bluuebunny/crossref_metadata_2025 huggingface dataset:
Granulocyte-macrophage colony-stimulating factor and interleukin-3 signaling pathways converge on the CREB-binding site in the human egr-1 promoter.
Authors: Sakamoto K M , Fraser J K , Lee H J , Lehman E , Gasson J C
Published: January 2012

Granulocyte-macrophage colony-stimulating factor (GM-CSF) stimulates myeloid progenitor cell proliferation and enhances the function of terminally differentiated effector cells. Interleukin-3 (IL-3) stimulation results in the proliferation and maturation of early bone marrow progenitor cells. These activities are mediated by non-tyrosine kinase-containing receptors which consist of ligand-specific alpha subunits that complex with a common beta subunit required for signal transduction. Both GM-CSF and IL-3 rapidly and transiently induce expression of early growth response gene 1 (egr-1) in the human factor-dependent cell line TF-1. To define the mechanism of early response gene induction by GM-CSF and IL-3, growth factor- and serum-starved TF-1 cells transfected with recombinant constructs containing sequences of the human egr-1 promoter were stimulated with GM-CSF or IL-3. A 116-nucleotide (nt) region of the egr-1 promoter which contains sequences inducible by GM-CSF and IL-3 was defined. DNase I footprint analysis identified a 20-nt region, including nt -57 to -76, which contains a potential cyclic AMP (cAMP) response element (CRE). Electrophoretic mobility shift assays performed with CREB antibody confirmed the presence of CREB in the DNA-binding complex. Mutational analysis of the cytokine-responsive region of the egr-1 promoter revealed that both the cAMP response and serum response elements are required for induction by GM-CSF and IL-3. Nuclear extracts from GM-CSF- or IL-3-stimulated but not unstimulated TF-1 cells contain factors which specifically bind to the Egr-1-binding site in the nt -600 to -480 region of the promoter. Electrophoretic mobility shift assays were performed with antibodies against the Egr-1 protein to demonstrate the presence of the protein product in the shifted complex. Our studies suggest that the Egr-1 protein may further stimulate transcription of the egr-1 gene in response to GM-CSF as a secondary event.
c-Fos-induced activation of a TATA-box-containing promoter involves direct contact with TATA-box-binding protein.
Authors: Metz R , Bannister A J , Sutherland J A , Hagemeier C , O'Rourke E C , Cook A , Bravo R , Kouzarides T
Published: January 2012

Transcriptional activation in eukaryotes involves protein-protein interactions between regulatory transcription factors and components of the basal transcription machinery. Here we show that c-Fos, but not a related protein, Fra-1, can bind the TATA-box-binding protein (TBP) both in vitro and in vivo and that c-Fos can also interact with the transcription factor IID complex. High-affinity binding to TBP requires c-Fos activation modules which cooperate to activate transcription. One of these activation modules contains a TBP-binding motif (TBM) which was identified through its homology to TBP-binding viral activators. This motif is required for transcriptional activation, as well as TBP binding. Domain swap experiments indicate that a domain containing the TBM can confer TBP binding on Fra-1 both in vitro and in vivo. In vivo activation experiments indicate that a GAL4-Fos fusion can activate a promoter bearing a GAL4 site linked to a TATA box but that this activity does not occur at high concentrations of GAL4-Fos. This inhibition (squelching) of c-Fos activity is relieved by the presence of excess TBP, indicating that TBP is a direct functional target of c-Fos. Removing the TBM from c-Fos severely abrogates activation of a promoter containing a TATA box but does not affect activation of a promoter driven only by an initiator element. Collectively, these results suggest that c-Fos is able to activate via two distinct mechanisms, only one of which requires contact with TBP. Since TBP binding is not exhibited by Fra-1, TBP-mediated activation may be one characteristic that discriminates the function of Fos-related proteins.
A role for RNA synthesis in homologous pairing events.
Authors: Kotani H , Kmiec E B
Published: January 2012

The relationship between RNA synthesis and homologous pairing in vitro, catalyzed by RecA protein, was examined by using an established strand transfer assay system. When a short DNA duplex is mixed with single-stranded circles, RecA protein promotes the transfer of the minus strand of the duplex onto the complementary region of the plus-strand circle, with the displacement of the plus strand of the duplex. However, if minus-strand RNA is synthesized from the duplex pairing partner, joint molecules containing the RNA transcript, the plus strand of the DNA duplex, and the plus-strand circle are also observed to form. This reaction, which is dependent on RNA polymerase, sequence homology, and RecA protein, produces a joint molecule that can be dissolved by treatment with RNase H but not RNase A. Under these reaction conditions, product molecules form even when the length of shared homology between duplex and circle is reduced to 15 bp.
Plasmid maintenance functions encoded on Dictyostelium discoideum nuclear plasmid Ddp1.
Authors: Hughes J E , Kiyosawa H , Welker D L
Published: January 2012

