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

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

Growth performance and nutrient balance of pigs fed low protein diets without mineral phosphate supplementation

The 48 pigs were blocked by gender, body weight (BW), and litter, assigned to 1 of the 4 treatments (C=control, N-=low crude protein (CP) with amino acid (AA) addition, P-=no MP, and N-P-=combination of N- and P-), fed ad libitum, and all housed in one pen. Grower and finisher diets with C contained respectively 15.5% and 13.5% CP, 0.47% and 0.41% P, and 0.29% and 0.26% digestible P (dP), diets with N- contained 10% and 15% less CP, and diets with P- contained 20% and 22% less P, leading to 24% and 21% less dP than C. Diets with N- were optimized to use minimal amounts of imported soybean meal, replaced by Swiss-origin protein beans and rapeseed meal, and synthetic AAs to reach minimal CP but equal digestible AA contents as in C. In P-, phosphate was removed and calcium:dP ratios were fixed as in C by adjusting calcium carbonate. Individual feed intake and weekly BW were recorded. Average daily feed intake and gain, and feed conversion ratio (FCR) were calculated. Over grower and finisher phases (47±4.0d and 40±8.2d, respectively), nutrient balance data were derived by differences between nutrient intake and body nutrient accretion which was derived from body composition assessment by dual X-ray absorptiometry at the start (22.3±3.35kg BW), middle (≈60kg BW at diet change from grower to finisher), and end (BW≥100kg) of the experiment. Urinary and daily fecal samples were obtained during two 4-d collection periods (40-50kg BW grower and 75-85kg BW finisher). There were no interactions (P>0.05) between N- and P- effects on any measured parameter. No differences (P>0.10) were observed in growth performance due to N- or P- effects, except finisher pigs with P- had a higher FCR (P<0.05, 2.66 vs 2.60). In grower, finisher, and overall periods, the intake and excretion of N and P were reduced (P<0.01) in pigs fed respectively diets N- and P-, and female pigs had better nutrient utilization rates (P≤0.001) regardless of treatments. The findings suggest replacing imported soybean meal with local protein sources and AA supplementation while simultaneously reducing CP contents and the MP removal in growing-finishing pig’s diet can maintain animal growth and reduce N and P excretion into the environment

Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD

The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius’ eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profle of the frst Pompeian’ genome, which has strong afnities with the surrounding central Italian population from the Roman Imperial Age. Our fndings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identifed the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confrms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial fndings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site

The Political Legacy of Entertainment TV

We study the political impact of commercial television in Italy exploiting the staggered introduction of Berlusconi's private TV network, Mediaset, in the early 1980s. We find that individuals with early access to Mediaset all-entertainment content were more likely to vote for Berlusconi's party in 1994, when he first ran for office. The effect persists for five elections and is driven by heavy TV viewers, namely the very young and the elderly. Regarding possible mechanisms, we find that individuals exposed to entertainment TV as children were less cognitively sophisticated and civic-minded as adults, and ultimately more vulnerable to Berlusconi's populist rhetoric. © 2019 AE

Estudio de prospectiva estratégica sobre la Agricultura Periurbana (AP) en la Ciudad de Corrientes: horizonte temporal 2020. Grupo Buenos Aires

Tesis presentada para la Especialización en Prospectiva Estratégica. Tutor: Eduardo Raúl Balbi Co-Tutor: Norberto Ramis

Randomized trial on adjuvant treatment with FOLFIRI followed by docetaxel and cisplatin versus 5-fluorouracil and folinic acid for radically resected gastric cancer

Some trial have demonstrated a benefit of adjuvant fluoropirimidine with or without platinum compounds compared with surgery alone. ITACA-S study was designed to evaluate whether a sequential treatment of FOLFIRI [irinotecan plus 5-fluorouracil/folinic acid (5-FU/LV)] followed by docetaxel plus cisplatin improves disease-free survival in comparison with 5-FU/LV in patients with radically resected gastric cancer. Patients with resectable adenocarcinoma of the stomach or gastroesophageal junction were randomly assigned to either FOLFIRI (irinotecan 180 mg/m(2) day 1, LV 100 mg/m(2) as 2 h infusion and 5-FU 400 mg/m(2) as bolus, days 1 and 2 followed by 600 mg/m(2)/day as 22 h continuous infusion, q14 for four cycles) followed by docetaxel 75 mg/m(2) day 1, cisplatin 75 mg/m(2) day 1, q21 for three cycles (sequential arm) or De Gramont regimen (5-FU/LV arm). From February 2005 to August 2009, 1106 patients were enrolled, and 1100 included in the analysis: 562 in the sequential arm and 538 in the 5-FU/LV arm. With a median follow-up of 57.4 months, 581 patients recurred or died (297 sequential arm and 284 5-FU/LV arm), and 483 died (243 and 240, respectively). No statistically significant difference was detected for both disease-free [hazard ratio (HR) 1.00; 95% confidence interval (CI): 0.85-1.17; P = 0.974] and overall survival (OS) (HR 0.98; 95% CI: 0.82-1.18; P = 0.865). Five-year disease-free and OS rates were 44.6% and 44.6%, 51.0% and 50.6% in the sequential and 5-FU/LV arm, respectively. A more intensive regimen failed to show any benefit in disease-free and OS versus monotherapy

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