Top PDF Decomposition of Parallel Copies with Duplication

Decomposition of Parallel Copies with Duplication

Decomposition of Parallel Copies with Duplication

SSA form is becoming more popular in the context of JIT compilation since it allows the compiler to perform important optimizations like common sub-expression elimination or constant propagation without the drawbacks of keeping huge data structures in memory or requiring a lot of computing power. The recent approach of SSA-based register allocation performs SSA elimination after register allocation. F. Bouchez et al. proposed parallel copy motion to prevent the splitting of edges when going out of colored SSA by moving the code that should be assigned to the edges to a more convenient place. Duplications in parallel copies pose some problems when moving them. In this paper an approach has been developed to decompose parallel copies so that duplications can be handled separately and parallel copies can be easily moved away without duplication. A simple and elegant application is moving duplicated copies out of critical edges. This is often beneficial compared to the alternative splitting the edge.
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Drosophila duplication hotspots are associated with late-replicating regions of the genome.

Drosophila duplication hotspots are associated with late-replicating regions of the genome.

Understanding the evolutionary forces shaping the evolution of CNVs is also important from a medical and evolutionary perspective. Despite their pervasiveness, analyses of the genomic distribution of CNVs among different functional regions clearly indicate that a large fraction is under purifying selection. Population genetic models that address both demographic and selection processes have been used to estimate the strength of selection acting on different classes of CNVs. In both flies [36] and humans [37] coding CNVs are under the strongest purifying selection followed by intronic CNVs and finally intergenic CNVs. Evidence for positive selection has been less clear. There are examples of CNVs under positive selection in humans, such as the copy number variation of the amylase [10] and CCL3L1 [38] genes, and in flies (e.g. duplication of the Cyp6G1 locus) [36,39]. However, on a genome-wide scale, the over-representation of certain classes of genes in CNVs, namely ‘‘environmental’’ genes, is best explained by reduced purifying selection acting on these variants than by positive selection [40]. Although genome-scale studies of CNVs have only recently become technically feasible [41], the study of gene duplication can be traced back to as early as 1911 [12,42]. An important problem is to determine the relative roles of positive selection and genetic drift in the fixation of new gene duplicates [43]. Most population genetic models assume that gene duplicates are fixed by genetic drift and that their subsequent fate in genomes (being retained or lost) is determined by ensuing mutations in one or both copies [43,44]. An alternative hypothesis is that gene duplications are fixed by positive selection. Assessing
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Detecção multiusuário baseada em tensores para sistemas de comunicação sem fio cooperativos

Detecção multiusuário baseada em tensores para sistemas de comunicação sem fio cooperativos

Abstract— In the present paper, a semi-blind receiver for a multiuser uplink DS-CDMA (Direct-Sequence Code-Division Multiple-Access) system based on relay aided cooperative com- munications is proposed. For the received signal, a quadrilinear Parallel Factor (PARAFAC) tensor decomposition is adopted, such that the proposed receiver can semi-blindly estimate the transmitted symbols, channel gains and spatial signatures of all users. The estimation is done by fitting the tensor model using the Alternating Least Squares (ALS) algorithm. With computa- tional simulations, we provide the performance evaluation of the proposed receiver for various scenarios.
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art alfalmeidaA Constrained Factor Decomposition With

art alfalmeidaA Constrained Factor Decomposition With

Abstract— In this paper, we formulate a new tensor decomposi- tion herein called constrained factor (CONFAC) decomposition. It consists in decomposing a third-order tensor into a triple sum of rank-one tensor factors, where interactions involving the com- ponents of different tensor factors are allowed. The interaction pattern is controlled by three constraint matrices the columns of which are canonical vectors. Each constraint matrix is associated with a given dimension, or mode, of the tensor. The explicit use of these constraint matrices provides degrees of freedom to the CONFAC decomposition for modeling tensor signals with con- strained structures which cannot be handled with the standard parallel factor (PARAFAC) decomposition. The uniqueness of this decomposition is discussed and an application to multiple-input multiple-output (MIMO) antenna systems is presented. A new transmission structure is proposed, the core of which consists of a precoder tensor decomposed as a function of the CONFAC constraint matrices. By adjusting the precoder constraint ma- trices, we can control the allocation of data streams and spreading codes to transmit antennas. Based on a CONFAC model of the received signal, blind symbol/code/channel recovery is possible using the alternating least squares algorithm. For illustrating this application, we evaluate the bit-error-rate (BER) performance for some configurations of the precoder constraint matrices.
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Duplication 9p and their implication to phenotype