All of the plasmid-carried genes expressed during vegetative growth are essential for long-term maintenance of plasmid Ddp1 in the nucleus of Dictyostelium discoideum. Deletion of Ddp1 genes expressed only during development had no detectable effect on plasmid maintenance. Deletion of vegetatively expressed genes, either singly or in pairs, resulted in (i) a rapid loss of plasmid from cells grown in the absence of selection for plasmid retention, (ii) variation in the proportion of monomer to multimer forms of the plasmid molecules, and/or (iii) abnormalities in plasmid copy number. At least two plasmid-encoded gene products influence patterns of expression of plasmid genes.
Control of transcription arrest in intron 1 of the murine adenosine deaminase gene.
Authors: Kash S F , Kellems R E
Published: January 2012

Transcription arrest plays a key role in the regulation of the murine adenosine deaminase (ADA) gene, as well as a number of other cellular and viral genes. We have previously characterized the ADA intron 1 arrest site, located 145 nucleotides downstream of the transcription start site, with respect to sequence and elongation factor requirements. Here, we show that the optimal conditions for both intron 1 arrest and overall ADA transcription involve the addition of high concentrations of KCl soon after initiation. As we have further delineated the sequence requirements for intron 1 arrest, we have found that sequences downstream of the arrest site are unnecessary for arrest. Also, a 24-bp fragment containing sequences upstream of the arrest site is sufficient to generate arrest downstream of the adenovirus major late promoter only in the native orientation. Surprisingly, we found that deletion of sequences encompassing the ADA transcription start site substantially reduced intron 1 arrest, with no effect on overall levels of transcription. At the same time, deletion of sequences upstream of the TATA box had no significant effect on either process. We believe the start site mutations have disrupted either the assembly or the composition of the transcription complex such that intron 1 site read-through is now favored. This finding, coupled with the increase in overall transcription after high-concentration KCl treatment, allows us to further refine our model of ADA gene regulation.
Hypoxia induces accumulation of p53 protein, but activation of a G1-phase checkpoint by low-oxygen conditions is independent of p53 status.
Authors: Graeber T G , Peterson J F , Tsai M , Monica K , Fornace A J , Giaccia A J
Published: January 2012

It has been convincingly demonstrated that genotoxic stresses cause the accumulation of the tumor suppressor gene p53. One important consequence of increased p53 protein levels in response to DNA damage is the activation of a G1-phase cell cycle checkpoint. It has also been shown that G1-phase cell cycle checkpoints are activated in response to other stresses, such as lack of oxygen. Here we show that hypoxia and heat, agents that induce cellular stress primarily by inhibiting oxygen-dependent metabolism and denaturing proteins, respectively, also cause an increase in p53 protein levels. The p53 protein induced by heat is localized in the cytoplasm and forms a complex with the heat shock protein hsc70. The increase in nuclear p53 protein levels and DNA-binding activity and the induction of reporter gene constructs containing p53 binding sites following hypoxia occur in cells that are wild type for p53 but not in cells that possess mutant p53. However, unlike ionizing radiation, the accumulation of cells in G1 phase by hypoxia is not strictly dependent on wild-type p53 function. In addition, cells expressing the human papillomavirus E6 gene, which show increased degradation of p53 by ubiquitination and fail to accumulate p53 in response to DNA-damaging agents, do increase their p53 levels following heat and hypoxia. These results suggest that hypoxia is an example of a "nongenotoxic" stress which induces p53 activity by a different pathway than DNA-damaging agents.
Introns are cis effectors of the nonsense-codon-mediated reduction in nuclear mRNA abundance.
Authors: Cheng J , Belgrader P , Zhou X , Maquat L E
Published: January 2012

The translation of human triosephosphate isomerase (TPI) mRNA normally terminates at codon 249 within exon 7, the final exon. Frameshift and nonsense mutations of the type that cause translation to terminate prematurely at or upstream of codon 189 within exon 6 reduce the level of nuclear TPI mRNA to 20 to 30% of normal by a mechanism that is not a function of the distance of the nonsense codon from either the translation initiation or termination codon. In contrast, frameshift and nonsense mutations of another type that cause translation to terminate prematurely at or downstream of codon 208, also within exon 6, have no effect on the level of nuclear TPI mRNA. In this work, quantitations of RNA that derived from TPI alleles in which nonsense codons had been generated between codons 189 and 208 revealed that the boundary between the two types of nonsense codons resides between codons 192 and 195. The analysis of TPI gene insertions and deletions indicated that the positional feature differentiating the two types of nonsense codons is the distance of the nonsense codon upstream of intron 6. For example, the movement of intron 6 to a position downstream of its normal location resulted in a concomitant downstream movement of the boundary between the two types of nonsense codons. The analysis of intron 6 mutations indicated that the intron 6 effect is stipulated by the 88 nucleotides residing between the 5' and 3' splice sites. Since the deletion of intron 6 resulted in only partial abrogation of the nonsense codon-mediated reduction in the level of TPI mRNA, other sequences within TPI pre-mRNA must function in the effect. One of these sequences may be intron 2, since the deletion of intron 2 also resulted in partial abrogation of the effect. In experiments that switched introns 2 and 6, the replacement of intron 6 with intron 2 was of no consequence to the effect of a nonsense codon within either exon 1 or exon 6. In contrast, the replacement of intron 2 with intron 6 was inconsequential to the effect of a nonsense codon in exon 6 but resulted in partial abrogation of a nonsense codon in exon 1.
Incremental Cycle Detection, Topological Ordering, and Strong Component Maintenance
Authors: Haeupler Bernhard , Kavitha Telikepalli , Mathew Rogers , Sen Siddhartha , Tarjan Robert E.
Published: January 2012

