bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical Accuracy of a PLEX-ID Flu Device for Simultaneous Detection and Identification of Influenza Viruses A and B
Authors: Tang Yi-Wei , Lowery Kristin S. , Valsamakis Alexandra , Schaefer Virginia C. , Chappell James D. , White-Abell Jill , Quinn Criziel D. , Li Haijing , Washington Cicely A. , Cromwell Jenna , Giamanco Chantel M. , Forman Michael , Holden Jeffery , Rothman Richard E. , Parker Michelle L. , Ortenberg Elaine V. , Zhang Lei , Lin Yea-Lin , Gaydos Charlotte A.
Published: October 2012

Respiratory tract infections caused by influenza A and B viruses often present nonspecifically, and a rapid, high-throughput laboratory technique that can identify influenza viruses is clinically and epidemiologically desirable. The PLEX-ID Flu assay (Abbott Molecular Inc., Des Plaines, IL) incorporates multilocus PCR and electrospray ionization-mass spectrometry to detect and differentiate influenza A 2009 H1N1 (H1N1-p), seasonal H1N1 (H1N1-s), influenza A H3N2, and influenza B viruses in nasopharyngeal swab (NPS) specimens. The clinical performance characteristics of the PLEX-ID Flu assay in symptomatic patients were determined in this multicenter trial. A total of 2,617 prospectively and retrospectively collected NPS specimens from patients with influenza-like illness between February 2008 and 28 May 2010 were eligible for inclusion in the study. Each specimen was tested in parallel by the PLEX-ID Flu assay and by the Prodesse ProFLU+ assay (Prodesse Inc., Madison, WI), to detect influenza A and B viruses. Specimens testing positive for influenza A virus by ProFLU+ were subtyped as H1N1-p, H1N1-s, or H3N2 by using the ProFAST+ assay (Gen-Probe Prodesse Inc.). The reproducibility of the PLEX-ID Flu assay ranged from 98.3 to 100.0%, as determined by testing a nine-specimen panel at three clinical sites on each of 5 days. Positive percent agreements (PPAs) and negative percent agreements (NPAs) of the PLEX-ID Flu assay were 94.5% and 99.0% for influenza A virus and 96.0% and 99.9% for influenza B virus, respectively. For the influenza A virus subtyping characterization, the PLEX-ID Flu assay had PPAs and NPAs of 98.3% and 97.5% for H1N1-p, 88.6% and 100.0% for H1N1-s, and 98.0% and 99.9% for H3N2, respectively. The overall agreements between the PLEX-ID and Prodesse ProFLU+/ProFAST+ assays were 97.1 to 100.0%. Bidirectional Sanger sequencing analysis revealed that 87.5% of 96 discrepant results between the PLEX-ID Flu and ProFLU+/ProFAST+ assays were found upon influenza A virus detection and H1N1-p subtyping. The PLEX-ID Flu assay demonstrated a high level of accuracy for the simultaneous detection and identification of influenza A and B viruses in patient specimens, providing a new laboratory tool for the rapid diagnosis and management of influenza A and B virus infections.
Taxonomy and Antifungal Susceptibility of Clinically Important Rasamsonia Species
Authors: Houbraken J. , Giraud S. , Meijer M. , Bertout S. , Frisvad J. C. , Meis J. F. , Bouchara J. P. , Samson R. A.
Published: October 2012

In recent years,
Geosmithia argillacea
has been increasingly reported in humans and animals and can be considered an emerging pathogen. The taxonomy of
Geosmithia
was recently studied, and
Geosmithia argillacea
and related species were transferred to the new genus
Rasamsonia
. The diversity among a set of
Rasamsonia argillacea
strains, including 28 clinical strains, was studied, and antifungal susceptibility profiles were generated. Data obtained from morphological studies and from phylogenetic analyses of internal transcribed spacer (ITS) and partial β-tubulin and calmodulin sequences revealed the presence of four species in the
Rasamsonia argillacea
complex, two of which are newly described here:
R. piperina
sp. nov. and
R. aegroticola
sp. nov. In contrast to other related genera, all
Rasamsonia
species can be identified with ITS sequences. A retrospective identification was performed on recently reported clinical isolates from animal or human patients. Susceptibility tests showed that the antifungal susceptibility profiles of the four members of the
R. argillacea
complex are similar, and caspofungin showed significant activity
in vitro
, followed by amphotericin B and posaconazole. Voriconazole was the least active of the antifungals tested. The phenotypically similar species
R. brevistipitata
and
R. cylindrospora
had different antifungal susceptibility profiles, and this indicates that correct species identification is important to help guide appropriate antifungal therapy.
Inhibition of Reverse Transcriptase Activity Increases Stability of the HIV-1 Core
Authors: Yang Yang , Fricke Thomas , Diaz-Griffero Felipe
Published: October 2012

Previous studies showed that HIV-1 reverse transcription occurs during or before uncoating, linking mechanistically reverse transcription with uncoating. Here we show that inhibition of reverse transcriptase (RT) during HIV-1 infection by pharmacologic or genetic means increased the stability of the HIV-1 core during infection. Interestingly, HIV-1 particles with increased core stability were resistant to the core-destabilizing effects of rhesus TRIM5α (TRIM5α
rh
). Collectively, this work implies that the surface of the HIV-1 core is dynamic and changes upon the ongoing processes within the core.
Investigation of Influenza Virus Polymerase Activity in Pig Cells
Authors: Moncorgé Olivier , Long Jason S. , Cauldwell Anna V. , Zhou Hongbo , Lycett Samantha J. , Barclay Wendy S.
Published: October 2012

