A Bulk-Parallel Priority Queue in External Memory with STXXL

We propose the design and an implementation of a bulk-parallel external memory priority queue to take advantage of both shared-memory parallelism and high external memory transfer speeds to parallel disks. To achieve higher performance by decoupling item insertions and extractions, we offer two parallelization interfaces: one using "bulk" sequences, the other by defining "limit" items. In the design, we discuss how to parallelize insertions using multiple heaps, and how to calculate a dynamic prediction sequence to prefetch blocks and apply parallel multiway merge for extraction. Our experimental results show that in the selected benchmarks the priority queue reaches 75% of the full parallel I/O bandwidth of rotational disks and and 65% of SSDs, or the speed of sorting in external memory when bounded by computation.Comment: extended version of SEA'15 conference pape

Formación de megacristales de feldespato potásico en el sector sur del batolito Cerro Aspero-Alpa Corral (32°40'S y 64°50'W), Sierras Pampeanas, Córdoba, Argentina

The surrounding rocks of studied area are composed by a metamorphic sequence which includes gneisses, schists, amphibolites, marbles and heterogeneous migmatites in non-conformity intruded by a granitic pluton. All this sequence is dated as having late-Precambric to mid-Paleozoic age.Three facies, mostly of monzogranitic composition, were identified. This study focuses on the porphiric facies; detailed petroestructural studies being performed, the orientation of large microcline crystal and associated microgranular enclaves being measured.Different primary flow directions were determined with track variation of microcline megacrystal and enclaves from subvertical to nearly horizontal positions.These changes have been interpreted as a convective system within the pluton.The presence of a marked planar fabric in microcline megacrystals along with phenomena such a size-variation of crystal, synneusis, crystal trending at the enclave's border and crystal accumulation, proves their early magmatic origin. The enclaves show a cinematic of deformation produced by simple shear.El entorno encajante de la zona estudiada está integrado por una secuencia metamórfica que incluye gneises, esquistos, anfibolitas, calizas cristalinas y migmatitas heterogéneas, intruidas discordantemente por el plutón granítico. A este conjunto puede asignársele una edad precámbrica superior-paleozoica media.Se identificaron tres facies, en su mayoría de composición monzogranítica, diques micrograníticos a aplíticos y enclaves. En este trabajo se pone énfasis en la facies porfiroide efectuándose estudios petroestructurales de detalle, tomando como indicadores la orientación de los grandes cristales de microclina y enclaves microgranulares asociados.Se determinaron distintas direcciones de flujo primario con variaciones en la trayectoria de los megacristales de microclina y enclaves desde posiciones subverticales hasta aproximadamente horizontales. Estos cambios han sido interpretados como un sistema convectivo dentro del plutón.La presencia de una marcada fábrica planar en los megacristales de microclina, conjuntamente con fenómenos de gradaciones en el tamaño de cristales, sineusis, alineaciones en los bordes de enclaves y aglomeraciones de cristales evidencian su origen temprano magmático. Los enclaves muestran una cinemática de deformación producida por cizalla simple

Biofortification of selenium in black soldier fly (Hermetia illucens) prepupae reared on seaweed or selenium enriched substrates

Selenium (Se) is an essential trace element for livestock. The element can be supplemented to feed in inorganic or organic Se forms, where the chemical form in the diet affects the accumulation of Se in animal tissues. Insects are known to be natural bioaccumulators of different nutrients, but no studies have so far looked up on the capacity of insects to be biofortified with Se, as a potential future source for Se in feed. In this study, black soldier fly (BSF, Hermetia illucens) larvae were reared on three different substrates: (1) a control substrate (CTR diet) of plant-ingredients (Gainesville diet); (2) Ascophyllum nodosum diet (AN30%), with 30% substitution of the alfalfa meal with the brown algae; and (3) a Se diet, where the CTR diet was fortified with 0.3 mg/kg of Se. All experiments were carried out under dark condition, at 25 °C with 70% relative humidity for two weeks, and the final BSF prepupae were analysed for Se, metals and minerals, and Se species. The mean total Se content in the prepupae reared on Se dietary group was over five times higher compared to the CTR group, whereas lower Se levels were detected in AN30% dietary group. Se speciation analyses showed that organic selenomethionine (SeMet) was the major Se species present, both in CTR and AN30% group. For the Se group, SeMet was accounting for 54% of the total Se. The levels of SeMet were higher in the Se group compared to the CTR group, indicating that BSF prepupae are able to convert inorganic Se to organic Se. The overall results show that the substrates hereby studied affect the total Se and Se species, as well as the levels of other elements, in the BSF prepupae.publishedVersio

