A Memory Bandwidth-Efficient Hybrid Radix Sort on GPUs

Sorting is at the core of many database operations, such as index creation, sort-merge joins, and user-requested output sorting. As GPUs are emerging as a promising platform to accelerate various operations, sorting on GPUs becomes a viable endeavour. Over the past few years, several improvements have been proposed for sorting on GPUs, leading to the first radix sort implementations that achieve a sorting rate of over one billion 32-bit keys per second. Yet, state-of-the-art approaches are heavily memory bandwidth-bound, as they require substantially more memory transfers than their CPU-based counterparts. Our work proposes a novel approach that almost halves the amount of memory transfers and, therefore, considerably lifts the memory bandwidth limitation. Being able to sort two gigabytes of eight-byte records in as little as 50 milliseconds, our approach achieves a 2.32-fold improvement over the state-of-the-art GPU-based radix sort for uniform distributions, sustaining a minimum speed-up of no less than a factor of 1.66 for skewed distributions. To address inputs that either do not reside on the GPU or exceed the available device memory, we build on our efficient GPU sorting approach with a pipelined heterogeneous sorting algorithm that mitigates the overhead associated with PCIe data transfers. Comparing the end-to-end sorting performance to the state-of-the-art CPU-based radix sort running 16 threads, our heterogeneous approach achieves a 2.06-fold and a 1.53-fold improvement for sorting 64 GB key-value pairs with a skewed and a uniform distribution, respectively.Comment: 16 pages, accepted at SIGMOD 201

Tree-based Coarsening and Partitioning of Complex Networks

Many applications produce massive complex networks whose analysis would benefit from parallel processing. Parallel algorithms, in turn, often require a suitable network partition. For solving optimization tasks such as graph partitioning on large networks, multilevel methods are preferred in practice. Yet, complex networks pose challenges to established multilevel algorithms, in particular to their coarsening phase. One way to specify a (recursive) coarsening of a graph is to rate its edges and then contract the edges as prioritized by the rating. In this paper we (i) define weights for the edges of a network that express the edges' importance for connectivity, (ii) compute a minimum weight spanning tree $T^m$ with respect to these weights, and (iii) rate the network edges based on the conductance values of $T^m$'s fundamental cuts. To this end, we also (iv) develop the first optimal linear-time algorithm to compute the conductance values of \emph{all} fundamental cuts of a given spanning tree. We integrate the new edge rating into a leading multilevel graph partitioner and equip the latter with a new greedy postprocessing for optimizing the maximum communication volume (MCV). Experiments on bipartitioning frequently used benchmark networks show that the postprocessing already reduces MCV by 11.3%. Our new edge rating further reduces MCV by 10.3% compared to the previously best rating with the postprocessing in place for both ratings. In total, with a modest increase in running time, our new approach reduces the MCV of complex network partitions by 20.4%

Synergistic Embryotoxicity of Polycyclic Aromatic Hydrocarbon Aryl Hydrocarbon Receptor Agonists with Cytochrome P4501A Inhibitors in Fundulus heteroclitus

Widespread contamination of aquatic systems with polycyclic aromatic hydrocarbons (PAHs) has led to concern about effects of PAHs on aquatic life. Some PAHs have been shown to cause deformities in early life stages of fish that resemble those elicited by planar halogenated aromatic hydrocarbons (pHAHs) that are agonists for the aryl hydrocarbon receptor (AHR). Previous studies have suggested that activity of cytochrome P4501A, a member of the AHR gene battery, is important to the toxicity of pHAHs, and inhibition of CYP1A can reduce the early-life-stage toxicity of pHAHs. In light of the effects of CYP1A inhibition on pHAH-derived toxicity, we explored the impact of both model and environmentally relevant CYP1A inhibitors on PAH-derived embryotoxicity. We exposed Fundulus heteroclitus embryos to two PAH-type AHR agonists, β-naphthoflavone and benzo(a)pyrene, and one pHAH-type AHR agonist, 3,3′,4,4′,5-pentachlorobiphenyl (PCB-126), alone and in combination with several CYP1A inhibitors. In agreement with previous studies, coexposure of embryos to PCB-126 with the AHR antagonist and CYP1A inhibitor α-naphthoflavone decreased frequency and severity of deformities compared with embryos exposed to PCB-126 alone. In contrast, embryos coexposed to the PAHs with each of the CYP1A inhibitors tested were deformed with increased severity and frequency compared with embryos dosed with PAH alone. The mechanism by which inhibition of CYP1A increased embryotoxicity of the PAHs tested is not understood, but these results may be helpful in elucidating mechanisms by which PAHs are embryotoxic. Additionally, these results call into question additive models of PAH embryotoxicity for environmental PAH mixtures that contain both AHR agonists and CYP1A inhibitors