Reassortant influenza viruses with combinations of avian, human, and/or swine genomic segments have been detected frequently in pigs. As a consequence, pigs have been accused of being a “mixing vessel” for influenza viruses. This implies that pig cells support transcription and replication of avian influenza viruses, in contrast to human cells, in which most avian influenza virus polymerases display limited activity. Although influenza virus polymerase activity has been studied in human and avian cells for many years by use of a minigenome assay, similar investigations in pig cells have not been reported. We developed the first minigenome assay for pig cells and compared the activities of polymerases of avian or human influenza virus origin in pig, human, and avian cells. We also investigated in pig cells the consequences of some known mammalian host range determinants that enhance influenza virus polymerase activity in human cells, such as PB2 mutations E627K, D701N, G590S/Q591R, and T271A. The two typical avian influenza virus polymerases used in this study were poorly active in pig cells, similar to what is seen in human cells, and mutations that adapt the avian influenza virus polymerase for human cells also increased activity in pig cells. In contrast, a different pattern was observed in avian cells. Finally, highly pathogenic avian influenza virus H5N1 polymerase activity was tested because this subtype has been reported to replicate only poorly in pigs. H5N1 polymerase was active in swine cells, suggesting that other barriers restrict these viruses from becoming endemic in pigs.
Attenuation of Porcine Reproductive and Respiratory Syndrome Virus by Molecular Breeding of Virus Envelope Genes from Genetically Divergent Strains
Authors: Ni Yan-Yan , Opriessnig Tanja , Zhou Lei , Cao Dianjun , Huang Yao-Wei , Halbur Patrick G. , Meng Xiang-Jin
Published: October 2012

Molecular breeding via DNA shuffling can direct the evolution of viruses with desired traits. By using a positive-strand RNA virus, porcine reproductive and respiratory syndrome virus (PRRSV), as a model, rapid attenuation of the virus was achieved in this study by DNA shuffling of the viral envelope genes from multiple strains. The GP5 envelope genes of 7 genetically divergent PRRSV strains and the GP5-M genes of 6 different PRRSV strains were molecularly bred by DNA shuffling and iteration of the process, and the shuffled genes were cloned into the backbone of a DNA-launched PRRSV infectious clone. Two representative chimeric viruses, DS722 with shuffled GP5 genes and DS5M3 with shuffled GP5-M genes, were rescued and shown to replicate at a lower level and to form smaller plaques
in vitro
than their parental virus. An
in vivo
pathogenicity study revealed that pigs infected with the two chimeric viruses had significant reductions in viral-RNA loads in sera and lungs and in gross and microscopic lung lesions, indicating attenuation of the chimeric viruses. Furthermore, pigs vaccinated with the chimeric virus DS722, but not pigs vaccinated with DS5M3, still acquired protection against PRRSV challenge at a level similar to that of the parental virus. Therefore, this study reveals a unique approach through DNA shuffling of viral envelope genes to attenuate a positive-strand RNA virus. The results have important implications for future vaccine development and will generate broad general interest in the scientific community in rapidly attenuating other important human and veterinary viruses.
Mechanism for Active Membrane Fusion Triggering by Morbillivirus Attachment Protein
Authors: Ader Nadine , Brindley Melinda , Avila Mislay , Örvell Claes , Horvat Branka , Hiltensperger Georg , Schneider-Schaulies Jürgen , Vandevelde Marc , Zurbriggen Andreas , Plemper Richard K. , Plattet Philippe
Published: October 2012

The paramyxovirus entry machinery consists of two glycoproteins that tightly cooperate to achieve membrane fusion for cell entry: the tetrameric attachment protein (HN, H, or G, depending on the paramyxovirus genus) and the trimeric fusion protein (F). Here, we explore whether receptor-induced conformational changes within morbillivirus H proteins promote membrane fusion by a mechanism requiring the active destabilization of prefusion F or by the dissociation of prefusion F from intracellularly preformed glycoprotein complexes. To properly probe F conformations, we identified anti-F monoclonal antibodies (MAbs) that recognize conformation-dependent epitopes. Through heat treatment as a surrogate for H-mediated F triggering, we demonstrate with these MAbs that the morbillivirus F trimer contains a sufficiently high inherent activation energy barrier to maintain the metastable prefusion state even in the absence of H. This notion was further validated by exploring the conformational states of destabilized F mutants and stabilized soluble F variants combined with the use of a membrane fusion inhibitor (3g). Taken together, our findings reveal that the morbillivirus H protein must lower the activation energy barrier of metastable prefusion F for fusion triggering.
Role of Interferon Regulatory Factor 3-Mediated Apoptosis in the Establishment and Maintenance of Persistent Infection by Sendai Virus
Authors: Chattopadhyay Saurabh , Fensterl Volker , Zhang Ying , Veleeparambil Manoj , Yamashita Michifumi , Sen Ganes C.
Published: October 2012

