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.

A Gain Scheduling Model Predictive Controller for Blood Glucose Control in Type 1 Diabetes

This paper presents a control strategy for blood glucose(BG) level regulation in type 1 diabetic patients. To design the controller, model-based predictive control scheme has been applied to a newly developed diabetic patient model. The controller is provided with a feedforward loop to improve meal compensation, a gain-scheduling scheme to account for different BG levels, and an asymmetric cost function to reduce hypoglycemic risk. A simulation environment that has been approved for testing of artificial pancreas control algorithms has been used to test thecontroller. The simulation results show a good controller performance in fasting conditions and meal disturbance rejection, and robustness against model–patient mismatch and errors in mealestimation

Modifying effect of dual antiplatelet therapy on incidence of stent thrombosis according to implanted drug-eluting stent type.

AIM: To investigate the putative modifying effect of dual antiplatelet therapy (DAPT) use on the incidence of stent thrombosis at 3 years in patients randomized to Endeavor zotarolimus-eluting stent (E-ZES) or Cypher sirolimus-eluting stent (C-SES). METHODS AND RESULTS: Of 8709 patients in PROTECT, 4357 were randomized to E-ZES and 4352 to C-SES. Aspirin was to be given indefinitely, and clopidogrel/ticlopidine for ≥3 months or up to 12 months after implantation. Main outcome measures were definite or probable stent thrombosis at 3 years. Multivariable Cox regression analysis was applied, with stent type, DAPT, and their interaction as the main outcome determinants. Dual antiplatelet therapy adherence remained the same in the E-ZES and C-SES groups (79.6% at 1 year, 32.8% at 2 years, and 21.6% at 3 years). We observed a statistically significant (P = 0.0052) heterogeneity in treatment effect of stent type in relation to DAPT. In the absence of DAPT, stent thrombosis was lower with E-ZES  vs. C-SES (adjusted hazard ratio 0.38, 95% confidence interval 0.19, 0.75; P = 0.0056). In the presence of DAPT, no difference was found (1.18; 0.79, 1.77; P = 0.43). CONCLUSION: A strong interaction was observed between drug-eluting stent type and DAPT use, most likely prompted by the vascular healing response induced by the implanted DES system. These results suggest that the incidence of stent thrombosis in DES trials should not be evaluated independently of DAPT use, and the optimal duration of DAPT will likely depend upon stent type (Clinicaltrials.gov number NCT00476957).

Design, synthesis and biological evaluation of a class of bioisosteric oximes of the novel dual peroxisome proliferator-activated receptor α/γ ligand LT175.

The effects resulting from the introduction of an oxime group in place of the distal aromatic ring of the diphenyl moiety of LT175, previously reported as a PPARα/γ dual agonist, have been investigated. This modification allowed the identification of new bioisosteric ligands with fairly good activity on PPARα and fine-tuned moderate activity on PPARγ. For the most interesting compound (S)-3, docking studies in PPARα and PPARγ provided a molecular explanation for its different behavior as full and partial agonist of the two receptor isotypes, respectively. A further investigation of this compound was carried out performing gene expression studies on HepaRG cells. The results obtained allowed to hypothesize a possible mechanism through which this ligand could be useful in the treatment of metabolic disorders. The higher induction of the expression of some genes, compared to selective agonists, seems to confirm the importance of a dual PPARα/γ activity which probably involves a synergistic effect on both receptor subtypes.

L'incontinence urinaire chez des personnes âgées hospitalisées en unité de gériatrie: est-ce vraiment une priorité pour les infirmières [Urinary incontinence in hospitalized geriatric patients : is it really a priority for nurses?].

