2995 research outputs found
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Twister2 Demonstrations for BDEC2
No full textData-driven applications are essential to handle the ever-increasing volume, velocity, and veracity of data generated by sources such as the Web and Internet of Things (IoT) devices. Simulta- neously, an event-driven computational paradigm is emerging as the core of modern systems designed for database queries, data analytics, and on-demand applications. Modern big data pro- cessing runtimes and asynchronous many task (AMT) systems from high performance computing (HPC) community have adopted dataflow event-driven model. The services are increasingly mov- ing to an event-driven model in the form of Function as a Service (FaaS) to compose services. An event-driven runtime designed for data processing consists of well-understood components such as communication, scheduling, and fault tolerance. Different design choices adopted by these components determine the type of applications a system can support efficiently. We find that modern systems are limited to specific sets of applications because they have been designed with fixed choices that cannot be changed easily. In this paper, we present a loosely coupled component-based design of a big data toolkit where each component can have different imple- mentations to support various applications. Such a polymorphic design would allow services and data analytics to be integrated seamlessly and expand from edge to cloud to HPC environments
Understanding ML Driven HPC: Applications and Infrastructure
No full textWe recently outlined the vision of "Learning Everywhere" which captures the possibility and impact of how learning methods and traditional HPC methods can be coupled together. A primary driver of such coupling is the promise that Machine Learning (ML) will give major performance improvements for traditional HPC simulations. Motivated by this potential, the ML around HPC class of integration is of particular significance. In a related follow-up paper, we provided an initial taxonomy for integrating learning around HPC methods. In this paper, which is part of the Learning Everywhere series, we discuss "how" learning methods and HPC simulations are being integrated to enhance effective performance of computations. This paper identifies several modes --- substitution, assimilation, and control, in which learning methods integrate with HPC simulations and provide representative applications in each mode. This paper discusses some open research questions and we hope will motivate and clear the ground for MLaroundHPC benchmarks
ManyClasses 1: Assessing the generalizable effect of immediate versus delayed feedback across many college classes
No full textPsychology researchers have long attempted to identify educational practices that improve student learning. However, experimental research on these practices is often conducted in laboratory contexts or in a single class, threatening the external validity of the results. In this paper, we establish an experimental paradigm for evaluating the benefits of recommended practices across a variety of authentic educational contexts – a model we call ManyClasses. The core feature is that researchers examine the same research question and measure the same experimental effect across many classes spanning a range of topics, institutions, teacher implementations, and student populations. We report the first ManyClasses study, which examined how the timing of feedback on class assignments, either immediate or delayed by a few days, affected subsequent performance on class assessments. Across XX classes, [summarize effect of feedback timing, including key moderators]. More broadly, these findings provide evidence regarding the feasibility of conducting within-class randomized experiments across a range of naturally occurring learning environments
U.S. Medical Examiner/Coroner capability to handle highly infectious decedents
No full textIn the United States of America, Medical Examiners and Coroners (ME/Cs) investigate approximately 20% of all deaths. Unexpected deaths, such as those occurring due to a deceased person under investigation for a highly infectious disease, are likely to fall under ME/C jurisdiction, thereby placing the ME/C and other morgue personnel at increased risk of contracting an occupationally acquired infection. This survey of U.S. ME/Cs′ capabilities to address highly infectious decedents aimed to determine opportunities for improvement at ME/C facilities serving a state or metropolitan area. Data for this study was gathered via an electronic survey. Of the 177 electronic surveys that were distributed, the overall response rate was N = 108 (61%), with 99 of those 108 respondents completing all the questions within the survey. At least one ME/C responded from 47 of 50 states, and the District of Columbia. Select results were: less than half of respondents (44%) stated that their office had been involved in handling a suspected or confirmed highly infectious remains case and responses indicated medical examiners. Additionally, ME/C altered their personal protective equipment based on suspected versus confirmed highly infectious remains rather than taking an all-hazards approach. Standard operating procedures or guidelines should be updated to take an all-hazards approach, best-practices on handling highly infectious remains could be integrated into a standardized education, and evidence-based information on appropriate personal protective equipment selection could be incorporated into a widely disseminated learning module for addressing suspected or confirmed highly infectious remains, as those areas were revealed to be currently lacking