Infection of cultured cells by paramyxoviruses causes cell death, mediated by a newly discovered apoptotic pathway activated by virus infection. The key proapoptotic protein in this pathway is interferon regulatory factor 3 (IRF-3), which upon activation by virus infection binds BAX, translocates it to mitochondria, and triggers apoptosis. When IRF-3-knockdown cells were infected with Sendai virus (SeV), persistent infection (PI) was established. The PI cells produced infectious SeV continuously and constitutively expressed many innate immune genes. Interferon signaling was blocked in these cells. The elevated levels of IRF-3-driven genes in the PI cells indicated that the amount of residual IRF-3 activated by endogenous SeV was high enough to drive the transcriptional effects of IRF-3 but too low to trigger its apoptotic activity. We confirmed this IRF-3 threshold idea by generating a tetracycline (Tet)-inducible cell line for IRF-3 expression, which enabled us to express various levels of IRF-3. PI could be established in the Tet-off cell line, and as expected, when doxycycline was withdrawn, the cells underwent apoptosis. Finally, we tested for PI establishment in 12 mouse embryo fibroblasts by natural selection. Eleven lines became persistently infected; although seven out of them had low IRF-3 levels, four did not. When one of the latter four was further analyzed, we observed that it expressed a very low level of caspase 3, the final executor protease of the apoptotic pathway. These results demonstrated that SeV PI can arise from infection of normal wild-type cells, but only if they can find a way to impair the IRF-3-dependent apoptotic pathway.
A Single-Amino-Acid Change in Murine Norovirus NS1/2 Is Sufficient for Colonic Tropism and Persistence
Authors: Nice Timothy J. , Strong David W. , McCune Broc T. , Pohl Calvin S. , Virgin Herbert W.
Published: October 2012

Human norovirus (HuNoV) is the major cause of acute nonbacterial gastroenteritis worldwide but has no clear animal reservoir. HuNoV can persist after the resolution of symptoms, and this persistence may be essential for viral maintenance within the population. Many strains of the related murine norovirus (MNV) also persist, providing a tractable animal model for studying norovirus (NoV) persistence. We have used recombinant cDNA clones of representative persistent (CR6) and nonpersistent (CW3) strains to identify a domain within the nonstructural gene NS1/2 that is necessary and sufficient for persistence. Furthermore, we found that a single change of aspartic acid to glutamic acid in CW3 NS1/2 was sufficient for persistence. This same conservative change also caused increased growth of CW3 in the proximal colon, which we found to be a major tissue reservoir of MNV persistence, suggesting that NS1/2 determines viral tropism that is necessary for persistence. These findings represent the first identified function for NoV NS1/2 during infection and establish a novel model system for the study of enteric viral persistence.
Essential Role of Rta in Lytic DNA Replication of Epstein-Barr Virus
Authors: El-Guindy Ayman , Ghiassi-Nejad Maryam , Golden Sean , Delecluse Henri-Jacques , Miller George
Published: October 2012

Two transcription factors, ZEBRA and Rta, switch Epstein-Barr virus (EBV) from the latent to the lytic state. While ZEBRA also plays an obligatory role as an activator of replication, it is not known whether Rta is directly required for replication. Rta is dispensable for amplification of an oriLyt-containing plasmid in a transient-replication assay. Here, we assessed the requirement for Rta in activation of viral DNA synthesis from the endogenous viral genome, a function that has not been established. Initially, we searched for a ZEBRA mutant that supports viral replication but not transcription. We found that Z(S186A), a mutant of ZEBRA unable to activate transcription of Rta or viral genes encoding replication proteins, is competent to bind to oriLyt and to function as an origin recognition protein. Ectopic expression of the six components of the EBV lytic replication machinery failed to rescue replication by Z(S186A). However, addition of Rta to Z(S186A) and the mixture of replication factors activated viral replication and late gene expression. Deletion mutagenesis of Rta indicated that the C-terminal 10 amino acids (aa) were essential for the function of Rta in replication.
In vivo
DNA binding studies revealed that Rta interacted with the enhancer region of oriLyt. In addition, expression of Rta and Z(S186A) together, but not individually, activated synthesis of the BHLF1 transcript, a lytic transcript required for the process of viral DNA replication. Our findings demonstrate that Rta plays an indispensable role in the process of lytic DNA replication.
High Frequency of Herpesvirus-Specific Clonotypes in the Human T Cell Repertoire Can Remain Stable over Decades with Minimal Turnover
Authors: Neller M. A. , Burrows J. M. , Rist M. J. , Miles J. J. , Burrows S. R.
Published: October 2012

High-throughput T cell receptor sequencing on sequentially banked blood samples from healthy individuals has shown that high-frequency clonotypes can remain relatively stable for up to 18 years, with minimal inflation, deflation, or turnover. These populations included T cell expansions specific for Epstein-Barr virus. Thus, in spite of exposure to a barrage of microorganisms over the course of life, the dominant clonotypes in the mature peripheral T cell repertoire can alter surprisingly little.
Recombinant Parainfluenza Virus 5 Expressing Hemagglutinin of Influenza A Virus H5N1 Protected Mice against Lethal Highly Pathogenic Avian Influenza Virus H5N1 Challenge
Authors: Li Zhuo , Mooney Alaina J. , Gabbard Jon D. , Gao Xiudan , Xu Pei , Place Ryan J. , Hogan Robert J. , Tompkins S. Mark , He Biao
Published: October 2012

