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In this paper, a source to source parallelizing complier system, AutoPar, is presentd. The system transforms FORTRAN programs to multi-level hybrid MPI/OpenMP parallel programs. Integrated parallel optimizing technologies are utilized extensively to derive an effective program decomposition in the whole program scope. Other features such as synchronization optimization and communication optimization improve the performance scalability of the generated parallel programs, from both intra-node and inter-node. The system makes great effort to boost automation of parallelization. Profiling feedback is used in performance estimation which is the basis of automatic program decomposition. Performance results for eight benchmarks in NPB1.0 from NAS on an SMP cluster are given, and the speedup is desirable. It is noticeable that in the experiment, at most one data distribution directive and a reduction directive are inserted by the user in BT/SP/LU. The compiler is based on ORC, Open Research Compiler. ORC is a powerful compiler infrastructure, with such features as robustness, flexibility and efficiency. Strong analysis capability and well-defined infrastructure of ORC make the system implementation quite fast.

Purpose: To investigate whether secreted phosphoprotein-1iSPP1j promoter variants are associated with susceptibility to ankylosing spondylitis (AS) in the western China.Methods: The rs5860110 variant of SPP1 promoter was genotyped using direct sequencing in 120 unrelated AS patients and 106 ethnically matched healthy controls. All the patients were human leukocyte antigen iHLAj-B27 positive. Frequencies of different genotypes and alleles were analyzedamong the AS patients and the controls.Results: In AS patient group, frequency of +254 SPP1 promoter genotype was 0.483 in base TG/TG homozygotes and 0.517 in TG-(deletion)/TG-(deletion) homozygotes, while the values for the control group were 0.311 and 0.689, respectively. However, TG-(deletion)/TG heterozygote was not detected in this study. The rs5860110 single nucleotide polymorphism (SNP) in SPP1 was significantly different when all AS patients were compared to controls (p < 0.01).Conclusion: The rs5860110 SNP in SPP1 has a protective role against AS in the selected Chinese population.Keywords: Polymorphism, Ankylosing spondylitis, Secreted phosphoprotein-1, Sequencing, Genotype, Alleles

To initiate homologous recombination, sequence similarity between two DNA molecules must be searched for and homology recognized. How the search for and recognition of homology occurs remains unproven. We have examined the influences of DNA topology and the polarity of RecA–single-stranded (ss)DNA filaments on the formation of synaptic complexes promoted by RecA. Using two complementary methods and various ssDNA and duplex DNA molecules as substrates, we demonstrate that topological constraints on a small circular RecA–ssDNA filament prevent it from interwinding with its duplex DNA target at the homologous region. We were unable to detect homologous pairing between a circular RecA–ssDNA filament and its relaxed or supercoiled circular duplex DNA targets. However, the formation of synaptic complexes between an invading linear RecA–ssDNA filament and covalently closed circular duplex DNAs is promoted by supercoiling of the duplex DNA. The results imply that a triplex structure formed by non-Watson–Crick hydrogen bonding is unlikely to be an intermediate in homology searching promoted by RecA. Rather, a model in which RecA-mediated homology searching requires unwinding of the duplex DNA coupled with local strand exchange is the likely mechanism. Furthermore, we show that polarity of the invading RecA–ssDNA does not affect its ability to pair and interwind with its circular target duplex DNA.

One of the most intellectual steps in compiling for distributed memory parallel machines is to determine a suitable data partitioning scheme for a particular program. Most of the parallelizing compilers for these machines provide no or little support to the user in this difficult task. We have developed DPART, an automatic data partitioning system for Fortran 77 procedures. This paper describes the partitioning strategics of alignment, distribution, and processor layout in DPART. Finally we present experimental results for TRED2, DGEFA, and JACOBI procedures to demonstrate the effectiveness of this system.

A set of methods for interprocedural analysis is proposed. First, an approach for interprocedural constant propagation is given. Then the concept of constant propagation is extended so as to meet the needs of data dependence analysis. Besides certain constant, constant range can also be propagated. The related propagating rules are introduced, and an idea for computing Return function is given. This approach can solve almost all interprocedural constant propagation problems with non-recursive calls. Second, a multiple-version parallelizing technique is also proposed for alias problem. The work related to this paper has been implemented on a shared-memory parallel computer.

