Parallel application-level behavioral attributes for performance and energy management of high-performance computing systems

Run time variability of parallel applications continues to present significant challenges to their performance and energy efficiency in high-performance computing (HPC) systems. When run times are extended and unpredictable, application developers perceive this as a degradation of system (or subsystem) performance. Extended run times directly contribute to proportionally higher energy consumption, potentially negating efforts by applications, or the HPC system, to optimize energy consumption using low-level control techniques, such as dynamic voltage and frequency scaling (DVFS). Therefore, successful systemic management of application run time performance can result in less wasted energy, or even energy savings. We have been studying run time variability in terms of communication time, from the perspective of the application, focusing on the interconnection network. More recently, our focus has shifted to developing a more complete understanding of the effects of HPC subsystem interactions on parallel applications. In this context, the set of executing applications on the HPC system is treated as a subsystem, along with more traditional subsystems like the communication subsystem, storage subsystem, etc. To gain insight into the run time variability problem, our earlier work developed a framework to emulate parallel applications (PACE) that stresses the communication subsystem. Evaluation of run time sensitivity to network performance of real applications is performed with a tool called PARSE, which uses PACE. In this paper, we propose a model defining application-level behavioral attributes, that collectively describes how applications behave in terms of their run time performance, as functions of their process distribution on the system (spacial locality), and subsystem interactions (communication subsystem degradation). These subsystem interactions are produced when multiple applications execute concurrently on the same HPC system. We also revisit our evaluation framework and tools to demonstrate the flexibility of our application characterization techniques, and the ease with which attributes can be quantified. The validity of the model is demonstrated using our tools with several parallel benchmarks and application fragments. Results suggest that it is possible to articulate application-level behavioral attributes as a tuple of numeric values that describe course-grained performance behavior.     

Comparative genomics of NAD biosynthesis in cyanobacteria

Biosynthesis of NAD(P) cofactors is of special importance for cyanobacteria due to their role in photosynthesis and respiration. Despite significant progress in understanding NAD(P) biosynthetic machinery in some model organisms, relatively little is known about its implementation in cyanobacteria. We addressed this problem by a combination of comparative genome analysis with verification experiments in the model system of Synechocystis sp. strain PCC 6803. A detailed reconstruction of the NAD(P) metabolic subsystem using the SEED genomic platform (http://theseed.uchicago.edu/FIG/index.cgi) helped us accurately annotate respective genes in the entire set of 13 cyanobacterial species with completely sequenced genomes available at the time. Comparative analysis of operational variants implemented in this divergent group allowed us to elucidate both conserved (de novo and universal pathways) and variable (recycling and salvage pathways) aspects of this subsystem. Focused genetic and biochemical experiments confirmed several conjectures about the key aspects of this subsystem. (i) The product of the slr1691 gene, a homolog of Escherichia coli gene nadE containing an additional nitrilase-like N-terminal domain, is a NAD synthetase capable of utilizing glutamine as an amide donor in vitro. (ii) The product of the sll1916 gene, a homolog of E. coli gene nadD, is a nicotinic acid mononucleotide-preferring adenylyltransferase. This gene is essential for survival and cannot be compensated for by an alternative nicotinamide mononucleotide (NMN)-preferring adenylyltransferase (slr0787 gene). (iii) The product of the slr0788 gene is a nicotinamide-preferring phosphoribosyltransferase involved in the first step of the two-step non-deamidating utilization of nicotinamide (NMN shunt). (iv) The physiological role of this pathway encoded by a conserved gene cluster, slr0787-slr0788, is likely in the recycling of endogenously generated nicotinamide, as supported by the inability of this organism to utilize exogenously provided niacin. Positional clustering and the co-occurrence profile of the respective genes across a diverse collection of cellular organisms provide evidence of horizontal transfer events in the evolutionary history of this pathway.     