A safe and effective vaccine is the best way to prevent large-scale highly pathogenic avian influenza virus (HPAI) H5N1 outbreaks in the human population. The current FDA-approved H5N1 vaccine has serious limitations. A more efficacious H5N1 vaccine is urgently needed. Parainfluenza virus 5 (PIV5), a paramyxovirus, is not known to cause any illness in humans. PIV5 is an attractive vaccine vector. In our studies, a single dose of a live recombinant PIV5 expressing a hemagglutinin (HA) gene of H5N1 (rPIV5-H5) from the H5N1 subtype provided sterilizing immunity against lethal doses of HPAI H5N1 infection in mice. Furthermore, we have examined the effect of insertion of H5N1 HA at different locations within the PIV5 genome on the efficacy of a PIV5-based vaccine. Interestingly, insertion of H5N1 HA between the leader sequence, thede factopromoter of PIV5, and the first viral gene, nucleoprotein (NP), did not lead to a viable virus. Insertion of H5N1 HA between NP and the next gene, V/phosphorprotein (V/P), led to a virus that was defective in growth. We have found that insertion of H5N1 HA at the junction between the small hydrophobic (SH) gene and the hemagglutinin-neuraminidase (HN) gene gave the best immunity against HPAI H5N1 challenge: a dose as low as 1,000 PFU was sufficient to protect against lethal HPAI H5N1 challenge in mice. The work suggests that recombinant PIV5 expressing H5N1 HA has great potential as an HPAI H5N1 vaccine.
THE SUPERLUMINAL NEUTRINOS FROM DEFORMED LORENTZ INVARIANCE
Authors: HUO YUNJIE , LI TIANJUN , LIAO YI , NANOPOULOS DIMITRI V. , QI YONGHUI , WANG FEI
Published: October 2012

We study two superluminal neutrino scenarios where [Formula: see text] is a constant. To be consistent with the OPERA, Borexino and ICARUS experiments and with the SN1987a observations, we assume that δvν on the Earth is about three-order larger than that on the interstellar scale. To explain the theoretical challenges from the Bremsstrahlung effects and pion decays, we consider the deformed Lorentz invariance, and show that the superluminal neutrino dispersion relations can be realized properly while the modifications to the dispersion relations of the other Standard Model particles can be negligible. In addition, we propose the deformed energy and momentum conservation laws for a generic physical process. In Scenario I the momentum conservation law is preserved while the energy conservation law is deformed. In Scenario II the energy conservation law is preserved while the momentum conservation law is deformed. We present the energy and momentum conservation laws in terms of neutrino momentum in Scenario I and in terms of neutrino energy in Scenario II. In such formats, the energy and momentum conservation laws are exactly the same as those in the traditional quantum field theory with Lorentz symmetry. Thus, all the above theoretical challenges can be automatically solved. We show explicitly that the Bremsstrahlung processes are forbidden and there is no problem for pion decays.
LEARNING BETTER INSPECTION OPTIMIZATION POLICIES
Authors: LUMPE MARKUS , VASA RAJESH , MENZIES TIM , RUSH REBECCA , TURHAN BURAK
Published: October 2012

Recent research has shown the value of social metrics for defect prediction. Yet many repositories lack the information required for a social analysis. So, what other means exist to infer how developers interact around their code? One option is static code metrics that have already demonstrated their usefulness in analyzing change in evolving software systems. But do they also help in defect prediction? To address this question we selected a set of static code metrics to determine what classes are most "active" (i.e., the classes where the developers spend much time interacting with each other's design and implementation decisions) in 33 open-source Java systems that lack details about individual developers. In particular, we assessed the merit of these activity-centric measures in the context of "inspection optimization" — a technique that allows for reading the fewest lines of code in order to find the most defects. For the task of inspection optimization these activity measures perform as well as (usually, within 4%) a theoretical upper bound on the performance of any set of measures. As a result, we argue that activity-centric static code metrics are an excellent predictor for defects.
A FRAMEWORK FOR AUTOMATED CONSTRUCTION OF NODE SOFTWARE USING LOW-LEVEL ATTRIBUTES IN USN APPLICATION DEVELOPMENT
Authors: LEE WOOJIN , KIM JUIL , KANG JANGMOOK
Published: October 2012

Nodes comprising ubiquitous sensor networks have limited processing speed, storage capacity and communication bandwidth. Developing a USN application considering such problems is a difficult task. In this paper, a framework for automated construction of node software using low-level attributes is presented in order to support the developers who are not familiar with developing USN applications for their effective development of USN applications. The presented framework consists of attributes necessary for designing an application, code templates necessary for generating softwares for sensor nodes in the application, and tools necessary for designing and generating the application. Through the presented framework, the developers can easily design a USN application by using low-level attributes and automatically generate node softwares for the USN application. Therefore, development productivity will be increased.
AUTOMATED DEBUGGING OF VERILOG DESIGNS
Authors: PEISCHL BERNHARD , RIAZ NAVEED , WOTAWA FRANZ
Published: October 2012

