A performance comparison of the contiguous allocation strategies in 3D mesh connected multicomputers

The performance of contiguous allocation strategies can be significantly affected by the distribution of job execution times. In this paper, the performance of the existing contiguous allocation strategies for 3D mesh multicomputers is re-visited in the context of heavy-tailed distributions (e.g., a Bounded Pareto distribution). The strategies are evaluated and compared using simulation experiments for both First-Come-First-Served (FCFS) and Shortest-Service-Demand (SSD) scheduling strategies under a variety of system loads and system sizes. The results show that the performance of the allocation strategies degrades considerably when job execution times follow a heavy-tailed distribution. Moreover, SSD copes much better than FCFS scheduling strategy in the presence of heavy-tailed job execution times. The results also show that the strategies that depend on a list of allocated sub-meshes for both allocation and deallocation have lower allocation overhead and deliver good system performance in terms of average turnaround time and mean system utilization

On the nature and impact of self-similarity in real-time systems

In real-time systems with highly variable task execution times simplistic task models are insufficient to accurately model and to analyze the system. Variability can be tackled using distributions rather than a single value, but the proper charac- terization depends on the degree of variability. Self-similarity is one of the deep- est kinds of variability. It characterizes the fact that a workload is not only highly variable, but it is also bursty on many time-scales. This paper identifies in which situations this source of indeterminism can appear in a real-time system: the com- bination of variability in task inter-arrival times and execution times. Although self- similarity is not a claim for all systems with variable execution times, it is not unusual in some applications with real-time requirements, like video processing, networking and gaming. The paper shows how to properly model and to analyze self-similar task sets and how improper modeling can mask deadline misses. The paper derives an analyti- cal expression for the dependence of the deadline miss ratio on the degree of self- similarity and proofs its negative impact on real-time systems performance through system¿s modeling and simulation. This study about the nature and impact of self- similarity on soft real-time systems can help to reduce its effects, to choose the proper scheduling policies, and to avoid its causes at system design time.This work was developed under a grant from the European Union (FRESCOR-FP6/2005/IST/5-03402).Enrique Hernández-Orallo; Vila Carbó, JA. (2012). On the nature and impact of self-similarity in real-time systems. Real-Time Systems. 48(3):294-319. doi:10.1007/s11241-012-9146-0S294319483Abdelzaher TF, Sharma V, Lu C (2004) A utilization bound for aperiodic tasks and priority driven scheduling. IEEE Trans Comput 53(3):334–350Abeni L, Buttazzo G (1999) QoS guarantee using probabilistic deadlines. In: Proc of the Euromicro confererence on real-time systemsAbeni L, Buttazzo G (2004) Resource reservation in dynamic real-time systems. Real-Time Syst 37(2):123–167Anantharam V (1999) Scheduling strategies and long-range dependence. Queueing Syst 33(1–3):73–89Beran J (1994) Statistics for long-memory processes. Chapman and Hall, LondonBeran J, Sherman R, Taqqu M, Willinger W (1995) Long-range dependence in variable-bit-rate video traffic. IEEE Trans Commun 43(2):1566–1579Boxma O, Zwart B (2007) Tails in scheduling. SIGMETRICS Perform Eval Rev 34(4):13–20Brichet F, Roberts J, Simonian A, Veitch D (1996) Heavy traffic analysis of a storage model with long range dependent on/off sources. Queueing Syst 23(1):197–215Crovella M, Bestavros A (1997) Self-similarity in world wide web traffic: evidence and possible causes. IEEE/ACM Trans Netw 5(6):835–846Dìaz J, Garcìa D, Kim K, Lee C, Bello LL, López J, Min LS, Mirabella O (2002) Stochastic analysis of periodic real-time systems. In: Proc of the 23rd IEEE real-time systems symposium, pp 289–300Erramilli A, Narayan O, Willinger W (1996) Experimental queueing analysis with long-range dependent packet traffic. IEEE/ACM Trans Netw 4(2):209–223Erramilli A, Roughan M, Veitch