Machine translation (MT), with its broad potential use, has gained increased attention from both researchers and software vendors. To generate high quality translations, however, MT decoders can be highly computation intensive. With significant raw computing power, multi-core microprocessors have the potential to speed up MT software on desktop machines. However, retrofitting existing MT decoders is a nontrivial issue. Race conditions and atomicity issues are among those complications making parallelization difficult. In this article, we show that, to parallelize a state-of-the-art MT decoder, it is much easier to overcome such difficulties by using a process-based parallelization method, called functional task parallelism, than using conventional thread-based methods. We achieve a 7.60 times speed up on an 8-core desktop machine while making significantly less changes to the original sequential code than required by using multiple threads.

The problem of M activities of NM > parallel activities being adjusted to a procedure chain is one type of the project scheduling. In allusion to 3 M = , a new polynomial algorithm is proposed to minimize the total tardiness criterion. In order to present this algorithm, and search the optimal procedure chain, we propose a Normal Chain Theory by virtue of the relationships of activities' time parameters, together with the properties that the optimal chain contains the activities with the minimum of earliest finish time. By the analysis of this algorithm, we get the time complexity is (l og ) ON N.

ATP-dependent chromatin-remodeling enzymes are linked to changes in gene expression; however, it is not clear how the multiple remodeling enzymes found in eukaryotes differ in function and work together. In this report, we demonstrate that the ATP-dependent remodeling enzymes ACF and Mi2β can direct consecutive, opposing chromatin-remodeling events, when recruited to chromatin by different transcription factors. In a cell-free system based on the immunoglobulin heavy chain gene enhancer, we show that TFE3 induces a DNase I-hypersensitive site in an ATP-dependent reaction that requires ACF following transcription factor binding to chromatin. In a second step, PU.1 directs Mi2β to erase an established DNase I-hypersensitive site, in an ATP-dependent reaction subsequent to PU.1 binding to chromatin, whereas ACF will not support erasure. Erasure occurred without displacing the transcription factor that initiated the site. Other tested enzymes were unable to erase the DNase I-hypersensitive site. Establishing and erasing the DNase I-hypersensitive site required transcriptional activation domains from TFE3 and PU.1, respectively. Together, these results provide important new mechanistic insight into the combinatorial control of chromatin structure.

On today's microprocessors, there often exist several different types of registers, e.g. general purpose registers and floating point registers. A given program may use one type of registers much more frequently than other types. This creates an opportunity to employ the infrequently used registers as spill destinations for the more frequently used register types. In this paper, we present a code optimization method named idle register exploitation (IRE) to exploit such opportunities. We developed a model, called the IRE model, or IREM, to determine the static performance gains of IRE versus spilling to the stack. On a microprocessor with fast data paths between different types of registers, we find that IRE method speeds up the execution of the SPECint benchmark suite from 1.7% to 10%. In contrast, on microprocessors with less efficient data transfer paths, the performance gain is limited. In some cases, performance may even suffer degradation. This result argues strongly for the adoption of fast data paths between different types of registers for the purpose of reducing register spills, which is important in view of the increased significance of memory bottlenecks on future microprocessors.

The Open Research Compiler (ORC), jointly developed by Intel Microprocessor Technology Labs and the Institute of Computing Technology at Chinese Academy of Sciences, has become the leading open source compiler on the ItaniumTM Processor Family (IPF, previously known as IA-64). Since its first release in 2002, it has been widely used in academia and industry worldwide as a compiler and architecture research infrastructure and as code base for further development. In this paper, we present an overview of the design of the major components in ORC, especially those new features in the code generator. We discuss the development methodology that is important to achieving the objectives of ORC. Performance comparisons with other IPF compilers and a brief summary of the research work based on ORC are also presented.

