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Multi-threaded programming is part of mainstream software development. It adds several issues not present on serial applications. Among the issues an important one is data races, i.e. the unsynchronized access of data by multiple threads. They are particularly hard to debug since they typically occur sporadically and often invisibly corrupt the internal state. Generally, the tool used to identify those kinds of issues is a data race analyzer. Due to the subtlety of data race bugs, the user at this point would already have tried to understand the problem using an application debugger. Debuggers offer a variety of features to analyze and modify the execution state of programs. Such features are typically not offered by data race analyzers. Integrating a data race analyzer into a debugger would improve the user workflow. This is usually prohibited by the huge performance overhead of a whole-program data race analysis. We propose in this work a method to reduce the overhead by allowing the user to define the scope of the analysis. A sufficiently narrow scope reduces the performance overhead to less than 5 $$\times $$ , thus allowing its integration into a debugger. Defining the analysis scope fits naturally into the debugger workflow of focusing on one problem at a time. The work here presented has been implemented in a commercial debugger product. [ABSTRACT FROM AUTHOR]

Abstract: Here we tested whether ‘insular woodiness’, a striking evolutionary pattern that commonly occurs on islands, has also appeared in QTP continental endemics. Parapteropyrum, a monotypic shrubby genus occurring in the central QTP, has been previously placed in the tribe Atraphaxideae of the family Polygonaceae, while all the other woody species of this tribe mainly occur in western and central Asia. We studied sequence variations of nuclear ITS (internal transcribed spacer) and cp (chloroplast) DNA (rbcL and accD) of this genus and the other ten genera. The constructed phylogenies based on ITS, cpDNA or a combination of both datasets, suggest that the woody Parapteropyrum is nested within and most likely evolved from the herbaceous Fagopyrum. We propose that the large-scale uplift of the QTP not only promoted continental species radiation, but also the secondary feature of woodiness in a few herbaceous lineages in response to strong selection pressures, similar to those acting on island flora. In addition, the confirmation of Parapteropyrum within Fagopyrum highlights its potential use as a new, perennial source of buckwheat. [Copyright &y& Elsevier]

Abstract: This paper presents the design and implementation of a parallelization framework and OpenMP runtime support in Intel C++ & Fortran compilers for exploiting nested parallelism in applications using OpenMP pragmas or directives. We conduct the performance evaluation of two multimedia applications parallelized with OpenMP pragmas and compiled with the Intel C++ compiler on Hyper-Threading Technology (HT) enabled multiprocessor systems. The performance results show that the multithreaded code generated by the Intel compiler achieved a speedup up to 4.69 on 4 processors with HT enabled for five different input video sequences for the H.264 encoder workload, and a 1.28 speedup on an HT enabled single-CPU system and 1.99 speedup on an HT-enabled dual-CPU system for the audio–visual speech recognition workload. The performance gain due to exploiting nested parallelism for leveraging Hyper-Threading Technology is up to 70% for two multimedia workloads under different multiprocessor system configurations. These results demonstrate that hyper-threading benefits can be achieved by exploiting nested parallelism through Intel compiler and runtime system support for OpenMP programs. [Copyright &y& Elsevier]

Ranunculaceae is a large family of angiosperms comprising 2500 known species—a few with medicinal and ornamental values. Despite this, only two mitochondrial genomes (mitogenomes) of the family have been released in GenBank. Isopyrum anemonoides is a medicinal plant belonging to the family Ranunculaceae, and its chloroplast genome has recently been reported; however, its mitogenome remains unexplored. In this study, we assembled and analyzed the complete mitochondrial genome of I. anemonoides and performed a comparative analysis against different Ranunculaceae species, reconstructing the phylogenetic framework of Isopyrum. The circular mitogenome of I. anemonoides has a length of 206,722 bp, with a nucleotide composition of A (26.4%), T (26.4%), C (23.6%), and G (23.6%), and contains 62 genes, comprising 37 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. Abundantly interspersed repetitive and simple sequence repeat (SSR) loci were detected in the I. anemonoides mitogenome, with tetranucleotide repeats accounting for the highest proportion of SSRs. By detecting gene migration, we observed gene exchange between the chloroplast and mitogenome in I. anemonoides, including six intact tRNA genes, six PCG fragments, and fragments from two rRNA genes. Comparative mitogenome analysis of three Ranunculaceae species indicated that the PCG contents were conserved and the GC contents were similar. Selective pressure analysis revealed that only two genes (nad1 and rpl5) were under positive selection during their evolution in Ranunculales, and two specific RNA editing sites (atp6 and mttB) were detected in the I. anemonoides mitogenome. Moreover, a phylogenetic analysis based on the mitogenomes of I. anemonoides and the other 15 taxa accurately reflected the evolutionary and taxonomic status of I. anemonoides. Overall, this study provides new insights into the genetics, systematics, and evolution of mitochondrial evolution in Ranunculaceae, particularly I. anemonoides. [ABSTRACT FROM AUTHOR]