INTRODUCTION: urinary incontinence (UI) is a phenomenon with high prevalence in hospitalized elderly patients, effecting up to 70% of patients requiring long term care. However, despite the discomfort it causes and its association with functional decline, it seems to be given insufficient attention by nurses in geriatric care. OBJECTIVES: to assess the prevalence of urinary incontinence in geriatric patients at admission and the level of nurse involvement as characterized by the explicit documentation of UI diagnosis in the patient's record, prescription of nursing intervention, or nursing actions related to UI. METHODS: cross-sectional retrospective chart review. One hundred cases were randomly selected from those patients 65 years or older admitted to the geriatric ward of a university hospital. The variables examined included: total and continence scores on the Measure of Functional Independence (MIF), socio-demographic variables, presence of a nursing diagnosis in the medical record, prescription of or documentation of a nursing intervention related to UI. RESULTS: the prevalence of urinary incontinence was 72 % and UI was positively correlated with a low MIF score, age and status of awaiting placement. Of the examined cases, nursing diagnosis of UI was only documented in 1.4 % of cases, nursing interventions were prescribed in 54 % of cases, and at least one nursing intervention was performed in 72 % of cases. The vast majority of the interventions were palliative. DISCUSSION: the results on the prevalence of IU are similar to those reported in several other studies. This is also the case in relation to nursing interventions. In this study, people with UI were given the same care regardless of their MIF score MIF, age or gender. One limitation of this study is that it is retrospective and therefore dependent on the quality of the nursing documentation. CONCLUSIONS: this study is novel because it examines UI in relation to nursing interventions. It demonstrates that despite a high prevalence of UI, the general level of concern for nurses remains relatively low. Individualized care is desirable and clinical innovations must be developed for primary and secondary prevention of UI during hospitalization.

Bax-induced apoptosis in Leber's congenital amaurosis: a dual role in rod and cone degeneration.

Pathogenesis in the Rpe65(-/-) mouse model of Leber's congenital amaurosis (LCA) is characterized by a slow and progressive degeneration of the rod photoreceptors. On the opposite, cones degenerate rapidly at early ages. Retinal degeneration in Rpe65(-/-) mice, showing a null mutation in the gene encoding the retinal pigment epithelium 65-kDa protein (Rpe65), was previously reported to depend on continuous activation of a residual transduction cascade by unliganded opsin. However, the mechanisms of apoptotic signals triggered by abnormal phototransduction remain elusive. We previously reported that activation of a Bcl-2-dependent pathway was associated with apoptosis of rod photoreceptors in Rpe65(-/-) mice during the course of the disease. In this study we first assessed whether activation of Bcl-2-mediated apoptotic pathway was dependent on constitutive activation of the visual cascade through opsin apoprotein. We then challenged the direct role of pro-apoptotic Bax protein in triggering apoptosis of rod and cone photoreceptors.Quantitative PCR analysis showed that increased expression of pro-apoptotic Bax and decreased level of anti-apoptotic Bcl-2 were restored in Rpe65(-/-)/Gnat1(-/-) mice lacking the Gnat1 gene encoding rod transducin. Moreover, photoreceptor apoptosis was prevented as assessed by TUNEL assay. These data indicate that abnormal activity of opsin apoprotein induces retinal cell apoptosis through the Bcl-2-mediated pathway. Following immunohistological and real-time PCR analyses, we further observed that decreased expression of rod genes in Rpe65-deficient mice was rescued in Rpe65(-/-)/Bax(-/-) mice. Histological and TUNEL studies confirmed that rod cell demise and apoptosis in diseased Rpe65(-/-) mice were dependent on Bax-induced pathway. Surprisingly, early loss of cones was not prevented in Rpe65(-/-)/Bax(-/-) mice, indicating that pro-apoptotic Bax was not involved in the pathogenesis of cone cell death in Rpe65-deficient mice.This is the first report, to our knowledge, that a single genetic mutation can trigger two independent apoptotic pathways in rod and cone photoreceptors in Rpe65-dependent LCA disease. These results highlight the necessity to investigate and understand the specific death signaling pathways committed in rods and cones to develop effective therapeutic approaches to treat RP diseases.