Duplication 9p and their implication to phenotype

Based on the UCSC Genome Browser database (https:// genome.ucsc.edu), the duplicated region in our patients contains several annotated genes. DMRT1 (doublesex- and mab-3-related transcription factor 1) and DMRT2 (double- sex- and mab-3-related transcription factor 2) are genes related to gonadal development causing hypospadia, abnormal external genitalia, or XY sex reversal, as well as gonadal dysgenesis [19-21]. Only our male patients (P1 and P4) presented gonadal malformation. FREM1 (FRAS1-related extracellular matrix 1) gene encodes a basement membrane protein that may play a role in cra- niofacial and renal development. Although none of our patients presented renal abnormality, P1 presented microcephaly and P2, P3 and P4 present brachycephaly. PSIP1 (PC4 and SFRS1 interacting protein 1), SIGMAR1 (Sigma non-opioid intracellular receptor 1), PAX5 (paired box 5) and CNTNAP3 (contactin associated protein-like 3) genes are involved in the development of central nervous system and are responsible for learning processes, memory and mood alteration. All of our patients presented intellectual disability. Dele- tion of FOXD4 (forkhead box D4) gene is associated with speech and language delays [22] as found in eight patients from Table 2. The genes described above cause abnormalities when deleted or mutated. However, in our patients, these genes are present in three copies, probably resulting in overexpression of these genes causing impairment of its function. It is possible that some of the duplicated genes are dosage-sensitive gene and the interaction with other factors, such as regu- latory elements (transcription factors and growth factors), may contribute to phenotype and cerebral malformation. In fact, the phenotypic heterogeneity in trisomy 9p can be caused by the variable expression of duplicated genes, which can change the development phenotype [23].
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DUPLICATION OF BOWEL PRESENTING AS CHRONIC ABDOMINAL PAIN

DUPLICATION OF BOWEL PRESENTING AS CHRONIC ABDOMINAL PAIN

An ultra sonological report of abdomen revealed a multiloculated cystic mass, suggesting a mesenteric cyst. In view of chronic pain in the abdomen, we obtained consent for exploratory laparotomy. The procedure revealed an ileal duplication 38-cm long with a cystic dilatation that had adhesions to the transverse colon (Fig.1). The base of the cyst was fibrotic, suggesting that recurrent obstruction at this level resulted in the patient’s periodic episodes of abdominal pain. We resected the cyst and the parallel segment of small bowel and conducted a primary anastomosis. The patient had an uneventful postoperative period.
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A System’s Approach to Cache Hierarchy-Aware Decomposition of Data-Parallel Computations

A System’s Approach to Cache Hierarchy-Aware Decomposition of Data-Parallel Computations

The authors recognize that, although compiler and runtime optimizations increase the efficiency of a program up to a certain degree, when dealing with architectures with complex memory hierarchies the greatest performance gains can only be attained by op- timizing the way the application uses these hierarchies. However, the increasing levels of the hardware hierarchy and the wide variety of system architectures make it difficult for compilers to perform efficient tunnings. Therefore, it is highly unlikely that compiler or runtime systems will perform a good distribution of data and tasks across the hier- archy to meet the user’s computational needs. This means that one should emphasize enhancements of the programming model as much as improving the compiler or run- time libraries.
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Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.

Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis.

One of the PsbC homologs (Nsp37500) possesses a considerable C terminal extension (total length 477 amino acids compared to 319–344 residues for the other PsbC homologs). A closer inspection revealed that Nsp37500 possesses a PsaL domain in this additional segment and that nine transmembrane regions are predicted for the PsbC-PsaL hybrid protein (SI, Fig. S2). Similar genes have recently been identified in several more cyanobacterial genomes and the PsbC-PsaL hybrid proteins have been classified as chlorophyll binding proteins type V (CBPV) [69]. Analysis of a PsaL-less mutant of Synechocystis sp. PCC 6803 indicated that PsaL is required for the formation PSI trimers. However, iron- starved cells of this mutant were still able to form IsiA rings around PSI monomers but to a lesser extent [66,70]. The PsbC-PsaL fusion present in Nsp37500 suggests that this strain is hard-wired for the addition of chlorophyll-antenna to PSI monomers over and above the IsiA-rings associated with PSI trimers. This possibility is supported by the results of a recent homology modelling and insertion of the PsaL-like domain into the PSI structure [69]. Such an antenna complex may be a particularly efficient form of light- harvesting by PSI in the ecological niche of N. spumigena. The regulation of these genes in N. spumigena is not known, but at least for F. muscicola PCC 73103 the iron-stress-regulation of a comparable large operon with Pcb/PsbC homologs was detected [68].
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Rev. Bras. Hematol. Hemoter.  vol.39 número3