We present two online algorithms for maintaining a topological order of a directed
n
-vertex acyclic graph as arcs are added, and detecting a cycle when one is created. Our first algorithm handles
m
arc additions in O(
m
3/2
) time. For sparse graphs (
m
/
n
= O(1)), this bound improves the best previous bound by a logarithmic factor, and is tight to within a constant factor among algorithms satisfying a natural locality property. Our second algorithm handles an arbitrary sequence of arc additions in O(
n
5/2
) time. For sufficiently dense graphs, this bound improves the best previous bound by a polynomial factor. Our bound may be far from tight: we show that the algorithm can take Ω(
n
2
2
√2 lg
n
) time by relating its performance to a generalization of the
k
-levels problem of combinatorial geometry. A completely different algorithm running in Θ(
n
2
log
n
) time was given recently by Bender, Fineman, and Gilbert. We extend both of our algorithms to the maintenance of strong components, without affecting the asymptotic time bounds.
A 10 Point Checklist for Getting it Off the Shelf
Authors: Denning Peter J.
Published: January 2012

Far too many R&D programs in industry as well as government result in reports or prototypes that represent fundamentally good ideas but end up gathering dust on a shelf. Ellison "Dick" Urban, formerly of DARPA (Defense Advanced Research Projects Agency) and now the Director of Washington Operations at Draper Laboratory, has had considerable experience with technology transition. We talked to him about his guidelines for success.
The social life of robots
Authors: Wright Alex
Published: January 2012

Researchers are trying to build robots capable of working together with minimal human supervision. But will they ever learn to get along?
Bahurupi
Authors: Pricopi Mihai , Mitra Tulika
Published: January 2012

Computing systems have made an irreversible transition towards parallel architectures with the emergence of multi-cores. Moreover, power and thermal limits in embedded systems mandate the deployment of many simpler cores rather than a few complex cores on chip. Consumer electronic devices, on the other hand, need to support an ever-changing set of diverse applications with varying performance demands. While some applications can benefit from thread-level parallelism offered by multi-core solutions, there still exist a large number of applications with substantial amount of sequential code. The sequential programs suffer from limited exploitation of instruction-level parallelism in simple cores. We propose a reconfigurable multi-core architecture, called Bahurupi, that can successfully reconcile the conflicting demands of instruction-level and thread-level parallelism. Bahurupi can accelerate the performance of serial code by dynamically forming coalition of two or more simple cores to offer increased instruction-level parallelism. In particular, Bahurupi can efficiently merge 2-4 simple 2-way out-of-order cores to reach or even surpass the performance of more complex and power-hungry 4-way or 8-way out-of-order core. Compared to baseline 2-way core, quad-core Bahurupi achieves up to 5.61 speedup (average 4.08 speedup) for embedded workloads. On an average, quad-core Bahurupi achieves 17% performance improvement and 43% improvement in energy consumption compared to 8-way out-of-order baseline core on a diverse set of embedded benchmark applications.
Efficiently exploiting memory level parallelism on asymmetric coupled cores in the dark silicon era
Authors: Patsilaras George , Choudhary Niket K. , Tuck James
Published: January 2012

Extracting high memory-level parallelism (MLP) is essential for speeding up single-threaded applications which are memory bound. At the same time, the projected amount of dark silicon (the fraction of the chip powered off) on a chip is growing. Hence, Asymmetric Multicore Processors (AMP) offer a unique opportunity to integrate many types of cores, each powered at different times, in order to optimize for different regions of execution. In this work, we quantify the potential for exploiting core customization to speedup programs during regions of high MLP. Based on a careful design space exploration, we discover that an AMP that includes a narrow and fast specialized core has the potential to efficiently exploit MLP.

Using the results of our analysis, we design an AMP with both an MLP and ILP specialized core, and we propose a hardware-level, application steering mechanism called Symbiotic Core Execution (SCE). SCE detects MLP phases by monitoring the L2 miss rate of the application, and it uses that information to steer the application to the best core. Interestingly, we show that L2 miss rates are important for deciding when an MLP region begins and when it ends. As a program runs, its execution migrates to a core customized for MLP during regions of high MLP; when the region ends, it is re-scheduled on the core that fits the application characteristics.

Compared to a monolithic core optimized for both modes of operation, our AMP design provides a harmonic mean performance improvement of 5.3% and 6.6% for SPEC2000 and SPEC2006, respectively, with a maximum speedup of 14.5%. For the same study, it achieves a 18.3% and 21.1% energy delay
2
reduction for SPEC2000 and SPEC2006, respectively. Our findings yield an important message for designing AMPs with specialized cores: core customization enables efficient exploitation of MLP, and application steering mechanisms for MLP are simple to implement and effective.
Making wide-issue VLIW processors viable on FPGAs
Authors: Purnaprajna Madhura , Ienne Paolo
Published: January 2012

