bluuebunny/crossref_metadata_2025 huggingface dataset:
Meat Tenderness Genetic and Genomic Variation Sources in Commercial Beef Cattle
Authors: Rubio Lozano María Salud , Alfaro‐Zavala Selene , Sifuentes‐Rincón Ana María , Parra‐Bracamonte Gaspar Manuel , Braña Varela Diego , Medina Rubén Danilo Méndez , Pérez Linares Cristina , Ríos Rincón Francisco , Sánchez Escalante Armida , Torrescano Urrutia Gastón , Figueroa Saavedra Fernando
Published: December 2015

To assess genetic group (GGR; Bos indicus [Bi], Bos taurus [Bt] and crosses [BtxBi]) and to confirm the calpain (CAPN316 and CAPN4751) and calpastatin (CAST‐T1) single nucleotide polymorphism (SNP) effects on Warner–Bratzler shear force (WBSF), 196 animals under commercial conditions were analyzed. A model was fitted including the effect of GGR and considering residuals as adjusted WBSF (aWBSF). Another model was fitted to evaluate the SNP effect on aWBSF. Allele substitution effect (α) and combined favorable alleles in CAPN and CAST on aWBSF were evaluated. GGR showed a significant effect (P < 0.0001) on WBSF; Bt and BtxBi had the lower WBSF. CAPN316 showed significant effect on aWBSF with an α = −0.549 kg. The combined effect of CAPN and CAST showed significant (P < 0.0056) reduction on aWBSF of 0.239 kg by favorable allele. The results remarked the importance of GGR and confirmed CAPN316 and combined effect of CAPN and CAST on prediction of meat tenderness.

Practical Applications

Knowledge of main factors related to tenderness, as a key related factor to beef consumer satisfaction, would serve as a resource for commercial beef classification and management under slaughterhouse conditions. Confirmation on combined marker effects provides strong validation for marker‐assisted management use of these technologies under industry conditions. Additionally, the presented results may be used as a reference for research in the beef industry aimed to provide improvement on beef tenderness to the final product.
Genetic Characterization of Enterococcus Faecalis N1‐33 Bacteriocin and Obtained of the Mutant Strain that Produce Many Bacteriocin by Novobiocin Agent Effect, its Merit as A Food Preservative in Steamed Rice Model
Authors: Hata Tomomi , Sato Toyoki , Morimitsu Yasujiro
Published: December 2015

Enterococcus faecalis strain N1‐33 produces a peptide that shows bacteriocin activity, enterocin MR10A (EntMR10A). We cloned and sequenced the structural gene of the EntMR10A locus (entMR10A), and the peripheral region of entMR10A was analyzed. Inverted repeat‐like structure was found for at both ends of entMR10A and so that it suggested entMR10A of strain N1‐33 could be formed from an insertion sequence. Attempting to eliminate the plasmid from strain N1‐33 using the plasmid‐curing agent novobiocin was obtained the mutant strain of N1‐33 which seemed to overproduction of bacteriocin than the original strain, termed N41‐51. The number of originated bacteriocin structural genes detected by real‐time PCR showed that its level of the strain N41‐51 was about twofold higher than that of N1‐33, and correspondingly appeared to produce about twofold more bacteriocin compared with the original strain in these culture broth, respectively. This difference as a food preservative potential was examined whether it proves the same result in the actual food systems, by using steamed rice. The culture supernatant of strain N41‐51 has confirmed to inhibit the growth of Bacillus cereus by significantly less amount added to steamed rice than that of N1‐33.

Practical Applications

Besides having it with their usual meals, Japanese often eat steamed rice such as rice balls and in their lunch. The most important point we care at these cases is the food poisoning caused by Bacillus cereus, and thus, growth inhibition of B. cereus in steamed rice has been an important task for food industry. In this study, efficacy of the bacteriocin produced by Enterococcus faecalis N1‐33 against B. cereus in steamed rice had shown. The difference in bacteriocin activity of the wild‐type strain N1‐33 and its mutant strain N41‐51, which showed about twice as much bacteriocin production, was also reshown well in the actual food system. Also that, the high bacteriocin producing strain of N1‐33, termed N41‐51, could be obtained with a simple plasmid curing process.
Renin‐Angiotensin‐Aldosterone System Blockers in Elderly Adults with Chronic Kidney Disease without Diabetes Mellitus or Proteinuria
Authors: Arora Pradeep , Golzy Mojgan , Patel Nilang , Quigg Richard , Carter Randolph L. , Lohr James W.
Published: December 2015

Objectives

To compare the effect of renin‐angiotensin‐aldosterone system (RAAS) blockers with that of other antihypertensive agents on outcomes in a cohort of elderly veterans with incident chronic kidney disease (CKD) without diabetes mellitus or proteinuria.

Design

Retrospective cohort study.

Setting

Veterans Affairs (VA) Upstate New York Healthcare System.

Participants

All participants were seen in primary care clinic in Veterans Integrated Service Network 2, which comprises five VA medical centers and 29 community‐based outpatient clinics, from April 2001 to April 2008. Veterans with incident CKD who were taking antihypertensive medications and did not have proteinuria or diabetes mellitus on the date of onset of CKD were selected from this population.