京郊农业生物循环系统生态经济能值评估——以密云尖岩村为例

国内外学术界和决策者对于循环农业给予了相当关注,但关于循环农业研究,从产业经济角度进行定量分析目前仍处于相对匮乏状态.以京郊典型的尖岩村农业生物循环农业范式为案例,采用能值方法,以翔实的数据描述了从种植、养殖到食用菌生产的各个阶段能量输入与输出,通过能值评估指标体系判断在整个循环产业链条中,各生产环节对环境经济产生的影响,结果显示:(1)农业生物循环系统的能值投资率(2.57)较养殖(116.23)、食用菌子系统(158.73)低;环境负荷率(1.40)也较养殖子系统(7.24)、食用菌子系统(13)低,表明,该循环模式可减少对自然资源和外来经济投入的依赖,能够获得自身的资源补偿.(2)农业生物循环系统的净能值产出率和可持续发展指数较高,说明,该模式有较强的获利性,是较理想的产业系统,在北京郊区推广价值较高.     

Dying under the bird's shadow: narrative representations of degedege and child survival among the Zaramo of Tanzania

In this article, I examine the cultural interpretations of degedege, an indigenous illness commonly recognized by the Zaramo people of coastal Tanzania as life threatening. Drawing on the narratives of three bereaved parents who lost a child to degedege, I analyze the contextual and circumstantial factors involved in these parents' negotiation of the identity of an illness and in their subsequent therapy seeking behavior. I show that even though cultural knowledge and etiological beliefs about degedege may be shared locally, there is significant variation in the therapeutic pathways that parents follow to deal with an actual episode of the illness. I emphasize the need for more contextualized data on health-seeking behaviors, and argue that it is necessary to pay attention to the micropolitics of health care decision making at the household level. Finally, I also call attention to the politics of provider-patient communication at public health facilities as a means to improve public health interventions to increase child survival.     

Symptomatic differences between the sexes in rural Mexico

This paper addresses the problem of the differential presentation of illness by women and men in two Spiritualist temples and a physician's office situated in rural Mexico. Women's morbidity raises the broader anthropological questions of the interplay between symptomatic expression and women's unequal status in the social structure, their cognitive evaluation of specific life experiences, cultural etiological explanations and Western models of dysphoria. Symptoms presented by patients in different health care delivery sites are compared and case vignettes of patients' illnesses and attributions are presented to demonstrate the ways in which culturally constructed illness attributions and illness expressions comprise a somatic grammar for the articulation of experiential distress. The sick population is compared with a control group of healthy women to highlight the socio-cultural and psychosocial variables that promote illness in women from the same sociocultural strata of rural Mexico. Collective understandings of the role of life events and emotional expression in illness attributions legitimize somatization as a coping style under adverse existential conditions.     

黄河三角洲区域生态经济系统动态耦合过程及趋势

黄河三角洲地区正处于快速开发建设时期,资源丰富,但生态环境脆弱,区域生态经济耦合状况影响着区域可持续发展的态势。借鉴一般系统论的思想,构建了区域生态经济系统耦合过程模型,定量分析了黄河三角洲区域生态经济系统的耦合过程与演进趋势。结果表明:1990年以来黄河三角洲区域生态系统综合指数与经济系统综合指数均呈上升趋势,区域资源供给和生态环境调节能力逐渐提高,经济生产能力和社会消费水平不断提升;黄河三角洲区域生态系统与经济系统总体上处于互动协调发展状态,1990—2007年区域生态经济系统耦合度指数先增加后减少,耦合过程经历了由相悖发展到良性耦合的过程;按照区域生态经济系统耦合趋势外推,2019年将接近最佳耦合点45°;区域生态经济系统仍处于较低水平的良性耦合,区域生态经济发展的速度和质量有待进一步提升。应协同推进区域经济生态化和生态经济化建设,建立高效生态经济体系,努力实现区域生态资源资产化、价值化,提升区域生态经济系统耦合的状态水平。     

New data (smaller foraminifers and correlation with depositional sequences) on the Las Llacerias section (Late Pennsylvanian,Cantabrian Mountains,NW Spain)

