Memory-based scheduling of scientific computing clusters

This study looks at how increased memory utilisation affects throughput and energy consumption in scientific computing, especially in high-energy physics. Our aim is to minimise energy consumed by a set of jobs without increasing the processing time. The earlier tests indicated that, especially in data analysis, throughput can increase over 100% and energy consumption decrease 50% by processing multiple jobs in parallel per CPU core. Since jobs are heterogeneous, it is not possible to find an optimum value for the number of parallel jobs. A better solution is based on memory utilisation, but finding an optimum memory threshold is not straightforward. Therefore, a fuzzy logic-based algorithm was developed that can dynamically adapt the memory threshold based on the overall load. In this way, it is possible to keep memory consumption stable with different workloads while achieving significantly higher throughput and energy-efficiency than using a traditional fixed number of jobs or fixed memory threshold approaches.

Streamlining the medication process improves safety in the intensive care unit.

BACKGROUND: Multiple interventions were made to optimize the medication process in our intensive care unit (ICU). 1 Transcriptions from the medical order form to the administration plan were eliminated by merging both into a single document; 2 the new form was built in a logical sequence and was highly structured to promote completeness and standardization of information; 3 frequently used drug names, approved units, and fixed routes were pre-printed; 4 physicians and nurses were trained with regard to the correct use of the new form. This study was aimed at evaluating the impact of these interventions on clinically significant types of medication errors. METHODS: Eight types of medication errors were measured by a prospective chart review before and after the interventions in the ICU of a public tertiary care hospital. We used an interrupted time-series design to control the secular trends. RESULTS: Over 85 days, 9298 lines of drug prescription and/or administration to 294 patients, corresponding to 754 patient-days were collected and analysed for the three series before and three series following the intervention. Global error rate decreased from 4.95 to 2.14% (-56.8%, P < 0.001). CONCLUSIONS: The safety of the medication process in our ICU was improved by simple and inexpensive interventions. In addition to the optimization of the prescription writing process, the documentation of intravenous preparation, and the scheduling of administration, the elimination of the transcription in combination with the training of users contributed to reducing errors and carried an interesting potential to increase safety.

Objectifying psychomental stress in the workplace--an example.

BACKGROUND: Psychomental stress is a major source of illness and reduced productivity. Data objectifying physiological stress responses are scarce. We studied salivary cortisol levels in a highly stressful environment, the pediatric critical care unit. The aim was to identify targets for organizational changes, to implement these changes and to assess their impact on cortisol levels. DESIGN: Repeated measurements observational cohort study (before and after intervention). SUBJECTS: 84 nurses working in two independent teams (A and B) in a 19 bed pediatric intensive care unit. Between study periods team A experienced a major exchange of experienced staff while the turnover rate in team B remained average. MEASUREMENTS AND INTERVENTIONS: Salivary cortisol samples were collected every 2 h and after stressful events. Nurses in study period I showed elevated cortisol levels at the beginning of the late shift, interpreted as an anticipatory stress reaction. To ease conditions during the early part of the late shift (conflicting tasks, noise and crowding), we postponed the afternoon ward round, limited non-urgent procedures and introduced a change in visiting hours. The early shift, which was not affected by the intervention, served as control. MAIN RESULTS: Both crude and adjusted analysis revealed a decrease of cortisol levels at the beginning of the late shift in team B (p = 0.0009), but not in team A (p = 0.464). The control situation showed no difference between teams and study periods. INTERPRETATION: We demonstrated reduced cortisol secretions in one team following organizational changes, which was probably overridden by the disruption of social coherence in the second team.

Comparison of in-hospital mortality for acute myocardial infarction in Switzerland with admission during routine duty hours versus admission during out of hours (insight into the AMIS plus registry).

To improve long-term survival, prompt revascularization of the infarct-related artery should be done in patients with acute myocardial infarction (AMI); therefore, a large proportion of these patients would be hospitalized during out of hours. The clinical effects of out-of-hours AMI management were already questioned, with conflicting results. The purpose of this investigation was to compare the in-hospital outcome of patients admitted for AMI during out of hours and working hours. All patients with AMI included in the AMIS Plus Registry from January 1, 1997, to March 30, 2006, were analyzed. The working-hours group included patients admitted from 7 a.m. to 7 p.m. on weekdays, and the out-of-hours group included patients admitted from 7 p.m. to 7 a.m. on weekdays or weekends. Major cardiac events were defined as cardiovascular death, reinfarction, and stroke. The study primary end points were in-hospital death and major adverse cardiac event (MACE) rates. A total of 12,480 patients met the inclusion criteria, with 52% admitted during normal working hours, and 48%, during out of hours. Patients admitted during weekdays included more women (28.1% vs 26%; p = 0.009), older patients (65.5 +/- 13 vs 64.1 +/- 13 years; p = 0.0011), less current smokers (40.1% vs 43.5%; p <0.001), and less patients with a history of ischemic heart disease (31.5% vs 34.5%; p = 0.001). A significantly higher proportion of patients admitted during out of hours had Killip's class III and IV. No differences in terms of in-hospital survival rates between the 2 groups (91.5% vs 91.2%; p = 0.633) or MACE-free survival rates (both 88.5%; p = 1.000) were noted. In conclusion, the outcome of patients with AMI admitted out of hours was the same compared with those with a weekday admission. Of predictors for in-hospital outcome, timing of admission had no significant influence on mortality and/or MACE incidence.