Measurements

The outcome variables studied were progression of kidney disease (doubling of serum creatinine level or Stage 5 CKD (estimated glomerular filtration rate <15 mL/min per 1.73 m2)), all‐cause mortality, and combined outcome.

Results

Analysis included 2,474 participants, 47.9% of whom were taking RAAS blockers at baseline and the rest other antihypertensives. Time‐varying Cox proportional hazards analyses did not reveal a statistically significant difference in primary combined outcome in participants taking RAAS blockers and those taking other antihypertensives (hazard ratio = 1.09, 95% confidence interval = 0.93–1.27). There was also no significant effect on individual outcomes (death or progression of kidney disease).

Conclusion

Use of RAAS blockers was not associated with less hazard of combined and individual outcomes (doubling of serum creatinine, Stage 5 CKD, death) in elderly veterans with incident CKD without diabetes mellitus or proteinuria.
The Environmental Impact of Two Australian Rock Lobster Fishery Supply Chains under a Changing Climate
Authors: van Putten Ingrid E. , Farmery Anna K. , Green Bridget S. , Hobday Alistair J. , Lim‐Camacho Lilly , Norman‐López Ana , Parker Robert W.
Published: December 2015

Understanding the potential future impacts of climate change along the supply chain for highly traded fisheries products can inform choices to enhance future global seafood security. We examine the supply chains of the Australian tropical rock lobster fishery (TRL) and southern rock lobster fishery (SRL), with similar destination markets but different catch methods and fishing communities. A boat‐to‐market analysis allows for comparison and illustration of the effects of single supply‐chain aspects. We used life cycle assessment to provide an overview of the environmental footprint, expressed as global warming potential (GWP), eutrophication, and cumulative energy demand, for two lobster products: live animals and frozen tails. The export phase contributed 44% and 56% of GWP of live‐weight lobster for SRL and TRL, respectively. The SRL fishery currently produces 68% of the combined 1,806.7 tonnes of lobster product and 78% of the combined global warming for the two fisheries over the whole supply chain. We develop climate adaptation options that: (1) reduce the overall footprint; (2) consider alternative supply‐chain strategies (e.g., reduce cost); and (3) predicted impact of future climate change. Adaptation options include: more direct export routes and change in the export transport mode. Value adding and product differentiation, which can level out seasonality and thus spread risk, is likely to become increasingly important for both increases and decreases in predicted climate‐induced abundance of fish species.
Weight under Steel Wheels: Material Stock and Flow Analysis of High‐Speed Rail in China
Authors: Wang Tao , Zhou Jun , Yue Ye , Yang Jie , Hashimoto Seiji
Published: December 2015

The construction of a nation‐wide high‐speed rail (HSR) network has emerged as a hugely expensive and ambitious infrastructure project in China. As of December 2012, some 8,800 kilometers (km) of double‐track HSR lines came into service in the country, accounting for 40% of the total HSR length in the world. The network is expected to expand to 34,000 km or longer in around two decades. As the first HSR system specially built and operated in an economically developing country, it helps integrate the sprawling economy and lift the quality of life of the increasing urban population. China's experiences in HSR are expected to be of value to other countries aiming to adopt bullet train systems, especially those at a similar level of industrialization and urbanization. This work specifically examines material stocks and flows associated with the HSR infrastructure construction in China. A major distinction from the construction of HSR tracks in Europe is that nearly 70% of the HSR tracks in China are laid upon bridges or inside tunnels, which are structures that demand great amounts of raw materials. The entire network, once completed by 2030, will cumulatively require 83 to 137 million tonnes (Mt) of steel and 560 to 920 Mt of cement. This is still a small share of China's use of material resources. Nonetheless, the massive application of the steel‐ and cement‐intensive structures deserves consideration when assessing the environmental performance of HSR over its entire life cycle.
Annexin A5 levels or circulating microparticles: what we see depends mainly on what we look for
Authors: Patil R. , Ghosh K. , Shetty S.
Published: December 2015

Click here to view the article Letter to the Editor by C. Reutelingsperger et al.
Is the Expert Admissibility Game Fixed?: Judicial Gatekeeping of Fire and Arson Evidence
Authors: Dioso‐Villa Rachel
Published: December 2015

Anecdotal evidence claims that in criminal cases, trial judges admit the prosecution's expert witnesses more readily than the defendants', and in civil cases the reverse is true; judges exclude plaintiffs' experts more often than civil defendants' experts. This occurs despite the fact that, with few exceptions, the same rules of admissibility apply to all parties and, in most jurisdictions, across criminal and civil cases. This article empirically tests this differential by reviewing judicial decisions to admit or exclude evidence holding the type of expert testimony constant, fire and arson evidence, across criminal and civil cases in the United States. The study examines the admissibility of fire and arson investigation experts in criminal and civil cases across all legal parties in fifty‐seven federal and state opinions in the United States. The findings offer empirical support of a bias in criminal cases and in civil cases which present expert witnesses at trial, and is less pronounced, but still evident, on appeal. Specifically, the role of the party that offers the evidence has a profound effect on whether arson evidence is admitted, even when factors around the judge's political affiliation, attorney experience, expert qualifications, and rules of evidence are taken into account.
Investigating Transfer of Academic Proficiency Among Trilingual Immigrant Students: A Holistic Tri‐Directional Approach
Authors: HAIM ORLY
Published: December 2015