New sedimentological and paleontological information on the uppermost Moscovian and Kasimovian strata of the Las Llacerias section, a succession exposed in the Picos de Europa region (Cantabrian Mountains) that is considered to bear interest for the global correlation of the Upper Pennsylvanian subsystem, are presented. Based on sedimentological studies, three stratigraphic intervals can be established which record three successive episodes in the evolution of the carbonate platform. The study of the environmental evolution and sea-level fluctuations, as well as biostratigraphic fusulinoidean information, allow the correlation of this section with the synorogenic deposits of the Gamonedo-Cabrales area (northern Picos de Europa region). It is recognized that in the Las Llacerias strata, 7 of the 11 depositional sequences of the latter area are represented. The taxonomy and distribution of smaller foraminifers, a fossil group never studied before in this section, have been analysed. Data obtained show the presence of, at least, 30 genera. In some cases (Syzrania aff. bulbosa, Tezaquina, Mesolasiodiscus, Pseudotaxis and Hemidiscus), their record in the Las Llacerias section significantly extends the stratigraphic genus or species range. The potential role of Protonodosaria and Nodosinelloides species, as well as the acme of Hemigordius schlumbergeri for the correlation of the Kasimovian deposits is reinforced within this study.     

京津冀地区城市化与生态环境交互耦合关系定量测度

城市化与生态环境之间客观上存在着极其复杂的交互耦合关系,如何实现城市化与生态环境协调发展将是世界经济社会发展的核心议题,也是近年来国内外研究的热点命题。首先构建了城市化和生态环境系统综合评价指标体系,然后借助物理学耦合模型,构建了城市化与生态环境动态耦合协调度模型,定量分析了1980—2011年京津冀地区城市化与生态环境的耦合过程与演进趋势。结果表明:人口城市化和生态压力分别对城市化子系统与生态环境子系统的贡献份额最大,明显高于其他因素;在耦合协调度测算模型中,城市化子系统与生态环境子系统3种不同贡献份额所得出的耦合协调度的变化趋势是一致的,表明耦合协调度模型受城市化与生态环境子系统贡献份额比例的影响很小;1980年以来京津冀地区的城市化与生态环境耦合协调度呈现出S型曲线变化,协调类型从严重不协调-城市化受阻发展到高级协调-生态环境滞后类型;正确认识城市化与生态环境交互胁迫的时空动态耦合规律,采取恰当的区域发展政策和适当的城市发展战略,对进一步加快区域城市化进程,改善生态环境,实现京津冀地区城市化与生态环境的协调和可持续发展具有重要的指导意义。     

沙滩-社区系统健康韧性评价——以深圳市大鹏半岛为例

沙滩既是海岸带旅游活动热点区,也是应对陆海交互影响以及人为气候变化的最前沿。如何将韧性和健康理念融入到海岸带发展建设规划,建立自免疫、自适应、自修复的区域健康韧性发展机制已成为亟待解决的问题。定位于深圳大鹏半岛的沙滩-社区系统,从社会-生态系统的应对力和适应力出发,构建健康韧性评估框架。结果显示：（1）大鹏沙滩-社区复合系统中,社会子系统健康韧性水平（0.38±0.16,均值±标准差）低于生态子系统（0.65±0.10）;（2）依据沙滩管理分类,I类沙滩的社会（0.53±0.16）、生态子系统（0.67±0.08）健康韧性均最高,沙滩浴场类复合系统的健康韧性大于围合管理类和封闭管理类,而开放管理类沙滩耦合系统的健康韧性在社会、生态子系统间差异明显,其生态子系统得分最低而社会子系统得分偏高;（3）沙滩-社区复合系统健康韧性差异的主控因子包括紧急避难场所覆盖率（19.4%,贡献度）、沙滩整洁度（16.5%）、公共卫生设施覆盖率（16.1%）,提升此类健康指标是提升沙滩-社区系统健康韧性的关键。本研究揭示了大鹏半岛的沙滩-社区系统存在自然资源分散、健康基础设施服务供给质量差异显著等问题,为大鹏半岛可持续发展和沙滩生态产品价值实现提供了科学评估基础。     

