bluuebunny/crossref_metadata_2025 huggingface dataset:
Complete Nucleotide Sequences of Two
bla
KPC-2
-Bearing IncN Plasmids Isolated from Sequence Type 442 Klebsiella pneumoniae Clinical Strains Four Years Apart
Authors: Pérez-Chaparro Paula Juliana , Cerdeira Louise Teixeira , Queiroz Maíse Gomes , de Lima Clayton Pereira Silva , Levy Carlos Emílio , Pavez Mónica , Lincopan Nilton , Gonçalves Evonnildo Costa , Mamizuka Elsa Masae , Sampaio Jorge Luiz Mello , Nunes Marcio Roberto Teixeira , McCulloch John Anthony
Published: February 2014

We sequenced the oldest
bla
KPC-2
-bearing plasmid isolated in Brazil and another plasmid also carried by a
Klebsiella pneumoniae
strain of sequence type 442 (ST442), isolated 52 months later. Both plasmids present an IncN backbone and few acquired regions. Because the 2005 plasmid presented deletions and a truncated gene within Tn
4401b
compared to the 2009 plasmid, we can thus infer that IncN
bla
KPC-2
-bearing plasmids pFCF1305 and pFCF3SP had a common ancestor circulating in Brazil prior to May 2005.
Identification of CMY-2-Type Cephalosporinases in Clinical Isolates of Enterobacteriaceae by MALDI-TOF MS
Authors: Papagiannitsis C. C. , Kotsakis S. D. , Tuma Z. , Gniadkowski M. , Miriagou V. , Hrabak J.
Published: February 2014

This study exploited the possibility to detect
Citrobacter freundii
-derived CMY-2-like cephalosporinases in
Enterobacteriaceae
clinical isolates using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). Periplasmic proteins were prepared using a modified sucrose method and analyzed by MALDI-TOF MS. A ca. 39,850-
m
/
z
peak, confirmed to represent a
C. freundii
-like β-lactamase by in-gel tryptic digestion followed by MALDI-TOF/TOF MS, was observed only in CMY-producing isolates. We have also shown the potential of the assay to detect ACC- and DHA-like AmpC-type β-lactamases.
Fitness Costs for Influenza B Viruses Carrying Neuraminidase Inhibitor-Resistant Substitutions: Underscoring the Importance of E119A and H274Y
Authors: Burnham Andrew J. , Baranovich Tatiana , Marathe Bindumadhav M. , Armstrong Jianling , Webster Robert G. , Govorkova Elena A.
Published: February 2014

Influenza B viruses cause annual outbreaks of respiratory illness in humans and are increasingly recognized as a major cause of influenza-associated pediatric mortality. Neuraminidase (NA) inhibitors (NAIs) are the only available therapy for patients infected with influenza B viruses, and the potential emergence of NAI-resistant viruses is a public health concern. The NA substitutions located within the enzyme active site could not only reduce NAI susceptibility of influenza B virus but also affect virus fitness. In this study, we investigated the effect of single NA substitutions on the fitness of influenza B/Yamanashi/166/1998 viruses (Yamagata lineage). We generated recombinant viruses containing either wild-type (WT) NA or NA with a substitution in the catalytic (R371K) or framework (E119A, D198E, D198Y, I222T, H274Y, and N294S) residues. We assessed NAI susceptibility, NA biochemical properties, NA protein expression, and virus replication
in vitro
and in differentiated normal human bronchial epithelial (NHBE) cells. Our results showed that four NA substitutions (D198E, I222T, H274Y, and N294S) conferred reduced inhibition by oseltamivir and three (E119A, D198Y, and R371K) conferred highly reduced inhibition by oseltamivir, zanamivir, and peramivir. All NA substitutions, except for D198Y and R371K, were genetically stable after seven passages in MDCK cells. Cell surface NA protein expression was significantly increased by H274Y and N294S substitutions. Viruses with the E119A, I222T, H274Y, or N294S substitution were not attenuated in replication efficiency
in vitro
or in NHBE cells. Overall, viruses with the E119A or H274Y NA substitution possess fitness comparable to NAI-susceptible virus, and the acquisition of these substitutions by influenza B viruses should be closely monitored.
Novel Liquid Chromatography-Tandem Mass Spectrometry Method for Simultaneous Detection of Anti-HIV Drugs Lopinavir, Ritonavir, and Tenofovir in Plasma
Authors: Koehn Josefin , Ho Rodney J. Y.
Published: February 2014