The study addresses the degree of transfer of literacy dimensions of academic proficiency (AP), that is, reading comprehension and writing, across three languages—Russian (L1), Hebrew (L2), and English (L3)—and investigates whether a common conceptual source underlies the linguistic and cognitive operations of the trilingual learner (Grosjean, 1985). The sample included 274 Russian‐speaking 11th graders studying Hebrew (L2) and English (L3). The instruments for assessing AP were (a) an L1 writing task and ‘can do’ questionnaire and (b) AP tests in L2 and L3. Questionnaires were administered to gather information about the participants’ background variables. The results indicate interdependence of AP across the 3 languages. AP in L1 contributed significantly to the prediction of AP performance in L2 and L3 independent of interaction with arrival age, gender, and socioeconomic status. Reading comprehension and writing in Hebrew (L2) significantly predicted performance on the parallel measures in English (L3). L3 writing proved to be a better predictor of AP in L2 compared to L3 reading comprehension and predicted not only L2 writing but also L2 reading. The results indicate that the Interdependence Hypothesis transpires in the context of 3 languages and can be interpreted to comply with holistic views of bi/trilingualism (Cummins, 2008; Jessner, 2008c).
Molecular characterization of endosperm and amino acids modifications among quality protein maize inbreds
Authors: Pandey Neha , Hossain Firoz , Kumar Krishan , Vishwakarma Ashish K. , Muthusamy Vignesh , Saha Supradip , Agrawal Pawan K. , Guleria Satish K. , Reddy Sallaram S. , Thirunavukkarasu Nepolean , Gupta Hari S.
Published: December 2015

Modifier loci in QPM play a vital role in achieving acceptable degree of kernel hardness and accumulation of lysine and tryptophan. This study was undertaken to characterize a set of diverse QPM inbreds using SSRs linked to endosperm and amino acids modifier loci for their effective utilization in the breeding programme. Significant variation was observed for endosperm modification (25–100% opaqueness), tryptophan (0.056–0.111%) and lysine (0.223–0.444%). Generally, inbreds with soft endosperm possessed more tryptophan and lysine than inbreds with higher vitreousness. SSRs generated 341 alleles with two to seven alleles per locus. The frequency of unique and rare alleles was more for amino acid modifications, compared to endosperm modifications. Phylogenetic analyses grouped the inbreds into three major clusters, and the study identified suitable crosses for accumulation of endosperm and amino acids modifiers. QPM inbreds with desirable modifications identified here would serve as suitable donor for both opaque2 and modifier loci in the marker‐assisted backcross breeding. Further, contrasting inbreds can be used for generating mapping populations to identify new modifier loci underlying both endosperm and amino acids modifications.
QTL mapping of seedling traits in cucumber using recombinant inbred lines
Authors: Wang Min , Liu Shulin , Zhang Shengping , Miao Han , Tian Guili , Lu Hongwei , Liu Panna , Wang Ye , Gu Xingfang
Published: December 2015

Seedling traits are important for development, flower bud differentiation, fruit production and fruit quality of cucumber (Cucumis sativus L.). In this study, 160 recombinant inbred lines (RILs), derived from crossing wild cucumber inbred line PI 183967 (C. sativus var. hardwickii) with ‘931’ northern China cultivated cucumber inbred line 931, were employed to identify quantitative trait loci (QTLs) of cotyledon length (Cl), cotyledon width (Cw), hypocotyl length (Hl), first true leaf length (Fll), first true leaf width (Flw), aboveground fresh biomass (Afb) and aboveground dry biomass (Adb) at seedling stage. A genetic map including 307 SSR markers was developed which spanned 993.3 cM, with an average genetic distance of 3.23 cM between adjacent markers. 36 QTLs associated with the seven traits were detected on chromosomes 1, 2, 3, 5 and 6 in four environments (spring and autumn of 2012 and 2013), explaining 6.1 to 23.6% of the observed phenotypic variations. Among the 36 QTLs, 21 were responsible for more than 10% of observed phenotypic variations. We obtained 2, 2, 1 and 3 QTL loci for the traits of Fll, Flw, Afw and Adw, respectively. In addition, genes in the genetic region spanned by SSR15321‐SSR07711 on chr. 5 may contribute to Flw, Afw and Adw.
Wheat streak mosaic virus resistance in eight wheat germplasm lines
Authors: Zhang Xinzhong , Bai Guihua , Xu Rugen , Zhang Guorong
Published: December 2015

Wheat streak mosaic virus (WSMV) is a destructive pathogen in wheat (Triticum aestivum L.). Host resistance is the most effective way to control this virus. To date, Wsm2 is the only wheat resistance gene that is genetically mapped. The objective of this study was to identify germplasm lines that might carry resistance genes different from Wsm2. Eight newly reported resistant germplasm lines were examined by allelic tests. To validate the allelic test results, five of them were further analysed for the inheritance of WSMV resistance. A Wsm2‐linked marker was also genotyped on populations developed for the inheritance study. Our results suggested that the WSMV resistance in lines CItr9358, PI225288, PI243652, PI245439, PI245526 and PI478095 was controlled by either Wsm2 or a gene very closely linked to Wsm2. The resistance in PI243753 and PI321730, however, is likely controlled by a gene different from, but linked to Wsm2. The resistance in PI321730 might also involve some minor genes. This study provided useful information for breeders to select appropriate resistant lines to improve WSMV resistance in wheat.
Silage yield and quality traits in elite maize hybrids and their relationship to elemental concentrations in juvenile plants
Authors: Melchinger Albrecht E. , Utz Friedrich H. , Bay Alexander , Mirdita Vilson , Ludewig Uwe
Published: December 2015