In this article we report on novel insights in model-based software debugging of hardware description languages (HDLs). Today's simulation driven working process emphasizes the need for exploiting test suites not only for detecting but also for localizing the root cause of misbehavior. We discuss the modeling approaches for the various artifacts of the Verilog hardware description language (blocking and non-blocking statements, expressions, execution ordering) and present a novel model incorporating test suites. The evaluation of our approach on the well-known ISCAS89 benchmarks concerning single and double-fault diagnoses clearly indicates that incorporating test suites into the fault localization technique (and development process) considerably improves the accuracy of the obtained diagnosis candidates.
HOLOGRAPHY, QUANTUM GRAVITY AND CONFINEMENT
Authors: HUSAIN VIQAR , KOTHAWALA DAWOOD
Published: October 2012

In the holographic dictionary between gauge theory in four dimensions and gravity in five dimensions, there is an encoding in the bulk geometry of the phases of the gauge theory. If the correspondence holds at all scales, it is natural to expect that gauge theory contains information about quantum gravity in one higher dimension. We argue that the confining phase of gauge theory has a correspondence with singularity avoidance in quantum gravity. This comes from the observation that confinement appears to be generically associated with repulsion deep in the bulk on the gravity side, which in turn is a consequence of the violation of energy conditions in quantum gravity that lead to singularity avoidance.
FRW TYPE OF COSMOLOGY WITH A CHAPLYGIN GAS
Authors: PANIGRAHI D. , CHATTERJEE S.
Published: October 2012

The evolution of a universe modeled as a mixture of generalized Chaplygin gas (GCG) and ordinary matter field is studied for a Robertson–Walker type of spacetime. This model could interpolate periods of radiation-dominated, matter-dominated and cosmological constant-dominated universes. Depending on the arbitrary constants appearing in our theory, the instant of flip changes. Interestingly, we also get a bouncing model when the signature of one of the constants changes. The velocity of sound may become imaginary under certain situations pointing to a perturbative state and consequently the possibility of structure formation. We also discuss the whole situation in the backdrop of the well-known Raychaudhuri equation and a comparison is made with the previous results.
HOMOTHETIC KILLING VECTORS IN EXPANDING $\mathcal{HH}$-SPACES WITH Λ
Authors: CHUDECKI ADAM
Published: October 2012

Conformal Killing equations and their integrability conditions for expanding hyperheavenly spaces with Λ in spinorial formalism are studied. It is shown that any conformal Killing vector reduces to homothetic or isometric Killing vector. Reduction of respective Killing equation to one master equation is presented. Classification of homothetic and isometric Killing vectors is given. Type [D] ⊗ [any] is analyzed in detail and some expanding [Formula: see text] complex metrics of types [III, N] ⊗ [III, N] with Λ admitting isometric Killing vectors are found.
CONFORMAL COURANT ALGEBROIDS AND ORIENTIFOLD T-DUALITY
Authors: BARAGLIA DAVID
Published: October 2012

We introduce conformal Courant algebroids, a mild generalization of Courant algebroids in which only a conformal structure rather than a bilinear form is assumed. We introduce exact conformal Courant algebroids and show they are classified by pairs (L, H) with L a flat line bundle and H ∈ H3(M, L) a degree 3 class with coefficients in L. As a special case gerbes for the crossed module (U(1) → ℤ2) can be used to twist TM ⊕ T*M into a conformal Courant algebroid. In the exact case there is a twisted cohomology which is 4-periodic if L2= 1. The structure of Conformal Courant algebroids on circle bundles leads us to construct a T-duality for orientifolds with free involution. This incarnation of T-duality yields an isomorphism of 4-periodic twisted cohomology. We conjecture that the isomorphism extends to an isomorphism in twisted KR-theory and give some calculations to support this claim.
An Algorithm for Jointly Optimizing Quantization and Multiple Constant Multiplication
Authors: Gately Matthew B. , Yeary Mark B. , Tang Choon Yik
Published: October 2012

This article presents a joint framework for quantization and Multiple Constant Multiplication (MCM) optimization, which yields a computationally efficient implementation of multiplierless multiplication in hardware and software. Frameworks of this nature have been developed in the context of Finite Impulse Response (FIR) filters, where frequency response specifications are used to drive the design. In this work, we look at a general case, considering as given a vector of ideal, real constants, which may come from any application and do not necessarily represent FIR filter coefficients. We first formulate a joint optimization problem for finding a fixed-point vector and a shift-add network that are optimal in terms of quantization error and MCM complexity. We then describe ways to finitize and prune the search space, leading to an efficient algorithm called JOINT_SOLVE that solves the problem. Finally, via extensive randomized experiments, we show that our joint framework is notably more computationally efficient than a disjointed one, reducing the MCM cost by 15%--60% on moderate size problems.
Conditional Diagnosability of k-Ary n-Cubes under the PMC Model
Authors: Chang Nai-Wen , Lin Tzu-Yin , Hsieh Sun-Yuan
Published: October 2012

Processor fault diagnosis plays an important role in measuring the reliability of multiprocessor systems and the diagnosis of many well-known interconnection networks. The conditional diagnosability, which is more general than the classical diagnosability, is to measure the diagnosability of a multiprocessor system under the assumption that all of the neighbors of any node in the system cannot fail at the same time. This study shows that the conditional diagnosability for
k
-ary
n
-cubes under the PMC model is 8
n
 − 7 for
k
 ≥ 4 and
n
 ≥ 4.
Migration-Resistant Policies for Probe-Wear Leveling in MEMS Storage Devices
Authors: Khatib Mohammed G.
Published: October 2012

Probes (read/write heads) in a MEMS storage device are susceptible to wear. We study probe wear, and analyze the causes of uneven wear. We show that under real-world workloads some probes can wear one order of magnitude faster than others. This premature expiry has severe consequences for reliability, timing performance, energy efficiency, and lifetime. Wear leveling precludes premature expiry and is thus necessary. We discuss the fundamental differences between probe wear in MEMS storage and medium wear in Flash, calling for a different treatment.