Suaeda salsa is an important salt- and drought-tolerant plant with important ecological restoration roles. However, little is known about its underlying molecular regulatory mechanisms. Therefore, understanding the response mechanisms of plants to salt and drought stress is of great importance. In this study, metabolomics analysis was performed to evaluate the effects of salt and drought stress on S. salsa. The experiment consisted of three treatments: (1) control (CK); (2) salt stress (Ps); and (3) drought stress (Pd). The results showed that compared with the control group, S. salsa showed significant differences in phenotypes under salt and drought stress conditions. First, a total of 207 and 292 differential metabolites were identified in the Ps/CK and Pd/CK groups, respectively. Second, some soluble sugars and amino acids, such as raffinose, maltopentoses, D-altro-beptulose, D-proline, valine-proline, proline, tryptophan and glycine-L-leucine, showed increased activity under salt and drought stress conditions, suggesting that these metabolites may be responsible for salt and drought resistance in S. salsa. Third, the flavonoid biosynthetic and phenylalanine metabolic pathways were significantly enriched under both salt and drought stress conditions, indicating that these two metabolic pathways play important roles in salt and drought stress resistance in S. salsa. The findings of this study provide new insights into the salt and drought tolerance mechanisms of S. salsa. This study used liquid chromatography-mass spectrometry (LC-MS) to study the changes of small molecule metabolites of Suaeda salsa under salt and drought stress. We showed the main metabolites and metabolic pathways that changed under salt and drought stress environments, and revealed the molecular responses of S. salsa in response to salt and drought from the level of metabolomics. [ABSTRACT FROM AUTHOR]

Range expansion caused by climate oscillations in the past probably promoted morphological radiation in a few plant groups. In this study, we aim to test this hypothesis through phylogeographical analysis of the cold-tolerant fir genus ( A bies) in the Qinghai- Tibet Plateau ( QTP) and Himalayas, where it comprises 12 described species. We examined sequence variation in two maternally inherited mitochondrial (mt) DNA fragments ( nad5-4 and nad7-1) and two paternally inherited plastid DNA fragments ( trnS- G and trnL- F) for 733 individuals from 75 populations of the species in a monophyletic group. Only six mtDNA haplotypes were recovered, but five were shared between multiple species and one occurred at a high frequency, providing strong evidence of range expansion. Forty-three plastid DNA haplotypes were detected, 19 of which were shared between species and three occurred at high frequency. Network, mismatch and Bayesian skyline plot analyses of all plastid DNA haplotypes from this clade clearly suggested range expansion. This expansion was dated as having occurred during the longest and most extensive glaciation in the Pleistocene. Our results therefore supported the range expansion hypothesis for this clade of A bies during the Pleistocene; expansion probably drove the morphological radiation of the clade in the QTP and Himalayas, although it remains unclear whether the different morphotypes should be acknowledged as independent, reproductively isolated species. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179, 444-453. [ABSTRACT FROM AUTHOR]