European silage maize is cultivated for animal feed and biogas production. We evaluated 210 factorial crosses of elite dent and flint lines in multilocation trials for agronomic and quality traits together with biomass and shoot concentrations of 10 elements in juvenile plants. Significant genotypic variances, mainly due to general combining ability variance of the dent lines, and high heritabilities were observed for dry matter yield (DMY) and quality traits. DMY was not correlated with quality traits, but methane fermentation yield (MFY) and metabolizable energy content (MEC) showed significant correlations with starch and fibre content. Concentrations of elements N,P,S,K were positively correlated with each other but only in few cases correlated with DMY and quality traits. Parent lines with contrasting P concentrations differed in root morphology traits. Results support DMY as primary trait for selection of silage maize hybrids, but MFY is of negligible importance in breeding for biogas contrary to MEC for animal feed. Neither biomass nor elemental composition of juvenile plants were of predictive value for final DMY or quality traits.
Functional dyspepsia and irritable bowel syndrome in teenagers: Internet survey
Authors: Kumagai Hideki , Yokoyama Koji , Imagawa Tomoyuki , Yamagata Takanori
Published: December 2015

Background

Only a handful of studies have investigated children with functional dyspepsia (FD) and irritable bowel syndrome (IBS) classified according to the Rome III criteria, and limited information is available on the lifestyle of affected patients.

Methods

We conducted an Internet questionnaire survey of 2060 parents among the general public in Japan who lived with their children aged 10–15, who were screened for FD and IBS.

Results

The prevalence of FD and IBS was 2.8% and 6.1%, respectively, and 1.4% of the subjects met the criteria for both FD and IBS. The lifestyles of 155 subjects who met the criteria for FD, IBS, or both were compared with those of 1745 control subjects. In comparison with the controls, a significantly higher percentage of subjects with FD, IBS, or both thought that their sleep was insufficient, ate meals irregularly, were susceptible to stress and to dizziness on standing, had difficulty in getting out of bed or felt sluggish in the morning, had a tendency to faint when standing, and had migraine/chronic headache.

Conclusions

Children with FD and IBS are susceptible to stress, have impaired sleep and eating habits, and have more frequent symptoms of comorbid orthostatic dysregulation and headache.
Cytomegalovirus transmission in pediatric renal transplant recipients during the window period
Authors: Gangopadhyay Sanhita , Rampersaud Howard , Pelletier J. Peter R. , Herman Lettie , Goldstein Steven , Upadhyay Kiran
Published: December 2015

We report two CMV naïve children who received deceased donor renal transplants from a CMV IgG‐negative single donor. CMV IgG in both recipients and the donor were negative immediately prior to transplant. Both recipients had early recurrences of their original disease in their transplants, requiring multiple sessions of plasmapheresis. All blood products used were leukoreduced or CMV seronegative. A few days post‐transplant, both recipients developed significant positive CMV viremia. Both required initiation of oral valganciclovir. Case 1 responded to oral valganciclovir only while the case 2 had a delayed response to it and hence required intravenous ganciclovir with good response. When checked retrospectively, CMV IgM in the donor was positive along with positive CMV DNA PCR from the white cells. Here we describe a very unusual scenario of CMV transmission in two pediatric renal transplant recipients from a single donor during the CMV window period.
Defending Exclusivity
Authors: Archer Sophie
Published: December 2015

‘Exclusivity’ is the claim that when deliberating about whether to believe that p one can only be consciously motivated to reach one's conclusion by considerations one takes to pertain to the truth of p. The pragmatist tradition has long offered inspiration to those who doubt this claim. Recently, a neo‐pragmatist movement (Carl Ginet (), Keith Frankish (), and Conor McHugh ()) has given rise to a serious challenge to exclusivity. In this article, I defend exclusivity in the face of this challenge. First, I dispute a crucial assumption underlying the challenge, namely, that one can have evidence sufficient to enable but not compel belief. Secondly, I examine several cases that McHugh in particular offers to call exclusivity into question and argue on independent grounds that these cases do not threaten exclusivity. Whether or not exclusivity holds, in addition to being of intrinsic interest, has a decisive consequence for the contemporary debate over Bernard Williams’ () claim that “beliefs aim at truth”. If exclusivity is true, as David Owens () has argued, the deliberator cannot be said to literally aim at truth. So, in defending exclusivity, I thereby show that the notion of ‘aiming’ fails to illuminate the nature of belief.
Stop Making Sense? On a Puzzle about Rationality
Authors: Littlejohn Clayton
Published: December 2015