In this paper we develop a new region-based compilation framework driven by the considerations of performance opportunities and compilation resources. In addition, we allow some optimization-directed attributes communicated from one optimization phase to another on a region basis to guide subsequent optimizations. This region-based framework has been implemented in the Open Research Compiler targeting Itanium/sup /spl reg// Processor Family (IPF). Experimental results from the SPEC2000Int programs show that this infrastructure provides an effective control on forming regions to meet the requirements of different optimizations. For example, the compilation time of instruction scheduling is significantly reduced by this region formation infrastructure while preserving or improving the overall performance. At the highest optimization level, the performance of one program has a 15.6% improvement by employing this region-based infrastructure.

Maximizing parallelism and minimizing communication overheads are important issues on distributed-memory systems. This paper presents a communication optimization technique named redundant computation partitioning, and also gives its implementation. The main idea is to select computation redundancy, represented by a redundant vector, properly for each partitioned loop nest in a parallel loop sequence, so as to acquire a larger parallel region. The technique can eliminate inter-loop communications which will be introduced using ordinary computation partitionings. Some data redistribution points may be eliminated, so the global deduction of data and computation partition can be simplified.

A hardware managed register stack, Register Stack Engine (RSE), is implemented in Itanium® architecture to provide a unified and flexible register structure to software. The compiler allocates each procedure a register stack frame with its size explicitly specified using an alloc instruction. When the total number of registers used by the procedures on the call stack exceeds the number of physical registers, RSE performs automatically register overflows and fills to ensure that the current procedure has its requested registers available. The virtual register stack frames and RSE alleviate the need of explicit spills by the compiler, but our experimental results indicate that a trade-off exists between using stacked registers and explicit spills under high register pressure due to the uneven cost between them. In this work, we introduce the stacked register quota assignment problem based on the observation that reducing stacked register usage in some procedures could reduce the total memory access time of spilling registers, which includes the time caused by the loads/stores due to explicit register spills and RSE overflows/fills. We propose a new inter-procedural algorithm to solve the problem by allocating stacked registers across procedures based on a quantitative cost model. The results show that our approach can improve performance significantly for the programs with high RSE overflow cost, e.g. perlbmk and crafty, improved by 14% and 3.7%, respectively.

Program languages with sophisticated usage of pointers as C are hard to analyze. Recent researches on pointer analysis focus on tracking the possible values of pointers, when a program point is reached, and great progress has been achieved. However, how to apply the result of pointer analysis to dataflow analysis and other program optimization/parallelization is not well studied. This paper presents an efficient interprocedural framework based on two insights in real C program and its use in deriving an context-sensitive pointer analysis algorithm and an accurate interprocedural modification side effects (MOD) computation. Based on the result of the pointer analysis, the inaccuracy induced by merging aliasing information is also studied.

We report the first experimental observation of anisotropic magnetocaloric effect (MCE) in the Fe8 clusters. It is found that the magnetic anisotropy plays a very important role in the determination of the magnetocaloric effect. The maximum and minimum MCE's are observed when the applied magnetic fields are parallel and perpendicular to the easy axis, respectively. The quantum spin Hamiltonian of a Fe8 cluster is used to calculate the partition function and the magnetization in a range of temperature and magnetic field. Excellent quantitative agreement between the experimental data and calculation is observed.

The DNA-dependent ATPase activity of the Escherichia coli RecA protein has been recognized for more than two decades. Yet, the role of ATP hydrolysis in the RecA-promoted strand exchange reaction remains unclear. Here, we demonstrate that ATP hydrolysis is required as part of a proofreading process during homology recognition. It enables the RecA-ssDNA complex, after determining that the strand-exchanged duplex is mismatched, to dissociate from the synaptic complex, which allows it to re-initiate the search for a "true" homologous region. Furthermore, the results suggest that when non-homologous sequences are present at the proximal end, ATP hydrolysis is required to allow ssDNA-RecA to reinitiate the strand exchange from an internal homologous region.

Despite its merits, software DSM has a serious drawback, that is, over-simplified data distribution schemes. Most software DSM systems are page-based and often fail to exactly satisfy the data partition required by the programmer and cause a serious communication overhead. In order to reduce communication cost incurred by the limitation of the underlying DSM system, we present two communicative primitives to easier utilize software pipelining, giving good legibility to paralellized code. We performed software pipelining on appbt, a program in the NAS benchmark, on a software DSM called JIAJIA. Experiments show that the speed-up is greatly improved.

