bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiple sequence elements and a maternal mRNA product control cdk2 RNA polyadenylation and translation during early Xenopus development.
Authors: Stebbins-Boaz B , Richter J D
Published: January 2012

Cytoplasmic poly(A) elongation is one mechanism that regulates translational recruitment of maternal mRNA in early development. In Xenopus laevis, poly(A) elongation is controlled by two cis elements in the 3' untranslated regions of responsive mRNAs: the hexanucleotide AAUAAA and a U-rich structure with the general sequence UUUUUAAU, which is referred to as the cytoplasmic polyadenylation element (CPE). B4 RNA, which contains these sequences, is polyadenylated during oocyte maturation and maintains a poly(A) tail in early embryos. However, cdk2 RNA, which also contains these sequences, is polyadenylated during maturation but deadenylated after fertilization. This suggests that cis-acting elements in cdk2 RNA signal the removal of the poly(A) tail at this time. By using poly(A) RNA-injected eggs, we showed that two elements which reside 5' of the CPE and 3' of the hexanucleotide act synergistically to promote embryonic deadenylation of this RNA. When an identical RNA lacking a poly(A) tail was injected, these sequences also prevented poly(A) addition. When fused to CAT RNA, the cdk2 3' untranslated region, which contains these elements, as well as the CPE and the hexanucleotide, promoted poly(A) addition and enhanced chloramphenicol acetyltransferase activity during maturation, as well as repression of these events after fertilization. Incubation of fertilized eggs with cycloheximide prevented the embryonic inhibition of cdk2 RNA polyadenylation but did not affect the robust polyadenylation of B4 RNA. This suggests that a maternal mRNA, whose translation occurs only after fertilization, is necessary for the cdk2 deadenylation or inhibition of RNA polyadenylation. This was further suggested when poly(A)+ RNA isolated from two-cell embryos was injected into oocytes that were then allowed to mature. Such oocytes became deficient for cdk2 RNA polyadenylation but remained proficient for B4 RNA polyadenylation. These data show that CPE function is developmentally regulated by multiple sequences and factors.
Genetic analysis of a phosphatidylinositol 3-kinase SH2 domain reveals determinants of specificity.
Authors: Yoakim M , Hou W , Songyang Z , Liu Y , Cantley L , Schaffhausen B
Published: January 2012

Phosphatidylinositol 3-kinase is an important element in both normal and oncogenic signal transduction. Polyomavirus middle T antigen transforms cells in a manner depending on association of its tyrosine 315 phosphorylation site with Src homology 2 (SH2) domains on the p85 subunit of the phosphatidylinositol 3-kinase. Both nonselective and site-directed mutagenesis have been used to probe the interaction of middle T with the N-terminal SH2 domain of p85. Most of the 24 mutants obtained showed reduced middle T binding. However, mutations that showed increased binding were also found. Comparison of middle T binding to that of the platelet-derived growth factor receptor showed that some mutations altered the specificity of recognition by the SH2 domain. Mutations altering S-393, D-394, and P-395 were shown to affect the ability of the SH2 domain to select peptides from a degenerate phosphopeptide library. These results focus attention on the role of the EF loop in the SH2 domain in determining binding selectivity at the third position after the phosphotyrosine.
A small family of elements with long inverted repeats is located near sites of developmentally regulated DNA rearrangement in Tetrahymena thermophila.
Authors: Wells J M , Ellingson J L , Catt D M , Berger P J , Karrer K M
Published: January 2012

Extensive DNA rearrangement occurs during the development of the somatic macronucleus from the germ line micronucleus in ciliated protozoans. The micronuclear junctions and the macronuclear product of a developmentally regulated DNA rearrangement in Tetrahymena thermophila, Tlr1, have been cloned. The intrachromosomal rearrangement joins sequences that are separated by more than 13 kb in the micronucleus with the elimination of moderately repeated micronucleus-specific DNA sequences. There is a long, 825-bp, inverted repeat near the micronuclear junctions. The inverted repeat contains two different 19-bp tandem repeats. The 19-bp repeats are associated with each other and with DNA rearrangements at seven locations in the micronuclear genome. Southern blot analysis is consistent with the occurrence of the 19-bp repeats within pairs of larger repeated sequences. Another family member was isolated. The 19-mers in that clone are also in close proximity to a rearrangement junction. We propose that the 19-mers define a small family of developmentally regulated DNA rearrangements having elements with long inverted repeats near the junction sites. We discuss the possibility that transposable elements evolve by capture of molecular machinery required for essential cellular functions.
Activation of AP-1 and of a nuclear redox factor, Ref-1, in the response of HT29 colon cancer cells to hypoxia.
Authors: Yao K S , Xanthoudakis S , Curran T , O'Dwyer P J
Published: January 2012