In this paper, I present a puzzle about epistemic rationality. It seems plausible that it should be rational to believe a proposition if you have sufficient evidential support for it. It seems plausible that it rationality requires you to conform to the categorical requirements of rationality. It also seems plausible that our first‐order attitudes ought to mesh with our higher‐order attitudes. It seems unfortunate that we cannot accept all three claims about rationality. I will present three ways of trying to resolve this tension and argue that the best way to do this is to reject the idea that strong evidential support is the stuff rationality is made of. In the course of doing this, I shall argue that there is a special class of propositions about the requirements of rationality that we cannot make rational mistakes about and explain how this can be.
Rural Disadvantage and Malaria in Less‐Developed Nations: A Cross‐National Investigation of a Neglected Disease
Authors: Noble Mark D. , Austin Kelly F.
Published: December 2015

Although often forgotten among people in affluent nations, malaria represents a leading global health concern in poor, rural countries. Malaria is traditionally thought of as a rural disease, given the close proximity of rural households to mosquito disease vectors. However, more insight is needed to investigate the larger social, economic, and environmental conditions that perhaps interact with rurality to explain why some nations continue to have high levels of prevalence of this preventable and eradicable parasitic infection. We employ structural equation modeling to efficiently test for both direct and indirect effects of rurality. The results demonstrate that rurality works in important indirect ways; although rurality has indirect links to malaria through export agriculture, health spending, and sociohealth resources, careful decomposition of the indirect effects illustrates that the indirect effects through heath spending and sociohealth resources are most important. Overall, the findings suggest that rural vulnerabilities to malaria are not inherent and can be largely addressed by increasing public health provisions among rural populations.
Narcissism and coach interpersonal style: A self‐determination theory perspective
Authors: Matosic D. , Ntoumanis N. , Boardley I. D. , Sedikides C. , Stewart B. D. , Chatzisarantis N.
Published: December 2015

Athletes’ sport experiences are often influenced by the interpersonal styles of communication used by their coaches. Research on personality antecedents of such styles is scarce. We examined the link between a well‐researched personality trait, namely narcissism, and two types of coaching interpersonal style, namely autonomy‐supportive and controlling styles. We also tested the mediating roles of dominance and empathic concern in explaining the relations between narcissism and the two coaching interpersonal styles. United Kingdom‐based coaches (N = 211) from various sports completed a multi‐section questionnaire assessing the study variables. Regression analyses revealed a positive direct relation between narcissism and controlling coach behaviors. Furthermore, empathy (but not dominance) mediated the positive and negative indirect effects of narcissism on controlling and autonomy‐supported interpersonal styles, respectively. We discuss these findings in terms of their implications for coaching and the quality of athletes’ sport experiences.
The Effect of Primary School Absence and Closure on Inward and Outward Flows of Families
Authors: Elshof Hans , Haartsen Tialda , Mulder Clara H.
Published: December 2015

Due to ageing and depopulation, the continued existence of many primary schools in villages in rural North‐Netherlands is threatened. It is believed that villages without a primary school will no longer be attractive to families with children, which could strengthen the process of population decline. This research examines to what extent the absence and closure of a primary school in a village influence the inward and outward flows of families with children in rural villages. We used population register data to acquire the flows at village level for the period 1996 to 2011. Data on primary schools were provided by the Dutch Ministry of Education, Culture and Science. Linear regression analyses of relative inward and outward flows show that villages without a primary school, and villages that have experienced the closure of a primary school, have similar influx, but larger outward flows of families with children compared with villages with a primary school.
Some non-finitely generated Cox rings
Authors: González José Luis , Karu Kalle
Published: December 2015

We give a large family of weighted projective planes, blown up at a smooth point, that do not have finitely generated Cox rings. We then use the method of Castravet and Tevelev to prove that the moduli space$\overline{M}_{0,n}$of stable$n$-pointed genus-zero curves does not have a finitely generated Cox ring if$n$is at least$13$.
Unbalanced data leads to obsolete economic advice
Authors: Wiederhold Gio
Published: December 2015

Few computer scientists and technological workers worry about their role in the economies of their industries and their countries.
Why knowledge representation matters
Authors: Shoham Yoav
Published: December 2015

A personal story: From philosophy to software.
Time is an illusion lunchtime doubly so
Authors: Neville-Neil George V.
Published: December 2015

Ford Prefect to Arthur Dent in
The Hitchhiker's Guide to the Galaxy
Non-volatile storage
Authors: Nanavati Mihir , Schwarzkopf Malte , Wires Jake , Warfield Andrew
Published: December 2015

Implications of the datacenter's shifting center.
PARSECSs
Authors: Chasapis Dimitrios , Casas Marc , Moretó Miquel , Vidal Raul , Ayguadé Eduard , Labarta Jesús , Valero Mateo
Published: December 2015

In this work, we show how parallel applications can be implemented efficiently using task parallelism. We also evaluate the benefits of such parallel paradigm with respect to other approaches. We use the PARSEC benchmark suite as our test bed, which includes applications representative of a wide range of domains from HPC to desktop and server applications. We adopt different parallelization techniques, tailored to the needs of each application, to fully exploit the task-based model. Our evaluation shows that task parallelism achieves better performance than thread-based parallelization models, such as Pthreads. Our experimental results show that we can obtain scalability improvements up to 42% on a 16-core system and code size reductions up to 81%. Such reductions are achieved by removing from the source code application specific schedulers or thread pooling systems and transferring these responsibilities to the runtime system software.
Sensible Energy Accounting with Abstract Metering for Multicore Systems
Authors: Liu Qixiao , Moreto Miquel , Abella Jaume , Cazorla Francisco J. , Jimenez Daniel A. , Valero Mateo
Published: December 2015

