Speculative dynamic vectorization

Traditional vector architectures have shown to be very effective for regular codes where the compiler can detect data-level parallelism. However, this SIMD parallelism is also present in irregular or pointer-rich codes, for which the compiler is quite limited to discover it. In this paper we propose a microarchitecture extension in order to exploit SIMD parallelism in a speculative way. The idea is to predict when certain operations are likely to be vectorizable, based on some previous history information. In this case, these scalar instructions are executed in a vector mode. These vector instructions operate on several elements (vector operands) that are anticipated to be their input operands and produce a number of outputs that are stored on a vector register in order to be used by further instructions. Verification of the correctness of the applied vectorization eventually changes the status of a given vector element from speculative to non-speculative, or alternatively, generates a recovery action in case of misspeculation. The proposed microarchitecture extension applied to a 4-way issue superscalar processor with one wide bus is 19% faster than the,same processor with 4 scalar buses to Ll data cache. This speed up is due basically to 1) the reduction in number of memory accesses, 15% for SpecInt and 20% for SpecFP, 2) the transformation of scalar arithmetic instructions into their vector counterpart, 28% for SpecInt and 23% for SpecFP, and 3) the exploitation of control independence for mispredicted branches.Peer ReviewedPostprint (published version

Lowering costs of microbial cellulose

We have been conducting research with Acetobacter xylinium for microbial conversion of sugars to cellulose. A rotating disk biological contactor should lower costs considerably because its production rates are greater than for the usual method of surface culture. Another major cost saving comes from replacing expensive sugars in the medium with sugars derived from wastes. Extracts of spent grapes from wastes of Portuguese wine factories supply suitable sugars for good production of microbial cellulose

A neuroimaging study of pleasant and unpleasant olfactory perceptions of virgin olive oil

Functional magnetic resonance imaging (fMRI) has been used to collect information from neurons that receive direct input from olfactory bulbs when subjects smell virgin olive oil. The pleasant aroma of three extra virgin olive oils (var. Royal, Arbequina and Picual) and three virgin olive oils with sensory defects (rancid, fusty and winey/vinegary) were presented to 14 subjects while a fMRI scan acquired data from the brain activity. Data were subjected to a two-sample t test analysis, which allows a better interpretation of results particularly when data are studied across different subjects. Most of the activations, which were located in the frontal lobe, are related to the olfactory task regardless of the hedonic component of perception (e.g. Brodmann areas 10, 11). Comparing the samples with pleasant and unpleasant aromas, differences were found at the anterior cingu�late gyrus (Brodmann area 32), at the temporal lobe (Brodmann area 38), and inferior frontal gyrus (Brodmann area 47), while intense aromas activated Brodmann area 6. The actual perceptions described by the subjects and the concentration of the odorant compounds in the samples were considered in the interpretation of the results.Estudio mediante neuroimagen de percepciones olfativas agradables y desagradables de aceites de oliva virgen. La imagen por resonancia magnética funcional (fMRI) ha sido empleada para estudiar la información de la respuesta cerebral producida al estimular las neuronas que participan en el proceso olfatorio tras percibir el aroma del aceite de oliva virgen (AOV). Se utilizó fMRI para la adquisición de los datos de la actividad cerebral de 14 sujetos a los que se presentaron tres aceites de oliva vírgenes de aroma agradable (var. Royal, Arbequina and Picual) y tres aceites de oliva vírgenes con defectos sensoriales (rancio, atrojado, avinado/avinagrado). Los datos se sometieron a una prueba t para observar diferencias entre dos grupos, la cual permite una mejor interpretación de los resultados, particularmente cuando los datos se estudian a través de diferentes sujetos. La mayoría de las activaciones, que se localizaron en lóbulos frontales, se relacionaron con la tarea olfatoria independientemente de la componente hedónica de la percepción (por ejemplo, áreas Brodmann 10, 11). Al comparar las muestras con aromas agradables y desagradables, se encontraron diferencias significativas en el giro cingulado anterior (área Brodmann 32), el lóbulo temporal (área Brodmann 38) y el giro frontal inferior (área Brodmann 47), mientras que los aromas más intensos activaron el área Brodmann 6. En la interpretación de los resultados se tuvo en cuenta tanto la percepción descrita por los sujetos como las concentraciones de los compuestos volátiles en las muestras.Ramón y Cajal Program AGL2008-01411, AGL2011- 30371-C02-01/02