For HIV infection, anti-HIV drug combinations are typically used as highly active antiretroviral therapy (HAART), intended to maximize viral suppression. Three drugs used frequently in combination are the protease inhibitors lopinavir and ritonavir and the nucleotide reverse transcriptase inhibitor tenofovir. We have successfully developed a simple, efficient, and sensitive method to simultaneously extract and determine the concentrations of lopinavir, ritonavir, and tenofovir in plasma samples. The plasma extractions were performed using a liquid-liquid extraction followed by protein precipitation of the remaining aqueous layer. The collected fractions were combined, dried, and reconstituted in the mobile phase. The drugs were quantified using liquid chromatography coupled with tandem mass spectrometry. The assay was applied to a study of plasma drug levels in two primates (
Macaca nemestrina
). The bioanalytical assay was optimized and validated to exhibit a high extraction efficiency and good sensitivity and reproducibility. When the assay was applied in a primate study, all three drugs could be detected in plasma within minutes of subcutaneous dosing. This validated assay will be useful for evaluation of drug concentrations in an efficient, selective, and sensitive manner.
An
ethA-ethR
-Deficient Mycobacterium bovis BCG Mutant Displays Increased Adherence to Mammalian Cells and Greater Persistence
In Vivo
, Which Correlate with Altered Mycolic Acid Composition
Authors: Ang Michelle Lay Teng , Siti Zarina Zainul Rahim , Shui Guanghou , Dianišková Petronela , Madacki Jan , Lin Wenwei , Koh Vanessa Hui Qi , Martinez Gomez Julia Maria , Sudarkodi Sukumar , Bendt Anne , Wenk Markus , Mikušová Katarína , Korduláková Jana , Pethe Kevin , Alonso Sylvie
Published: February 2014

Tuberculosis remains a major worldwide epidemic because of its sole etiological agent,
Mycobacterium tuberculosis
. Ethionamide (ETH) is one of the major antitubercular drugs used to treat infections with multidrug-resistant
M. tuberculosis
strains. ETH is a prodrug that requires activation within the mycobacterial cell; its bioactivation involves the
ethA-ethR
locus, which encodes the monooxygenase EthA, while EthR is a transcriptional regulator that binds to the intergenic promoter region of the
ethA-ethR
locus. While most studies have focused on the role of EthA-EthR in ETH bioactivation, its physiological role in mycobacteria has remained elusive, although a role in bacterial cell detoxification has been proposed. Moreover, the importance of EthA-EthR
in vivo
has never been reported on. Here we constructed and characterized an EthA-EthR-deficient mutant of
Mycobacterium bovis
BCG. Our results indicate that absence of the
ethA-ethR
locus led to greater persistence of
M. bovis
BCG in the mouse model of mycobacterial infection, which correlated with greater adherence to mammalian cells. Furthermore, analysis of cell wall lipid composition by thin-layer chromatography and mass spectrometry revealed differences between the
ethA-ethR
KO mutant and the parental strain in the relative amounts of α- and keto-mycolates. Therefore, we propose here that
M. bovis
BCG
ethA-ethR
is involved in the cell wall-bound mycolate profile, which impacts mycobacterial adherence properties and
in vivo
persistence. This study thus provides some experimental clues to the possible physiological role of
ethA-ethR
and proposes that this locus is a novel factor involved in the modulation of mycobacterial virulence.
Inflammatory Bone Loss in Experimental Periodontitis Induced by Aggregatibacter actinomycetemcomitans in Interleukin-1 Receptor Antagonist Knockout Mice
Authors: Izawa A. , Ishihara Y. , Mizutani H. , Kobayashi S. , Goto H. , Okabe E. , Takeda H. , Ozawa Y. , Kamiya Y. , Sugita Y. , Kubo K. , Kamei H. , Kikuchi T. , Mitani A. , Hayashi J. , Nishihara T. , Maeda H. , Noguchi T.
Published: February 2014