Many solid tumors contain substantial fractions of hypoxic cells which are relatively resistant to both radiation therapy and certain cytotoxic drugs. We have previously shown that exposure of human HT29 cells to hypoxic conditions results in the overexpression of certain enzymes involved in the detoxication of xenobiotics, including NAD(P)H:(quinone acceptor) oxidoreductase (DT)-diaphorase, and gamma-glutamylcysteine synthetase, the rate-limiting enzyme in glutathione synthesis. This hypoxic effect on DT-diaphorase was shown to involve both transcriptional induction and altered message stability. We have investigated the effects of hypoxia on elements in the promoter region of DT-diaphorase. Electrophoretic mobility shift assays demonstrate the induction of a binding activity to the AP-1 response element of DT-diaphorase. Supershift assays suggest that this binding is due to AP-1 nuclear factors and that members of the jun family are induced to a greater degree than fos by hypoxia. Analysis of the kinetics of transcription factor expression indicates that the expression of c-jun and junD is induced during hypoxic exposure; mRNA levels fall during reoxygenation. Induction of fos on the other hand is not as florid during hypoxia (5-fold) and is most pronounced (17-fold) 24 h after the restoration of an oxic environment. Thus, the hypoxic response of DT-diaphorase expression is mediated in part through AP-1, initially by a jun-related mechanism and then by the involvement of fos. The affinity of transcription factors for the AP-1 binding site depends on the redox state of a cysteine residue located close to the DNA-binding region of both Fos and Jun. A nuclear protein, Ref-1, maintains the reduced state of Fos and Jun and promotes binding to AP-1. Nuclear extracts of HT29 cells exposed to hypoxia show markedly increased Ref-1 protein content. Elevation of ref-1 steady-state mRNA levels occurs as an early event following induction of hypoxia and persists when cells are restored to a normally oxygenated environment. Nuclear run-on analysis demonstrates that induction of transcription is the mechanism of ref-1 mRNA elevation. Electrophoretic mobility shift assays and immunodepletion assays were used to further define the interaction of Ref-1 with specific AP-1-binding proteins under hypoxic conditions. These data demonstrate that the induction of detoxicating enzyme expression in HT29 cells exposed to hypoxia results from the induction of both transactivating factors that bind to the AP-1 element and of redox proteins that enhance their affinity for this element.
Characterization of a delayed early serum response region.
Authors: Groskopf J C , Linzer D I
Published: January 2012

The proliferin (PLF) gene promoter provides a relatively simple model system for the study of growth-regulated gene expression in mouse cells. The promoter elements required for this serum-induced regulation have been identified and include an AP-1 site as well as an adjacent element comprised of three imperfect repeats that are similar in sequence to the simian virus 40 (SV40) Sph motif. Distinct protein complexes bound independently to the AP-1 and Sph elements, and both of these juxtaposed sites could be occupied simultaneously. Furthermore, serum stimulation of mouse fibroblasts resulted in similar increases in protein binding to the AP-1 and Sph elements. Consistent with this increase in AP-1 and Sph binding activity, the PLF AP-1 and Sph elements were independently able to confer serum responsiveness to a minimal promoter, and together these two elements acted synergistically in response to serum. Although several members of the AP-1 family were able to activate the PLF gene promoter in transient cotransfection experiments, the predominant AP-1 components interacting with the PLF gene promoter in serum-stimulated cells were Fra-1, JunB, and JunD. Analysis of the Sph element revealed that mutation of Sph repeats I or III abolished serum responsiveness of the PLF gene promoter, and mutation of Sph repeat III decreased protein binding to this element. Although the Sph element is similar in sequence to the SV40 element, the PLF Sph-binding factor is distinct from TEF-1, the factor that binds to the SV40 Sph motif.
Mutation of the gene encoding protein kinase C 1 stimulates mitotic recombination in Saccharomyces cerevisiae.
Authors: Huang K N , Symington L S
Published: January 2012

We have isolated a recessive allele of the yeast protein kinase C gene (PKC1) which promotes an elevated rate of mitotic recombination and confers a temperature-sensitive growth defect. The rate of recombination was increased between genes in direct repeat and at a series of heteroalleles and was dependent upon the RAD52 gene product. The mutant pkc1 allele was sequenced and found to encode a single amino acid change within the catalytic domain. Osmotic stabilizing agents rescued the temperature-sensitive growth defect but not the hyperrecombination phenotype, indicating that the two traits are separable. This separability suggests that the PKC1 gene product (Pkc1p) regulates DNA metabolism by an alternate pathway to that used in the regulation of cell lysis. The regulation of recombination is a previously unidentified role for Pkc1p.
Identification of functional domains of the aryl hydrocarbon receptor nuclear translocator protein (ARNT).
Authors: Reisz-Porszasz S , Probst M R , Fukunaga B N , Hankinson O
Published: January 2012

The activated aryl hydrocarbon receptor (AHR) and the AHR nuclear translocator (ARNT) bind DNA as a heterodimer. Both proteins represent a novel class of basic helix-loop-helix (bHLH)-containing transcription factors in that (i) activation of AHR requires the binding of ligand (e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin [TCDD]), (ii) the xenobiotic responsive element (XRE) recognized by the AHR/ARNT heterodimer differs from the recognition sequence for nearly all other bHLH proteins, and (iii) both proteins contain a PAS homology region, which in the Drosophila PER and SIM proteins functions as a dimerization domain. A cDNA for mouse ARNT has been cloned, and potential functional domains of ARNT were investigated by deletion analysis. A mutant lacking all regions of ARNT other than the bHLH and PAS regions is unimpaired in TCDD-dependent dimerization and subsequent XRE binding and only modestly reduced in ability to complement an ARNT-deficient mutant cell line, c4, in vivo. Both the first and second alpha helices of the bHLH region are required for dimerization. The basic region is required for XRE binding but not for dimerization. Deletion of either the A or B segments of the PAS region slightly affects TCDD-induced heterodimerization, while deletion of the complete PAS region severely affects (but does not eliminate) dimerization. Thus, ARNT possesses multiple domains required for maximal heterodimerization. Mutants deleted for PAS A, PAS B, and the complete PAS region all retain some degree of XRE binding, yet none can rescue the c4 mutant. Therefore, both the PAS A and PAS B segments, besides contributing to dimerization, apparently fulfill additional, unknown functions required for biological activity of ARNT.
petD mRNA maturation in Chlamydomonas reinhardtii chloroplasts: role of 5' endonucleolytic processing.
Authors: Sakamoto W , Sturm N R , Kindle K L , Stern D B
Published: January 2012