Soft and highly-customized processors are emerging as a common way to efficiently control large amount of computing resources available on FPGAs. Yet, some processor architectures of choice for DSP and media applications, such as wide-issue VLIW processors, remain impractical: the multi-ported register file makes a very inefficient use of the resources in the FPGA fabric. This paper proposes modifications to existing FPGAs to make soft-VLIW processor viable. We introduce an embedded multi-ported RAM that can be customized to match the issue-width of VLIW processors. To ascertain the benefits of this approach, we map an extensible VLIW processor onto a standard FPGA from Xilinx. For the register file implemented in the modified FPGA, the area occupied is at least 102× smaller and the dynamic power is reduced by 41% as compared to the implementation using configurable logic blocks in existing standard FPGAs. A subset of this embedded multi-ported RAM can also be used for mapping the register file in soft-RISC processors. For the soft-RISC processor, the register file in the modified FPGA is at least 22× smaller than its equivalent that uses configurable logic blocks and 1.5× the size in comparison to the implementation using block RAMs. Reduction of routing area and the maximum net length is about 39% and 51% respectively for RISC processors. As a result, this approach works towards enhancing soft-processor density in FPGAs by orders of magnitude.
Polyhedral parallelization of binary code
Authors: Pradelle Benoit , Ketterlin Alain , Clauss Philippe
Published: January 2012

Many automatic software parallelization systems have been proposed in the past decades, but most of them are dedicated to source-to-source transformations. This paper shows that parallelizing executable programs is feasible, even if they require complex transformations, and in effect decouples parallelization from compilation, for example, for closed-source or legacy software, where binary code is the only available representation.

We propose an automatic parallelizer, which is able to perform advanced parallelization on binary code. It first parses the binary code and extracts high-level information. From this information, a C program is generated. This program captures only a subset of the program semantics, namely, loops and memory accesses. This C program is then parallelized using existing, state-of-the-art parallelizers, including advanced polyhedral parallelizers. The original program semantics is then re-injected, and the transformed parallel loop nests are recompiled by a standard C compiler.

We show on the PolyBench benchmark suite that our system successfully detects and parallelizes almost all the loop nests from the binary code, using a recent polyhedral loop parallelizer as a backend. The paper ends by elaborating a strategy to parallelize more complex programs, such as those containing non-linear accesses to memory, and provides a few example case-studies.
ReNIC
Authors: Dong Yaozu , Chen Yu , Pan Zhenhao , Dai Jinquan , Jiang Yunhong
Published: January 2012

Virtualization is gaining popularity in cloud computing and has become the key enabling technology in cloud infrastructure. By replicating the virtual server state to multiple independent platforms, virtualization improves the reliability and availability of cloud systems. Unfortunately, existing Virtual Machine (VM) replication solutions were designed only for software virtualized I/O, which suffers from large performance and scalability overheads. Although hardware-assisted I/O virtualization (such as SR-IOV) can achieve close to native performance and very good scalability, they cannot be properly replicated across different physical machines due to architectural limitations (such as lack of efficient device state read/write, buffering outbound packets, etc.).

In this paper, we address those architectural limitations, by proposing ReNIC, an architectural extension to SR-IOV I/O virtualization for efficient I/O replications. We have extended Xen hypervisor and the Remus rapid checkpoint solution to support this new architectural extension. We developed a system simulator on multi-core systems to extensively evaluate ReNIC. The experimental results demonstrate that ReNIC achieves up to 54% CPU usage reduction, compared to software based I/O virtualization at runtime, and up to 16.2% performance advantage over software based I/O virtualization in rapid checkpoint. During migration, ReNIC reduces service shutdown time by about 50%, compared to device emulation and paravirtualized I/O, and over 71% compared to teaming driver.
Thread Tranquilizer
Authors: Pusukuri Kishore Kumar , Gupta Rajiv , Bhuyan Laxmi N.
Published: January 2012

To realize the performance potential of multicore systems, we must effectively manage the interactions between memory reference behavior and the operating system policies for thread scheduling and migration decisions. We observe that these interactions lead to significant variations in the performance of a given application, from one execution to the next, even when the program input remains unchanged and no other applications are being run on the system. Our experiments with multithreaded programs, including the TATP database application, SPECjbb2005, and a subset of PARSEC and SPEC OMP programs, on a 24-core Dell PowerEdge R905 server running OpenSolaris confirms the above observation. In this work we develop Thread Tranquilizer, an automatic technique for simultaneously reducing performance variation and improving performance by dynamically choosing appropriate memory allocation and process scheduling policies. Thread Tranquilizer uses simple utilities available on modern Operating Systems for monitoring cache misses and thread context-switches and then utilizes the collected information to dynamically select appropriate memory allocation and scheduling policies. In our experiments, Thread Tranquilizer yields up to 98% (average 68%) reduction in performance variation and up to 43% (average 15%) improvement in performance over default policies of OpenSolaris. We also demonstrate that Thread Tranquilizer simultaneously reduces performance variation and improves performance of the programs on Linux. Thread Tranquilizer is easy to use as it does not require any changes to the application source code or the OS kernel.
Using machine learning to improve automatic vectorization
Authors: Stock Kevin , Pouchet Louis-Noël , Sadayappan P.
Published: January 2012

Automatic vectorization is critical to enhancing performance of compute-intensive programs on modern processors. However, there is much room for improvement over the auto-vectorization capabilities of current production compilers through careful vector-code synthesis that utilizes a variety of loop transformations (e.g., unroll-and-jam, interchange, etc.).

