Characterizing Task-Based OpenMP Programs

Programmers struggle to understand performance of task-based OpenMP programs since profiling tools only report thread-based performance. Performance tuning also requires task-based performance in order to balance per-task memory hierarchy utilization against exposed task parallelism. We provide a cost-effective method to extract detailed task-based performance information from OpenMP programs. We demonstrate the utility of our method by quickly diagnosing performance problems and characterizing exposed task parallelism and per-task instruction profiles of benchmarks in the widely-used Barcelona OpenMP Tasks Suite. Programmers can tune performance faster and understand performance tradeoffs more effectively than existing tools by using our method to characterize task-based performance.     

Optimization of SAMtools sorting using OpenMP tasks

SAMtools is a widely-used genomics application for post-processing high-throughput sequence alignment data. Such sequence alignment data are commonly sorted to make downstream analysis more efficient. However, this sorting process itself can be computationally- and I/O-intensive: high-throughput sequence alignment files in the de facto standard binary alignment/map (BAM) format can be many gigabytes in size, and may need to be decompressed before sorting and compressed afterwards. As a result, BAM-file sorting can be a bottleneck in genomics workflows. This paper describes a case study on the performance analysis and optimization of SAMtools for sorting large BAM files. OpenMP task parallelism and memory optimization techniques resulted in a speedup of 5.9X versus the upstream SAMtools 1.3.1 for an internal (in-memory) sort of 24.6 GiB of compressed BAM data (102.6 GiB uncompressed) with 32 processor cores, while a 1.98X speedup was achieved for an external (out-of-core) sort of a 271.4 GiB BAM file.     

Task-Based Core-Periphery Organization of Human Brain Dynamics

As a person learns a new skill, distinct synapses, brain regions, and circuits are engaged and change over time. In this paper, we develop methods to examine patterns of correlated activity across a large set of brain regions. Our goal is to identify properties that enable robust learning of a motor skill. We measure brain activity during motor sequencing and characterize network properties based on coherent activity between brain regions. Using recently developed algorithms to detect time-evolving communities, we find that the complex reconfiguration patterns of the brain''s putative functional modules that control learning can be described parsimoniously by the combined presence of a relatively stiff temporal core that is composed primarily of sensorimotor and visual regions whose connectivity changes little in time and a flexible temporal periphery that is composed primarily of multimodal association regions whose connectivity changes frequently. The separation between temporal core and periphery changes over the course of training and, importantly, is a good predictor of individual differences in learning success. The core of dynamically stiff regions exhibits dense connectivity, which is consistent with notions of core-periphery organization established previously in social networks. Our results demonstrate that core-periphery organization provides an insightful way to understand how putative functional modules are linked. This, in turn, enables the prediction of fundamental human capacities, including the production of complex goal-directed behavior.     

Embodied Emotion Modulates Neural Signature of Performance Monitoring

Background

Recent research on the “embodiment of emotion” implies that experiencing an emotion may involve perceptual, somatovisceral, and motor feedback aspects. For example, manipulations of facial expression and posture appear to induce emotional states and influence how affective information is processed. The present study investigates whether performance monitoring, a cognitive process known to be under heavy control of the dopaminergic system, is modulated by induced facial expressions. In particular, we focused on the error-related negativity, an electrophysiological correlate of performance monitoring.

Methods/Principal Findings

During a choice reaction task, participants held a Chinese chop stick either horizontally between the teeth (“smile” condition) or, in different runs, vertically (“no smile”) with the upper lip. In a third control condition, no chop stick was used (“no stick”). It could be shown on a separate sample that the facial feedback procedure is feasible to induce mild changes in positive affect. In the ERP sample, the smile condition, hypothesized to lead to an increase in dopaminergic activity, was associated with a decrease of ERN amplitude relative to “no smile” and “no stick” conditions.

Conclusion

Embodying emotions by induced facial expressions leads to a changes in the neural correlates of error detection. We suggest that this is due to the joint influence of the dopaminergic system on positive affect and performance monitoring.     

Systematic Monitoring of Male Circumcision Scale-Up in Nyanza,Kenya: Exploratory Factor Analysis of Service Quality Instrument and Performance Ranking

Background

Considerable conceptual and operational complexities related to service quality measurements and variability in delivery contexts of scaled-up medical male circumcision, pose real challenges to monitoring implementation of quality and safety. Clarifying latent factors of the quality instruments can enhance contextual applicability and the likelihood that observed service outcomes are appropriately assessed.

Objective

To explore factors underlying SYMMACS service quality assessment tool (adopted from the WHO VMMC quality toolkit) and; determine service quality performance using composite quality index derived from the latent factors.