D, Willinger W (2002) Self-similar traffic and network dynamics. Proc IEEE 90(5):800–819Gardner M (1999) Probabilistic analysis and scheduling of critical soft real-time systems. Phd thesis, University of Illinois, Urbana-ChampaignGarrett MW, Willinger W (1994) Analysis, modeling and generation of self-similar vbr video traffic. In: ACM SIGCOMMHarchol-Balter M (2002) Task assignment with unknown duration. J ACM 49(2):260–288Harchol-Balter M (2007) Foreword: Special issue on new perspective in scheduling. SIGMETRICS Perform Eval Rev 34(4):2–3Harchol-Balter M, Downey AB (1997) Exploiting process lifetime distributions for dynamic load balancing. ACM Trans Comput Syst 15(3):253–285Hernandez-Orallo E, Vila-Carbo J (2007) Network performance analysis based on histogram workload models. In: Proceedings of the 15th international symposium on modeling, analysis, and simulation of computer and telecommunication systems (MASCOTS), pp 331–336Hernandez-Orallo E, Vila-Carbo J (2010) Analysis of self-similar workload on real-time systems. In: IEEE real-time and embedded technology and applications symposium (RTAS). IEEE Computer Society, Washington, pp 343–352Hernández-Orallo E, Vila-Carbó J (2010) Network queue and loss analysis using histogram-based traffic models. Comput Commun 33(2):190–201Hughes CJ, Kaul P, Adve SV, Jain R, Park C, Srinivasan J (2001) Variability in the execution of multimedia applications and implications for architecture. SIGARCH Comput Archit News 29(2):254–265Leland W, Ott TJ (1986) Load-balancing heuristics and process behavior. SIGMETRICS Perform Eval Rev 14(1):54–69Leland WE, Taqqu MS, Willinger W, Wilson DV (1994) On the self-similar nature of ethernet traffic (extended version). IEEE/ACM Trans Netw 2(1):1–15Liu CL, Layland JW (1973) Scheduling algorithms for multiprogramming in a hard-real-time environment. J ACM 20(1):46–61Mandelbrot B (1965) Self-similar error clusters in communication systems and the concept of conditional stationarity. IEEE Trans Commun 13(1):71–90Mandelbrot BB (1969) Long run linearity, locally Gaussian processes, h-spectra and infinite variances. Int Econ Rev 10:82–113Norros I (1994) A storage model with self-similar input. Queueing Syst 16(3):387–396Norros I (2000) Queueing behavior under fractional Brownian traffic. In: Park K, Willinger W (eds) Self-similar network traffic and performance evaluation. Willey, New York, Chap 4Park K, Willinger W (2000) Self-similar network traffic: An overview. In: Park K, Willinger W (eds) Self-similar network traffic and performance evaluation. Willey, New York, Chap 1Paxson V, Floyd S (1995) Wide area traffic: the failure of Poisson modeling. IEEE/ACM Trans Netw 3(3):226–244Rolls DA, Michailidis G, Hernández-Campos F (2005) Queueing analysis of network traffic: methodology and visualization tools. Comput Netw 48(3):447–473Rose O (1995) Statistical properties of mpeg video traffic and their impact on traffic modeling in atm systems. In: Conference on local computer networksRoy N, Hamm N, Madhukar M, Schmidt DC, Dowdy L (2009) The impact of variability on soft real-time system scheduling. In: RTCSA ’09: Proceedings of the 2009 15th IEEE international conference on embedded and real-time computing systems and applications. IEEE Computer Society, Washington, pp 527–532Sha L, Abdelzaher T, Årzén KE, Cervin A, Baker T, Burns A, Buttazzo G, Caccamo M, Lehoczky J, Mok AK (2004) Real time scheduling theory: A historical perspective. Real-Time Syst 28(2):101–155Taqqu MS, Willinger W, Sherman R (1997) Proof of a fundamental result in self-similar traffic modeling. SIGCOMM Comput Commun Rev 27(2):5–23Tia T, Deng Z, Shankar M, Storch M, Sun J, Wu L, Liu J (1995) Probabilistic performance guarantee for real-time tasks with varying computation times. In: Proc of the real-time technology and applications symposium, pp 164–173Vila-Carbó J, Hernández-Orallo E (2008) An analysis method for variable execution time tasks based on histograms. Real-Time Syst 38(1):1–37Willinger W, Taqqu M, Erramilli A (1996) A bibliographical guide to self-similar traffic and performance modeling for modern high-speed networks. In: Stochastic networks: Theory and applications, pp 339–366Willinger W, Taqqu MS, Sherman R, Wilson DV (1997) Self-similarity through high-variability: statistical analysis of ethernet lan traffic at the source level. IEEE/ACM Trans Netw 5(1):71–8