Fate of Salmonella enterica Typhimurium and Listeria monocytogenes in Black Soldier Fly (Hermetia illucens) Larvae Reared on Two Artificial Diets

Ensuring food security is one of the main challenges facing the world over the next 30 years. There is, thus, an urgent need to significantly increase the supply of sustainable protein that can be transformed into animal feed. Proteins from insects offer a valuable alternative. This article presents the results of challenge tests conducted to investigate the dynamics of the microbial load of Salmonella enterica Typhimurium and Listeria monocytogenes in black soldier fly (Hermetia illucens) larvae grown on contaminated substrates. Four separate challenge tests were performed on two substrates: the Gainesville diet and a homemade diet. The challenge test procedure was carried out in accordance with ISO/DIS 20976-2 (under development). The results of this study show that, when grown on contaminated substrates, BSF larvae do not eliminate Salmonella Typhimurium or L. monocytogenes, but can reduce their microbial load. Sanitation processes downstream of the breeding of BSF larvae are, however, required to reduce the microbiological risks of this novel food

Stops making sense: translational trade-offs and stop codon reassignment

Background Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences. Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants

Light microscopy with a differential staining technique for the characterization and discrimination of insects versus marine arthropods in processed animal proteins

The aim of this study was to evaluate the use of light microscopy with a differential staining technique for the discrimination of insect material from marine arthropods - classified as fishmeal. Specifically, three samples of single species insect material, Hermetia illucens (HI), Bombyx mori (BM) and Tenebrio molitor (TM) and two samples of marine arthropods, shrimp material and krill, have been analysed and compared after staining by two reagents to enhance fragment identification. Alizarin Red (AR) and Chlorazol black (CB), which react respectively with calcium salts and chitin, were tested for their potential efficacy in distinguishing between insect and marine materials. Results indicated that AR failed to stain HI, BM and TM materials. By contrast, the three insect species materials tested (HI, BM and TM) were stained by CB. When shrimp fragments and krill were considered, AR and CB stained marine materials reddish-pink and light blue to black, respectively. By combining these results it can be suggested that CB staining may efficiently be used to mark insect materials; AR does stain shrimp fragments but does not stain the tested insect material, indicating a possible approach for discriminating between insects and marine arthropods. However, since the present study has only been done on pure materials and on a small set of samples, possible implementation of this technique still needs to be confirmed in complex matrices such as compound feed

Pronounced dys-autonomic symptoms announcing a primary Sjögren's syndrome

Sjögren’s syndrome (SS) is an autoimmune disease that involves the nervous system in about 20% of cases. In 25-92% of patients affected by Sjögren’s syndrome, neurological symptoms may precede the sicca syndrome. A 65-year-old male presented with a seven-month history of episodes of near-syncope, constipation, anhidrosis, disabling fatigue and asthenia. Physical examination was unremarkable, whilst the ECG revealed sinus bradycardia. Laboratory tests showed lymphopenia and normal inflammatory markers. In order to assess a potential autonomic neuropathy, “Deep Breathing Test” (E/I 1.02), “Lying to Standing Test” (R/R’ 0.95), and “Orthostatic Hypotension Tests” (T 120s Systolic reduction >20 mmHg and Diastolic reduction >10 mmHg) were performed, all of which were abnormal. ECG Holter monitoring revealed sinus bradycardia, and right bundle branch block with 24-h blood pressure monitoring revealing a diurnal hypotensive profile. The patient reported a three-month history of worsening dry mouth. On physical examination, the patient had anisocoria in response to light stimulation. Auto-antibody testing was performed to evaluate the presence of any autoimmune disease. The results of these studies included an abnormal elevation of ANA (1:320 speckled pattern), Ro/SS-a (>240U/l), and La/SS-b (162 U/ml) antibodies. The patient was discharged with a diagnosis of “Autonomic Neuropathy Most Likely Due to Primary Sjögren’s Syndrome (SS)” and started the immunotherapy. After one month, he reported a significant improvement in his symptoms with a concomitant normalization of his “Orthostatic Hypotension Tests.” This case underlines the potential for dys-autonomic symptoms to precede the onset of sicca syndrome in patients with Sjogren’s Syndrome

P-110 Hepatocellular carcinoma in elderly patients: Final results of the Italian cohort of GIDEON study

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