processors in the implemented multiprocessor SoC architectures. In this article, we consider the issue of communication cost reduction during multithreaded code generation from partitioned Simulink models to help designers in code optimization to improve system performance. We first propose a technique combining message aggregation and communication pipeline methods, which groups communications with the same destinations and sources and parallelizes communication and computation tasks. We also present a method to apply static analysis and dynamic emulation for efficient communication buffer allocation to further reduce synchronization cost and increase processor utilization. The existing cyclic dependency in the mapped model may hinder the effectiveness of the two techniques. We further propose a set of optimizations involving repartition with strongly connected threads to maximize the degree of communication reduction and preprocessing strategies with available delays in the model to reduce the number of communication channels that cannot be optimized. Experimental results demonstrate the advantages of the proposed optimizations with 11--143% throughput improvement.

Differences in Allosteric Communication Pipelines in the Inactive and Active States of a GPCR

G-protein-coupled receptors (GPCRs) are membrane proteins that allosterically transduce the signal of ligand binding in the extracellular (EC) domain to couple to proteins in the intracellular (IC) domain. However, the complete pathway of allosteric communication from the EC to the IC domain, including the role of individual amino acids in the pathway is not known. Using the correlation in torsion angle movements calculated from microseconds-long molecular-dynamics simulations, we elucidated the allosteric pathways in three different conformational states of β2-adrenergic receptor (β2AR): 1), the inverse-agonist-bound inactive state; 2), the agonist-bound intermediate state; and (3), the agonist- and G-protein-bound fully active state. The inactive state is less dynamic compared with the intermediate and active states, showing dense clusters of allosteric pathways (allosteric pipelines) connecting the EC with the IC domain. The allosteric pipelines from the EC domain to the IC domain are weakened in the intermediate state, thus decoupling the EC domain from the IC domain and making the receptor more dynamic compared with the other states. Also, the orthosteric ligand-binding site becomes the initiator region for allosteric communication in the intermediate state. This finding agrees with the paradigm that the nature of the agonist governs the specific signaling state of the receptor. These results provide an understanding of the mechanism of allosteric communication in class A GPCRs. In addition, our analysis shows that mutations that affect the ligand efficacy, but not the binding affinity, are located in the allosteric pipelines. This clarifies the role of such mutations, which has hitherto been unexplained.

Mapping Allosteric Communication Pipelines in GPCRs from Microsecond Timescale Molecular Dynamics Simulations

G protein coupled receptors (GPCRs) are 7 transmembrane (TM) helical proteins that signal through effector proteins bound at the intracellular (IC) interface. Agonist binding at the extracellular (EC) domain triggers conformational change at the IC domain leading to receptor activation. However, the mechanism of allosteric communication and the amino acids involved in the pipelines of allosteric communication (allosteric pathways) are not known yet. In this study, we have mapped the allosteric pipelines of communication in β2-adrenergic receptor (β2AR) using microseconds timescale Molecular Dynamics trajectories. Using mutual information in the internal coordinates, we have compared the allosteric pipelines among three β2AR conformations; inverse agonist bound inactive state, agonist bound intermediate state, and agonist and G protein bound active state. Strong allosteric communication along the TM domains stabilize the receptor in the inactive and active conformations. However the agonist bound intermediate state is dynamic showing weakened communication between the EC and IC domains. We have identified the residues that mediate multiple allosteric pipelines as allosteric hubs. These allosteric hubs have also been identified with the mutations that alter the receptor efficacy without altering the ligand binding. The role of such mutations were not previously understood.We have identified the residue networks involved in a continuous communication pipeline from the EC loops to the G protein coupling site. One of the termination points of the activation signal is the engineered Zn2+ binding site at the IC interface, which is a known positive allosteric modulator binding site in β2AR. We have shown how our method in conjunction with MD simulations can identify allosteric pockets which can then be used for screening allosteric drugs in GPCRs.