Study design

Using a comparative process evaluation of Voluntary Medical Male Circumcision Scale-Up in Kenya site level data was collected among health facilities providing VMMC over two years. Systematic Monitoring of the Medical Male Circumcision Scale-Up quality instrument was used to assess availability of guidelines, supplies and equipment, infection control, and continuity of care services. Exploratory factor analysis was performed to clarify quality structure.

Results

Fifty four items and 246 responses were analyzed. Based on Eigenvalue >1.00 cut-off, factors 1, 2 & 3 were retained each respectively having eigenvalues of 5.78; 4.29; 2.99. These cumulatively accounted for 29.1% of the total variance (12.9%; 9.5%; 6.7%) with final communality estimates being 13.06. Using a cut-off factor loading value of ≥0.4, fifteen items loading on factor 1, five on factor 2 and one on factor 3 were retained. Factor 1closely relates to preparedness to deliver safe male circumcisions while factor two depicts skilled task performance and compliance with protocols. Of the 28 facilities, 32% attained between 90^th and 95^th percentile (excellent); 45% between 50^th and 75^th percentiles (average) and 14.3% below 25^th percentile (poor).

Conclusion

the service quality assessment instrument may be simplified to have nearly 20 items that relate more closely to service outcomes. Ranking of facilities and circumcision procedure using a composite index based on these items indicates that majority performed above average.     

2种治疗药物监测结果分析

目的:通过对治疗药物(462例地高辛、171例氨茶碱)的血药浓度监测,提出个体化给药建议,以有效指导临床合理用药。方法:用全自动微粒子化学发光免疫分析系统(EMIA)测定地高辛和氨茶碱在病人体内的血药浓度,进行血药浓度监测。结果:浓度在有效范围内比例逐年上升,低于治疗范围的比例较高,高出治疗范围的比例较低,我院共监测地高辛血药浓度462例,在有效血药浓度范围(0.8μg·L~(-1)～2μg·L~(-1))248例,有效率为53.7%;氨茶碱血药浓度171例,在有效血药浓度范围(10mg·L~(-1)～20mg·L~(-1)) 83例,有效率为48.5%。结论:该方法快速、敏感、简便,本研究提示在应用地高辛和氨茶碱等安全范围窄的药物时,应注意血药浓度监测(TDM),并密切注意患者的生理、病理、联合用药等影响因素。     

应用远程质量控制体系对CT性能监测的效果评价

目的 通过对CT远程质量控制体系应用前后其性能状态对比分析,检验CT远程质量控制模式的价值与效果。方法 收集3家医疗机构41份CT指标检测数据,对远程质量控制体系应用前、后CT的性能指标数据进行对比分析。结果 CT远程质量控制体系应用后,CT性能指标（噪声、空间分辨力)较前显著改善（P﹤0.01）,CT合格率明显提高（P﹤0.01）。结论 质量控制是提高临床质量,促进精准医疗发展的重要保障,远程质量控制体系可靠性好,为全国各医疗机构开展CT远程质量控制工作提供了借鉴依据,也为实现MRI、DSA、DR等大型设备远程质量控制开辟了可靠路径。     

No Evidence That Gratitude Enhances Neural Performance Monitoring or Conflict-Driven Control

It has recently been suggested that gratitude can benefit self-regulation by reducing impulsivity during economic decision making. We tested if comparable benefits of gratitude are observed for neural performance monitoring and conflict-driven self-control. In a pre-post design, 61 participants were randomly assigned to either a gratitude or happiness condition, and then performed a pre-induction flanker task. Subsequently, participants recalled an autobiographical event where they had felt grateful or happy, followed by a post-induction flanker task. Despite closely following existing protocols, participants in the gratitude condition did not report elevated gratefulness compared to the happy group. In regard to self-control, we found no association between gratitude—operationalized by experimental condition or as a continuous predictor—and any control metric, including flanker interference, post-error adjustments, or neural monitoring (the error-related negativity, ERN). Thus, while gratitude might increase economic patience, such benefits may not generalize to conflict-driven control processes.     

Eprobe Mediated Real-Time PCR Monitoring and Melting Curve Analysis

Real-time monitoring of PCR is one of the most important methods for DNA and RNA detection widely used in research and medical diagnostics. Here we describe a new approach for combined real-time PCR monitoring and melting curve analysis using a 3′ end-blocked Exciton-Controlled Hybridization-sensitive fluorescent Oligonucleotide (ECHO) called Eprobe. Eprobes contain two dye moieties attached to the same nucleotide and their fluorescent signal is strongly suppressed as single-stranded oligonucleotides by an excitonic interaction between the dyes. Upon hybridization to a complementary DNA strand, the dyes are separated and intercalate into the double-strand leading to strong fluorescence signals. Intercalation of dyes can further stabilize the DNA/DNA hybrid and increase the melting temperature compared to standard DNA oligonucleotides. Eprobes allow for specific real-time monitoring of amplification reactions by hybridizing to the amplicon in a sequence-dependent manner. Similarly, Eprobes allow for analysis of reaction products by melting curve analysis. The function of different Eprobes was studied using the L858R mutation in the human epidermal growth factor receptor (EGFR) gene, and multiplex detection was demonstrated for the human EGFR and KRAS genes using Eprobes with two different dyes. Combining amplification and melting curve analysis in a single-tube reaction provides powerful means for new mutation detection assays. Functioning as “sequence-specific dyes”, Eprobes hold great promises for future applications not only in PCR but also as hybridization probes in other applications.     