Political attitudes vary with detection of androstenone
No full textBuilding on a growing body of research that suggests political attitudes are part of broader individual and biological orientations, we test whether the detection of the hormone androstenone is predictive of political attitudes. The particular social chemical analyzed in this study is androstenone, a non-androgenic steroid found in the sweat and saliva of many mammals, including humans. A primary reason for scholarly interest in odor detection is that it varies so dramatically from person to person. Using participants’ self-reported perception of androstenone intensity, together with a battery of survey items testing social and political preferences and orientations, this research supports the idea that perceptions of androstenone intensity relate to political orientations, most notably preferences for social order, lending further support to theories positing the influence of underlying biological traits on sociopolitical attitudes and behaviors
An emerging form of public engagement with science: Ask Me Anything (AMA) sessions on Reddit r/science
No full textOriginally, online public engagement with science tended to be one directional—from experts to the general population via news media. Such an arrangement allowed for little to no direct interaction between the public and scientists. However, the emergence of social media has opened the door to meaningful engagement between scientists and the general public. The current study examines scientists’ perspectives on the interactions between laypeople and scientists by asking questions and sharing information on social media platforms, specifically, through Ask Me Anything (AMA) sessions on Reddit’s “Science” subreddit (r/science). By analyzing the content of six different r/science AMAs and surveying scientists who participated as r/science AMA hosts, our research attempts to gain a richer understanding of direct communication between scientists and lay audiences online. We had three main questions: (1) who are the participant scientists hosting r/science AMAs, (2) what are their experiences like as hosts, and (3) what type of discussions do they have on this platform? Survey results suggested that these scientists recognize the promising interactive nature of Reddit and are interested in continuing to use this platform as a tool for public engagement. Survey respondents generally had positive experiences as AMA hosts, but further research is needed to examine negative experiences. Overall, this study has significant implications for how scientists can engage public audiences online and more effectively communicate scientific findings to the general populace
In Situ Structure of an Intact Lipopolysaccharide-Bound Bacterial Surface Layer
No full textMost bacterial and all archaeal cells are encapsulated by a paracrystalline, protective, and cell-shape-determining proteinaceous surface layer (S-layer). On Gram-negative bacteria, S-layers are anchored to cells via lipopolysaccharide. Here, we report an electron cryomicroscopy structure of the Caulobacter crescentus S-layer bound to the O-antigen of lipopolysaccharide. Using native mass spectrometry and molecular dynamics simulations, we deduce the length of the O-antigen on cells and show how lipopolysaccharide binding and S-layer assembly is regulated by calcium. Finally, we present a near-atomic resolution in situ structure of the complete S-layer using cellular electron cryotomography, showing S-layer arrangement at the tip of the O-antigen. A complete atomic structure of the S-layer shows the power of cellular tomography for in situ structural biology and sheds light on a very abundant class of self-assembling molecules with important roles in prokaryotic physiology with marked potential for synthetic biology and surface-display applications
A Multiprotein Complex Anchors Adhesive Holdfast at the Outer Membrane of Caulobacter crescentus