Effets du travail de nuit sur la santé

Dans les pays industrialisés, 20% des salariés sont concernés par le travail de nuit. Pourtant, les effets du travail de nuit sur la santé sont peu traités par les revues médicales générales, alors que le travail de nuit a des conséquences non négligeables sur les systèmes cardiovasculaires et digestifs entre autres, comme l'ont démontré de nombreuses études ces dernières décennies. Le travail de nuit a encore récemment attiré l'attention quand il a été déclaré cancérigène probable (catégorie 2A) par le Centre international de recherches sur le cancer. Ainsi dans cet article, seront passés en revue les troubles de la santé qui peuvent être générés ou aggravés par le travail de nuit. Deux cas pratiques illustreront la problématique et permettront d'aborder la conduite à tenir. 20% of employees in industrialized countries are concerned by shift work. Nevertheless, there is very little information in general medical journals about the effects of shift work on health. Shift work can have several major effects on health such as cardiovascular and digestive disorders among others, as demonstrated by several studies in recent decades. Shift work has attracted considerable attention recently when it was declared probable carcinogen by the International Agency for research on cancer. We review the health disorders that may be generated or aggravated by shift work and illustrate the problem by two case studies of occupational medicine and discuss the appropriate attitude to take

Circadian and circaseptan patterns of natality and perinatal mortality of infants with different birth weights

OBJECTIVE. Data on human natality, stillbirth and perinatal mortality from Switzerland (1979-1987), available in four birthweight categories, are reexamined to assess any about-weekly (circaseptan) and changes in about-daily (circadian) patterns in central Europe over a century and a halfDESIGN. Retrospective analyses on archived data.SETTING. Federal Office of Statistics for Switzerland.RESULTS. In addition to prominent circadians, weekly patterns are also documented.CONCLUSION. Exogenous variations, prominent in early extrauterine life, such as changes of scheduling in obstetrics, may contribute to circadian and cireaseptan natality patterns. Information on these patterns serves in the optimization of neonatal care. Partly endogenous, partly physical environmental aspects, at least of about-weekly patterns, remain to be elucidated in series consisting exclusively of spontaneous parturitions.

Production Flow Analysis - cases from manufacturing and service industry

Production flow analysis (PFA) is a well-established methodology used for transforming traditional functional layout into product-oriented layout. The method uses part routings to find natural clusters of workstations forming production cells able to complete parts and components swiftly with simplified material flow. Once implemented, the scheduling system is based on period batch control aiming to establish fixed planning, production and delivery cycles for the whole production unit. PFA is traditionally applied to job-shops with functional layouts, and after reorganization within groups lead times reduce, quality improves and motivation among personnel improves. Several papers have documented this, yet no research has studied its application to service operations management. This paper aims to show that PFA can well be applied not only to job-shop and assembly operations, but also to back-office and service processes with real cases. The cases clearly show that PFA reduces non-value adding operations, introduces flow by evening out bottlenecks and diminishes process variability, all of which contribute to efficient operations management.

Cancer chronotherapeutics: experimental, theoretical, and clinical aspects.

The circadian timing system controls cell cycle, apoptosis, drug bioactivation, and transport and detoxification mechanisms in healthy tissues. As a consequence, the tolerability of cancer chemotherapy varies up to several folds as a function of circadian timing of drug administration in experimental models. Best antitumor efficacy of single-agent or combination chemotherapy usually corresponds to the delivery of anticancer drugs near their respective times of best tolerability. Mathematical models reveal that such coincidence between chronotolerance and chronoefficacy is best explained by differences in the circadian and cell cycle dynamics of host and cancer cells, especially with regard circadian entrainment and cell cycle variability. In the clinic, a large improvement in tolerability was shown in international randomized trials where cancer patients received the same sinusoidal chronotherapy schedule over 24h as compared to constant-rate infusion or wrongly timed chronotherapy. However, sex, genetic background, and lifestyle were found to influence optimal chronotherapy scheduling. These findings support systems biology approaches to cancer chronotherapeutics. They involve the systematic experimental mapping and modeling of chronopharmacology pathways in synchronized cell cultures and their adjustment to mouse models of both sexes and distinct genetic background, as recently shown for irinotecan. Model-based personalized circadian drug delivery aims at jointly improving tolerability and efficacy of anticancer drugs based on the circadian timing system of individual patients, using dedicated circadian biomarker and drug delivery technologies.