The interleukin-1 receptor antagonist (IL-1Ra) binds to IL-1 receptors and inhibits IL-1 activity. However, it is not clear whether IL-1Ra plays a protective role in periodontal disease. This study was undertaken to compare experimental periodontitis induced by
Aggregatibacter actinomycetemcomitans
in IL-1Ra knockout (KO) mice and wild-type (WT) mice. Computed tomography (CT) analysis and hematoxylin-and-eosin (H&E) and tartrate-resistant acid phosphatase (TRAP) staining were performed. In addition, osteoblasts were isolated; the mRNA expression of relevant genes was assessed by real-time quantitative PCR (qPCR); and calcification was detected by Alizarin Red staining. Infected IL-1Ra KO mice exhibited elevated (
P
, <0.05) levels of antibody against
A. actinomycetemcomitans
, bone loss in furcation areas, and alveolar fenestrations. Moreover, protein for tumor necrosis factor alpha (TNF-α) and IL-6, mRNA for macrophage colony-stimulating factor (M-CSF), and receptor activator of NF-κB ligand (RANKL) in IL-1Ra KO mouse osteoblasts stimulated with
A. actinomycetemcomitans
were increased (
P
, <0.05) compared to in WT mice. Alkaline phosphatase (ALP), bone sialoprotein (BSP), osteocalcin (OCN)/bone gla protein (BGP), and runt-related gene 2 (Runx2) mRNA levels were decreased (
P
, <0.05). IL-1α mRNA expression was increased, and calcification was not observed, in IL-1 Ra KO mouse osteoblasts. In brief, IL-1Ra deficiency promoted the expression of inflammatory cytokines beyond IL-1 and altered the expression of genes involved in bone resorption in
A. actinomycetemcomitans
-infected osteoblasts. Alterations consistent with rapid bone loss in infected IL-Ra KO mice were also observed for genes expressed in bone formation and calcification. In short, these data suggest that IL-1Ra may serve as a potential therapeutic drug for periodontal disease.
Hypercalcaemia: atypical presentation of miliary tuberculosis
Authors: So Edison , Bolger Dennis Thomas
Published: February 2014

We report an unusual case of miliary tuberculosis in a 77-year-old Filipino man with hypertension, diabetes mellitus, nephrolithiasis status-post left nephrectomy, presenting with 1 month of fever, generalised weakness and weight loss. Laboratory data were significant for anaemia, hypercalcaemia and acute kidney injury. Chest radiograph showed ground glass opacities and interstitial infiltrates. Extensive workup was performed to evaluate fever and hypercalcaemia. Malignancy, hormonal and septic workup were all unremarkable. Tuberculin skin test was negative. Sputum, pleural fluid, bronchoalveolar lavage and cerebrospinal fluid were acid-fast bacilli (AFB) smear negative. Remarkably, urine AFB smear was positive. Caseating granulomas were seen on transbronchial biopsy. Antituberculosis therapy was initiated which lead to defervescence and initial clinical improvement. However, hospital course became complicated by small bowel obstruction and respiratory failure. He subsequently developed pulseless electrical activity and expired. An autopsy confirmed the presence of tuberculosis in multiple organs including his remaining kidney.
Ketoacidosis is not always due to diabetes
Authors: Chandrasekara Hemantha , Fernando Pasan , Danjuma Mohammed , Jayawarna Chaminda
Published: February 2014