Rev. Bras. Hematol. Hemoter. vol.39 número3

who have a good from those with a dismal prognosis. In fact, chromosomal abnormalities detected by G-banding karyotype and gene rearrangements revealed by molecular tests are important tools to stratify patients into favorable, intermediate or unfavorable prognoses. The World Health Organization (WHO) classification of hematopoietic tumors lists recurrent genetic abnormalities. 2

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A two-fluid model describing the finite-collisionality, stationary Alfvén wave in anisotropic plasma

A two-fluid model describing the finite-collisionality, stationary Alfvén wave in anisotropic plasma

“inertial” and “kinetic”, respectively, and together they are known as a dispersive Alfv´en wave (e.g., Stasiewicz, 2005). The dispersive Alfv´en wave has been studied extensively because of its possible role in accelerating electrons in the Earth’s magnetosphere, particularly the auroral ionosphere, where the inertial wave can generate transient ( ∼1 s) bursts of electron energy at energies up to ∼1 keV (e.g., Hui and Seyler, 1992; Kletzing, 1994; Lysak and Song, 2003; Chas- ton et al., 2004; Seyler and Liu, 2007). The dispersive Alfv´en wave also leads to electron acceleration as a result of inter- hemispheric field-line resonances having periods of ∼10 min (e.g., Streltsov and Lotko, 1995; Rankin et al., 1999). See the comprehensive review by Stasiewicz et al. (2000). The lin- ear dispersion relation for the dispersive Alfv´en wave in both the inertial and kinetic limits has been verified in laboratory experiments (e.g., Allen et al., 1959; Jephcott, 1959; Wilcox et al., 1960; Jephcott and Stocker, 1962; Gekelman et al., 1997; Leneman et al., 1999; Vincena et al., 2004).
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Duplication cyst of the stomach with ectopic pancreatic tissue in an asymptomatic adult.

Duplication cyst of the stomach with ectopic pancreatic tissue in an asymptomatic adult.

The authors describe a rare case of a gastric duplication cyst in a 55-year-old man. The past history revealed that the patient was treated one year before for gastroduodenal ulcer. The cyst was discovered incidentally at upper gastrointestinal endoscopy. Biopsies showed inflammation without evidence of tumor. On abdominal ultrasonography and CT scan, a left upper quadrant mass was noted. At laparotomy, a mass measuring 6,0 cm in contact with the stomach was excised. Histopathology showed a gastric duplication cyst containing pancreatic mucosa.

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Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase

Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase

Figure 2 Identification of the intron gain in potatoes. The phylogenetic tree was constructed using the coding sequences of the gene PGSC0003DMG402000361.L and its orthologs Solyc12g008410.1 in S. lycopersicum, Sopen12g003370.2 in S. pennellii, Capana09g000243 in C. annuum, Niben101Scf04189g00002 in N. benthamiana, and Migut.K00531 in M. guttatus as well as the orthologous regions manually annotated in S. commersonii, S. habrochaites, and S. melongena. Numbers above the branches indicate the percentage of bootstrap support after 1,000 replicates. In the schematic diagram of the gene structures, the presented sequences start from the initiation codon ATG, the boxes represent exons, and the horizontal lines represent introns. Because of space limitations, the extraordinarily long introns are not scaled according to their lengths, and they are represented by broken lines. To avoid crowding together the slashed lines, the introns of M. guttatus have been scaled up by a factor of two. The new intron/exon structure is marked in red. Abbreviations: Stub, S. tuberosum; Scom, S. commersonii; Slyc, S. lycopersicum; Shab, S. habrochaites; Spen, S. pennellii; Smel, S. melongena; Cann, C. annuum; Nben, N. benthamiana; Mgut, M. guttatus.
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Vibration analysis of parallel misaligned shaft with ball bearing system