• Three diploid-containing sections of Enkianthus (Meisteria, Andromedina and Enkianthus) are monophyletic groups. • Sect. Enkiantella in China likely arose from allopolyploidy, their diploid progenitors may be members of sect. Meisteria and sect. Andromedina. • E. tubulatus may be a diploid species of hybrid origin. Enkianthus is a small genus of Ericaceae mostly in east Asia, most constituent species with important ornamental and ecological values. Due to limited sampling of Chinese species and neglect of the origin of polyploid species in previous studies, phylogenetic relationships within this genus remain elusive. Using six chloroplast DNA fragments (psb A- trn H, rpl 32- trn L, trn L- trn F, rps 16- trn Q, psb J- pet A and mat K), nuclear ribosomal internal transcribed spacer (nrITS) and one single-copy nuclear gene (OG9899), we reconstructed the phylogenetic relationships of most Enkianthus species, with a special attempt to decipher the origin of polyploids within the genus. The phylogenetic trees excluding polyploid species indicated that the sections of Meisteria, Andromedina and Enkianthus were all monophyletic groups, with sect. Enkianthus first branching out. The position of E. tubulatus was in conflict between cpDNA and nuclear gene trees, indicating that this species could be of hybrid origin. After the inclusion of polyploid species, we found that members of sect. Enkiantella clustered either with sect. Meisteria or with sect. Andromedina in nuclear gene trees , suggesting this section might be derived from allopolyploidy. The close affinity of sect. Enkiantella with sect. Meisteria in cpDNA tree implies that the members of sect. Meisteria might be the maternal progenitor of sect. Enkiantella. In addition, the octoploid species E. campanulatus might be either an autopolyploid or an allopolyploid with one of its progenitors originating from sect. Meisteria. Our findings provide a robust phylogenetic framework for the evolutionary study and the utility of germplasm resources of Enkianthus. The results of this study will also be helpful for the breeding of Enkianthus cultivars. [ABSTRACT FROM AUTHOR]

The complexity of modern processors poses increasingly more difficult challenges to software optimization. Modern optimizing compilers have become essential tools for leveraging the power of recent processors by means of high-level optimizations to exploit multi-core platforms and single-instruction-multiple-data (SIMD) instructions, as well as advanced code generation to deal with microarchitectural performance aspects. Using the Intel® CoreTM 2 Duo processor and Intel Fortran/C++ compiler as a case study, this paper gives a detailed account of the sort of optimizations required to obtain high performance on modern processors. [ABSTRACT FROM AUTHOR]

Protein secondary structure prediction has a fundamental influence on today’s bioinformatics research. In this work, tertiary classifiers for the protein secondary structure prediction are implemented on Denoeux Belief Neural Network (DBNN) architecture. Hydrophobicity matrix, orthogonal matrix, BLOSUM62 matrix and PSSM matrix are experimented separately as the encoding schemes for DBNN. Hydrophobicity matrix, BLOSUM62 matrix and PSSM matrix are applied to DBNN architecture for the first time. The experimental results contribute to the design of new encoding schemes. Our accuracy of the tertiary classifier with PSSM encoding scheme reaches 72.01%, which is almost 10% better than the previous results obtained in 2003. Due to the time consuming task of training the neural networks, Pthread and OpenMP are employed to parallelize DBNN in the Hyper-Threading enabled Intel architecture. Speedup for 16 Pthreads is 4.9 and speedup for 16 OpenMP threads is 4 in the 4 processors shared memory architecture. Both speedup performance of OpenMP and Pthread is superior to that of other research. With the new parallel training algorithm, thousands of amino acids can be processed in reasonable amount of time. Our research also shows that Hyper-Threading technology for Intel architecture is efficient for parallel biological algorithms. [ABSTRACT FROM AUTHOR]

Recent extensions to the Intel® Architecture feature the SIMD technique to enhance the performance of computational intensive applications that perform the same operation on different elements in a data set. To date, much of the code that exploits these extensions has been hand-coded. The task of the programmer is substantially simplified, however, if a compiler does this exploitation automatically. The high-performance Intel® C++/Fortran compiler supports automatic translation of serial loops into code that uses the SIMD extensions to the Intel® Architecture. This paper provides a detailed overview of the automatic vectorization methods used by this compiler together with an experimental validation of their effectiveness. [ABSTRACT FROM AUTHOR]