ConfocalCheck - A Software Tool for the Automated Monitoring of Confocal Microscope Performance

Laser scanning confocal microscopy has become an invaluable tool in biomedical research but regular quality testing is vital to maintain the system’s performance for diagnostic and research purposes.Although many methods have been devised over the years to characterise specific aspects of a confocal microscope like measuring the optical point spread function or the field illumination, only very few analysis tools are available. Our aim was to develop a comprehensive quality assurance framework ranging from image acquisition to automated analysis and documentation. We created standardised test data to assess the performance of the lasers, the objective lenses and other key components required for optimum confocal operation.The ConfocalCheck software presented here analyses the data fully automatically. It creates numerous visual outputs indicating potential issues requiring further investigation. By storing results in a web browser compatible file format the software greatly simplifies record keeping allowing the operator to quickly compare old and new data and to spot developing trends.We demonstrate that the systematic monitoring of confocal performance is essential in a core facility environment and how the quantitative measurements obtained can be used for the detailed characterisation of system components as well as for comparisons across multiple instruments.     

综合性医院绩效评价的现状调查与分析

目的 了解医院绩效评价现状与存在的主要问题,为医院探索新的绩效评价方法和构建以战略为导向的绩效评价体系提供依据。方法 采用问卷调查法获得医院绩效评价的基本数据,运用统计描述法对问卷进行分析。结果 现行医院的绩效评价缺乏系统性,与外部环境相脱节,未能反映利益相关者需求,在指标设计时缺少员工参与,重视短期财务结果,在实施、反馈等方面缺乏有效沟通,绩效考评没能实现与医院战略的有效连接。结论 现行绩效评价体系同医院战略脱节,未能有效体现医院战略,评价指标侧重于医院内部评价与财务类指标,而忽视非财务类指标,绩效评价指标设置与评价结果的应用存在矛盾。     

Performance Analysis of a Myrinet-Based Cluster

In recent years, there has been a growing interest in the cluster system as an accepted form of supercomputing, due to its high performance at an affordable cost. This paper attempts to elaborate performance analysis of Myrinet-based cluster. The communication performance and effect of background load on parallel applications were analyzed. For point-to-point communication, it was found that an extension to the Hockney's model was required to estimate the performance. The proposed model suggested that there should be two ranges to be used for the performance metrics to cope with the cache effect. Moreover, based on the extension of the point-to-point communication model, the Xu and Hwang's model for collective communication performance was also extended. Results showed that our models can make better estimation of the communication performance than the previous models. Finally, the interference of other user processes to the cluster system is evaluated by using synthetic background load generation programs.     

Identification and Monitoring of Host Cell Proteins by Mass Spectrometry Combined with High Performance Immunochemistry Testing

Biotherapeutics are often produced in non-human host cells like Escherichia coli, yeast, and various mammalian cell lines. A major focus of any therapeutic protein purification process is to reduce host cell proteins to an acceptable low level. In this study, various E. coli host cell proteins were identified at different purifications steps by HPLC fractionation, SDS-PAGE analysis, and tryptic peptide mapping combined with online liquid chromatography mass spectrometry (LC-MS). However, no host cell proteins could be verified by direct LC-MS analysis of final drug substance material. In contrast, the application of affinity enrichment chromatography prior to comprehensive LC-MS was adequate to identify several low abundant host cell proteins at the final drug substance level. Bacterial alkaline phosphatase (BAP) was identified as being the most abundant host cell protein at several purification steps. Thus, we firstly established two different assays for enzymatic and immunological BAP monitoring using the cobas® technology. By using this strategy we were able to demonstrate an almost complete removal of BAP enzymatic activity by the established therapeutic protein purification process. In summary, the impact of fermentation, purification, and formulation conditions on host cell protein removal and biological activity can be conducted by monitoring process-specific host cell proteins in a GMP-compatible and high-throughput (> 1000 samples/day) manner.     