Chip multicore processors (CMPs) are the preferred processing platform across different domains such as data centers, real-time systems, and mobile devices. In all those domains, energy is arguably the most expensive resource in a computing system. Accurately quantifying energy usage in a multicore environment presents a challenge as well as an opportunity for optimization. Standard metering approaches are not capable of delivering consistent results with shared resources, since the same task with the same inputs may have different energy consumption based on the mix of co-running tasks. However, it is reasonable for data-center operators to charge on the basis of estimated energy usage rather than time since energy is more correlated with their actual cost.

This article introduces the concept of Sensible Energy Accounting (SEA). For a task running in a multicore system, SEA accurately estimates the energy the task would have consumed running in isolation with a given fraction of the CMP shared resources. We explain the potential benefits of SEA in different domains and describe two hardware techniques to implement it for a shared last-level cache and on-core resources in SMT processors. Moreover, with SEA, an energy-aware scheduler can find a highly efficient on-chip resource assignment, reducing by up to 39% the total processor energy for a 4-core system.
Falcon
Authors: Cheramangalath Unnikrishnan , Nasre Rupesh , Srikant Y. N.
Published: December 2015

Graph algorithms have been shown to possess enough parallelism to keep several computing resources busy—even hundreds of cores on a GPU. Unfortunately, tuning their implementation for efficient execution on a particular hardware configuration of heterogeneous systems consisting of multicore CPUs and GPUs is challenging, time consuming, and error prone. To address these issues, we propose a domain-specific language (DSL), Falcon, for implementing graph algorithms that (i) abstracts the hardware, (ii) provides constructs to write explicitly parallel programs at a higher level, and (iii) can work with general algorithms that may change the graph structure (morph algorithms). We illustrate the usage of our DSL to implement local computation algorithms (that do not change the graph structure) and morph algorithms such as Delaunay mesh refinement, survey propagation, and dynamic SSSP on GPU and multicore CPUs. Using a set of benchmark graphs, we illustrate that the generated code performs close to the state-of-the-art hand-tuned implementations.
QoS-Aware Autonomic Resource Management in Cloud Computing
Authors: Singh Sukhpal , Chana Inderveer
Published: December 2015

As computing infrastructure expands, resource management in a large, heterogeneous, and distributed environment becomes a challenging task. In a cloud environment, with uncertainty and dispersion of resources, one encounters problems of allocation of resources, which is caused by things such as heterogeneity, dynamism, and failures. Unfortunately, existing resource management techniques, frameworks, and mechanisms are insufficient to handle these environments, applications, and resource behaviors. To provide efficient performance of workloads and applications, the aforementioned characteristics should be addressed effectively. This research depicts a broad methodical literature analysis of autonomic resource management in the area of the cloud in general and QoS (Quality of Service)-aware autonomic resource management specifically. The current status of autonomic resource management in cloud computing is distributed into various categories. Methodical analysis of autonomic resource management in cloud computing and its techniques are described as developed by various industry and academic groups. Further, taxonomy of autonomic resource management in the cloud has been presented. This research work will help researchers find the important characteristics of autonomic resource management and will also help to select the most suitable technique for autonomic resource management in a specific application along with significant future research directions.
High performance locks for multi-level NUMA systems
Authors: Chabbi Milind , Fagan Michael , Mellor-Crummey John
Published: December 2015

Efficient locking mechanisms are critically important for high performance computers. On highly-threaded systems with a deep memory hierarchy, the throughput of traditional queueing locks, e.g., MCS locks, falls off due to NUMA effects. Two-level cohort locks perform better on NUMA systems, but fail to deliver top performance for deep NUMA hierarchies. In this paper, we describe a hierarchical variant of the MCS lock that adapts the principles of cohort locking for architectures with deep NUMA hierarchies. We describe analytical models for throughput and fairness of Cohort-MCS (C-MCS) and Hierarchical MCS (HMCS) locks that enable us to tailor these locks for high performance on any target platform without empirical tuning. Using these models, one can select parameters such that an HMCS lock will deliver better fairness than a C-MCS lock for a given throughput, or deliver better throughput for a given fairness. Our experiments show that, under high contention, a three-level HMCS lock delivers up to 7.6x higher lock throughput than a C-MCS lock on a 128-thread IBM Power 755 and a five-level HMCS lock delivers up to 72x higher lock throughput on a 4096-thread SGI UV 1000. On the K-means clustering code from the MineBench suit, a three-level HMCS lock reduces the running time by up to 55% compared to the C-MCS lock on a IBM Power 755.
Performance implications of dynamic memory allocators on transactional memory systems
Authors: Baldassin Alexandro , Borin Edson , Araujo Guido
Published: December 2015