As the set of transformations considered is increased, the selection of the most effective combination of transformations becomes a significant challenge: Currently used cost models in vectorizing compilers are often unable to identify the best choices. In this paper, we address this problem using machine learning models to predict the performance of SIMD codes. In contrast to existing approaches that have used high-level features of the program, we develop machine learning models based on features extracted from the generated assembly code. The models are trained offline on a number of benchmarks and used at compile-time to discriminate between numerous possible vectorized variants generated from the input code.

We demonstrate the effectiveness of the machine learning model by using it to guide automatic vectorization on a variety of tensor contraction kernels, with improvements ranging from 2× to 8× over Intel ICC's auto-vectorized code. We also evaluate the effectiveness of the model on a number of stencil computations and show good improvement over auto-vectorized code.
VSim
Authors: Ryckbosch Frederick , Polfliet Stijn , Eeckhout Lieven
Published: January 2012

Simulating contemporary computer systems is a challenging endeavor, especially when it comes to simulating high-end setups involving multiple servers. The simulation environment needs to run complete software stacks, including operating systems, middleware, and application software, and it needs to simulate network and disk activity next to CPU performance. In addition, it needs the ability to scale out to a large number of server nodes while attaining good accuracy and reasonable simulation speeds.

This paper presents VSim, a novel simulation methodology for multi-server systems. VSim leverages virtualization technology for simulating a target system on a host system. VSim controls CPU, network and disk performance on the host, and it gives the illusion to the software stack to run on a target system through time dilation. VSim can simulate multiple targets per host, and it employs a distributed simulation scheme across multiple hosts for simulations at scale. Our experimental results demonstrate VSim's accuracy: typical errors are below 6% for CPU, disk, and network performance. Real-life workloads involving the Lucene search engine and the Olio Web 2.0 benchmark illustrate VSim's utility and accuracy (average error of 3.2%). Our current setup can simulate up to five target servers per host, and we provide a Hadoop workload case study in which we simulate 25 servers. These simulation results are obtained at a simulation slowdown of one order of magnitude compared to native hardware execution.
A transactional memory with automatic performance tuning
Authors: Wang Qingping , Kulkarni Sameer , Cavazos John , Spear Michael
Published: January 2012

A significant obstacle to the acceptance of transactional memory (TM) in real-world parallel programs is the abundance of substantially different TM algorithms. Each TM algorithm appears well-suited to certain workload characteristics, but the best choice of algorithm is sensitive to program inputs, available cores, and program phases. Furthermore, operating system and hardware characteristics can affect which algorithm is best, with tradeoffs changing across iterations of a single ISA.

This paper introduces methods for constructing policies to dynamically select the most appropriate TM algorithm based on static and dynamic information. We leverage intraprocedural static analysis to create a static profile of the application. We also introduce a low-overhead framework for dynamic profiling of a running transactional application. Armed with these complementary descriptions of a program's behavior, we present novel expert adaptivity policies as well as machine learning policies that are trained off-line using simple microbenchmarks. In our evaluation, we find that both the expert and learned policies provide better performance than any single TM algorithm across the entire STAMP benchmark suite. In addition, policies that combine expert and learned policies offer the best combination of performance, maintainability, and flexibility.
Automatic authoring of interactive multimedia documents via media-oriented operators
Authors: Martins Diogo Santana , Vega-Oliveros Didier Augusto , da Graça Campos Pimentel Maria
Published: January 2012

When capturing multimedia records of collaborative activities (e.g. lectures, meetings, etc.), later access to the captured activity is usually provided by a linear video comprising the contents of the exchanged media. Such alternative impairs the review of the activity to the extent that the user only counts on the traditional timeline-based video controls. In scenarios in which automated tools generate interactive multimedia documents as a result of capturing an activity, the literature reports the use of ink-based and audio-based operators that allow the identification of points of interaction in the resulting document. In previous work, we defined a taxonomy of media-based operators in order to take into account user interactions with boards and videos, and extended the audio and ink-based operators with action-based alternatives. In this paper, the applicability of the operators is demonstrated in the context of the automatic generation of multimedia documents for interactive TV. Results from the user evaluation suggest that the operators provide means for faster review of a session when compared to a linear video.
Efficient page caching algorithm with prediction and migration for a hybrid main memory
Authors: Seok Hyunchul , Park Youngwoo , Park Ki-Woong , Park Kyu Ho
Published: January 2012

Emerging next generation memories, NVRAMs, such as Phase-change RAM (PRAM), Ferroelectric RAM (FRAM), and Magnetic RAM (MRAM) are rapidly becoming promising candidates for large scale main memory because of their high density and low power consumption. Many researchers have attempted to construct a main memory with NVRAMs, in order to make up for the limits of NVRAMs. However, we find that the preexisting page caching algorithms, such as LRU, LIRS, and CLOCK-Pro, are often sub-optimal for NVRAMs due to its DRAM-oriented design including uniform access latency and unlimited endurance. Consequently, the algorithms cannot be directly adapted to the hybrid main memory architecture with PRAM.