医院绩效管理与医院运营成本控制研究

公立医院的公益性质要求医院建立一套既注重服务数量质量又避免以追求创收为目的,既注重服务效率又能够进行成本控制的绩效评价体系。医院管理者应采用科学的绩效管理方法,利用合理的绩效管理手段,降低医院运营成本,从而实现为患者提供更好的医疗服务和提高医院效益的双重目标。     

Testing Global Positioning System Performance for Wildlife Monitoring Using Mobile Collars and Known Reference Points

Abstract: To determine the spatial resolution of Global Positioning System (GPS) receiver data, rigorous testing is essential. We tested performance of the Lotek 3300 GPS collar for medium-sized mammals (Lotek Engineering, Inc., Newmarket, ON, Canada). To mimic real wildlife monitoring situations, we performed both static (stationary receiver) and mobile tests, placing the receiver collar on a dog. We compared fix locations of the mobile receiver with the actual trajectory described by a portable Trimble high-precision GPS. We determined performance in relation to habitat type and leaf cover. Location error was habitat-dependent, with the best results in open habitat and much poorer ones in forest, particularly coniferous-dominated forest. For both static and mobile tests, location accuracy was higher when the number of satellites contacted was high and when the residual positional dilution of precision (PDOP) value was low. However, location error was highly variable, even for a given PDOP value and a given number of satellites contacted. Finally, mobile collars performed less well than their static counterparts, presumably because of frequent changes of GPS position and orientation.     

Performance Measurement Via Sap Flow Monitoring of Three Eucalyptus Species for Mine Site and Dryland Salinity Phytoremediation

Monitoring of trees with reliable technology is essential in phytoremediation. Sap flow instrumentation on three Eucalyptus species at a mine site in western Victoria, Australia, was used to determine which species is best suited to meet the goals of a phytoremediation project. Specifically, the aim of the monitoring was to determine which species could better tolerate the hypersaline soil, potentially lower saline ground water, and cope with expected hotter and drier weather given climate change scenarios. Over a summer period, average daily water use of E. cladocalyx was approximately six times greater than E. melliodora and four times greater than E. polybractea. During a three day heat wave event, E. cladocalyx was found to have a higher tolerance to extreme temperature. The optimal VPD / temperature for tree transpiration was 2.6 kPa / 26.2 °C for E. cladocalyx, 2.1 kPa / 23.9 °C for E. melliodora, and 2.0 kPa / 23.2 °C for E. polybractea. Through sap flow monitoring, it was determined that E. cladocalyx could better tolerate saline soils, hotter and drier weather, and had greater potential to lower saline ground water.     

Reliability of Task-Based fMRI for Preoperative Planning: A Test-Retest Study in Brain Tumor Patients and Healthy Controls

Background

Functional magnetic resonance imaging (fMRI) continues to develop as a clinical tool for patients with brain cancer, offering data that may directly influence surgical decisions. Unfortunately, routine integration of preoperative fMRI has been limited by concerns about reliability. Many pertinent studies have been undertaken involving healthy controls, but work involving brain tumor patients has been limited. To develop fMRI fully as a clinical tool, it will be critical to examine these reliability issues among patients with brain tumors. The present work is the first to extensively characterize differences in activation map quality between brain tumor patients and healthy controls, including the effects of tumor grade and the chosen behavioral testing paradigm on reliability outcomes.

Method

Test-retest data were collected for a group of low-grade (n = 6) and high-grade glioma (n = 6) patients, and for matched healthy controls (n = 12), who performed motor and language tasks during a single fMRI session. Reliability was characterized by the spatial overlap and displacement of brain activity clusters, BOLD signal stability, and the laterality index. Significance testing was performed to assess differences in reliability between the patients and controls, and low-grade and high-grade patients; as well as between different fMRI testing paradigms.

Results

There were few significant differences in fMRI reliability measures between patients and controls. Reliability was significantly lower when comparing high-grade tumor patients to controls, or to low-grade tumor patients. The motor task produced more reliable activation patterns than the language tasks, as did the rhyming task in comparison to the phonemic fluency task.

Conclusion

In low-grade glioma patients, fMRI data are as reliable as healthy control subjects. For high-grade glioma patients, further investigation is required to determine the underlying causes of reduced reliability. To maximize reliability outcomes, testing paradigms should be carefully selected to generate robust activation patterns.     

Anaesthesia Monitoring by Recurrence Quantification Analysis of EEG Data

Appropriate monitoring of the depth of anaesthesia is crucial to prevent deleterious effects of insufficient anaesthesia on surgical patients. Since cardiovascular parameters and motor response testing may fail to display awareness during surgery, attempts are made to utilise alterations in brain activity as reliable markers of the anaesthetic state. Here we present a novel, promising approach for anaesthesia monitoring, basing on recurrence quantification analysis (RQA) of EEG recordings. This nonlinear time series analysis technique separates consciousness from unconsciousness during both remifentanil/sevoflurane and remifentanil/propofol anaesthesia with an overall prediction probability of more than 85%, when applied to spontaneous one-channel EEG activity in surgical patients.