We devise three policies to level probe wear. The policies provide a spectrum between best lifetime and least influence on the response time and energy efficiency of a MEMS storage device. We make the case that data migration can be prevented by augmenting the policies with a simple rule. We study the influence of the data layout configuration on the leveling performance of the policies.
Fast Statistical Full-Chip Leakage Analysis for Nanometer VLSI Systems
Authors: Shen Ruijing , Tan Sheldon X.-D. , Wang Hai , Xiong Jinjun
Published: October 2012

In this article, we present a new full-chip statistical leakage estimation considering the spatial correlation condition (strong or weak). The new algorithm can deliver linear time,
O
(
N
), time complexity, where
N
is the number of grids on chip. The proposed algorithm adopts a set of uncorrelated virtual variables over grid cells to represent the original physical random variables and the cell size is determined by the spatial correlation length. In this way, each physical variable is always represented by virtual variables locally. We prove the number of neighbor cells for each grid cell is not related to the condition of spatial correlation (from no correlation to 100% correlated), which leads to linear time complexity in terms of number of gates. We compute the gate leakage by the orthogonal polynomials-based collocation method. The total leakage of a whole chip can be computed by simply summing up the coefficients of corresponding orthogonal polynomials in each grid cell. Furthermore, we develop a look-up table to cache statistical information for each
type
of gate instead of calculating leakage for every single instance of gate on a chip. As a result, a new statistical leakage characterization in Standard Cell Library (SCL) is put forward. Furthermore, an incremental analysis algorithm is proposed to update the chip-level statistical leakage information efficiently after a few changes are made. The proposed method has no restrictions on static leakage models, or types of leakage distributions. The large circuit examples in 45nm CMOS process demonstrate the proposed algorithm is 1000X faster than a recently proposed grid-based method with similar accuracy and many orders of magnitude times speedup over the Monte Carlo method. Experimental results also show the incremental analysis provides about 10X further speedup. We expect the incremental analysis could achieve more speedup over the full leakage analysis for larger problem sizes.
Enhancing Reconfigurable Platforms Programmability for Synchronous Data-Flow Applications
Authors: Gantel Laurent , Khiar Amel , Miramond Benoit , Benkhelifa Mohamed El Amine , Kessal Lounis , Lemonnier Fabrice , Le Rhun Jimmy
Published: October 2012

Recent FPGAs allow the design of efficient and complex
Heterogeneous Systems-on-Chip
(HSoC). Namely, these systems are composed of several processors, hardware accelerators as well as communication media between all these components. Performances provided by HSoCs make them really interesting for data-flow applications, especially image processing applications. The use of this kind of architecture provides good performances but the drawback is an increase of the programming complexity.

This complexity is due to the heterogeneous deployment of the application on the platform. Some functions are implemented in software to run on a processor, whereas other functions are implemented in hardware to run in a reconfigurable partition of the FPGA. This article aims to define a programming model based on the Synchronous Data-Flow model, in order to abstract the heterogeneity of the implementation and to leverage the communication issue between software and hardware actors.
Secure Extension of FPGA General Purpose Processors for Symmetric Key Cryptography with Partial Reconfiguration Capabilities
Authors: Gaspar Lubos , Fischer Viktor , Bossuet Lilian , Fouquet Robert
Published: October 2012

In data security systems, general purpose processors (GPPs) are often extended by a cryptographic accelerator. The article presents three ways of extending GPPs for symmetric key cryptography applications. Proposed extensions guarantee secure key storage and management even if the system is facing protocol, software and cache memory attacks. The system is partitioned into processor, cipher, and key memory zones. The three security zones are separated at protocol, system, architecture and physical levels. The proposed principle was validated on Altera NIOS II, Xilinx MicroBlaze and Microsemi Cortex M1 soft-core processor extensions. We show that stringent separation of the cipher zone is helpful for partial reconfiguration of the security module, if the enciphering algorithm needs to be dynamically changed. However, the key zone including reconfiguration controller must remain static in order to maintain the high level of security required. We demonstrate that the principle is feasible in partially reconfigurable field programmable gate arrays (FPGAs) such as Altera Stratix V or Xilinx Virtex 6 and also to some extent in FPGAs featuring hardwired general purpose processors such as Cortex M3 in Microsemi SmartFusion FPGA. Although the three GPPs feature different data interfaces, we show that the processors with their extensions reach the required high security level while maintaining partial reconfiguration capability.
Privacy perception and fall detection accuracy for in-home video assistive monitoring with privacy enhancements
Authors: Edgcomb Alex , Vahid Frank
Published: October 2012