Vibration analysis of parallel misaligned shaft with ball bearing system

From the literature it is clearly understood that mis- alignment produces significant vibration levels in the bear- ings. It is strongly influenced by machine speed and stiffness of the coupling. Softer coupling are more forgiving, and tend to produce very less amount of vibration levels. Single point vibration spectrum for a given operating speed does not provide a reliable indication of misalignment. A machine can have parallel misalignment without exhibiting significant 2X vibration levels (Ganeriwala et al., 1999; Piotrowski, 2006). Vibration due to misalignment is usually characterized by a 2X running speed component and high axial vibration levels. When a misaligned shaft is supported by rolling-element bearing, these characteristic frequencies may also appear.
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Synthesis of nanoparticeles in ductile iron with small additions of vanadium and niobium and its mechanical properties

Synthesis of nanoparticeles in ductile iron with small additions of vanadium and niobium and its mechanical properties

Ductile iron is a modern construction material and offers wide range of mechanical properties with simultaneous high wear resistance and dumping capacity [1]. From foundry practice result that in many cases production of ductile iron ensure fulfillment the Standard regarding tensile strength as well as elongation but not always yield strength archives required value. Investigations enabling affirm whether the foregoing problem can be resolve by means of small additions of vanadium, niobium and nitrogen and heat treatment are the aim of this work.
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Evolutionary history of chordate PAX genes: dynamics of change in a complex gene family.

Evolutionary history of chordate PAX genes: dynamics of change in a complex gene family.

These results could indicate that a round of complete vertebrate genome duplication most likely involved PAX2 and PAX5 ancestor, whereas PAX8 emerged through local gene duplication. This would support the idea that PAX8 is the most recent gene to appear by duplication in this family. An alternative scenario to evolution of the PAX2/5/8 subfamily is that after 1 RWGD, two copies of the subfamily genes emerged, one resembling PAX2/5 and the other PAX8. A second duplication event (2 WRGD), resulted in 4 copies of the PAX2/5/8 subfamily, followed by loss of one of the PAX8 duplicates. The result is the presence of PAX2, PAX5, and PAX8 genes in jawed vertebrates [19,20]. The relaxation of selective pressure immediately after this last partial/total duplication would be expected, which could explain the higher variation observed in PAX8 relative to its outgroup (PAX2/5/8). The higher evolutionary rate (inferred by v = dN/dS; see Material and Methods and next section) could be an alternative explanation; however, the 2 above mentioned possi- bilities, relative to PAX8, are not mutually exclusive. Redundancy in the expression of these genes likely played a central role in the loss and/or higher divergence rate of PAX8. In mammals, PAX8 is mainly expressed in the kidney, ear, and thyroid gland during development, whereas PAX2 is expressed not only in these organs and tissues, but also in others, such as the eye, pharyngeal arches, and brain [2,3,5,7,19,20,44]. Amphioxus (here considered as an outgroup) contains only PAX2/5/8 and shows pleiotropic expres- sion in most organs and tissues, implying that PAX2, PAX5, and PAX8 have retained most of their ancestral expression patterns [19,20,44].
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A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment

A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment

The alignment among three or more nucleotides/amino-acids sequences at the same time is known as Multiple Sequence Alignment (MSA), an NP-hard optimization problem. The time complexity of finding an op- timal alignment raises exponentially when the number of sequences to align increases. In this work, we deal with a multiobjective version of the MSA problem where the goal is to simultaneously optimize the accuracy and conservation of the alignment. A parallel version of the Hybrid Mul- tiobjective Memetic Metaheuristics for Multiple Sequence Alignment is proposed. In order to evaluate the parallel performance of our proposal, we have selected a pull of datasets with different number of sequences (up to 1000 sequences) and study its parallel performance against other well-known parallel metaheuristics published in the literature, such as MSAProbs, T-Coffee, Clustal Ω, and MAFFT. The comparative study reveals that our parallel aligner is around 25 times faster than the sequen- tial version with 32 cores, obtaining a parallel efficiency around 80%.
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Therapeutic advances in 5q-linked spinal muscular atrophy

Therapeutic advances in 5q-linked spinal muscular atrophy

[29-O-(2-methoxyethyl)] and marketed by Biogen after receiv- ing approval from the Food and Drug Administration in 2016, and the European Medicines Agency in 2017. The intrathe- cal route was considered the best option to deliver the ASO to the spinal motor neurons, and a first study demonstrated safety, tolerability, adequate cerebrospinal fluid levels and, as a side effect, post-puncture syndrome, which is routinely found during treatments for other conditions when using this pathway 31,32 . An open-label phase 2 study of 20 patients with