Although dynamic memory management accounts for a significant part of the execution time on many modern software systems, its impact on the performance of transactional memory systems has been mostly overlooked. In order to shed some light into this subject, this paper conducts a thorough investigation of the interplay between memory allocators and software transactional memory (STM) systems. We show that allocators can interfere with the way memory addresses are mapped to versioned locks on state-of-the-art software transactional memory implementations. Moreover, we observed that key aspects of allocators such as false sharing avoidance, scalability, and locality have a drastic impact on the final performance. For instance, we have detected performance differences of up to 171% in the STAMP applications when using distinct allocators. Moreover, we show that optimizations at the STM-level (such as caching transactional objects) are not effective when a modern allocator is already in use. All in all, our study highlights the importance of reporting the allocator utilized in the performance evaluation of transactional memory systems.
Diagnosing the causes and severity of one-sided message contention
Authors: Tallent Nathan R. , Vishnu Abhinav , Van Dam Hubertus , Daily Jeff , Kerbyson Darren J. , Hoisie Adolfy
Published: December 2015

Two trends suggest network contention for one-sided messages is poised to become a performance problem that concerns application developers: an increased interest in one-sided programming models and a rising ratio of hardware threads to network injection bandwidth. Often it is difficult to reason about when one-sided tasks decrease or increase network contention. We present effective and portable techniques for diagnosing the causes and severity of one-sided message contention. To detect that a message is affected by contention, we maintain statistics representing instantaneous network resource demand. Using lightweight measurement and modeling, we identify the portion of a message's latency that is due to contention and whether contention occurs at the initiator or target. We attribute these metrics to program statements in their full static and dynamic context. We characterize contention for an important computational chemistry benchmark on InfiniBand, Cray Aries, and IBM Blue Gene/Q interconnects. We pinpoint the sources of contention, estimate their severity, and show that when message delivery time deviates from an ideal model, there are other messages contending for the same network links. With a small change to the benchmark, we reduce contention by 50% and improve total runtime by 20%.
Scalable and efficient implementation of 3d unstructured meshes computation: a case study on matrix assembly
Authors: Thébault Loïc , Petit Eric , Dinh Quang
Published: December 2015

Exposing massive parallelism on 3D unstructured meshes computation with efficient load balancing and minimal synchronizations is challenging. Current approaches relying on domain decomposition and mesh coloring struggle to scale with the increasing number of cores per nodes, especially with new many-core processors. In this paper, we propose an hybrid approach using domain decomposition to exploit distributed memory parallelism, Divide-and-Conquer, D&C, to exploit shared memory parallelism and improve locality, and mesh coloring at core level to exploit vectors. It illustrates a new trade-off for many-cores between structuredness, memory locality, and vectorization. We evaluate our approach on the finite element matrix assembly of an industrial fluid dynamic code developed by Dassault Aviation. We compare our D&C approach to domain decomposition and to mesh coloring. D&C achieves a high parallel efficiency, a good data locality as well as an improved bandwidth usage. It competes on current nodes with the optimized pure MPI version with a minimum 10% speed-up. D&C shows an impressive 319x strong scaling on 512 cores (32 nodes) with only 2000 vertices per core. Finally, the Intel Xeon Phi version has a performance similar to 10 Intel E5-2665 Xeon Sandy Bridge cores and 95% parallel efficiency on the 60 physical cores. Running on 4 Xeon Phi (240 cores), D&C has 92% efficiency on the physical cores and performance similar to 33 Intel E5-2665 Xeon Sandy Bridge cores.
Predicate RCU: an RCU for scalable concurrent updates
Authors: Arbel Maya , Morrison Adam
Published: December 2015

Read-copy update (RCU) is a shared memory synchronization mechanism with scalable synchronization-free reads that nevertheless execute correctly with concurrent updates. To guarantee the consistency of such reads, an RCU update transitioning the data structure between certain states must wait for the completion of all existing reads. Unfortunately, these waiting periods quickly become a bottleneck, and thus RCU remains unused in data structures that require scalable, fine-grained, update operations. To solve this problem, we present Predicate RCU (PRCU), an RCU variant in which an update waits only for the reads whose consistency it affects, which are specified by a user-supplied predicate. We explore the trade-offs in implementing PRCU, describing implementations that reduce wait times by 10--100x with varying overhead on reads on modern x86 multiprocessor machines. We demonstrate the applicability of PRCU by applying it to two RCU-based concurrent algorithms---the Citrus binary search tree and a resizable hash table---and show experimentally that PRCU significantly improves the performance of both algorithms.
MPI+Threads: runtime contention and remedies
Authors: Amer Abdelhalim , Lu Huiwei , Wei Yanjie , Balaji Pavan , Matsuoka Satoshi
Published: December 2015

Hybrid MPI+Threads programming has emerged as an alternative model to the “MPI everywhere” model to better handle the increasing core density in cluster nodes. While the MPI standard allows multithreaded concurrent communication, such flexibility comes with the cost of maintaining thread safety within the MPI implementation, typically implemented using critical sections. In contrast to previous works that studied the importance of critical-section granularity in MPI implementations, in this paper we investigate the implication of critical-section arbitration on communication performance. We first analyze the MPI runtime when multithreaded concurrent communication takes place on hierarchical memory systems. Our results indicate that the mutex-based approach that most MPI implementations use today can incur performance penalties due to unfair arbitration. We then present methods to mitigate these penalties with a first-come, first-served arbitration and a priority locking scheme that favors threads doing useful work. Through evaluations using several benchmarks and applications, we demonstrate up to 5-fold improvement in performance.
The lazy happens-before relation: better partial-order reduction for systematic concurrency testing
Authors: Thomson Paul , Donaldson Alastair F.
Published: December 2015