Communication-oriented performance optimisation during code generation from Simulink models

Increasing complexity of embedded systems brings a big challenge for designers to satisfy requirements for both high-performance and programmability. Automatic multi-threaded code generation facilitates MPSoC-based programming greatly. Apart from the savings on programming effort, system performance is also an important issue to be considered during code generation process. As thread communication is quite frequent in multi-threaded code, system performance will be improved by reducing communication cost. Communication pipeline technique applies distributed memory server for parallel execution between message passing and functional tasks, to reduce the cost caused by communication between different processors. The technique can be applied directly to communicating threads in acyclic topologies. To maximise its application, we also provide a solution to apply the technique to cyclic topologies with allocable delay units. Furthermore, we introduce a scheduling strategy for local threads to improve communication efficiency and processor usage. Experimental results demonstrate the performance improvements with the proposed techniques.

Three-Dimensional Reconstruction of Cardiac Sarcoplasmic Reticulum Reveals a Continuous Network Linking Transverse-Tubules

Rationale: The organization of the transverse-tubular (t-t) system and relationship to the sarcoplasmic reticulum (SR) underpins cardiac excitation–contraction coupling. The architecture of the SR, and relationship with the t-ts, is not well characterized at the whole-cell level. Furthermore, little is known regarding changes to SR ultrastructure in heart failure. Objective: The aim of this study was to unravel interspecies differences and commonalities between the relationship of SR and t-t networks within cardiac myocytes, as well as the modifications that occur in heart failure, using a novel high-resolution 3-dimensional (3D) imaging technique. Methods and Results: Using serial block face imaging coupled with scanning electron microscopy and image analysis, we have generated 3D reconstructions of whole cardiomyocytes from sheep and rat left ventricle, revealing that the SR forms a continuous network linking t-ts throughout the cell in both species. In sheep, but not rat, the SR has an intimate relationship with the sarcolemma forming junctional domains. 3D reconstructions also reveal details of the sheep t-t system. Using a model of tachypacing-induced heart failure, we show that there are populations of swollen and collapsed t-ts, patches of SR tangling, and disorder with rearrangement of the mitochondria. Conclusions: We provide the first high-resolution 3D structure of the SR network showing that it forms a cell-wide communication pipeline facilitating Ca 2+ diffusion, buffering, and synchronicity. The distribution of the SR within the cell is related to interspecies differences in excitation–contraction coupling, and we report the first detailed analysis of SR remodeling as a result of heart failure.

Seawater capacitance – a promising proxy for mapping and characterizing drifting hydrocarbon plumes in the deep ocean

Abstract. Hydrocarbons released into the deep ocean are an inevitable consequence of natural seep, seafloor drilling, and leaking wellhead-to-collection-point pipelines. The Macondo 252 (Deepwater Horizon) well blowout of 2010 was even larger than the Ixtoc event in the Gulf of Campeche in 1979. History suggests it will not be the last accidental release, as deepwater drilling expands to meet an ever-growing demand. For those who must respond to this kind of disaster, the first line of action should be to know what is going on. This includes knowing where an oil plume is at any given time, where and how fast it is moving, and how it is evolving or degrading. We have experimented in the laboratory with induced polarization as a method to track hydrocarbons in the seawater column and find that finely dispersed oil in seawater gives rise to a large distributed capacitance. From previous sea trials, we infer this could potentially be used to both map and characterize oil plumes, down to a ratio of less than 0.001 oil-to-seawater, drifting and evolving in the deep ocean. A side benefit demonstrated in some earlier sea trials is that this same approach in modified form can also map certain heavy placer minerals, as well as communication cables, pipelines, and wrecks buried beneath the seafloor.

Data Communication Support for Reusability of RT-Components – Converter Classification and Prototype Supporting Tool –

In RT-Middleware, a data-centric communication pipeline between RT-Components called Data Port is designed for improving software reusability. OMG standardization such as the Robotic Localization Service is also promoted. However, the actual I/O specification is different in each developer. In this paper, we first enumerate all connection patterns of possible communication by adjusting protocols. We then propose a supporting tool for flexible data communication. The proposed tool generates source code based on information on the desired conversion. We actually implement the prototype tool of the automatic source code generator and evaluate it.