To mitigate this design limitation, we propose a new page caching algorithm for the hybrid main memory. It is designed to overcome the long latency and low endurance of PRAM. On the basis of the LRU replacement algorithm, we propose a prediction of page access pattern and migration schemes to maintain write-bound access pages to DRAM. The experiment results have convinced us that our page caching algorithm minimizes the number of the write access of PRAM while maintaining the cache hit ratio. The results show that we can reduce the total write access count by a maximum of 52.9% and the consumed energy by 19.9%. Therefore, we can enhance the average page cache performance and reduce the endurance problem in the hybrid main memory.
A Survey of Open Source Products for Building a SIP Communication Platform
Authors: Segec Pavel , Kovacikova Tatiana
Published: January 2012

The Session Initiation Protocol (SIP) is a multimedia signalling protocol that has evolved into a widely adopted communication standard. The integration of SIP into existing IP networks has fostered IP networks becoming a convergence platform for both real-time and non-real-time multimedia communications. This converged platform integrates data, voice, video, presence, messaging, and conference services into a single network that offers new communication experiences for users. The open source community has contributed to SIP adoption through the development of open source software for both SIP clients and servers. In this paper, we provide a survey on open SIP systems that can be built using publically available software. We identify SIP features for service development and programming, services and applications of a SIP-converged platform, and the most important technologies supporting SIP functionalities. We propose an advanced converged IP communication platform that uses SIP for service delivery. The platform supports audio and video calls, along with media services such as audio conferences, voicemail, presence, and instant messaging. Using SIP Application Programming Interfaces (APIs), the platform allows the deployment of advanced integrated services. The platform is implemented with open source software. Architecture components run on standardized hardware with no need for special purpose investments.
Endovascular Treatment of a Giant Aneurysm of the Maxillary Artery
Authors: Stephenson J. A. , Panteleimonitis S. , Choke E. , Dennis M. , Glasby M.
Published: January 2012

Aneurysms of the maxillary artery are rare and the majority of the literature refers to false aneurysms. We report the first case of what we believe to be a spontaneous true maxillary artery aneurysm and its endovascular management.
Mangrove Rehabilitation on Highly Eroded Coastal Shorelines at Samut Sakhon, Thailand
Authors: Naohiro Matsui , Putth Songsangjinda , Keiyo Morimune
Published: January 2012

The study site is currently retreating at a rate of 20 m y−1due to severe coastal erosion and found to be highly polluted as revealed from the water, sediment and biological analysis. In an attempt to prevent coastal erosion, 14,000Rhizophora mucronata(RM) trees were planted across a heavily eroded shoreline at Samut Sakhon, Thailand. The survival rate of RM was high at the landward area and decreased at the offshore area. The most landward plot showed the highest survival rate when measured 4 years after planting (63.5%), while only 26.7% of trees survived at the most offshore plot. NPK and coconut fiber were shown to be significantly effective to enhance initial tree growths in heavily eroded area.
Conformal Cosmology and the Pioneer Anomaly
Authors: Varieschi Gabriele U.
Published: January 2012

We review the fundamental results of a new cosmological model, based on conformal gravity,
and apply them to the analysis of the early data of the Pioneer anomaly.
We show that our conformal cosmology can naturally explain the anomalous acceleration of the
Pioneer 10 and 11 spacecrafts, in terms of a local blueshift region extending around the solar system
and therefore affecting the frequencies of the navigational radio signals exchanged between Earth
and the spacecraft. By using our model, we explain the numerical coincidence between the value of the anomalous
acceleration and the Hubble constant at the present epoch and also confirm our previous determination of the cosmological parameters γ∼10−28 cm−1 and δ~10-4–10-5. New Pioneer data are
expected to be publicly available in the near future, which might enable more precise evaluations
of these parameters.
Nanostructured, Self-Assembling Peptide K5 Blocks TNF-αand PGE2Production by Suppression of the AP-1/p38 Pathway
Authors: Yang Woo Seok , Park Yung Chul , Kim Ji Hye , Kim Hye Ri , Yu Tao , Byeon Se Eun , Unsworth Larry D. , Lee Jaehwi , Cho Jae Youl
Published: January 2012

Nanostructured, self-assembling peptides hold promise for a variety of regenerative medical applications such as 3D cell culture systems, accelerated wound healing, and nerve repair. The aim of this study was to determine whether the self-assembling peptide K5 can be applied as a carrier of anti-inflammatory drugs. First, we examined whether the K5 self-assembling peptide itself can modulate various cellular inflammatory responses. We found that peptide K5 significantly suppressed the release of tumor-necrosis-factor- (TNF-)αand prostaglandin E2(PGE2) from RAW264.7 cells and peritoneal macrophages stimulated by lipopolysaccharide (LPS). Similarly, there was inhibition of cyclooxygenase- (COX-) 2 mRNA expression assessed by real-time PCR, indicating that the inhibition is at the transcriptional level. In agreement with this finding, peptide K5 suppressed the translocation of the transcription factors activator protein (AP-1) and c-Jun and inhibited upstream inflammatory effectors including mitogen activated protein kinase (MAPK), p38, and mitogen-activated protein kinase kinase 3/6 (MKK 3/6). Whether this peptide exerts its effects via a transmembrane or cytoplasmic receptor is not clear. However, our data strongly suggest that the nanostructured, self-assembling peptide K5 may possess significant anti-inflammatory activity via suppression of the p38/AP-1 pathway.
Design of an Effective WSN-Based Interactive u-Learning Model
Authors: Kim Hye-jin , Caytiles Ronnie D. , Kim Tai-hoon
Published: January 2012