We present the lazy happens-before relation (lazy HBR), which ignores mutex-induced edges to provide a more precise notion of state equivalence compared with the traditional happens-before relation. We demonstrate experimentally that the lazy HBR has the potential to provide greater schedule reduction during systematic concurrency testing with respect to a set of 79 Java benchmarks.
Towards batched linear solvers on accelerated hardware platforms
Authors: Haidar Azzam , Dong Tingxing , Luszczek Piotr , Tomov Stanimire , Dongarra Jack
Published: December 2015

As hardware evolves, an increasingly effective approach to develop energy efficient, high-performance solvers, is to design them to work on many small and independent problems. Indeed, many applications already need this functionality, especially for GPUs, which are known to be currently about four to five times more energy efficient than multicore CPUs for every floating-point operation. In this paper, we describe the development of the main one-sided factorizations: LU, QR, and Cholesky; that are needed for a set of small dense matrices to work in parallel. We refer to such algorithms as batched factorizations. Our approach is based on representing the algorithms as a sequence of batched BLAS routines for GPU-contained execution. Note that this is similar in functionality to the LAPACK and the hybrid MAGMA algorithms for large-matrix factorizations. But it is different from a straightforward approach, whereby each of GPU's symmetric multiprocessors factorizes a single problem at a time. We illustrate how our performance analysis together with the profiling and tracing tools guided the development of batched factorizations to achieve up to 2-fold speedup and 3-fold better energy efficiency compared to our highly optimized batched CPU implementations based on the MKL library on a two-sockets, Intel Sandy Bridge server. Compared to a batched LU factorization featured in the NVIDIA's CUBLAS library for GPUs, we achieves up to 2.5-fold speedup on the K40 GPU.
The lock-free k-LSM relaxed priority queue
Authors: Wimmer Martin , Gruber Jakob , Träff Jesper Larsson , Tsigas Philippas
Published: December 2015

We present a new, concurrent, lock-free priority queue that relaxes the delete-min operation to allow deletion of any of the ρ smallest keys instead of only a minimal one, where ρ is a parameter that can be configured at runtime. It is built from a logarithmic number of sorted arrays, similar to log-structured merge-trees (LSM). For keys added and removed by the same thread the behavior is identical to a non-relaxed priority queue. We compare to state-of-the-art lock-free priority queues with both relaxed and non-relaxed semantics, showing high performance and good scalability of our approach.
Tiles: a new language mechanism for heterogeneous parallelism
Authors: Chen Yifeng , Cui Xiang , Mei Hong
Published: December 2015

This paper studies the essence of heterogeneity from the perspective of language mechanism design. The proposed mechanism, called tiles, is a program construct that bridges two relative levels of computation: an outer level of source data in larger, slower or more distributed memory and an inner level of data blocks in smaller, faster or more localized memory.
Adaptive lock-free maps: purely-functional to scalable
Authors: Newton Ryan R. , Fogg Peter P. , Varamesh Ali
Published: December 2015

Purely functional data structures stored inside a mutable variable provide an excellent concurrent data structure—obviously correct, cheap to create, and supporting snapshots. They are not, however, scalable. We provide a way to retain the benefits of these pure-in-a-box data structures while dynamically converting to a more scalable lock-free data structure under contention. Our solution scales to any pair of pure and lock-free container types with key/value set semantics, while retaining lock-freedom. We demonstrate the principle in action on two very different platforms: first in the Glasgow Haskell Compiler and second in Java. To this end we extend GHC to support lock-free data structures and introduce a new approach for safe CAS in a lazy language.
Hygienic resugaring of compositional desugaring
Authors: Pombrio Justin , Krishnamurthi Shriram
Published: December 2015

Syntactic sugar is widely used in language implementation. Its benefits are, however, offset by the comprehension problems it presents to programmers once their program has been transformed. In particular, after a transformed program has begun to evaluate (or otherwise be altered by a black-box process), it can become unrecognizable. We present a new approach to _resugaring_ programs, which is the act of reflecting evaluation steps in the core language in terms of the syntactic sugar that the programmer used. Relative to prior work, our approach has two important advances: it handles hygiene, and it allows almost arbitrary rewriting rules (as opposed to restricted patterns). We do this in the context of a DAG representation of programs, rather than more traditional trees.
Functional pearl: two can keep a secret, if one of them uses Haskell
Authors: Russo Alejandro
Published: December 2015

For several decades, researchers from different communities have independently focused on protecting confidentiality of data. Two distinct technologies have emerged for such purposes: Mandatory Access Control (MAC) and Information-Flow Control (IFC)—the former belonging to operating systems (OS) research, while the latter to the programming languages community. These approaches restrict how data gets propagated within a system in order to avoid information leaks. In this scenario, Haskell plays a unique privileged role: it is able to protect confidentiality via libraries. This pearl presents a monadic API which statically protects confidentiality even in the presence of advanced features like exceptions, concurrency, and mutable data structures. Additionally, we present a mechanism to safely extend the library with new primitives, where library designers only need to indicate the read and write effects of new operations.