Complex processing of primary transcripts occurs during the expression of higher-plant chloroplast genes. In Chlamydomonas reinhardtii, most chloroplast genes appear to possess their own promoters, rather than being transcribed as part of multicistronic operons. By generating specific deletion mutants, we show that petD, which encodes subunit IV of the cytochrome b6/f complex, has an RNA processing site that is required for accumulation of monocistronic petD mRNA in petD promoter deletion mutants; in such mutants, transcription of petD originates from the upstream petA promoter. The 5' ends of transcripts initiated at the petD promoter are probably also generated by processing, since the 5' end of monocistronic petD mRNA is the same in wild-type strains as it is in the petD promoter mutants. The location and function of the processing site were further examined by inserting petD-uidA fusion genes into the chloroplast genome (uidA is an Escherichia coli gene that encodes beta-glucuronidase). When a promoterless petD-uidA fusion gene was inserted downstream of petA, a monocistronic uidA transcript accumulated, which was apparently initiated at the petA promoter and was processed at a site corresponding precisely to the petD mRNA 5' end. When a construct including only sequences downstream of +25 relative to the mature mRNA 5' end was inserted into the same site, a dicistronic petA-uidA transcript accumulated but no monocistronic uidA transcript could be detected, suggesting that a processing site lies at least partially within the region from -1 to +25. Beta-glucuronidase activity was not detected in transformants that accumulated only the dicistronic petA-uidA transcript, suggesting that the first 25 bp of the 5' untranslated region are required for translation initiation. One explanation for this translational defect is that Chlamydomonas chloroplasts cannot translate the second coding region of some dicistronic messages.
Dimerization through the helix-loop-helix motif enhances phosphorylation of the transcription activation domains of myogenin.
Authors: Zhou J , Olson E N
Published: January 2012

The muscle-specific basic helix-loop-helix (bHLH) protein myogenin activates muscle transcription by binding to target sequences in muscle-specific promoters and enhancers as a heterodimer with ubiquitous bHLH proteins, such as the E2A gene products E12 and E47. We show that dimerization with E2A products potentiates phosphorylation of myogenin at sites within its amino- and carboxyl-terminal transcription activation domains. Phosphorylation of myogenin at these sites was mediated by the bHLH region of E2A products and was dependent on dimerization but not on DNA binding. Mutations of the dimerization-dependent phosphorylation sites resulted in enhanced transcriptional activity of myogenin, suggesting that their phosphorylation diminishes myogenin's transcriptional activity. The ability of E2A products to potentiate myogenin phosphorylation suggests that dimerization induces a conformational change in myogenin that unmasks otherwise cryptic phosphorylation sites or that E2A proteins recruit a kinase for which myogenin is a substrate. That phosphorylation of these dimerization-dependent sites diminished myogenin's transcriptional activity suggests that these sites are targets for a kinase that interferes with muscle-specific gene expression.
Differential transformation of mammary epithelial cells by Wnt genes.
Authors: Wong G T , Gavin B J , McMahon A P
Published: January 2012

The mouse Wnt family includes at least 10 genes that encode structurally related secreted glycoproteins. Wnt-1 and Wnt-3 were originally identified as oncogenes activated by the insertion of mouse mammary tumor virus in virus-induced mammary adenocarcinomas, although they are not expressed in the normal mammary gland. However, five other Wnt genes are differentially expressed during development of adult mammary tissue, suggesting that they may play distinct roles in various phases of mammary gland growth and development. Induction of transformation by Wnt-1 and Wnt-3 may be due to interference with these normal regulatory events; however, there is no direct evidence for this hypothesis. We have tested Wnt family members for the ability to induce transformation of cultured mammary cells. The results demonstrate that the Wnt gene family can be divided into three groups depending on their ability to induce morphological transformation and altered growth characteristics of the C57MG mammary epithelial cell line. Wnt-1, Wnt-3A, and Wnt-7A were highly transforming and induced colonies which formed and shed balls of cells. Wnt-2, Wnt-5B, and Wnt-7B also induced transformation but with a lower frequency and an apparent decrease in saturation density. In contrast, Wnt-6 and two other family members which are normally expressed in C57MG cells, Wnt-4 and Wnt-5A, failed to induce transformation. These data demonstrate that the Wnt genes have distinct effects on cell growth and should not be regarded as functionally equivalent.
Structure of REC2, a recombinational repair gene of Ustilago maydis, and its function in homologous recombination between plasmid and chromosomal sequences.
Authors: Rubin B P , Ferguson D O , Holloman W K
Published: January 2012