Tracking Sensory Characteristics of Virgin Olive Oils During Storage: Interpretation of Their Changes from a Multiparametric Perspective

Virgin olive oil is inevitably subject to an oxidation process during storage that can affect its stability and quality due to off-flavors that develop before the oil surpasses its ‘best before’ date. Many parameters are involved in the oxidation process at moderate conditions. Therefore, a multiparametric study is necessary to establish a link between physico-chemical changes and sensory quality degradation in a real storage experiment. In this context, a storage experiment of 27 months was performed for four monovarietal virgin olive oils, bottled in transparent 500-mL PET bottles and subjected to conditions close to a supermarket scenario. Volatile composition, quality parameters and phenolic compounds were determined monthly. Simultaneously, an accredited sensory panel assessed their sensory characteristics. The stability of the fresh samples was also studied with the oxidative stability index (OSI) and mesh cell-FTIR. (E)-2-hexenal, (Z)-3-hexen-1-ol and (E)-2-hexen-1-ol were identified as markers of the fruity attribute. Hexanal and nonanal were also identified as compounds that were associated with the rise of median of defect during storage. Some disagreements were observed between the sensory assessment and the OSI analyzed by Rancimat. However, the increase of concentration of rancid markers agreed with the increase of aldehyde band measured with mesh cell-FTIR.Spanish Research State Agency (research projects AGL2015-69320-R and RTI2018-101546-B-C21

Control-flow independence reuse via dynamic vectorization

Current processors exploit out-of-order execution and branch prediction to improve instruction level parallelism. When a branch prediction is wrong, processors flush the pipeline and squash all the speculative work. However, control-flow independent instructions compute the same results when they re-enter the pipeline down the correct path. If these instructions are not squashed, branch misprediction penalty can significantly be reduced. In this paper we present a novel mechanism that detects control-flow independent instructions, executes them before the branch is resolved, and avoids their re-execution in the case of a branch misprediction. The mechanism can detect and exploit control-flow independence even for instructions that are far away from the corresponding branch and even out of the instruction window. Performance figures show that the proposed mechanism can exploit control-flow independence for nearly 50% of the mispredicted branches, which results in a performance improvement that ranges from 14% to 17,8% for realistic configurations of forthcoming microprocessors.Peer Reviewe

Control-flow independence reuse via dynamic vectorization

Current processors exploit out-of-order execution and branch prediction to improve instruction level parallelism. When a branch prediction is wrong, processors flush the pipeline and squash all the speculative work. However, control-flow independent instructions compute the same results when they re-enter the pipeline down the correct path. If these instructions are not squashed, branch misprediction penalty can significantly be reduced. In this paper we present a novel mechanism that detects control-flow independent instructions, executes them before the branch is resolved, and avoids their re-execution in the case of a branch misprediction. The mechanism can detect and exploit control-flow independence even for instructions that are far away from the corresponding branch and even out of the instruction window. Performance figures show that the proposed mechanism can exploit control-flow independence for nearly 50% of the mispredicted branches, which results in a performance improvement that ranges from 14% to 17,8% for realistic configurations of forthcoming microprocessors.Peer Reviewe

Speculative dynamic vectorization

Traditional vector architectures have shown to be very effective for regular codes where the compiler can detect data-level parallelism. However, this SIMD parallelism is also present in irregular or pointer-rich codes, for which the compiler is quite limited to discover it. In this paper we propose a microarchitecture extension in order to exploit SIMD parallelism in a speculative way. The idea is to predict when certain operations are likely to be vectorizable, based on some previous history information. In this case, these scalar instructions are executed in a vector mode. These vector instructions operate on several elements (vector operands) that are anticipated to be their input operands and produce a number of outputs that are stored on a vector register in order to be used by further instructions. Verification of the correctness of the applied vectorization eventually changes the status of a given vector element from speculative to non-speculative, or alternatively, generates a recovery action in case of misspeculation. The proposed microarchitecture extension applied to a 4-way issue superscalar processor with one wide bus is 19% faster than the,same processor with 4 scalar buses to Ll data cache. This speed up is due basically to 1) the reduction in number of memory accesses, 15% for SpecInt and 20% for SpecFP, 2) the transformation of scalar arithmetic instructions into their vector counterpart, 28% for SpecInt and 23% for SpecFP, and 3) the exploitation of control independence for mispredicted branches.Peer Reviewe

Microbial conversion of glycerol to 1,3-propanediol$ephysiological comparison of a natural producer, Clostridium butyricum VPI 3266, and an engineered strain, Clostridium acetobutylicum DG1 (pSPD5)

