Resampling Methods and Visualization Tools for Computer Performance Comparisons in the Presence of Performance Variation

Performance variability, stemming from non-deterministic hardware and software behaviors or deterministic behaviors such as measurement bias, is a well-known phenomenon of computer systems which increases the difficulty of comparing computer performance metrics and is slated to become even more of a concern as interest in Big Data Analytics increases. Conventional methods use various measures (such as geometric mean) to quantify the performance of different benchmarks to compare computers without considering this variability which may lead to wrong conclusions. In this paper, we propose three resampling methods for performance evaluation and comparison: a randomization test for a general performance comparison between two computers, bootstrapping confidence estimation, and an empirical distribution and five-number-summary for performance evaluation. The results show that for both PARSEC and high-variance BigDataBench benchmarks: 1) the randomization test substantially improves our chance to identify the difference between performance comparisons when the difference is not large; 2) bootstrapping confidence estimation provides an accurate confidence interval for the performance comparison measure (e.g. ratio of geometric means); and 3) when the difference is very small, a single test is often not enough to reveal the nature of the computer performance due to the variability of computer systems. We further propose using empirical distribution to evaluate computer performance and a five-number-summary to summarize computer performance. We use published SPEC 2006 results to investigate the sources of performance variation by predicting performance and relative variation for 8,236 machines. We achieve a correlation of predicted performances of 0.992 and a correlation of predicted and measured relative variation of 0.5. Finally, we propose the utilization of a novel Biplotting technique to visualize the effectiveness of benchmarks and cluster machines by behavior. We illustrate the results and conclusion through detailed Monte Carlo simulation studies and real examples

The role of light signaling on astrocytic morphological plasticity in the adult male rat suprachiasmatic nucleus

The body’s master clock lies at the base of the hypothalamus immediately above the optic chiasm. Because of the intimate connection to the optic chiasm, this hypothalamic nucleus was named the suprachiasmatic nucleus (SCN). Environmental light signaling conveys time of day and seasonal changes to the SCN via the retinohypothalamic tract (RHT). The SCN then relays this information to the brain and the rest of the body through synaptic signaling and indirectly through circadian regulation of hormonal signaling. The SCN is unique in that in the absence of external signaling, circadian rhythms will persist. This is accomplished through a transcription-translation feedback loop consisting of both positive and negative transcription factors. The interactions of the players within this loop create a near 24 hour rhythm. Although research within the SCN has focused primarily on neuronal signaling astrocytes comprise nearly a third of the total number of cells within the nucleus based on stereological analysis. Moreover, the astrocyte cytoskeletal marker, glial fibrillary acidic protein (GFAP), is expressed in much higher levels compared to other local hypothalamic regions containing neuronal fibers. GFAP allows for the rough estimation of the overall astrocyte cell shape and despite a lack of in vivo polymerization dynamics, in vitro GFAP filaments have been shown to be dynamically regulated by phosphorylation by known kinases. Additionally, the synaptic signals encoding light information, glutamate and pituitary adenylate cyclase activating peptide (PACAP), have been shown to bind to receptors that activate kinases responsible for GFAP phosphorylation. Based on this work, we hypothesized that the RHT regulates astrocytic cytoskeletal dynamics within the SCN of the male rat. To show this we established that GFAP immunofluorescence is significantly different between early day and early night within the SCN. We then showed that this observable difference is likely due to a shift in GFAP polymerization state from filaments into soluble monomers. Second, we clearly show that this polymerization shift is regulated by the optic nerve and not a circadian phenomenon. We further establish that long term enucleation decreases the overall GFAP levels relative to other local hypothalamic regions, suggesting that the higher levels of GFAP within the SCN is regulated by the optic nerve. Lastly, in order to establish a model system to study effects RHT signals have on SCN astrocytes we characterized the polymerization state of GFAP within the brain slice. Moreover, we studied the effects of glutamate and PACAP on the brain slice. In conclusion, we have determined that signals from the RHT drive the observed levels of GFAP as well as the polymerization state of the GFAP cytoskeleton in the adult male rat SCN