Video of in-home activity provides valuable information for assistive monitoring but raises privacy concerns. Raw video can be privacy-enhanced by obscuring the appearance of a person. We consider five privacy enhancements: blur, silhouette, oval, box, and trailing-arrows. We investigate whether a privacy enhancement exists that provides sufficient perceived privacy while enabling accurate fall detection by humans. We recorded 23 1-minute videos involving normal household activities, falling, and lying on the floor after an earlier fall, and created versions of each video for each privacy setting. We conducted an experiment with 376 undergraduate, non-engineering student participants to measure perceived privacy protection and the participant's fall detection accuracy for each privacy setting. Results indicate that the oval provides sufficient perceived privacy for 88% of participants while still supporting fall detection accuracy of 89%, and that the common privacy enhancements blur and silhouette were perceived to provide insufficient privacy.
Research challenges in measuring data for population health to enable predictive modeling for improving healthcare
Authors: Schatz Bruce , Marsh Clay , Gustafson David , Patrick Kevin , Krishnan Jerry , Kumar Santosh , Contractor Noshir
Published: October 2012

At the core of the healthcare crisis is a fundamental lack of actionable data, needed to stratify individuals within populations, to predict which persons have which outcomes. A new health system with better health management will require better health measurement, to improve cost and quality. It is now possible to use new technologies to provide the rich datasets necessary for adequate health measurement, which enables new information systems for new health systems.

This report is a summary of a workshop on
Measuring Data for Population Health
, sponsored by the NSF SmartHealth program with assistance from the NIH mHealth initiative, held on January 12--13, 2012 in Washington DC. There were 42 attendees, including invited researchers from academia, government and industry, plus program officers from NSF and NIH.

The workshop had background talks by leaders in health systems and information systems, followed by breakout discussions on future challenges and opportunities in measuring and managing population health. This report describes the observations on what problems of health systems should be addressed and what solutions of information systems should be developed. The recommendations cover how new information technologies can enable new health systems, with support from future initiatives of federal programs.

The workshop and its report identify research challenges that utilize new computing and information technologies to enable better measurement and management for practical healthcare. The measurement technologies focus on deeper monitoring of broader populations. The management technologies focus on utilizing new personal health records to provide personalized treatment guidelines, specialized for each population cohort. This would enable predictive modeling for health systems to support viable healthcare at acceptable cost and quality.

A workshop website contains background and discussion notes: https://wiki.engr.illinois.edu/display/hiworkshop/NSF+Workshop+Population+Health
Trends in computer-based medical systems
Authors: Soda Paolo , Antani Sameer , Tortorella Francesco , Cannataro Mario , Pechenizkiy Mykola , Tsymbal Alexey
Published: October 2012

The 25th IEEE International Symposium on Computer-Based Medical Systems, held June 20--22, 2012 in Rome, Italy, has been a forum for discussing the latest developments in the field of computational medicine, biomedical informatics, and related disciplines. The Symposium has covered a broad range of issues in several areas with accepted submissions gathered into one general track, addressing general questions of computational biomedicine, and twelve special tracks, each focused on a particular related sub-theme. Three keynote speakers have presented an overview of recent research and developments in their particular subareas of mining clinical data for biomedical research, multivariate and multiscale analysis of biomedical signals, and oncology image analysis.
Wellness interventions and HCI
Authors: Meyer Jochen , Boll Susanne , Lee Young S. , Mayora Oscar , Siek Katie , Röcker Carsten
Published: October 2012

In recent years, we have seen an explosion of wellness interventions and technology applications focused on human's wellness with the intention of helping people avoid needing medical care. Given the increasing emergence of wellness applications, there is a need to integrate existing diverse research endeavors and discuss key challenges and opportunities for next generation wellness interventions and applications. We therefore conducted a workshop that brought together researchers and practitioners in the wellness field to develop a shared understanding of existing approaches and findings around the wellness interventions and applications and identify key synergies, opportunities, and challenges for future research that lead to successful wellbeing.
Disaster Governance: Social, Political, and Economic Dimensions
Authors: Tierney Kathleen
Published: October 2012

Disaster governance is an emerging concept in the disaster research literature that is closely related to risk governance and environmental governance. Disaster governance arrangements and challenges are shaped by forces such as globalization, world-system dynamics, social inequality, and sociodemographic trends. Governance regimes are polycentric and multiscale, show variation across the hazards cycle, and tend to lack integration and to be formulated in response to particular large-scale disaster events. Disaster governance is nested within and influenced by overarching societal governance systems. Although governance failures can occur in societies with stable governance systems, as the governmental response to Hurricane Katrina shows, poorly governed societies and weak states are almost certain to exhibit deficiencies in disaster governance. State-civil society relationships, economic organization, and societal transitions have implications for disaster governance. Various measures can be employed to assess disaster governance; more research is needed in this nascent field of study on factors that contribute to effective governance and on other topics, such as the extent to which governance approaches contribute to long-term sustainability.
Homer 2 antagonizes protein degradation in slow-twitch skeletal muscles
Authors: Bortoloso Elena , Megighian Aram , Furlan Sandra , Gorza Luisa , Volpe Pompeo
Published: October 2012