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Expressiveness modulo Bisimilarity of Regular Expressions with Parallel Composition (Extended Abstract)

Expressiveness modulo Bisimilarity of Regular Expressions with Parallel Composition (Extended Abstract)

Casting our contributions mentioned above in process-theoretic terminology, we establish a strict expressiveness hierarchy on the process theories BPA ∗ 0,1 (A) (regular expressions) modulo bisimilarity, PA ∗ 0,1 (A) (regular expressions with interleaving) modulo bisimilarity and ACP ∗ 0,1 (A, γ) (regular expres- sions with ACP-style parallel composition and encapsulation) modulo bisimilarity. The differences be- tween the process theories BPA δ (A), PA δ (A) and ACP(A, γ ) considered [3, 4] and the process theories BPA ∗ 0,1 (A), PA ∗ 0,1 (A) and ACP ∗ 0,1 (A, γ) considered in this paper are as follows: we write 0 for the con- stant deadlock which is denoted by δ in [3, 4], we include the unary Kleene star instead of its binary variant, and we include a constant 1 denoting the successfully terminated process. The first difference is, of course, cosmetic, and with the addition of the constant 1 the unary and binary variants of Kleene’s star are interdefinable. So, our results pertaining to the relative expressiveness of BPA ∗ 0,1 (A), PA ∗ 0,1 (A) and ACP ∗ 0,1 (A, γ ) extend the expressiveness hierarchy of [3, 4] with the constant 1.
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Rev. Bras. Hematol. Hemoter.  vol.38 número4

Rev. Bras. Hematol. Hemoter. vol.38 número4

Acute promyelocytic leukemia has good prognosis in view of the high complete remission and survival rates achieved with therapies containing all-trans retinoic acid or arsenic tri- oxide. However, there is a significant risk of death during induction due to hemorrhage secondary to disseminated intravascular coagulation. This has contributed to a gap in the prognosis of patients between developed and developing countries. The International Con- sortium on Acute Promyelocytic Leukemia was created in 2005 and proposed a treatment protocol based on daunorubicin and all-trans retinoic acid stratified by risk geared toward developing countries. Herein are presented the results from the first patient cohort treated in a single developing country hospital employing a slightly modified version of the Interna- tional Consortium protocol in a real life setting. Twenty patients with acute promyelocytic leukemia were enrolled: 27.8% had low-risk, 55.6% intermediate risk and 16.7% high-risk. The complete remission rate was 94.4% after a median of 42 days. Both relapse rates and death rates were one patient (5.5%) each. No deaths were observed during consolidation. After a median follow-up of 29 months, the overall survival rate was 89.1%. Efficacy and safety of the International Consortium on Acute Promyelocytic Leukemia protocol has been reproduced in acute promyelocytic leukemia patients from a developing country.
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Exploring Strategies for Parallel Computing of RS Data Assimilation with SWAP-GA

Exploring Strategies for Parallel Computing of RS Data Assimilation with SWAP-GA

Abstract: An agro-hydrological simulation model is useful for agriculture monitoring. One issue in running such model is parameter identification, especially when the target area is large such as provincial or country level. Remote Sensing (RS) provides us with useful information over large area. RS cannot observe input parameters of agro-hydrological models directly. However, a method to estimate input parameters of such model from RS using data assimilation has been proposed by Ines [1] using the SWAP (Soil, Water, Atmosphere and Plant) model. Genetic Algorithm (GA) was used in this optimization process. The combined model of SWAP and GA is called SWAP-GA model. When dealing with sufficiently large and complex processing with RS data, single computers time processing extends to unacceptable limits. It becomes necessary to introduce methods for using higher processing power such as distributed computing. Cluster based computing support both high performance and load balancing parallel or distributed applications. Implementing SWAP-GA in Cluster computers will remove the computational time constraint, with this hypothesis three different parallel SWAP-GA approaches are proposed in this study. Distributed population (where GA will work on distributed manner), Distributed pixel (Pixels are processed in parallel) and Mixed of distributed population and pixel model called Hybrid model. The technical considerations of implementing such methodologies are visited here.
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