BifurKTM: Approximately Consistent Distributed Transactional Memory for GPUs

We present BifurKTM, the first read-optimized Distributed Transactional Memory system for GPU clusters. The BifurKTM design includes: GPU KoSTM, a new software transactional memory conflict detection scheme that exploits relaxed consistency to increase throughput; and KoDTM, a Distributed Transactional Memory model that combines the Data- and Control- flow models to greatly reduce communication overheads. Despite the allure of huge speedups, GPUs are limited in use due to their programmability and extreme sensitivity to workload characteristics. These become daunting concerns when considering a distributed GPU cluster, wherein a programmer must design algorithms to hide communication latency by exploiting data regularity, high compute intensity, etc. The BifurKTM design allows GPU programmers to exploit a new workload characteristic: the percentage of the workload that is Read-Only (e.g. reads but does not modify shared memory), even when this percentage is not known in advance. Programmers designate transactions that are suitable for Approximate Consistency, in which transactions "appear" to execute at the most convenient time for preventing conflicts. By leveraging Approximate Consistency for Read-Only transactions, the BifurKTM runtime system offers improved performance, application flexibility, and programmability without introducing any errors into shared memory. Our experiments show that Approximate Consistency can improve BkTM performance by up to 34x in applications with moderate network communication utilization and a read-intensive workload. Using Approximate Consistency, BkTM can reduce GPU-to-GPU network communication by 99%, reduce the number of aborts by up to 100%, and achieve an average speedup of 18x over a similarly sized CPU cluster while requiring minimal effort from the programmer

Telomerase Activation and Rejuvenation of Telomere Length in Stimulated T Cells Derived from Serially Transplanted Hematopoietic Stem Cells

Telomeres shorten in hematopoietic cells, including hematopoietic stem cells (HSCs), during aging and after transplantation, despite the presence of readily detectable levels of telomerase in these cells. In T cells, antigenic stimulation has been shown to result in a marked increase in the level of telomerase activity. We now show that stimulation of T cells derived from serially transplanted HSC results in a telomerase-dependent elongation of telomere length to a size similar to that observed in T cells isolated directly from young mice. Southern analysis of telomere length in resting and anti-CD3/CD28 stimulated donor-derived splenic T cells revealed an increase in telomere size by ∼7 kb for the population as a whole. Stimulation of donor-derived T cells from recipients of HSCs from telomerase-deficient mice did not result in regeneration of telomere length, demonstrating a dependence on telomerase. Furthermore, clonal anti-CD3/CD28 stimulation of donor-derived T cells followed by fluorescent in situ hybridization (FISH) analysis of telomeric signal intensity showed that telomeres had increased in size by ∼50% for all clonal expansions. Together, these results imply that one role for telomerase in T cells may be to renew or extend replicative potential via the rejuvenation of telomere length

Psychometric and biomedical outcomes of glycated haemoglobin target-setting in adults with type 1 and type 2 diabetes:Protocol for a mixed-methods parallel-group randomised feasibility study

BACKGROUND: The disease burden of diabetes can have wide-ranging implications on patients’ psychological well-being and health-related quality of life. Glycated haemoglobin targets are commonly used to guide patient management in diabetes to reduce the future risk of developing diabetes complications, but little is known of the psychological impact of glycated haemoglobin target-setting. This protocol describes a study to determine the feasibility of evaluating psychological outcomes when setting explicit glycated haemoglobin targets in people with diabetes. METHODS: This single-centre randomised feasibility study will follow a mixed-methods approach across four sub-studies. In sub-study A, eligible adults (aged 18 and over) with type 1 or type 2 diabetes will complete baseline validated psychometric questionnaires evaluating health-related quality of life (EuroQoL-5D-5L), diabetes-related distress (Problem Areas In Diabetes), self-care (Summary of Diabetes Self-Care Activities), well-being (Well-Being Quetionnaire-12) and diabetes-related psychosocial self-efficacy (Diabetes Empowerment Scale-Long Form). Participants will be randomised to receive explicit glycated haemoglobin intervention targets 5mmol/mol above or below current glycated haemoglobin readings. Rates of eligibility, recruitment, retention and questionnaire response rate will be measured. Psychometric outcomes will be re-evaluated 3-months post-intervention. Sub-studies B and C will use qualitative semi-structured interviews to evaluate experiences, views and opinions of diabetes patients and healthcare professionals in relation to the acceptability of study processes, the use of glycated haemoglobin targets, the impact of diabetes on psychological well-being and, in sub-study D, barriers to participation in diabetes research. DISCUSSION: This mixed-methods study aims to provide a novel insight into the psychological implications of glycated haemoglobin target-setting for people with diabetes in secondary care, alongside testing the feasibility of undertaking a larger project of this nature. TRIAL REGISTRATION: The study is registered with the ISRCTN (registration number: 12461724; date registered: 11(th) June 2021). Protocol version: 2.0.5, 26(th) February 2021