Evaluation of the Need for Longitudinal Median Joints in Bridge Decks on Dual Structures, TR-661, 2015

The primary objective of this project was to determine the effect of bridge width on deck cracking in bridges. Other parameters, such as bridge skew, girder spacing and type, abutment type, pier type, and number of bridge spans, were also studied. To achieve the above objectives, one bridge was selected for live-load and long-term testing. The data obtained from both field tests were used to calibrate a three-dimensional (3D) finite element model (FEM). Three different types of loading—live loading, thermal loading, and shrinkage loading—were applied. The predicted crack pattern from the FEM was compared to the crack pattern from bridge inspection results. A parametric study was conducted using the calibrated FEM. The general conclusions/recommendations are as follows: -- Longitudinal and diagonal cracking in the deck near the abutment on an integral abutment bridge is due to the temperature differences between the abutment and the deck. Although not likely to induce cracking, shrinkage of the deck concrete may further exacerbate cracks developed from thermal effects. -- Based upon a limited review of bridges in the Iowa DOT inventory, it appears that, regardless of bridge width, longitudinal and diagonal cracks are prevalent in integral abutment bridges but not in bridges with stub abutments. -- The parametric study results show that bridge width and skew have minimal effect on the strain in the deck bridge resulting from restrained thermal expansion. -- Pier type, girder type, girder spacing, and number of spans also appear to have no influence on the level of restrained thermal expansion strain in the deck near the abutment.

Dual inhibitors of beta-amyloid aggregation and acetylcholinesterase as multi-target anti-Alzheimer drug candidates

Notwithstanding the functional role that the aggregates of some amyloidogenic proteins can play in different organisms, protein aggregation plays a pivotal role in the pathogenesis of a large number of human diseases. One of such diseases is Alzheimer"s disease (AD), where the overproduction and aggregation of the β-amyloid peptide (Aβ) are regarded as early critical factors. Another protein that seems to occupy a prominent position within the complex pathological network of AD is the enzyme acetylcholinesterase (AChE), with classical and non-classical activities involved at the late (cholinergic deficit) and early (Aβ aggregation) phases of the disease. Dual inhibitors of Aβ aggregation and AChE are thus emerging as promising multi-target agents with potential to efficiently modify the natural course of AD. In the initial phases of the drug discovery process of such compounds, in vitro evaluation of the inhibition of Aβ aggregation is rather troublesome, as it is very sensitive to experimental assay conditions, and requires expensive synthetic Aβ peptides, which makes cost-prohibitive the screening of large compound libraries. Herein, we review recently developed multi-target anti-Alzheimer compounds that exhibit both Aβ aggregation and AChE inhibitory activities, and, in some cases also additional valuable activities such as BACE-1 inhibition or antioxidant properties. We also discuss the development of simplified in vivo methods for the rapid, simple, reliable, unexpensive, and high-throughput amenable screening of Aβ aggregation inhibitors that rely on the overexpression of Aβ42 alone or fused with reporter proteins in Escherichia coli.

In pancreatic carcinoma, dual EGFR/HER2 targeting with cetuximab/trastuzumab is more effective than treatment with trastuzumab/erlotinib or lapatinib alone: implication of receptors' down-regulation and dimers' disruption.

We previously demonstrated the synergistic therapeutic effect of the cetuximab (anti-epidermal growth factor receptor [EGFR] monoclonal antibody, mAb)-trastuzumab (anti-HER2 mAb) combination (2mAbs therapy) in HER2(low) human pancreatic carcinoma xenografts. Here, we compared the 2mAbs therapy, the erlotinib (EGFR tyrosine kinase inhibitor [TKI])-trastuzumab combination and lapatinib alone (dual HER2/EGFR TKI) and explored their possible mechanisms of action. The effects on tumor growth and animal survival of the three therapies were assessed in nude mice xenografted with the human pancreatic carcinoma cell lines Capan-1 and BxPC-3. After therapy, EGFR and HER2 expression and AKT phosphorylation in tumor cells were analyzed by Western blot analysis. EGFR/HER2 heterodimerization was quantified in BxPC-3 cells by time-resolved FRET. In K-ras-mutated Capan-1 xenografts, the 2mAbs therapy gave significantly higher inhibition of tumor growth than the erlotinib/trastuzumab combination, whereas in BxPC-3 (wild-type K-ras) xenografts, the erlotinib/trastuzumab combination showed similar growth inhibition but fewer tumor-free mice. Lapatinib showed no antitumor effect in both types of xenografts. The efficacy of the 2mAbs therapy was partly Fc-independent because F(ab')(2) fragments of the two mAbs significantly inhibited BxPC-3 growth, although with a time-limited therapeutic effect. The 2mAbs therapy was associated with a reduction of EGFR and HER2 expression and AKT phosphorylation. BxPC-3 cells preincubated with the two mAbs showed 50% less EGFR/HER2 heterodimers than controls. In pancreatic carcinoma xenografts, the 2mAbs therapy is more effective than treatments involving dual EGFR/HER2 TKIs. The mechanism of action may involve decreased AKT phosphorylation and/or disruption of EGFR/HER2 heterodimerization.