Mutation in the REC2 gene of Ustilago maydis leads to defects in DNA repair, recombination, and meiosis. Analysis of the primary sequence of the Rec2 protein reveals a region with significant homology to bacterial RecA protein and to the yeast recombination proteins Dmc1, Rad51, and Rad57. This homologous region in the U. maydis Rec2 protein was found to be functionally sensitive to mutation, lending support to the hypothesis that Rec2 has a functional RecA-like domain essential for activity in recombination and repair. Homologous recombination between plasmid and chromosomal DNA sequences is reduced substantially in the rec2 mutant following transformation. The frequency can be restored to a level approaching, but not exceeding, that observed in the wild-type strain if transformation is performed with cells containing multiple copies of REC2.
A novel DNA replication origin identified in the human heat shock protein 70 gene promoter.
Authors: Taira T , Iguchi-Ariga S M , Ariga H
Published: January 2012

A general and sensitive method for the mapping of initiation sites of DNA replication in vivo, developed by Vassilev and Johnson, has revealed replication origins in the region of simian virus 40 ori, in the regions upstream from the human c-myc gene and downstream from the Chinese hamster dihydrofolate reductase gene, and in the enhancer region of the mouse immunoglobulin heavy-chain gene. Here we report that the region containing the promoter of the human heat shock protein 70 (hsp70) gene was identified as a DNA replication origin in HeLa cells by this method. Several segments of the region were cloned into pUC19 and examined for autonomously replicating sequence (ARS) activity. The plasmids carrying the segments replicated episomally and semiconservatively when transfected into HeLa cells. The segments of ARS activity contained the sequences previously identified as binding sequences for a c-myc protein complex (T. Taira, Y. Negishi, F. Kihara, S. M. M. Iguchi-Ariga, and H. Ariga, Biochem. Biophys. Acta 1130:166-174, 1992). Mutations introduced within the c-myc protein complex binding sequences abolished the ARS activity. Moreover, the ARS plasmids stably replicated at episomal state for a long time in established cell lines. The results suggest that the promoter region of the human hsp70 gene plays a role in DNA replication as well as in transcription.
Insulating DNA directs ubiquitous transcription of the Drosophila melanogaster alpha 1-tubulin gene.
Authors: O'Donnell K H , Chen C T , Wensink P C
Published: January 2012

We identify DNA regions that are necessary for the ubiquitous expression of the Drosophila melanogaster alpha 1-tubulin (alpha 1t) gene. In vitro transcription showed that two upstream regions, tubulin element 1 (TE1 [29 bp]) and tubulin element 2 (TE2 [68 bp]), and a downstream region activate transcription. Germ line transformation demonstrated that these three regions are sufficient to direct the alpha 1t core promoter to begin transcribing at the stage of cellular blastoderm formation and to continue thereafter at high levels in all tissues and developmental stages. Remarkably, mutation of any one of these regions results in high sensitivity to chromosomal position effects, producing different but reproducible tissue-specific patterns of expression in each transformed line. None of these regions behaves as an enhancer in a conventional germ line transformation test. These observations show that these three regions, two of which bind the GAGA transcription factor, act ubiquitously to insulate from position effects and to activate transcription. The results also provide vectors for ubiquitous expression of gene products and for examining silencer activities.
Animal poisoning in Italy: 10 years of epidemiological data from the Poison Control Centre of Milan
Authors: Caloni F. , Cortinovis C. , Rivolta M. , Davanzo F.
Published: January 2012

From 2000 to 2010, the Poison Control Centre of Milan (CAV), in collaboration with the University of Milan, Faculty of Veterinary Medicine, Department of Veterinary Sciences and Technologies for Food Safety, Toxicology Section, collected epidemiological information related to animal poisoning and classified it in an organised and computerised data bank. Data recorded were predominantly related to small animals and to some extent to horses, ruminants and other food‐production animals. Few calls were registered involving exotics and no information was recorded on wildlife. The dog was reported to be the most common species involved in animal poisoning, and pesticides constituted the primary group of toxicants. In the case of pets, ‘drugs’ including veterinary parasiticide and drugs for human use constituted the second class of toxicants responsible for poisoning followed by household products, plants, zootoxins and metals. With regard to horses and farm animals, the second group consisted of phytotoxins, even if only episodically. In Italy, published data on this subject are scarce but this information is crucial for better management of the poisoning of domestic animals in an effort to reduce mortality.
The science of better science
Authors: Goth Gregory
Published: January 2012

Researchers are exploring networked computational analysis, formal classification, and topic modeling to better identify relevant scientists, ideas, and trends.
Incentive auctions
Authors: Rosston Gregory
Published: January 2012

Reallocating valuable wireless spectrum can generate billions of dollars in revenue to the U.S. federal government while also benefiting consumers.
Emotion and security
Authors: McDermott Rose
Published: January 2012

Examining the role of human emotional response in making complex security-related decisions.
You don't know jack about shared variables or memory models
Authors: Boehm Hans-J. , Adve Sarita V.
Published: January 2012

Data races are evil.
Software as a service for data scientists
Authors: Allen Bryce , Bresnahan John , Childers Lisa , Foster Ian , Kandaswamy Gopi , Kettimuthu Raj , Kordas Jack , Link Mike , Martin Stuart , Pickett Karl , Tuecke Steven
Published: January 2012