A review of some Cretaceous and Tertiary serpulid polychaetes of the genera Cementula and Spiraserpula Regenhardt 1961,Laqueoserpula Lommerzheim 1979 andProtectoconorca JÄger 1983

The genus Cementula was proposed by Nielsen (1931) without designating a type species. Regenhardt (1961) made the name Cementula available by designating Cementula sphaerica Nielsen 1931 as its type. Regenhardt (1961) and Lommerzheim (1979) retain Cementula as a genus distinct from Spiraserpula Regenhardt 1961, while JÄger (1983) synonymizes the latter with the former. Re-examination of their types, however, revealed an important additional character for retaining them as distinct genera, the presence of internal longitudinal ridges in Spiraserpula, which are absent in Cementula. Two other genera, Laqueoserpula Lommerzheim 1979 and Protectoconorca JÄger 1983 were also examined, but they lack such internal tube structures. This study yielded an available name among fossil genera, namely, Spiraserpula Regenhardt 1961, for several living Serpula-like species with internal tube structures, to be described in a separate paper.     

“There are many fevers”: Communities’ perception and management of Febrile illness and its relationship with human animal interactions in South-Western Uganda

Diagnosing the causative agent of febrile illness in resource-limited countries is a challenge in part due to lack of adequate diagnostic infrastructure to confirm cause of infection. Most febrile illnesses (>60%) are non-malarial, with a significant proportion being zoonotic and likely from animal origins. To better characterize the pathways for zoonotic disease transmission and control in vulnerable communities, adequate information on the communities’ experiences and lexicon describing fever, and their understanding and perceptions of risk pathways is required. We undertook an ethnographic study to understand behaviors, exposures, and attitudes toward fever at the community level. Our hope is to better elucidate areas of priority surveillance and diagnostic investment. A focused ethnography consisting of participant observation, informal conversations, 4 barazas (community meetings), and formal ethnographic interviews (13 Focus group discussions and 17 Key informant interviews) was conducted between April and November 2015 in Kasese and Hoima Districts in Uganda. Perception of illness and associated risk factors was heavily influenced by the predominant livelihood activity of the community. The term “fever” referred to multiple temperature elevating disease processes, recognized as distinct pathological occurrences. However, malaria was the illness often cited, treated, or diagnosed both at the health facilities and through self-diagnosis and treatment. As expected, fever is as an important health challenge affecting all ages. Recognition of malarial fever was consistent with a biomedical model of disease while non-malarial fevers were interpreted mainly through ethno etiological models of explanation. These models are currently being used to inform education and prevention strategies and treatment regimens toward the goal of improving patients’ outcomes and confidence in the health system. Development of treatment algorithms that consider social, cultural, and economic contexts, especially where human-animal interaction is prevalent, should factor animal exposure and zoonotic illnesses as important differentials.     

基于适应性循环理论与压力-状态-响应框架的区域社会-生态系统演进研究

21世纪以来都市圈快速扩张对区域社会-生态系统的可持续发展构成威胁,基于动态演进视角的区域社会-生态系统运行机制解析备受关注。以南京都市圈为例,从区域和城市两个尺度,基于适应性循环理论与压力-状态-响应框架解析2000—2019年近20年来都市圈社会-生态系统的交互适应循环阶段,以及每个阶段系统的差异化应激响应机制。研究表明南京都市圈社会-生态系统整体经历了3个适应循环周期,现处于新一轮的适应性循环阶段,系统适应性呈上升趋势,但社会子系统和生态子系统尚未取得协调。都市圈内各城市的社会-生态系统演进类型有所不同,可分为稳定增长型、波动增长型、不均衡发展型和生态危机型四类。未来需要采取差异化的社会-生态系统治理策略,确保都市圈整体优化发展。     

De novo acute infection and reactivation of hepatitis B virus in established cirrhosis.