Motor coordination, working memory, and academic achievement in a normative adolescent sample: Testing a mediation model

The aim of the present study was to examine whether the relationship between motor coordination and academic achievement is mediated by working memory (WM) in a normative adolescent sample. Participants included 93 adolescents aged 12–16. The Movement Assessment Battery for Children-2 provided three indicators of motor coordination (Manual Dexterity, Aiming and Catching, and Balance), the WM Index of the Wechsler Intelligence Scale for Children-IV and the N-back paradigm provided two indicators of WM, and the Wechsler Individual Achievement Test-II provided three indicators of academic achievement (Word Reading, Spelling, and Numerical Operations). Structural equation modeling, controlling for verbal comprehension, attention deficit hyperactivity disorder symptoms, and socioeconomic status, suggested that the association between motor coordination and academic achievement may be best understood in terms of a mechanism whereby motor coordination (specifically, Aiming and Catching skills) has an indirect impact on academic outcomes via WM. These findings have important implications for the assessment and treatment of motor coordination and learning difficulties as well as in increasing the understanding of the possible neural mechanisms underpinning the relationship between these areas

Nasal Colonization of Humans with Methicillin-Resistant Staphylococcus aureus (MRSA) CC398 with and without Exposure to Pigs

Background: Studies in several European countries and in North America revealed a frequent nasal colonization of livestock with MRSA CC398 and also in humans with direct professional exposure to colonized animals. The study presented here addresses the question of further transmission to non exposed humans. Methods: After selecting 47 farms with colonized pigs in different regions of Germany we sampled the nares of 113 humans working daily with pigs and of their 116 non exposed family members. The same was performed in 18 veterinarians attending pig farms and in 44 of their non exposed family members. For investigating transmission beyond families we samples the nares of 462 pupils attending a secondary school in a high density pig farming area. MRSA were detected by direct culture on selective agar. The isolates were typed by means of spa-sequence typing and classification of SCCmec elements. For attribution of spa sequence types to clonal lineages as defined by multi locus sequence typing we used the BURP algorithm. Antibiotic susceptibility testing was performed by microbroth dilution assay. Results: At the farms investigated 86% of humans exposed and only 4.3% of their family members were found to carry MRSA exhibiting spa-types corresponding to clonal complex CC398. Nasal colonization was also found in 45% of veterinarians caring for pig farms and in 9% of their non exposed family members. Multivariate analysis revealed that antibiotic usage prior to sampling beard no risk with respect to colonization. From 462 pupils only 3 were found colonized, all 3 were living on pig farms. Conclusion: These results indicate that so far the dissemination of MRSA CC398 to non exposed humans is infrequent and probably does not reach beyond familial communities

Survival estimates of bycatch individuals discarded from bivalve dredges

The fate of released bycatch is an issue of great interest for fisheries research and management. Survival experiments were carried out to assess the survival capacity of animals damaged and discarded during clam dredging operations. Three common bycatch species, two fish (Trachinus vipera; Dicologlossa cuneata) and one crab (Polybius henslowii), were collected during the sorting of catches from a commercial dredging boat. An arbitrary score scale was used to quantify the type and extent of damage to the organisms. Onboard, damaged individuals were placed in tanks containing seawater which were subsequently transferred to the laboratory. Survival experiments were conducted during the subsequent 48h. D. cuneata exhibited the lowest mortality after 48h (54%), followed by P. henslowii (65%) and T. vipera (81%). Despite the magnitude of the percentage mortalities determined, the average number of individuals estimated to die during a 15 minutes tow (standard commercial fishing time) was relatively small: 1.2, 3.24 and 11 for D. cuneata, T. vipera and P. henslowii, respectively. Nevertheless, when these figures are extrapolated to cover all the dredging fleet the impact of this practice on the populations of the species studied can be significant, particulary for D. cuneata