Clostridium acetobutylicum is not able to grow on glycerol as the sole carbon source since it cannot reoxidize the excess of NADH generated by glycerol catabolism. Nevertheless, when the pSPD5 plasmid, carrying the NADH-consuming 1,3-propanediol pathway from C. butyricum VPI 3266, was introduced into C. acetobutylicum DG1, growth on glycerol was achieved, and 1,3-propanediol was produced. In order to compare the physiological behavior of the recombinant C. acetobutylicum DG1(pSPD5) strain with that of the natural 1,3- propanediol producer C. butyricum VPI 3266, both strains were grown in chemostat cultures with glycerol as the sole carbon source. The same “global behavior” was observed for both strains: 1,3-propanediol was the main fermentation product, and the qH2 flux was very low. However, when looking at key intracellular enzyme levels, significant differences were observed. Firstly, the pathway for glycerol oxidation was different: C. butyricum uses a glycerol dehydrogenase and a dihydroxyacetone kinase, while C. acetobutylicum uses a glycerol kinase and a glycerol-3-phosphate dehydrogenase. Secondly, the electron flow is differentially regulated: (i) in C. butyricum VPI 3266, the in vitro hydrogenase activity is 10-fold lower than that in C. acetobutylicum DG1(pSPD5), and (ii) while the ferredoxin-NAD reductase activity is high and the NADH-ferredoxin reductase activity is low in C. acetobutylicum DG1(pSPD5), the reverse is observed for C. butyricum VPI 3266. Thirdly, lactate dehydrogenase activity is only detected in the C. acetobutylicum DG1(pSPD5) culture, explaining why this microorganism produces lactate

Metabolic engineering of clostridium acetobutylicum for the industrial production of 1,3-propanediol from glycerol

Clostridium butyricum is to our knowledge the best natural 1,3-propanediol producer from glycerol and the only microorganism identified so far to use a coenzyme B12-independent glycerol dehydratase. However, to develop an economical process of 1,3-propanediol production, it would be necessary to improve the strain by a metabolic engineering approach. Unfortunately, no genetic tools are currently available for C. butyricum and all our efforts to develop them have been so far unsuccessful. To obtain a better ‘‘vitamin B12-free’’ biological process, we developed a metabolic engineering strategy with Clostridium acetobutylicum. The 1,3- propanediol pathway from C. butyricum was introduced on a plasmid in several mutants of C. acetobutylicum altered in product formation. The DG1(pSPD5) recombinant strain was the most efficient strain and was further characterized from a physiological and biotechnological point of view. Chemostat cultures of this strain grown on glucose alone produced only acids (acetate, butyrate and lactate) and a high level of hydrogen. In contrast, when glycerol was metabolized in chemostat culture, 1,3-propanediol became the major product, the specific rate of acid formation decreased and a very low level of hydrogen was observed. In a fed-batch culture, the DG1(pSPD5) strain was able to produce 1,3-propanediol at a higher concentration (1104mM) and productivity than the natural producer C. butyricum VPI 3266. Furthermore, this strain was also successfully used for very long term continuous production of 1,3-propanediol at high volumetric productivity (3 g L⁻¹ h⁻¹) and titer (788 mM).N/

Maternal Lineages during the Roman Empire, in the Ancient City of Gadir (Cádiz, Spain): The Search for a Phoenician Identity

Phoenicians were probably the first eastern Mediterranean population to establish long-distance connections with the West, namely the Iberian Peninsula, from the final Bronze to the early Iron Age. For a long time, these colonies all over the Mediterranean Sea directly depended on an important city administration, Gadir, the most important metropolis in the Western Mediterranean. Modern archaeological excavations were discovered in Cadiz (Spain), the ancient city of Gadir, as well as possible Phoenician burial places. The purpose of the present work is the molecular study of 16 individuals, (V–IV millennium B.C, V A.D.) from several burial places found in Cadiz, attempting to disclose their maternal biogeographical ancestry. Furthermore, the determination of a possible biological link between two individuals found buried together was also an objective of this investigation. Of all the 16 analyzed individuals, eight of them produced positive results. Three main lineages were found: HV0, H and L3b. In general, the results support an Eastern origin for this set of individuals, reinforcing the theory of a Phoenician origin. Due to their historical period, in some cases, it was not possible to discard a Roman origin. Finally, the maternal kinship between two individuals found buried together was discarded