The scientific study of passive thinking: Methods of mind wandering research

The science of mind wandering has rapidly expanded over the past 20 years. During this boom, mind wandering researchers have relied on self-report methods, where participants rate whether their minds were wandering. This is not an historical quirk. Rather, we argue that self-report is indispensable for researchers who study passive phenomena like mind wandering. We consider purportedly “objective” methods that measure mind wandering with eye tracking and machine learning. These measures are validated in terms of how well they predict self-reports, which means that purportedly objective measures of mind wandering retain a subjective core. Mind wandering science cannot break from the cycle of self-report. Skeptics about self-report might conclude that mind wandering science has methodological foundations of sand. We take a rather more optimistic view. We present empirical and philosophical reasons to be confident in self-reports about mind wandering. Empirically, these self-reports are remarkably consistent in their contents and behavioral and neural correlates. Philosophically, self-reports are consistent with our best theories about the function of mind wandering. We argue that this triangulation gives us reason to trust both theory and method

Volcanic shutdown of the Panama Canal area following breakup of the Farallon plate

The Panama Canal area is a significant part of the Panama Isthmus, where prominent volcanic fronts of eastern Central America are interrupted by a topographic low of unclear tectonic and magmatic origin. Determining why no prominent volcanic system occurs along the Canal is essential to understand the formation of the Isthmus in an area believed to have hosted one of the last inter-American straits between the Atlantic and Pacific Oceans. We provide here new geochronological and geochemical constraints from volcanic units of the Panama Canal that belong to the recently-identified Central Panama Volcanic Field. Whole rock and mineralogical geochemical compositions document a secular magmatic change from ca. 25 to 16 Ma, with a progressive change from calc-alkaline to tholeiitic and possibly alkaline/transitional geochemical affinities. The age of the youngest volcanic unit of the Canal is similar to that of the youngest documented arc volcanism in eastern Panama ca. 18 Ma. We propose based on these observations and consistency with regional geological constraints that the Canal volcanism represents a unique example of magmatic cessation along a volcanic arc. This cessation occurred shortly after the breakup of the Farallon plate ca. 23 Ma, suggesting a causal link between volcanic shutdown and transition from orthogonal to oblique subduction along Central and Eastern Panama. We suggest that this tectonic event suppressed hydrous melting in the subduction zone and led to regional magmatic waning in Central and Eastern Panama ca. 16 Ma. The pre-existence of a transisthmian fault system in Central Panama probably facilitated extraction of the last supra-subduction melts during volcanic shutdown. Our results suggest that the end of volcanism, combined with transisthmian faulting, impeded the development of high topography in the Panama Canal area. Without this unusual tectono-magmatic evolution, the occurrence of a late inter-oceanic strait in Central Panama and the construction of the Panama Canal would not have been possible

Blame for Hum(e)an beings: The role of character information in judgments of blame

How does character information inform judgments of blame? Some argue that character information is indirectly relevant to blame because it enriches judgments about the mental states of a wrongdoer. Others argue that character information is directly relevant to blame, even when character traits are causally irrelevant to the wrongdoing. We propose an empirical synthesis of these views: a Two Channel Model of blame. The model predicts that character information directly affects blame when this information is relevant to the wrongdoing that elicits blame. Further, the effect of character information on blame depends on judgments about the true self that are independent of judgments of intentionality. Across three pre-registered studies (N = 662), we found support for all three predictions of the Two Channel Model. We propose that this reflects two distinct functions of blame: a social regulatory function that encourages norm compliance and a pedagogical function that encourages personal improvement