No full textAdhesion allows microbes to colonize surfaces and is the first stage in biofilm formation. Stable attachment of the freshwater alphaproteobacterium Caulobacter crescentus to surfaces requires an adhesive polysaccharide called holdfast, which is synthesized at a specific cell pole and ultimately found at the tip of cylindrical extensions of the cell envelope called stalks. Secretion and anchoring of holdfast to the cell surface are governed by proteins HfsDAB and HfaABD, respectively. The arrangement and organization of these proteins with respect to each other and the cell envelope, and the mechanism by which the holdfast is anchored on cells, are unknown. In this study, we have imaged a series of C. crescentus mutants using electron cryotomography, revealing the architecture and arrangement of the molecular machinery involved in holdfast anchoring in cells. We found that the holdfast is anchored to cells by a defined complex made up of the HfaABD proteins and that the HfsDAB secretion proteins are essential for proper assembly and localization of the HfaABD anchor. Subtomogram averaging of cell stalk tips showed that the HfaABD complex spans the outer membrane. The anchor protein HfaB is the major component of the anchor complex located on the periplasmic side of the outer membrane, while HfaA and HfaD are located on the cell surface. HfaB is the critical component of the complex, without which no HfaABD complex was observed in cells. These results allow us to propose a working model of holdfast anchoring, laying the groundwork for further structural and cell biological investigations
Semiparametric Estimation of Task-Based Dynamic Functional Connectivity on the Population Level
No full textDynamic functional connectivity (dFC) estimates time-dependent associations between pairs of brain region time series as typically acquired during functional MRI. dFC changes are most commonly quantified by pairwise correlation coefficients between the time series within a sliding window. Here, we applied a recently developed bootstrap-based technique (Kudela et al., 2017) to robustly estimate subject-level dFC and its confidence intervals in a task-based fMRI study (24 subjects who tasted their most frequently consumed beer and Gatorade as an appetitive control). We then combined information across subjects and scans utilizing semiparametric mixed models to obtain a group-level dFC estimate for each pair of brain regions, flavor, and the difference between flavors. The proposed approach relies on the estimated group-level dFC accounting for complex correlation structures of the fMRI data, multiple repeated observations per subject, experimental design, and subject-specific variability. It also provides condition-specific dFC and confidence intervals for the whole brain at the group level. As a summary dFC metric, we used the proportion of time when the estimated associations were either significantly positive or negative. For both flavors, our fully-data driven approach yielded regional associations that reflected known, biologically meaningful brain organization as shown in prior work, as well as closely resembled resting state networks (RSNs). Specifically, beer flavor-potentiated associations were detected between several reward-related regions, including the right ventral striatum (VST), lateral orbitofrontal cortex, and ventral anterior insular cortex (vAIC). The enhancement of right VST-vAIC association by a taste of beer independently validated the main activation-based finding (Oberlin et al., 2016). Most notably, our novel dFC methodology uncovered numerous associations undetected by the traditional static FC analysis. The data-driven, novel dFC methodology presented here can be used for a wide range of task-based fMRI designs to estimate the dFC at multiple levels—group-, individual-, and task-specific, utilizing a combination of well-established statistical methods
Intakes of long-chain omega-3 polyunsaturated fatty acids and non-fried fish in relation to incidence of chronic kidney disease in young adults: a 25-year follow-up
No full textPurpose: The prevalence of chronic kidney disease (CKD) is increasing rapidly in many countries and has become a major public health concern. Although intakes of long-chain omega-3 polyunsaturated fatty acids (LCω3PUFA) and its food source-fish-may have renal protective effects, little is known about the longitudinal association between these dietary factors and CKD incidence. Methods: A total of 4133 healthy individuals of black and white race aged 18-30 at baseline (1985-1986) from the Coronary Artery Risk Development in Young Adults study were enrolled and followed up over 25 years. LCω3PUFA and fish intake were assessed by an interview-based dietary history questionnaire at baseline, year 7 (1992-1993) and 20 (2005-2006). Results: Four hundred and eighty-nine incident cases of CKD were identified. After adjustment for potential confounders, LCω3PUFA intake was inversely associated with CKD incidence [HR = 0.73 (95% CI 0.60-0.89), P = 0.002, with one standard division (0.19 g/day) increment in LCω3PUFA]. This inverse association was persisted among females [0.64 (95% CI 0.48, 0.84; P = 0.002], but not males (Pinteraction = 0.070). A marginal significant inverse association was also found between non-fried fish consumption and CKD incidence (HR = 0.86, 95% CI 0.73, 1.01; P = 0.073). Conclusions: Dietary LCω3PUFA intake was inversely associated with incidence of CKD among American young adults over 25 years of follow-up. The suggestive evidence of the inverse association between non-fried fish consumption with CKD incidence needs further confirmation