Engage Students in Education Reform

![Figure][1] CREDIT: JAMES WOODSON/THINKSTOCK As a senior undergraduate student at a large public research university, I agree with W. A. Anderson et al. that excellent teaching and research are not mutually exclusive pursuits (“Changing the culture of science education at research universities,” Education Forum, 14 January, p. [152][2]). However, engagement with the students themselves is nowhere to be found in the authors' seven initiatives. Students—the largest stakeholders in the current landscape of science education reform—should be added to the list of chairs, deans, and presidents as parties to engage in the policy debate (initiative 7). Such an addition would add a fresh perspective on the issue, open valuable communication pipelines between students and policy-makers, and provide opportunities for students interested in educational policy to gain experience in the field. Restructuring the culture of education at research universities will require a new paradigm: Students should be considered not as passive consumers but as active participants in their education. [1]: pending:yes [2]: /lookup/doi/10.1126/science.1198280

Data Communication Support for Reusability of RT-Components : Converter Classification and Prototype Supporting Tool

In RT-Middleware, a data-centric communication pipeline between RT-Components called "Data Port" is designed for improving software reusability. Moreover, the OMG standardization such Robotic Localization Service is promoted. However, an actual I/O specification is different in each developer. In this paper, we first enumerates all the connection patterns of possible communication by adjusting protocols. And then, we propose a supporting tool for flexible data communication. The proposed tool generates source code based on information on the desired conversion. We actually implement the prototype tool of the automatic source code generator and evaluate it.

Exploring drug users’ attitudes and decisions regarding hepatitis C (HCV) treatment in the U.S.

Individuals with a history of injecting drugs are at the highest risk of becoming infected with the hepatitis C virus (HCV), with studies of patients in methadone maintenance treatment programmes (MMTPs) reporting that 60–90 percent of intravenous drug users (IDUs) have the virus. Fortunately, HCV therapy has been shown to be effective in 42–82 percent of all patients with chronic HCV infection, including IDUs. While the decision to start HCV therapy requires significant consideration, little research exists that explores the attitudes of drug users toward HCV therapy. Therefore, this paper examines how drug users perceive the treatment, as well as the processes by which HCV-positive individuals examined the advantages and disadvantages of starting the HCV medications. Interviews were conducted with 164 patients from 14 drug treatment programmes throughout the United States, and both uninfected and HCV-positive drug users described a pipeline of communication among their peers that conveys largely negative messages about the medications that are available to treat HCV. Although many of the HCV-positive individuals said that these messages heightened their anxiety about the side effects and difficulties of treatment, some patients said that their peers helped them to consider, initiate HCV treatment or both. Gaining a better understanding of drug users’ perceptions of HCV treatment is important, because so many of them, particularly IDUs, are already infected with HCV and may benefit from support in addressing their HCV treatment needs. In addition, currently uninfected drug users will likely remain at high risk for contracting HCV and may need to make decisions about whether or not to start the HCV medical regimen in the future.

Hypercube algorithms on mesh connected multicomputers

A new methodology named CALMANT (CC-cube Algorithms on Meshes and Tori) for mapping a type of algorithm that we call CC-cube algorithm onto multicomputers with hypercube, mesh, or torus interconnection topology is proposed. This methodology is suitable when the initial problem can be expressed as a set of processes that communicate through a hypercube topology (a CC-cube algorithm). There are many important algorithms that fit into the CC-cube type. CALMANT is based on three different techniques: (a) the standard embedding to assign the processes of the algorithm to the nodes of the mesh multicomputer; (b) the communication pipelining technique to increase the level of communication parallelism inherent in the CC-cube algorithms; and (c) optimal message-scheduling algorithms proposed in this work in order to avoid conflicts and minimizing in this way the communication time. Although CALMANT is proposed for multicomputers with different interconnection network topologies, the paper only focuses on the particular case of meshes.