Wireless sensor networks include a wide range of potential applications to improve the quality of teaching and learning in a ubiquitous environment. WSNs become an evolving technology that acts as the ultimate interface between the learners and the context, enhancing the interactivity and improving the acquisition or collection of learner's contextual information in ubiquitous learning. This paper presents a model of an effective and interactive ubiquitous learning environment system based on the concepts of ubiquitous computing technology that enables learning to take place anywhere at any time. The u-learning model is a web-based e-learning system utilizing various state-of-the-art features of WSN that could enable learners to acquire knowledge and skills through interaction between them and the ubiquitous learning environment. It is based on the theory of connectivism which asserts that knowledge and the learning of knowledge are distributive and are not located in any given place but rather consist of the network of connections formed from experiences and interactions with a knowing community. The communication between devices and the embedded computers in the environment allows learners to learn in an environment of their interest while they are moving, hence, attaching them to their learning environment.
Small Vessel Cerebrovascular Disease: The Past, Present, and Future
Authors: Behrouz Réza , Malek Ali R. , Torbey Michel T.
Published: January 2012

Brain infarction due to small vessel cerebrovascular disease (SVCD)—also known as small vessel infarct (SVI) or “lacunar” stroke—accounts for 20% to 25% of all ischemic strokes. Historically, SVIs have been associated with a favorable short-term prognosis. However, studies over the years have demonstrated that SVCD/SVI is perhaps a more complex and less benign phenomenon than generally presumed. The currently employed diagnostic and therapeutic strategies are based upon historical and contemporary perceptions of SVCD/SVI. What is discovered in the future will unmask the true countenance of SVCD/SVI and help furnish more accurate prognostication schemes and effective treatments for this condition. This paper is an overview of SVCD/SVI with respect to the discoveries of the past, what is known now, and what will the ongoing investigations evince in the future.
Is the Gut Microbiota a New Factor Contributing to Obesity and Its Metabolic Disorders?
Authors: Harris Kristina , Kassis Amira , Major Geneviève , Chou Chieh J.
Published: January 2012

The gut microbiota refers to the trillions of microorganisms residing in the intestine and is integral in multiple physiological processes of the host. Recent research has shown that gut bacteria play a role in metabolic disorders such as obesity, diabetes, and cardiovascular diseases. The mechanisms by which the gut microbiota affects metabolic diseases are by two major routes: (1) the innate immune response to the structural components of bacteria (e.g., lipopolysaccharide) resulting in inflammation and (2) bacterial metabolites of dietary compounds (e.g., SCFA from fiber), which have biological activities that regulate host functions. Gut microbiota has evolved with humans as a mutualistic partner, but dysbiosis in a form of altered gut metagenome and collected microbial activities, in combination with classic genetic and environmental factors, may promote the development of metabolic disorders. This paper reviews the available literature about the gut microbiota and aforementioned metabolic disorders and reveals the gaps in knowledge for future study.
Characterization of Nanocrystalline SiGe Thin Film Solar Cell with Double Graded-Dead Absorption Layer
Authors: Wang Chao-Chun , Wuu Dong-Sing , Lien Shui-Yang , Lin Yang-Shih , Liu Chueh-Yang , Hsu Chia-Hsum , Chen Chia-Fu
Published: January 2012

The nanocrystalline silicon-germanium (nc-SiGe) thin films were deposited by high-frequency (27.12 MHz) plasma-enhanced chemical vapor deposition (HF-PECVD). The films were used in a silicon-based thin film solar cell with graded-dead absorption layer. The characterization of the nc-SiGe films are analyzed by scanning electron microscopy, UV-visible spectroscopy, and Fourier transform infrared absorption spectroscopy. The band gap of SiGe alloy can be adjusted between 0.8 and 1.7 eV by varying the gas ratio. For thin film solar cell application, using double graded-dead i-SiGe layers mainly leads to an increase in short-circuit current and therefore cell conversion efficiency. An initial conversion efficiency of 5.06% and the stabilized efficiency of 4.63% for an nc-SiGe solar cell were achieved.
Characterization of Bacterial Etiologic Agents of Biofilm Formation in Medical Devices in Critical Care Setup
Authors: Revdiwala Sangita , Rajdev Bhaumesh M. , Mulla Summaiya
Published: January 2012

Background. Biofilms contaminate catheters, ventilators, and medical implants; they act as a source of disease for humans, animals, and plants.Aim. Critical care units of any healthcare institute follow various interventional strategies with use of medical devices for the management of critical cases. Bacteria contaminate medical devices and form biofilms.Material and Methods. The study was carried out on 100 positive bacteriological cultures of medical devices which were inserted in hospitalized patients. The bacterial isolates were processed as per microtitre plate. All the isolates were subjected to antibiotic susceptibility testing by VITEK 2 compact automated systems.Results. Out of the total 100 bacterial isolates tested, 88 of them were biofilm formers. A 16–20-hour incubation period was found to be optimum for biofilm development. 85% isolates were multidrug resistants and different mechanisms of bacterial drug resistance like ESBL, carbapenemase, and MRSA were found among isolates.Conclusion. Availability of nutrition in the form of glucose enhances the biofilm formation by bacteria. Time and availability of glucose are important factors for assessment of biofilm progress. It is an alarm for those who are associated with invasive procedures and indwelling medical devices especially in patients with low immunity.
High EGFR Gene Copy Number and Skin Rash as Predictive Markers for EGFR Tyrosine Kinase Inhibitors in Patients with Advanced Squamous Cell Lung Carcinoma
Authors: Lee Youngjoo , Shim Hyo Sup , Park Moo Suk , Kim Joo-Hang , Ha Sang-Jun , Kim Se Hoon , Cho Byoung Chul
Published: January 2012