Globus Online manages fire-and-forget file transfers for big-data, high-performance scientific collaborations.
ACM Fellows inducted
Authors: CACM Staff
Published: January 2012

Forty-six men and women are recognized as 2011 ACM Fellows.
An architecture-independent instruction shuffler to protect against side-channel attacks
Authors: Bayrak Ali Galip , Velickovic Nikola , Ienne Paolo , Burleson Wayne
Published: January 2012

Embedded cryptographic systems, such as smart cards, require secure implementations that are robust to a variety of low-level attacks.
Side-Channel Attacks (SCA)
exploit the information such as power consumption, electromagnetic radiation and acoustic leaking through the device to uncover the secret information. Attackers can mount successful attacks with very modest resources in a short time period. Therefore, many methods have been proposed to increase the security against SCA. Randomizing the execution order of the instructions that are independent, i.e.,
random shuffling
, is one of the most popular among them. Implementing instruction shuffling in software is either implementation specific or has a significant performance or code size overhead. To overcome these problems, we propose in this work a generic custom hardware unit to implement random instruction shuffling as an extension to existing processors. The unit operates between the CPU and the instruction cache (or memory, if no cache exists), without any modification to these components. Both true and pseudo random number generators are used to dynamically and locally provide the shuffling sequence. The unit is mainly designed for in-order processors, since the embedded devices subject to these kind of attacks use simple in-order processors. More advanced processors (e.g., superscalar, VLIW or EPIC processors) are already more resistant to these attacks because of their built-in ILP and wide word size. Our experiments on two different soft in-order processor cores, i.e., OpenRISC and MicroBlaze, implemented on FPGA show that the proposed unit could increase the security drastically with very modest resource overhead. With around 2% area, 1.5% power and no performance overhead, the shuffler increases the effort to mount a successful power analysis attack on AES software implementation over 360 times.
On-the-fly structure splitting for heap objects
Authors: Wang Zhenjiang , Wu Chenggang , Yew Pen-Chung , Li Jianjun , Xu Di
Published: January 2012

With the advent of multicore systems, the gap between processor speed and memory latency has grown worse because of their complex interconnect. Sophisticated techniques are needed more than ever to improve an application's spatial and temporal locality. This paper describes an optimization that aims to improve heap data layout by structure-splitting. It also provides runtime address checking by piggybacking on the existing page protection mechanism to guarantee the correctness of such optimization that has eluded many previous attempts due to safety concerns. The technique can be applied to both sequential and parallel programs at either compile time or runtime. However, we focus primarily on sequential programs (i.e., single-threaded programs) at runtime in this paper. Experimental results show that some benchmarks in SPEC 2000 and 2006 can achieve a speedup of up to 142.8%.
Efficient liveness computation using merge sets and DJ-graphs
Authors: Das Dibyendu , Dupont De Dinechin B. , Upadrasta Ramakrishna
Published: January 2012

In this work we devise an efficient algorithm that computes the liveness information of program variables. The algorithm employs SSA form and DJ-graphs as representation to build
Merge
sets. The
Merge
set of node
n
,
M
(
n
) is based on the structure of the Control Flow Graph (CFG) and consists of all nodes where a ϕ-function needs to be placed, if a definition of a variable appears in
n
. The merge sets of a CFG can be computed using DJ-graphs without prior knowledge of how the variables are used and defined. Later, we can answer the liveness query (as a part of other optimization or analysis phase) by utilizing the knowledge of the use/def of variables, the dominator tree and the pre-computed merge sets. On average, merge sets have been shown to be of size comparable to the Dominance Frontier(DF) set of a CFG and can be computed efficiently for all kinds of applications consisting of both reducible and irreducible loops. This is an advantage over existing algorithms which require additional complexities while handling applications using irreducible loops. For cases where the merge sets have already been created during the SSA construction step, the cost of our algorithm reduces even further when we use these merge sets for liveness computation. We have compared our new algorithm with a recent algorithm for computing liveness based on SSA form, and show how it performs better in practice, though being simpler to understand and implement.
Exploring the limits of GPGPU scheduling in control flow bound applications
Authors: Malits Roman , Bolotin Evgeny , Kolodny Avinoam , Mendelson Avi
Published: January 2012

GPGPUs are optimized for graphics, for that reason the hardware is optimized for massively data parallel applications characterized by predictable memory access patterns and little control flow. For such applications' e.g., matrix multiplication, GPGPU based system can achieve very high performance. However, many general purpose data parallel applications are characterized as having intensive control flow and unpredictable memory access patterns.

Optimizing the code in such problems for current hardware is often ineffective and even impractical since it exhibits low hardware utilization leading to relatively low performance.

This work tracks the root causes of execution inefficacies when running control flow intensive CUDA applications on NVIDIA GPGPU hardware.

We show both analytically and by simulations of various benchmarks that local thread scheduling has inherent limitations when dealing with applications that have high rate of branch divergence. To overcome those limitations we propose to use hierarchical warp scheduling and global warps reconstruction. We implement an ideal hierarchical warp scheduling mechanism we term ODGS (Oracle Dynamic Global Scheduling) designed to maximize machine utilization via global warp reconstruction. We show that in control flow bound applications that make no use of shared memory (1) there is still a substantial potential for performance improvement (2) we demonstrate, based on various synthetic and real benchmarks the feasible performance improvement.