Chronic alcoholism is a frequently unrecognised cause of ketoacidosis. Most patients with alcoholic ketoacidosis present with normal or low glucose, but this condition can present with hyperglycaemia. This can lead to misdiagnosis of diabetes ketoacidosis and, therefore, inappropriate treatment with insulin. We describe a 37-year-old Caucasian woman with chronic pancreatitis secondary to excess alcohol consumption, admitted with abdominal pain and vomiting, fulfilling the criteria for diabetes ketoacidosis. She was treated according to diabetes ketoacidosis protocol and experienced a hypoglycaemic attack within an hour of initiation of insulin. On review of her history, she was found to have three similar episodes over the past 12 months. Alcoholic ketoacidosis can present with hyperglycaemia due to relative deficiency of insulin and relative surplus in counter-regulatory stress hormones including glucagon. Awareness of the syndrome with a detailed history helps to differentiate alcohol ketoacidosis from diabetes ketoacidosis and prevent iatrogenic hypoglycaemia.
Expression of growth arrest-specific protein 6 and Axl molecules in the left internal mammary artery of patients undergoing coronary artery bypass grafting
Authors: Lee Chien-Hsing , Shieh Yi-Shing , Tsai Chien-Sung , Hung Yi-Jen , Tsai Yi-Ting , Lin Chih-Yuan
Published: February 2014

Aims

Studies have demonstrated that using a left internal mammary artery (LIMA) graft yields excellent long-term results in coronary artery bypass grafting (CABG). The growth arrest-specific 6 (Gas6) gene and its receptor, Axl, are crucial in vascular haemostasis and atherosclerosis. The objective of this study was to determine the expression of Gas6 and Axl molecules in the aorta and LIMA in patients undergoing CABG.

Methods

Plasma and tissue specimens were collected from 19 patients undergoing elective CABG. The expression of the Gas6 and Axl in the injured aorta and LIMA was examined using reverse transcription PCR (RT-PCR), real-time RT-PCR, western blot and immunohistochemical staining.

Results

In CABG patients, the mRNA, immunoreactivity and protein expressions of the Gas6 and Axl were considerably higher in the LIMA than those in the aorta. Further analysis revealed that the expression of the Gas6 positively correlated with that of Axl in the LIMA and aorta. The plasma Gas6 level was considerably and positively correlated with the expression of Gas6 protein in the LIMA and aorta.

Conclusions

The present study discovered that the higher expression of Gas6/Axl pathway components in the LIMA compared with that in the aorta may partly explain the less frequent atherosclerotic events involving the LIMA compared with other arteries. Moreover, Gas6 may play a critical and protective role in human vascular biology.
How much do soldiers know about the morphine they carry on operations? A questionnaire study of knowledge and understanding of the morphine auto-injector on Op HERRICK 17
Authors: Nelson Sarah C , Wedgwood J T A
Published: February 2014

Introduction

Morphine auto-injectors are issued to all British soldiers on operations in Afghanistan who deploy forward of Camp Bastion, the main British base. Previous studies have reviewed the effectiveness of various pre-hospital analgesics, but there is no record of the knowledge and confidence of the relatively medically untrained soldiers who carry and use intramuscular morphine on the battlefield. The aim of this study was to assess soldiers’ knowledge and confidence of the morphine auto-injector with a view to guiding further training.

Methods

Structured questionnaire distributed to soldiers in two patrol bases in Helmand Province during Op HERRICK 17.

Results

232 questionnaires were completed by a range of ranks and trades. 100% had received mandatory training on the auto-injector and over 70% had received more advanced training. Confidence in using the auto-injector was high, with 47% rating their confidence level as 10/10. Overall, factual knowledge was good with the mean score for the questionnaire being 7.9/10; 95% of respondents knew how to document the use of morphine and 79% knew when a second dose could safely be administered. Some misunderstanding of contraindications was revealed: 9% of answers were incorrect, and 47% wrongly answered that administering morphine to a patient changes the triage category.

Conclusions

The majority of soldiers received far more than the minimum required training on the use of the morphine auto-injector. Confidence in using the device is high and generally knowledge is good. The authors suggest that deployed medical personnel in forward locations maintain regular training to soldiers on the morphine auto-injector in order to ensure that casualties receive analgesia appropriately and promptly.
Combined use of Solitaire FR and Penumbra devices for endovascular treatment of cerebral venous sinus thrombosis in a child
Authors: Shaikh Hamza , Pukenas Bryan Anthony , McIntosh Adeka , Licht Daniel , Hurst Robert W
Published: February 2014