This paper presents a compiler algorithm for the distributed memory machines that automatically finds an optimal partitioning for the arrays and loops in a whole program at the presence of procedural calls. In this framework, the whole program is formulated as interprocedural iterations and data graph (IDG), and the interprocedural search space propagation and synthesis technique is proposed to determine an optimal search space of the loops and data partitioning. Based on the performance estimation model, the interprocedural candidate selection algorithm using dynamic programming technique is proposed to determine an optimal partitioning of the loops and data in the program. These ideas are adopted into the design and implementation of a parallelizing compiler targeted on the SIMD machines. We demonstrate the efficiency of this framework with encouraging experimental results.

It has been shown in vitro thatSaccharomyces cerevisiae strand exchange protein 1 (Sep1) promotes the transfer of one strand of a linear duplex DNA to a homologous single-stranded DNA circle. Sep1 also has an exonuclease active on DNA and RNA. By using exonuclease III-treated linear duplex DNA with various lengths of single-stranded tail as well as Ca2+ to inhibit the exonuclease activity of Sep1, we show that the processivity of exonuclease activity of Sep1 is greater than previously reported. The results in this work also demonstrate that the joint molecule between the linear duplex and single-stranded circle observed from the Sep1-promoted strand transfer reaction is just the pairing between the long single-stranded tail of the linear duplex DNA (generated by the exonuclease activity of Sep1) and the single-stranded circular DNA. When a synthetic Holliday junction was used as substrate, branch migration facilitated by Sep1 could not be detected. Finally, using electron microscopy no α-structure, a joint molecule with displaced single-stranded DNA tail that indicates branch migration could be observed. The results imply that Sep1 cannot promote branch migration in vitro. Further investigation is needed to determine the role of Sep1 in recombination in vivo.

The rigorous proof of the relation det A ( L ) = - [ ∏ i = 1 L q i i ] ( 1 + q 1 f L ( q 1 , q 2 ⋯ , q L ) ) is given. This relation has been used to obtain the exact critical surface and the correlation length exponents of the one-dimensional directed bond percolation problem with bonds connecting 1~Lth nearest neighbours. A(L) is related to the transfer-matrix by (7). qi is related to the occupation probability of the i-th nearest neighbour bond pi by qi=1–pi (i=1, 2, …, L). fL is a multi-variable polynomial in qi’s.

A first principle calculation is performed to investigate the electronic and the thermodynamic properties of a dimer in a potential characterized by the random site energy and the random screening length. The exact Hamiltonian from which the extended Hubbard model Hamiltonian is derived is formulated. All the coupling constants are calculated systematically using the analytical eigenfunctions. The breaking of the electron-hole symmetry leads to a temperature dependent chemical potential and so affects the thermoelectric power. In terms of the strengths of the coupling constants, the model Hamiltonian does not well approximate the exact Hamiltonian; and in terms of the properties of the eigensolutions, the model Hamiltonian does not yield a strong enough “band-narrowing” and therefore does not predict the correct low-temperature thermodynamical properties. The key conclusion also holds for bulk systems. Theoretical results can be applied to strongly dimerized charge-transfer salts such as BIP(TCNQ) 2 .

SummaryAlthough human induced pluripotent stem cells (hiPSCs) have enormous potential in regenerative medicine, their epigenetic variability suggests that some lines may not be suitable for human therapy. There are currently few benchmarks for assessing quality. Here we show that X-inactivation markers can be used to separate hiPSC lines into distinct epigenetic classes and that the classes are phenotypically distinct. Loss of XIST expression is strongly correlated with upregulation of X-linked oncogenes, accelerated growth rate in vitro, and poorer differentiation in vivo. Whereas differences in X-inactivation potential result in epigenetic variability of female hiPSC lines, male hiPSC lines generally resemble each other and do not overexpress the oncogenes. Neither physiological oxygen levels nor HDAC inhibitors offer advantages to culturing female hiPSC lines. We conclude that female hiPSCs may be epigenetically less stable in culture and caution that loss of XIST may result in qualitatively less desirable stem cell lines.