For example, MUM and BFS are parallel graph algorithms suffering from significant branch divergence. We show that in those algorithms it's possible to achieve performance gain of up to x4.4 and x2.6 relative to previously applied scheduling methods.
Non-monopolizable caches
Authors: Domnitser Leonid , Jaleel Aamer , Loew Jason , Abu-Ghazaleh Nael , Ponomarev Dmitry
Published: January 2012

We propose a flexibly-partitioned cache design that either drastically weakens or completely eliminates cache-based side channel attacks. The proposed Non-Monopolizable (NoMo) cache dynamically reserves cache lines for active threads and prevents other co-executing threads from evicting reserved lines. Unreserved lines remain available for dynamic sharing among threads. NoMo requires only simple modifications to the cache replacement logic, making it straightforward to adopt. It requires no software support enabling it to automatically protect pre-existing binaries. NoMo results in performance degradation of about 1% on average. We demonstrate that NoMo can provide strong security guarantees for the AES and Blowfish encryption algorithms.
PLDS
Authors: Feng Min , Lin Changhui , Gupta Rajiv
Published: January 2012

Recently, parallelization of computations in the presence of dynamic data structures has shown promising potential. In this paper, we present PLDS, a system for easily expressing and efficiently exploiting parallelism in computations that are based on dynamic linked data structures. PLDS improves the execution efficiency by providing support for data partitioning and then distributing computation across threads based on the partitioning. Such computations often require the use of speculation to exploit dynamic parallelism. PLDS supports a conditional speculation mechanism that reduces the cost of speculation. PLDS can be employed in the context of different forms of parallelism, which to cover a wide range of parallel applications. PLDS provides easy-to-use compiler directives, using enabling programmers to choose from among a variety of data partitionings to distribute computation across threads in a partitioning-sensitive fashion, and to use conditional speculation when required. We evaluate our implementation of PLDS using ten benchmarks, of which six are parallelized using speculation. PLDS achieves 1.3x--6.9x speedups on an 8-core machine.
Sabrewing
Authors: Bruintjes Tom M. , Walters Karel H. G. , Gerez Sabih H. , Molenkamp Bert , Smit Gerard J. M.
Published: January 2012

In spite of the fact that floating-point arithmetic is costly in terms of silicon area, the joint design of hardware for floating-point and integer arithmetic is seldom considered. While components like multipliers and adders can potentially be shared, floating-point and integer units in contemporary processors are practically disjoint. This work presents a new architecture which tightly integrates floating-point and integer arithmetic in a single datapath. It is mainly intended for use in low-power embedded digital signal processors and therefore the following design constraints were important: limited use of pipelining for the convenience of the compiler; maintaining compatibility with existing technology; minimal area and power consumption for applicability in embedded systems. The architecture is tailored to digital signal processing by combining
floating-point fused multiply-add
and
integer multiply-accumulate
. It could be deployed in a multi-core system-on-chip designed to support applications with and without dominance of floating-point calculations.

The VHDL structural description of this architecture is available for download under BSD license. Besides being configurable at design time, it has been thoroughly checked for IEEE-754 compliance by means of a floating-point test suite originating from the IBM Research Labs. A proof-of-concept has also been implemented using STMicroelectronics 65nm technology. This prototype supports 32-bit signed two's complement integers and 41-bit (8-bit exponent and 32-bit significand) floating-point numbers. Our evaluations show that over 67% energy and 19% area can be saved compared to a reference design in which floating-point and integer arithmetic are implemented separately. The area overhead caused by combining floating-point and integer is less than 5%.

Implemented in ST's general-purpose CMOS technology, the design can operate at a frequency of 1.35GHz, while 667MHz can be achieved in low-power CMOS. Considering that the entire datapath is partitioned in just three pipeline stages, and the fact that the design is intended for use in the low-power domain, these frequencies are adequate. They are in fact competitive with current technology low-power floating-point units. Post-layout estimates indicate that the required area of a low-power implementation can be as small as 0.04mm
2
. Power consumption is on the order of several milliwatts. Strengthened by the fact that clock gating could reduce power consumption even further, we think that a shared floating-point and integer architecture is a good choice for signal processing in low-power embedded systems.
Writeback-aware partitioning and replacement for last-level caches in phase change main memory systems
Authors: Zhou Miao , Du Yu , Childers Bruce , Melhem Rami , Mossé Daniel
Published: January 2012

Phase-Change Memory (PCM) has emerged as a promising low-power main memory candidate to replace DRAM. The main problems of PCM are that writes are much slower and more power hungry than reads, write bandwidth is much lower than read bandwidth, and limited write endurance. Adding an extra layer of cache, which is logically the
last-level cache
(LLC), can mitigate the drawbacks of PCM. However, writebacks from the LLC might (a) overwhelm the limited PCM write bandwidth and stall the application, (b) shorten lifetime, and (c) increase energy consumption. Cache partitioning and replacement schemes are important to achieve high throughput for multi-core systems. However, we noted that no existing partitioning and replacement policy takes into account the writeback information.