Clinical effectiveness of rapid tests for methicillin resistant Staphylococcus aureus (MRSA) in hospitalized patients: a systematic review

<p>Abstract</p> <p>Background</p> <p>Methicillin resistant <it>Staphylococcus aureus </it>(MRSA) are often resistant to multiple classes of antibiotics. The research objectives of this systematic review were to evaluate the clinical effectiveness of polymerase chain reaction (PCR) versus chromogenic agar for MRSA screening, and PCR versus no screening for several clinical outcomes, including MRSA colonization and infection rates.</p> <p>Methods</p> <p>An electronic literature search was conducted on studies evaluating polymerase chain reaction techniques and methicillin (also spelled meticillin) resistant <it>Staphylococcus aureus </it>that were published from 1993 onwards using Medline, Medline In-Process & Other Non-Indexed Citations, BIOSIS Previews, and EMBASE. Due to the presence of heterogeneity in the selected studies, the clinical findings of individual studies were described.</p> <p>Results</p> <p>Nine studies that compared screening for MRSA using PCR versus screening using chromogenic agar in a hospital setting, and two studies that compared screening using PCR with no or targeted screening were identified. Some studies found lower MRSA colonization and acquisition, infection, and transmission rates in screening with PCR versus screening with chromogenic agar, and the turnaround time for screening test results was lower for PCR. One study reported a lower number of unnecessary isolation days with screening using PCR versus screening with chromogenic agar, but the proportion of patients isolated was similar between both groups. The turnaround time for test results and number of isolation days were lower for PCR versus chromogenic agar for MRSA screening.</p> <p>Conclusions</p> <p>The use of PCR for MRSA screening demonstrated a lower turnaround time and number of isolation days compared with chromogenic agar. Given the mixed quality and number of studies (11 studies), gaps remain in the published literature and the evidence remains insufficient. In addition to screening, factors such as the number of contacts between healthcare workers and patients, number of patients attended by one healthcare worker per day, probability of colonization among healthcare workers, and MRSA status of hospital shared equipment and hospital environment must be considered to control the transmission of MRSA in a hospital setting.</p

Insights into the expanding phenotypic spectrum of inherited disorders of biogenic amines

Inherited disorders of neurotransmitter metabolism are rare neurodevelopmental diseases presenting with movement disorders and global developmental delay. This study presents the results of the first standardized deep phenotyping approach and describes the clinical and biochemical presentation at disease onset as well as diagnostic approaches of 275 patients from the registry of the International Working Group on Neurotransmitter related Disorders. The results reveal an increased rate of prematurity, a high risk for being small for gestational age and for congenital microcephaly in some disorders. Age at diagnosis and the diagnostic delay are influenced by the diagnostic methods applied and by disease-specific symptoms. The timepoint of investigation was also a significant factor: delay to diagnosis has decreased in recent years, possibly due to novel diagnostic approaches or raised awareness. Although each disorder has a specific biochemical pattern, we observed confounding exceptions to the rule. The data provide comprehensive insights into the phenotypic spectrum of neurotransmitter disorders

Persistence of Livestock Associated MRSA CC398 in Humans Is Dependent on Intensity of Animal Contact

INTRODUCTION: The presence of Livestock Associated MRSA (LA-MRSA) in humans is associated with intensity of animal contact. It is unknown whether the presence of LA-MRSA is a result of carriage or retention of MRSA-contaminated dust. We conducted a longitudinal study among 155 veal farmers in which repeated nasal and throat swabs were taken for MRSA detection. Periods with and without animal exposure were covered. METHODS: Randomly, 51 veal calf farms were visited from June-December 2008. Participants were asked to fill in questionnaires (n = 155) to identify potential risk factors for MRSA colonisation. Nasal and throat swabs were repeatedly taken from each participant for approximately 2 months. Swabs were analysed for MRSA and MSSA by selective bacteriological culturing. Spa-types of the isolates were identified and a ST398 specific PCR was performed. Data were analyzed using generalized estimation equations (GEE) to allow for correlated observations within individuals. RESULTS: Mean MRSA prevalence was 38% in farmers and 16% in family members. Presence of MRSA in farmers was strongly related to duration of animal contact and was strongly reduced in periods with absence of animal contact (-58%). Family members, especially children, were more often carriers when the farmer was a carrier (OR = 2,