Local optima networks of hard combinatorial landscapes

Combinatorial optimization involves finding an optimal solution in a finite set of options; many everyday life problems are of this kind. However, the number of options grows exponentially with the size of the problem, such that an exhaustive search for the best solution is practically infeasible beyond a certain problem size. When efficient algorithms are not available, a practical approach to obtain an approximate solution to the problem at hand, is to start with an educated guess and gradually refine it until we have a good-enough solution. Roughly speaking, this is how local search heuristics work. These stochastic algorithms navigate the problem search space by iteratively turning the current solution into new candidate solutions, guiding the search towards better solutions. The search performance, therefore, depends on structural aspects of the search space, which in turn depend on the move operator being used to modify solutions. A common way to characterize the search space of a problem is through the study of its fitness landscape, a mathematical object comprising the space of all possible solutions, their value with respect to the optimization objective, and a relationship of neighborhood defined by the move operator. The landscape metaphor is used to explain the search dynamics as a sort of potential function. The concept is indeed similar to that of potential energy surfaces in physical chemistry. Borrowing ideas from that field, we propose to extend to combinatorial landscapes the notion of the inherent network formed by energy minima in energy landscapes. In our case, energy minima are the local optima of the combinatorial problem, and we explore several definitions for the network edges. At first, we perform an exhaustive sampling of local optima basins of attraction, and define weighted transitions between basins by accounting for all the possible ways of crossing the basins frontier via one random move. Then, we reduce the computational burden by only counting the chances of escaping a given basin via random kick moves that start at the local optimum. Finally, we approximate network edges from the search trajectory of simple search heuristics, mining the frequency and inter-arrival time with which the heuristic visits local optima. Through these methodologies, we build a weighted directed graph that provides a synthetic view of the whole landscape, and that we can characterize using the tools of complex networks science. We argue that the network characterization can advance our understanding of the structural and dynamical properties of hard combinatorial landscapes. We apply our approach to prototypical problems such as the Quadratic Assignment Problem, the NK model of rugged landscapes, and the Permutation Flow-shop Scheduling Problem. We show that some network metrics can differentiate problem classes, correlate with problem non-linearity, and predict problem hardness as measured from the performances of trajectory-based local search heuristics.

Multi-institutional validation of the prognostic value of Ki-67 labeling index in patients treated with radical prostatectomy.

OBJECTIVE: Several smaller single-center studies have reported a prognostic role for Ki-67 labeling index in prostate cancer. Our aim was to test whether Ki-67 is an independent prognostic marker of biochemical recurrence (BCR) in a large international cohort of patients treated with radical prostatectomy (RP). METHODS: Ki-67 immunohistochemical staining on prostatectomy specimens from 3,123 patients who underwent RP for prostate cancer was retrospectively performed. Univariable and multivariable Cox regression models were used to assess the association of Ki-67 status with BCR. RESULTS: Ki-67 positive status was observed in 762 (24.4 %) patients and was associated with lymph node involvement (LNI) (p = 0.039). Six hundred and twenty-one (19.9 %) patients experienced BCR. The estimated 3-year biochemical-free survivals were 85 % for patients with negative Ki-67 status and 82.1 % for patients with positive Ki-67 status (log-rank test, p = 0.014). In multivariable analysis that adjusted for the effects of age, preoperative PSA, RP Gleason sum, seminal vesicle invasion, extracapsular extension, positive surgical margins, lymphovascular invasion, and LNI, Ki-67 was significantly associated with BCR (HR = 1.19; p = 0.019). Subgroup analysis revealed that Ki-67 is associated with BCR in patients without LNI (p = 0.004), those with RP Gleason sum 7 (p = 0.015), and those with negative surgical margins (p = 0.047). CONCLUSION: We confirmed Ki-67 as an independent predictor of BCR after RP. Ki-67 could be particularly informative in patients with favorable pathologic characteristics to help in the clinical decision-making regarding adjuvant therapy and optimized follow-up scheduling.

Le pool ou unité commune de personnel soignant

L'unité commune de personnel soignant ou pool infirmier du CHUV est un service de professionnels qualifiés, disponibles et capables de remplacer les défections du personnel régulier ou renforcer les effectifs lors de surcharge de travail occasionnel. [Table des matières] 1. Le pool: perspective historique: Origine du travail intérimaire; Le travail intérimaire en Suisse et son développement; Genèse du Pool; Développement du Pool. 2. Problématique du Pool : Perspective conceptuelle et théorique. L'hôpital, modèle d'organisation pris entre deux logiques; Marché-hiérarchie: théorie des coûts de transactions; La coordination collective des actions individuelles apport de l'économie des conventions. Concept de flexibilité. Connaissance tacite et explicite. 3. Le terrain d'observation. Annexes: Questionnaire des poolistes et résumé des commentaires; etc.