This paper proposes two writeback-aware schemes to manage the LLC for PCM main memory systems.
Writeback-aware Cache Partitioning
(WCP) is a runtime mechanism that partitions a shared LLC among multiple applications. Unlike past partitioning schemes, our scheme considers the reduction in cache misses as well as writebacks.
Write Queue Balancing
(WQB) replacement policy manages the cache partition of each application intelligently so that the writebacks are distributed evenly among PCM write queues. In this way, applications rarely stall due to unbalanced PCM write traffic among write queues. Our evaluation shows that WCP and WQB result in, on average, 21% improvement in throughput, 49% reduction in PCM writes, and 14% reduction in energy over a state-of-the-art cache partitioning scheme.
Protein secondary structures prediction based on evolutionary computation
Authors: Chamorro Alfonso E. Márquez , Divina Federico , Aguilar-Ruiz Jesús S.
Published: January 2012

In this paper we propose an approach based on evolutionary computation for the prediction of secondary protein structure motifs. The prediction model consists of a set of rules that predict both the beginning and the end of the regions corresponding to a secondary structure state conformation (α-helix or β-strand). The prediction is based on a set of specific amino acid physical-chemical properties. In addition we also propose a statistical study regarding the propensities of each pair of amino acids in capping regions of α-helix and β-strand. Experimental results confirm the validity of our proposal.
Ewing Sarcoma/Primitive Neuroectodermal Tumor of the Kidney: Two Unusual Presentations of a Rare Tumor
Authors: Castro E. C. , Parwani A. V.
Published: January 2012

Only few cases of primary renal Ewing's sarcoma have been reported in the literature to date. We present here two cases of renal ES/PNET with an uncanny presentation. The first case was discovered after the patient presented clinically with irradiating flank pain, mimicking the pain related with kidney stones. The second case had clinical presentation of pulmonary thromboembolism after the patient was involved in an automobilist accident. The tumors were mainly composed of small blue cells which by immunohistochemical were positive for neural markers, and FISH revealed the translocation 22q12 for the EWSR1 gene. The diagnosis of renal primitive neuroectodermal tumor/EWING tumor is very rare and usually involves several different diagnostic techniques. The differential diagnosis is usually broad with frequent overlapping features between the entities. The cases presented in this paper illustrated the difficulties with which routine anatomical pathologist is faced when dealing with rare renal poorly differentiated neoplasm in adults.
Large Eddy Simulation of Turbulent Flow and Heat Transfer in a Ribbed Coolant Passage
Authors: Ramgadia Abhishek G. , Saha Arun K.
Published: January 2012

Numerical simulations of hydrodynamic and thermally fully developed turbulent flow are presented for flow through a stationary duct with periodic array of inline transverse rib turbulators. The rib height to hydraulic diameter ratio (e/Dh) is 0.1 and the rib pitch to rib height ratio (P/e) is 10. The effect of secondary flow due to presence of rib turbulators on heat and mass transfer has been investigated. The present work reviews the use of a large eddy simulation (LES) turbulence model, known as shear‐improved Smagorinsky model (SISM), for predicting flow and heat transfer characteristics in the fully developed periodic flow region. The computations are performed for Reynolds number of 2,053 and the working fluid chosen to be air, the Prandtl number of which is 0.7. Instantaneous flow field, time‐mean, and turbulent quantities are reported together with heat transfer and a close match with experiments has been observed.
Preparation and Photocatalytic Property ofTiO2/Diatomite-Based Porous Ceramics Composite Materials
Authors: Zheng Shuilin , Bai Chunhua , Gao RuQin
Published: January 2012

The diatomite-based porous ceramics was made by low-temperature sintering. Then the nano-TiO2/diatomite-based porous ceramics composite materials were prepared by hydrolysis deposition method with titanium tetrachloride as the precursor ofTiO2and diatomite-based porous as the supporting body of the nano-TiO2. The structure and microscopic appearance of nano-TiO2/diatomite-based porous ceramics composite materials was characterized by XRD and SEM. The photocatalytic property of the composite was investigated by the degradation of malachite green. Results showed that, after calcination at550°C,TiO2thin film loaded on the diatomite-based porous ceramics is anataseTiO2and average grain size ofTiO2is about 10 nm. The degradation ratio of the composite for 5 mg/L malachite green solution reached 86.2% after irradiation for 6 h under ultraviolet.
Procedures and Properties for a Direct Nano-Micro Integration of Metal and Semiconductor Nanowires on Si Chips
Authors: Gedamu Dawit , Paulowicz Ingo , Jebril Seid , Kumar Mishra Yogendra , Adelung Rainer
Published: January 2012

1-dimensional metal and semiconductor nanostructures exhibit interesting physical properties, but their integration into modern electronic devices is often a very challenging task. Finding the appropriate supports for nanostructures and nanoscale contacts are highly desired aspects in this regard. In present work we demonstrate the fabrication of 1D nano- and mesostructures between microstructured contacts formed directly on a silicon chip either by a thin film fracture (TFF) approach or by a modified vapor-liquid-solid (MVLS) approach. In principle, both approaches offer the possibilities to integrate these nano-meso structures in wafer-level fabrications. Electrical properties of these nano-micro structures integrated on Si chips and their preliminary applications in the direction of sensors and field effect transistors are also presented.
Fate in Soil of Flavonoids Released from White Clover (Trifolium repensL.)
Authors: Carlsen Sandra C. K. , Pedersen Hans A. , Spliid Niels H. , Fomsgaard Inge S.
Published: January 2012