Aminoterminal amphipathic α-helix AH1 of hepatitis C virus nonstructural protein 4B possesses a dual role in RNA replication and virus production.

Nonstructural protein 4B (NS4B) is a key organizer of hepatitis C virus (HCV) replication complex formation. In concert with other nonstructural proteins, it induces a specific membrane rearrangement, designated as membranous web, which serves as a scaffold for the HCV replicase. The N-terminal part of NS4B comprises a predicted and a structurally resolved amphipathic α-helix, designated as AH1 and AH2, respectively. Here, we report a detailed structure-function analysis of NS4B AH1. Circular dichroism and nuclear magnetic resonance structural analyses revealed that AH1 folds into an amphipathic α-helix extending from NS4B amino acid 4 to 32, with positively charged residues flanking the helix. These residues are conserved among hepaciviruses. Mutagenesis and selection of pseudorevertants revealed an important role of these residues in RNA replication by affecting the biogenesis of double-membrane vesicles making up the membranous web. Moreover, alanine substitution of conserved acidic residues on the hydrophilic side of the helix reduced infectivity without significantly affecting RNA replication, indicating that AH1 is also involved in virus production. Selective membrane permeabilization and immunofluorescence microscopy analyses of a functional replicon harboring an epitope tag between NS4B AH1 and AH2 revealed a dual membrane topology of the N-terminal part of NS4B during HCV RNA replication. Luminal translocation was unaffected by the mutations introduced into AH1, but was abrogated by mutations introduced into AH2. In conclusion, our study reports the three-dimensional structure of AH1 from HCV NS4B, and highlights the importance of positively charged amino acid residues flanking this amphipathic α-helix in membranous web formation and RNA replication. In addition, we demonstrate that AH1 possesses a dual role in RNA replication and virus production, potentially governed by different topologies of the N-terminal part of NS4B.

High Priority Corridors for Access Management Near Large Urban Areas in Iowa, 2002

This research project was intended to produce a strategy for addressing current and future access management problems on state highway routes located just outside urban areas that serve as major routes for commuting into and out of major employment centers in Iowa. There were two basic goals: (1) to develop a ranking system for identifying high-priority segments for access management treatments on primary highways outside metro and urban areas and (2) to focus efforts on routes that are major commuting routes at present and in the future. The project focused on four-lane expressways and two-lane arterials most likely to serve extensive commuter traffic. Available spatial and statistical data were used to identify existing and possible future problem corridors with respect to access management. The research team developed a scheme for ranking commuter routes based on their need for attention to access management. This project was able to produce rankings for corridors based on a variety of factors, including proportion of crashes that appear to be access-related, severity of those crashes, and potential for improvement along corridors. Frequency and loss were found to be highly rank correlated; because of this, these indicators were not used together in developing final priority rankings. Most of the highest ranked routes are on two-lane rural cross sections, but a few are four-lane expressways with at-grade private driveways and public road intersections. The most important conclusion of the ranking system is that many of the poor-performing corridors are located in a single Iowa Department of Transportation district near two urban areas--Des Moines and Ames. A comprehensive approach to managing access along commuting corridors should be developed first in this district since the potential benefits would be highest in that region.