ALPS-Like Phenotype Caused by ADA2 Deficiency Rescued by Allogeneic Hematopoietic Stem Cell Transplantation

Adenosine deaminase 2 (ADA2) deficiency is an auto-inflammatory disease due to mutations in cat eye syndrome chromosome region candidate 1 (CECR1) gene, currently named ADA2. The disease has a wide clinical spectrum encompassing early-onset vasculopathy (targeting skin, gut and central nervous system), recurrent fever, immunodeficiency and bone marrow dysfunction. Different therapeutic options have been proposed in literature, but only steroids and anti-cytokine monoclonal antibodies (such as tumor necrosis factor inhibitor) proved to be effective. If a suitable donor is available, hematopoietic stem cell transplantation (HSCT) could be curative. Here we describe a case of ADA2 deficiency in a 4-year-old Caucasian girl. The patient was initially classified as autoimmune neutropenia and then she evolved toward an autoimmune lymphoproliferative syndrome (ALPS)-like phenotype. The diagnosis of ALPS became uncertain due to atypical clinical features and normal FAS-induced apoptosis test. She was treated with G-CSF first and subsequently with immunosuppressive drugs without improvement. Only HSCT from a 9/10 HLA-matched unrelated donor, following myeloablative conditioning, completely solved the clinical signs related to ADA2 deficiency. Early diagnosis in cases presenting with hematological manifestations, rather than classical vasculopathy, allows the patients to promptly undergo HSCT and avoid more severe evolution. Finally, in similar cases highly suspicious for genetic disease, it is desirable to obtain molecular diagnosis before performing HSCT, since it can influence the transplant procedure. However, if HSCT has to be performed without delay for clinical indication, related donors should be excluded to avoid the risk of relapse or partial benefit due to a hereditary genetic defect

Occupational Radiation Protection in Interventional Radiology: A Joint Guideline of the Cardiovascular and Interventional Radiology Society of Europe and the Society of Interventional Radiology

No Abstract

A multiscale hybrid model for pro-angiogenic calcium signals in a vascular endothelial cell

Cytosolic calcium machinery is one of the principal signaling mechanisms by which endothelial cells (ECs) respond to external stimuli during several biological processes, including vascular progression in both physiological and pathological conditions. Low concentrations of angiogenic factors (such as VEGF) activate in fact complex pathways involving, among others, second messengers arachidonic acid (AA) and nitric oxide (NO), which in turn control the activity of plasma membrane calcium channels. The subsequent increase in the intracellular level of the ion regulates fundamental biophysical properties of ECs (such as elasticity, intrinsic motility, and chemical strength), enhancing their migratory capacity. Previously, a number of continuous models have represented cytosolic calcium dynamics, while EC migration in angiogenesis has been separately approached with discrete, lattice-based techniques. These two components are here integrated and interfaced to provide a multiscale and hybrid Cellular Potts Model (CPM), where the phenomenology of a motile EC is realistically mediated by its calcium-dependent subcellular events. The model, based on a realistic 3-D cell morphology with a nuclear and a cytosolic region, is set with known biochemical and electrophysiological data. In particular, the resulting simulations are able to reproduce and describe the polarization process, typical of stimulated vascular cells, in various experimental conditions.Moreover, by analyzing the mutual interactions between multilevel biochemical and biomechanical aspects, our study investigates ways to inhibit cell migration: such strategies have in fact the potential to result in pharmacological interventions useful to disrupt malignant vascular progressio

Mosaic maternal ancestry in the Great Lakes region of East Africa

The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago

Mitochondrial haplogroup N1a phylogeography, with implication to the origin of European farmers