Five patients with cirrhosis proved by biopsy had clinical, biochemical, and serological evidence of an acute hepatitis B infection. In two the illness was fulminant and led to death. Only one patient completely recovered. Serological markers for the hepatitis B virus were absent before the onset of the acute illness in four patients, which suggested that a de novo infection had been acquired as a result of recent transfusions of blood or blood products. The fifth patient, who had Goodpasture''s syndrome, had antibody to the core of hepatitis B virus, indicating previous exposure to the virus; his acute hepatitis may have been related to immunosuppressive drug treatment, which may have reactivated a dormant virus infection. Thus an acute type B viral hepatitis due to either a de novo or a reactivated infection may be superimposed on cirrhosis.     

Explaining a complex disease process: talking to patients about Hansen's disease (leprosy) in Brazil

Patient explanatory models of Hansen's disease (leprosy) in Rio de Janeiro, Brazil, tend to be syntheses of folk models of illness and health, biomedical models to which patients are exposed at different stages in the treatment process, and individual patient experiences of illness. The sensitive presentation of biomedical information about Hansen's disease to patients has the potential to increase adherence to treatment programs and increase patient confidence in the biomedical system. Conversely, withholding or poor presentation of biomedical information can create misunderstanding and confusion for patients. In this article, I explore the ways in which people who are affected by Hansen's disease in Rio de Janeiro learn about different aspects of their illness and its treatment from health care professionals.     

Using Informatics and the Electronic Medical Record to Describe Antimicrobial Use in the Clinical Management of Diarrhea Cases at 12 Companion Animal Practices

Antimicrobial drugs may be used to treat diarrheal illness in companion animals. It is important to monitor antimicrobial use to better understand trends and patterns in antimicrobial resistance. There is no monitoring of antimicrobial use in companion animals in Canada. To explore how the use of electronic medical records could contribute to the ongoing, systematic collection of antimicrobial use data in companion animals, anonymized electronic medical records were extracted from 12 participating companion animal practices and warehoused at the University of Calgary. We used the pre-diagnostic, clinical features of diarrhea as the case definition in this study. Using text-mining technologies, cases of diarrhea were described by each of the following variables: diagnostic laboratory tests performed, the etiological diagnosis and antimicrobial therapies. The ability of the text miner to accurately describe the cases for each of the variables was evaluated. It could not reliably classify cases in terms of diagnostic tests or etiological diagnosis; a manual review of a random sample of 500 diarrhea cases determined that 88/500 (17.6%) of the target cases underwent diagnostic testing of which 36/88 (40.9%) had an etiological diagnosis. Text mining, compared to a human reviewer, could accurately identify cases that had been treated with antimicrobials with high sensitivity (92%, 95% confidence interval, 88.1%–95.4%) and specificity (85%, 95% confidence interval, 80.2%–89.1%). Overall, 7400/15,928 (46.5%) of pets presenting with diarrhea were treated with antimicrobials. Some temporal trends and patterns of the antimicrobial use are described. The results from this study suggest that informatics and the electronic medical records could be useful for monitoring trends in antimicrobial use.     

A Theoretical Approach on Controlling Agricultural Pest by Biological Controls

In this paper we propose and analyze a prey-predator type dynamical system for pest control where prey population is treated as the pest. We consider two classes for the pest namely susceptible pest and infected pest and the predator population is the natural enemy of the pest. We also consider average delay for both the predation rate i.e. predation to the susceptible pest and infected pest. Considering a subsystem of original system in the absence of infection, we analyze the existence of all possible non-negative equilibria and their stability criteria for both the subsystem as well as the original system. We present the conditions for transcritical bifurcation and Hopf bifurcation in the disease free system. The theoretical evaluations are demonstrated through numerical simulations.     