White clover is frequently used as a leguminous cover crop, serving as green manure, and is also included with grasses in cattle feed mixtures. Numerous biological effects reported for clover cultivation have been attributed to the production of bioactive secondary metabolites. Thus far the presence in soil of bioactive secondary metabolites from clover has received limited attention. In this paper we examine for the first time the release of flavonoids both from field-grown white clover and from soil-incorporated white clover plants of flavonoids, as analyzed by LC-MS/MS. The dominant flavonoid aglycones were formononetin, medicarpin, and kaempferol. Soil-incorporated white clover plants generated high concentrations of the glycosides kaempferol-Rha-Xyl-Gal and quercetin-Xyl-Gal. Substantial amounts of kaempferol persisted in the soil for days while the other compounds were degraded faster. These compounds should be considered in future studies of soil fatigue, allelopathic activity, and possible environmental risks from extended clover cultivation.
Anterior Segment Tomography with the Cirrus Optical Coherence Tomography
Authors: Rodrigues Eduardo B. , Johanson Margara , Penha Fernando M.
Published: January 2012

Optical coherence tomography (OCT) is an optical acquisition method to examine biological tissues. In recent years, OCT has become an important imaging technology used in diagnosing and following macular pathologies. Further development enabled application of optical coherence tomography in evaluation of the integrity of the nerve fiber layer, optic nerve cupping, anterior chamber angle, or corneal topography. In this manuscript we overview the use of OCT in the clinical practice to enable corneal, iris, ciliary body, and angle evaluation and diagnostics.
Deformation Behavior of Human Dentin under Uniaxial Compression
Authors: Zaytsev Dmitry , Grigoriev Sergey , Panfilov Peter
Published: January 2012

Deformation behavior of a human dentin under compression including size and rate effects is studied. No difference between mechanical properties of crown and root dentin is found. It is mechanically isotropic high elastic and strong hard tissue, which demonstrates considerable plasticity and ability to suppress a crack growth. Mechanical properties of dentin depend on a shape of samples and a deformation rate.
Loop‐Reduction LLL Algorithm and Architecture for Lattice‐Reduction‐Aided MIMO Detection
Authors: Liao Chun-Fu , Chai Li-Wei , Huang Yuan-Hao
Published: January 2012

We propose a loop‐reduction LLL (LR‐LLL) algorithm for lattice‐reduction‐aided (LRA) multi‐input multioutput
(MIMO) detection. The LLL algorithm is an iterative algorithm that contains many check and process operations; however, the
traditional LLL algorithm itself possesses a lot of redundant check operations. To solve this problem, we propose a look‐ahead
check technique that not only reduces the complexity of the LLL algorithm but also produces the lattice‐reduced matrix which
obeys the original LLL criterion. Simulation results show that the proposed LR‐LLL algorithm reduces the average number of
loops or computation complexity. Besides, it also shortens the latency of clock cycles about 19.4%, 29.1%, and 46.1% for 4 × 4, 8 × 8, and 12 × 12 MIMO systems, respectively.
Evaluation of Surface Slope Irregularity in Linear Parabolic Solar Collectors
Authors: Francini F. , Fontani D. , Sansoni P. , Mercatelli L. , Jafrancesco D. , Sani E.
Published: January 2012

The paper describes a methodology, very simple in its application, for measuring surface irregularities of linear parabolic collectors. This technique was principally developed to be applied in cases where it is difficult to use cumbersome instruments and to facilitate logistic management. The instruments to be employed are a digital camera and a grating. If the reflector surface is defective, the image of the grating, reflected on the solar collector, appears distorted. Analyzing the reflected image, we can obtain the local slope of the defective surface. These profilometric tests are useful to identify and monitor the mirror portions under mechanical stress and to estimate the losses caused by the light rays deflected outside the absorber.
Changes in Lipids and Lipoproteins after Selective LDL Apheresis (7-Year Experience)
Authors: Kolovou Genovefa , Hatzigeorgiou Georgios , Mihas Constantinos , Gontoras Nikos , Litras Panagiotis , Devekousos Dimitris , Kontodima Panagiota , Sorontila Constantina , Bilianou Helen , Mavrogeni Sophie
Published: January 2012

Background. The aim of the study was to investigate the changes in plasma lipids and lipoproteins and the cardiovascular events after selective LDL apheresis. Methods and Results. Two pediatric patients with familial hypercholesterolemia aged 11 and 13 years and 19 dyslipidemic adults aged 41 ± 14 years underwent direct adsorption of lipoproteins (DALI) sessions. The mean follow-up period was 47 ± 23 months. The total cholesterol (TC) values before and after treatment were 8.2 ± 2.2 and 3.1 ± 1.6 mmol/l (318 ± 86 and 122 ± 62 mg/dL), respectively. The interval mean of TC was 6.9 ± 1.9 mmol/l (268 ± 75 mg/dL). The LDL cholesterol concentrations before and after treatment were 6.6 ± 2.1 and 1.7 ± 1.1 mmol/l, (256 ± 82 mg/dL and 65 ± 41 mg/dL), respectively. The percentage of acute LDL cholesterol reduction was 75 ± 11%. Cardiovascular events were observed in seven patients. The average annual event rate was 5.51%. Conclusion. LDL apheresis is a very important therapeutic tool in managing patients at high risk for premature CAD or with aggressive CAD, despite adequate medical treatment.