<p>Abstract</p> <p>Background</p> <p>Tracing the genetic origin of central European farmer N1a lineages can provide a unique opportunity to assess the patterns of the farming technology spread into central Europe in the human prehistory. Here, we have chosen twelve N1a samples from modern populations which are most similar with the farmer N1a types and performed the complete mitochondrial DNA genome sequencing analysis. To assess the genetic and phylogeographic relationship, we performed a detailed survey of modern published N1a types from Eurasian and African populations.</p> <p>Results</p> <p>The geographic origin and expansion of farmer lineages related N1a subclades have been deduced from combined analysis of 19 complete sequences with 166 N1a haplotypes. The phylogeographic analysis revealed that the central European farmer lineages have originated from different sources: from eastern Europe, local central Europe, and from the Near East via southern Europe.</p> <p>Conclusions</p> <p>The results obtained emphasize that the arrival of central European farmer lineages did not occur via a single demic diffusion event from the Near East at the onset of the Neolithic spread of agriculture into Europe. Indeed these results indicate that the Neolithic transition process was more complex in central Europe and possibly the farmer N1a lineages were a result of a 'leapfrog' colonization process.</p

The Nature of the Dietary Protein Impacts the Tissue-to-Diet 15N Discrimination Factors in Laboratory Rats

Due to the existence of isotope effects on some metabolic pathways of amino acid and protein metabolism, animal tissues are 15N-enriched relative to their dietary nitrogen sources and this 15N enrichment varies among different tissues and metabolic pools. The magnitude of the tissue-to-diet discrimination (Δ15N) has also been shown to depend on dietary factors. Since dietary protein sources affect amino acid and protein metabolism, we hypothesized that they would impact this discrimination factor, with selective effects at the tissue level. To test this hypothesis, we investigated in rats the influence of a milk or soy protein-based diet on Δ15N in various nitrogen fractions (urea, protein and non-protein fractions) of blood and tissues, focusing on visceral tissues. Regardless of the diet, the different protein fractions of blood and tissues were generally 15N-enriched relative to their non-protein fraction and to the diet (Δ15N>0), with large variations in the Δ15N between tissue proteins. Δ15N values were markedly lower in tissue proteins of rats fed milk proteins compared to those fed soy proteins, in all sampled tissues except in the intestine, and the amplitude of Δ15N differences between diets differed between tissues. Both between-tissue and between-diet Δ15N differences are probably related to modulations of the relative orientation of dietary and endogenous amino acids in the different metabolic pathways. More specifically, the smaller Δ15N values observed in tissue proteins with milk than soy dietary protein may be due to a slightly more direct channeling of dietary amino acids for tissue protein renewal and to a lower recycling of amino acids through fractionating pathways. In conclusion, the present data indicate that natural Δ15N of tissue are sensitive markers of the specific subtle regional modifications of the protein and amino acid metabolism induced by the protein dietary source

Persistent DNA Damage after High Dose In Vivo Gamma Exposure of Minipig Skin

Exposure to high doses of ionizing radiation (IR) can lead to localized radiation injury of the skin and exposed cells suffer dsDNA breaks that may elicit cell death or stochastic changes. Little is known about the DNA damage response after high-dose exposure of the skin. Here, we investigate the cellular and DNA damage response in acutely irradiated minipig skin.IR-induced DNA damage, repair and cellular survival were studied in 15 cm(2) of minipig skin exposed in vivo to ~50 Co-60 γ rays. Skin biopsies of control and 4 h up to 96 days post exposure were investigated for radiation-induced foci (RIF) formation using γ-H2AX, 53BP1, and active ATM-p immunofluorescence. High-dose IR induced massive γ-H2AX phosphorylation and high 53BP1 RIF numbers 4 h, 20 h after IR. As time progressed RIF numbers dropped to a low of <1% of keratinocytes at 28-70 days. The latter contained large RIFs that included ATM-p, indicating the accumulation of complex DNA damage. At 96 days most of the cells with RIFs had disappeared. The frequency of active-caspase-3-positive apoptotic cells was 17-fold increased 3 days after IR and remained >3-fold elevated at all subsequent time points. Replicating basal cells (Ki67+) were reduced 3 days post IR followed by increased proliferation and recovery of epidermal cellularity after 28 days.Acute high dose irradiation of minipig epidermis impaired stem cell replication and induced elevated apoptosis from 3 days onward. DNA repair cleared the high numbers of DBSs in skin cells, while RIFs that persisted in <1% cells marked complex and potentially lethal DNA damage up to several weeks after exposure. An elevated frequency of keratinocytes with persistent RIFs may thus serve as indicator of previous acute radiation exposure, which may be useful in the follow up of nuclear or radiological accident scenarios