Purpose: This study aimed to search for predictors of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) efficacy in previously treated patients with advanced squamous cell lung carcinoma in which EGFR mutations are very rare.

Experimental Design: EGFR gene copy numbers were assessed by FISH and evaluated as predictors of EGFR-TKI efficacy in 71 patients with advanced squamous cell lung cancer who received gefitinib or erlotinib as a second-line or higher therapy. The tumors were classified into EGFR/FISH-positive (high polysomy/gene amplification) and EGFR/FISH-negative (other) groups.

Results: EGFR/FISH was positive in 19 (26.7%) patients. Only EGFR/FISH positive status was correlated with the EGFR-TKIs response (EGFR/FISH+ vs. EGFR/FISH−, 26.3% vs. 2.0%; P = 0.005). In a multivariate analysis, the risk of progression was lower in EGFR/FISH-positive patients (HR of EGFR/FISH+ vs. EGFR/FISH−, 0.57; P = 0.057) or patients experiencing grade 2 or more rash (HR for rash grade 2 or more vs. less than 2, 0.54; P = 0.042), compared with EGFR/FISH-negative patients or those experiencing grade of less than 2 rash, respectively. When the combined criteria of EGFR/FISH and skin rash severity were analyzed, EGFR/FISH-negative patients with grade less than 2 rash had poorer clinical outcomes than patients with positive EGFR/FISH or grade 2 or more rash, apparent as a lower response rate (0.0% vs. 21.4%; P = 0.003) and a shorter median progression-free survival (1.13 months vs. 3.90 months; P = 0.0002).

Conclusions: EGFR/FISH and skin rash severity may be used to identify which patients are likely to gain a benefit from EGFR-TKIs in this population. Clin Cancer Res; 18(6); 1760–8. ©2012 AACR.
The Antioxidant N-Acetylcysteine Prevents the Mitochondrial Fragmentation Induced by Soluble Amyloid-F Peptide Oligomers
Authors: SanMartin C.D. , Adasme T. , Hidalgo C. , Paula-Lima A.C.
Published: January 2012

Background: Soluble amyloid-F peptide oligomers (AFOs), which are centrally involved in the pathogenesis of Alzheimer’s disease, trigger Ca2+ influx through N-methyl-D-aspartate receptors and stimulate reactive oxygen species generation in primary hippocampal neurons. We have previously reported that AFOs promote Ca2+ release mediated by ryanodine receptors (RyR), which in turn triggers mitochondrial fragmentation. We have also reported that the antioxidant N-acetylcysteine (NAC) prevents AFOs-induced Ca2+ signal generation. Objectives: To determine if RyR-mediated Ca2+ release activated by the specific agonist 4-chloro-m-cresol (4-CMC) induces fragmentation of the mitochondrial network, and to ascertain if NAC prevents the mitochondrial fragmentation induced by AFOs and/or 4-CMC. Methods: Mature primary rat hippocampal neurons were incubated for 24 h with sublethal concentrations of AFOs (500 nM) or for 1–3 h with 4-CMC (0.5–1 mM), w10 mM NAC. Mitochondrial morphology was assessed by confocal microscopy of fixed neurons stained with anti-mHsp70. Intracellular Ca2+ levels were determined by time series microscopy of neurons preloaded with Fluo-4 AM. Results: Preincubation of neurons for 30 min with NAC prevented the mitochondrial fragmentation induced by AFOs or 4-CMC. In addition, we confirmed that preincubation with NAC abolished the stimulation of RyR-mediated Ca2+ release induced by AFOs or 4-CMC. Conclusion: The present results strongly suggest that the general antioxidant NAC prevents AFO-induced mitochondrial fragmentation by preventing RyR-mediated Ca2+-induced Ca2+ release. Copyright i 2012 S. Karger AG, Basel
Recognition of Face Identity and Emotion in Expressive Specific Language Impairment
Authors: Merkenschlager A. , Amorosa H. , Kiefl H. , Martinius J.
Published: January 2012

Objective: To study face and emotion recognition in children with mostly expressive specific language impairment (SLI-E). Subjects and Methods: A test movie to study perception and recognition of faces and mimic-gestural expression was applied to 24 children diagnosed as suffering from SLI-E and an age-matched control group of normally developing children. Results: Compared to a normal control group, the SLI-E children scored significantly worse in both the face and expression recognition tasks with a preponderant effect on emotion recognition. The performance of the SLI-E group could not be explained by reduced attention during the test session. Conclusion: We conclude that SLI-E is associated with a deficiency in decoding non-verbal emotional facial and gestural information, which might lead to profound and persistent problems in social interaction and development.