Material Spiraling in Stream Corridors: A Telescoping Ecosystem Model

Stream ecosystems consist of several subsystems that are spatially distributed concentrically, analogous to the elements of a simple telescope. Subsystems include the central surface stream, vertically and laterally arrayed saturated sediments (hyporheic and parafluvial zones), and the most distal element, the riparian zone. These zones are hydrologically connected; thus water and its dissolved and suspended load move through all of these subsystems as it flows downstream. In any given subsystem, chemical transformations result in a change in the quantity of materials in transport. Processing length is the length of subsystem required to “process” an amount of substrate equal to advective input. Long processing lengths reflect low rates of material cycling. Processing length provides the length dimension of each cylindrical element of the telescope and is specific to subsystem (for example, the surface stream), substrate (for instance, nitrate), and process (denitrification, for example). Disturbance causes processing length to increase. Processing length decreases during succession following disturbance. The whole stream-corridor ecosystem consists of several nested cylindrical elements that extend and retract, much as would a telescope, in response to disturbance regime. This telescoping ecosystem model (TEM) can improve understanding of material retention in running water systems; that is, their “nutrient filtration” capacity. We hypothesize that disturbance by flooding alters this capacity in proportion to both intensity of disturbance and to the relative effect of disturbance on each subsystem. We would expect more distal subsystems (for example, the riparian zone) to show the highest resistance to floods. In contrast, we predict that postflood recovery of functions such as material processing (that is, resilience) will be highest in central elements and decrease laterally. Resistance and resilience of subsystems are thus both inversely correlated and spatially separated. We further hypothesize that cross-linkages between adjacent subsystems will enhance resilience of the system as a whole. Whole-ecosystem retention, transformation, and transport are thus viewed as a function of subsystem extent, lateral and vertical linkage, and disturbance regime. Received 15 April 1997; accepted 1 September 1997.     

Neural cross-correlation and signal decorrelation: insights into coding of auditory space

The auditory systems of humans and many other species use the difference in the time of arrival of acoustic signals at the two ears to compute the lateral position of sound sources. This computation is assumed to initially occur in an assembly of neurons organized along a frequency-by-delay surface. Mathematically, the computations are equivalent to a two-dimensional cross-correlation of the input signals at the two ears, with the position of the peak activity along this surface designating the position of the source in space. In this study, partially correlated signals to the two ears are used to probe the mechanisms for encoding spatial cues in stationary or dynamic (moving) signals. It is demonstrated that a cross-correlation model of the auditory periphery coupled with statistical decision theory can predict the patterns of performance by human subjects for both stationary and motion stimuli as a function of stimulus decorrelation. Implications of these findings for the existence of a unique cortical motion system are discussed.     

A conceptual model of farmers' informational activity: a tool for improved support of livestock farming management

Farmers have been slow to adopt decision support system (DSS) models and their outputs, mainly owing to (i) the complexity of the data involved, which most potential users are unable to collect and process; and (ii) inability to integrate these models into real representations of their informational environments. This situation raises questions about the way farm management researchers have modelled information and information management, and especially about the quality of the information assessed by the farmers. We consider that to review advisory procedures we need to understand how farmers select and use farm management-related information, rather than focusing on decisions made in particular situations. The aim of this study was to build a conceptual model of the farmer-targeted farm management-related information system. This model was developed using data collected in commercial beef cattle farms. The design structure and operational procedures are based on (i) data categories representing the diversity of the informational activity; and (ii) selected criteria for supporting decisions. The model is composed of two subsystems, each composed of two units. First, an organizational subsystem organizes, finalizes and monitors informational activity. Second, a processing subsystem builds and exploits the informational resources. This conceptual model makes it possible to describe and understand the diverse range of farmers' informational activity by taking into account both the flow of information and the way farmers make sense of that information. This model could serve as a component of biodecisional DSS models for assigning information in the decision-making process. The next task will be to take into account the broad range of farmers' perceptions of the management situations in DSS models.