A Multi-Project Scheduling Procedure for Transportation Projects, Final Report, HR-339, 1993

This report proposes, that for certain types of highway construction projects undertaken by the Iowa Department of Transportation, a scheduling technique commonly referred to as linear scheduling may be more effective than the Critical Path Method scheduling technique that is currently being used. The types of projects that appear to be good candidates for the technique are those projects that have a strong linear orientation. Like a bar chart, this technique shows when an activity is scheduled to occur and like a CPM schedule it shows the sequence in which activities are expected to occur. During the 1992 construction season, the authors worked with an inlay project on Interstate 29 to demonstrate the linear scheduling technique to the Construction Office. The as-planned schedule was developed from the CPM schedule that the contractor had developed for the project. Therefore, this schedule represents what a linear representation of a CPM schedule would look like, and not necessarily what a true linear schedule would look like if it had been the only scheduling technique applied to the project. There is a need to expand the current repertoire of scheduling techniques to address those projects for which the bar chart and CPM may not be appropriate either because of the lack of control information or due to overly complex process for the actual project characteristics. The scheduling approaches used today on transportation projects have many shortcomings for properly modeling the real world constraints and conditions which are encountered. Linear project's predilection for activities with variable production rates, a concept very difficult to handle with the CPM, is easily handled and visualized with the linear technique. It is recommended that work proceed with the refinement of the method of linear scheduling described above and the development of a microcomputer based system for use by the Iowa Department of Transportation and contractors for its implementation. The system will be designed to provide the information needed to adjust schedules in a rational understandable method for monitoring progress on the projects and alerting Iowa Department of Transportation personnel when the contractor is deviating from the plan.

Do fire and seed additions alter strong seed timing and priority effects on prairie establishment?, 2011

Many prairie restoration projects are hampered by a lack of knowledge on how to restore the high diversity found in prairies, while at the same time preventing the establishment of a large weedy component. Methods are needed to increase diversity and abundance of native species while minimizing exotic species invasions in both 1) newly planted restorations and 2) established restorations. We established an experiment in Story and Monona counties in 2005 to determine the effects of different native cover crop species and timing of seeding on the establishment of new prairie restorations. We found that adding a 30-species prairie mix in early spring led to diverse native communities, but adding the mix in the late summer or the following year after cover crops established led to low diversity communities dominated by exotics. The identity of cover crops affected communities less than timing of seed additions. A second seed addition added to ash after a spring fire in the seventh year (Monona County site) increased recruitment from the prairie mix slightly, but the increase was not enough to cause convergence in the treatments. Surprisingly, the second seed addition increased diversity only in communities that were already the most diverse (i.e., in plots seeded with the prairie mix in early spring before cover crops established). These results imply that 1) cover crops are not effective for establishing prairie and 2) over seeding into established plots may not be an easy and efficient way to increase native recruitment and lower weedy species abundances. Therefore, focusing on establishing high levels of recruitment and diversity and excluding weedy species during the critical time early in establishment should be a priority for new projects.

Purpura de Henoch-Schönlein: une prise en charge entre pédiatre et néphrologue pédiatre [Henoch-Schönlein Purpura a dual follow up between pediatrician and pediatric nephrologist].

Henoch-Schönlein purpura is a well known paediatric disease characterized by the classic triad: purpura, arthritis and abdominal pain. Short term prognosis is excellent and is mostly dependant on abdominal complications. Long term morbidity depends essentially on the severity of renal involvement which occurs in 35% of cases. Microhematuria and light proteinuria are the only signs in 80% of cases. The remaining 20% presents with nephrotic or nephritic syndrome and acute renal insufficiency. Among patients with Henoch-Schönlein nephritis the risk of developing renal insufficiency varies between 11-30% of cases. Currently, the follow up guidelines are multiple and the optimal treatment of nephritis is controversial; this is what this article proposes to discuss.