Homer represents a new and diversified family of proteins made up of several isoforms. The presence of Homer isoforms, referable to 1b/c and 2a/b, was investigated in fast- and slow-twitch skeletal muscles from both rat and mouse. Homer 1b/c was identical irrespective of the muscle, and Homer 2a/b was instead characteristic of the slow-twitch phenotype. Transition in Homer isoform composition was studied in two established experimental models of atrophy, i.e., denervation and disuse of slow-twitch skeletal muscles of the rat. No change of Homer 1b/c was observed up to 14 days after denervation, whereas Homer 2a/b was found to be significantly decreased at 7 and 14 days after denervation by 70 and 90%, respectively, and in parallel to reduction of muscle mass; 3 days after denervation, relative mRNA was reduced by 90% and remained low thereafter. Seven-day hindlimb suspension decreased Homer 2a/b protein by 70%. Reconstitution of Homer 2 complement by in vivo transfection of denervated soleus allowed partial rescue of the atrophic phenotype, as far as muscle mass, muscle fiber size, and ubiquitinazion are concerned. The counteracting effects of exogenous Homer 2 were mediated by downregulation of MuRF1, Atrogin, and Myogenin, i.e., all genes known to be upregulated at the onset of atrophy. On the other hand, slow-to-fast transition of denervated soleus, another landmark of denervation atrophy, was not rescued by Homer 2 replacement. The present data show that 1) downregulation of Homer 2 is an early event of atrophy, and 2) Homer 2 participates in the control of ubiquitinization and ensuing proteolysis via transcriptional downregulation of MuRF1, Atrogin, and Myogenin. Homers are key players of skeletal muscle plasticity, and Homer 2 is required for trophic homeostasis of slow-twitch skeletal muscles.
GCN-2 dependent inhibition of protein synthesis activates osmosensitive gene transcription via WNK and Ste20 kinase signaling
Authors: Lee Elaine Choung-Hee , Strange Kevin
Published: October 2012

Increased gpdh-1 transcription is required for accumulation of the organic osmolyte glycerol and survival of Caenorhabditis elegans during hypertonic stress. Our previous work has shown that regulators of gpdh-1 ( rgpd) gene knockdown constitutively activates gpdh-1 expression. Fifty-five rgpd genes play essential roles in translation suggesting that inhibition of protein synthesis is an important signal for regulating osmoprotective gene transcription. We demonstrate here that translation is reduced dramatically by hypertonic stress or knockdown of rgpd genes encoding aminoacyl-tRNA synthetases and eukaryotic translation initiation factors (eIFs). Toxin-induced inhibition of translation also activates gpdh-1 expression. Hypertonicity-induced translation inhibition is mediated by general control nonderepressible (GCN)-2 kinase signaling and eIF-2α phosphoryation. Loss of gcn-1 or gcn-2 function prevents eIF-2α phosphorylation, completely blocks reductions in translation, and inhibits gpdh-1 transcription. gpdh-1 expression is regulated by the highly conserved with-no-lysine kinase (WNK) and Ste20 kinases WNK-1 and GCK-3, which function in the GCN-2 signaling pathway downstream from eIF-2α phosphorylation. Our previous work has shown that hypertonic stress causes rapid and dramatic protein damage in C. elegans and that inhibition of translation reduces this damage. The current studies demonstrate that reduced translation also serves as an essential signal for activation of WNK-1/GCK-3 kinase signaling and subsequent transcription of gpdh-1 and possibly other osmoprotective genes.
Disassociation of static and dynamic cerebral autoregulatory performance in healthy volunteers after lipopolysaccharide infusion and in patients with sepsis
Authors: Berg Ronan M. G. , Plovsing Ronni R. , Ronit Andreas , Bailey Damian M. , Holstein-Rathlou Niels-Henrik , Møller Kirsten
Published: October 2012

Sepsis is frequently complicated by brain dysfunction, which may be associated with disturbances in cerebral autoregulation, rendering the brain susceptible to hypoperfusion and hyperperfusion. The purpose of the present study was to assess static and dynamic cerebral autoregulation 1) in a human experimental model of the systemic inflammatory response during early sepsis and 2) in patients with advanced sepsis. Cerebral autoregulation was tested using transcranial Doppler ultrasound in healthy volunteers ( n = 9) before and after LPS infusion and in patients with sepsis ( n = 16). Static autoregulation was tested by norepinephrine infusion and dynamic autoregulation by transfer function analysis (TFA) of spontaneous oscillations between mean arterial blood pressure and middle cerebral artery blood flow velocity in the low frequency range (0.07–0.20 Hz). Static autoregulatory performance after LPS infusion and in patients with sepsis was similar to values in healthy volunteers at baseline. In contrast, TFA showed decreased gain and an increased phase difference between blood pressure and middle cerebral artery blood flow velocity after LPS (both P < 0.01 vs. baseline); patients exhibited similar gain but lower phase difference values ( P < 0.01 vs. baseline and LPS), indicating a slower dynamic autoregulatory response. Our findings imply that static and dynamic cerebral autoregulatory performance may disassociate in sepsis; thus static autoregulation was maintained both after LPS and in patients with sepsis, whereas dynamic autoregulation was enhanced after LPS and impaired with a prolonged response time in patients. Hence, acute surges in blood pressure may adversely affect cerebral perfusion in patients with sepsis.