A pre-teenager with newly diagnosed ulcerative colitis presented to an emergency department with acute headache, altered mental status and bilateral lower extremity weakness. Head CT demonstrated acute thrombus in the vein of Galen and straight sinus, and the patient was started on a heparin infusion. The patient clinically deteriorated and became unresponsive. In view of the rapid deterioration despite anticoagulation therapy, the patient was taken for endovascular treatment. A novel endovascular approach was performed with combined use of Solitaire FR and Penumbra devices to enhance access to the straight sinus and to limit intraprocedural blood loss. The post-treatment head CT demonstrated a decrease in hyperattenuation within the vein of Galen and straight sinus. The neurologic status improved within 24 h. The patient was discharged home with a normal neurologic examination.
Marine survival difference between wild and hatchery-reared steelhead trout determined during early downstream migration
Authors: Melnychuk Michael C. , Korman Josh , Hausch Stephen , Welch David W. , McCubbing Don J.F. , Walters Carl J.
Published: February 2014

We observed large survival differences between wild and hatchery-reared steelhead trout (Oncorhynchus mykiss) during the juvenile downstream migration immediately after release, which persisted through adult life. Following a railway spill of sodium hydroxide into the Cheakamus River, British Columbia, a short-term conservation hatchery rearing program was implemented for steelhead. We used acoustic telemetry and mark–recapture models to estimate survival of wild and (or) hatchery-reared steelhead during 4 years of the smolt migration, with both groups released in 2008. After adjusting for estimated freshwater residualization, 7%–13% of wild smolts and 30%–40% of hatchery smolts died in the first 3 km of the migration. Estimated survival from release to ocean entry was 71%–84% for wild fish and 26%–40% for hatchery fish and to exit from the Strait of Georgia system was 22%–33% for wild fish and 3.5%–6.7% for hatchery fish. A calculated 2.3-fold survival difference established during the downstream migration was similar to that after the return of adult spawners, as return rates were 8.0% for wild fish and 4.1% for hatchery fish. Contrary to current understanding, a large proportion of salmon mortality in the smolt-to-adult period, commonly termed “marine mortality”, may actually occur prior to ocean entry.
Variable effects of climate and density on the juvenile ecology of two salmonids in an Alaskan lake
Authors: Kovach Ryan P. , Joyce John E. , Vulstek Scott C. , Barrientos Evan M. , Tallmon David A.
Published: February 2014

Despite concerns over rapidly warming temperatures, an empirical understanding of climatic impacts on wild salmonid populations is limited. We tested how temperature and density affected juvenile coho (Oncorhynchus kisutch) and sockeye salmon (Oncorhynchus nerka) using a 31 year census from an Alaskan lake. There were positive effects of temperature on overall salmon biomass, sockeye biomass, and the length of age 2 sockeye smolts. There was, however, little evidence for relationships between temperature or length of growing season and coho biomass, coho length, smolts per spawner (both species), and age structure (both species). In some cases there were temporal changes contrary to what is generally expected in a warming Alaskan lake with longer growing seasons (e.g., increasing proportions of age 2 smolts). Intraspecific density was negatively related to sockeye length at out-migration, but there was no evidence for relationships between density and other response variables. Overall, patterns observed here and in other studies emphasize that responses to climatic variation can vary substantially across locations, between similar species occupying the same habitats, and among alternative life history strategies within populations.
Holographic dark energy and generalized second law
Authors: Mathew Titus K. , Praseetha P.
Published: February 2014

We explore the validity of the generalized second law (GSL) of thermodynamics in flat FRW universe with apparent horizon and event horizon as the boundary. We found that in a universe with holographic dark energy and dark matter, interacting with each other, the GSL is satisfied at the apparent horizon and partially satisfied at the event horizon under thermal equilibrium conditions. We also analyzed the GSL under non-equilibrium conditions and shows that the fulfillment of GSL at the apparent horizon implies that the temperature of the dark energy is greater than that of the horizon. Thus, there occurs a flow of dark energy towards the apparent horizon. As a result, the entropy of the dark energy decreases and that of the horizon increases. This is verified by finding the evolution of the dark energy entropy and horizon entropy in a dark energy dominated universe under non-equilibrium conditions.
GEOMETRY OF DOPAMINE ADSORPTION ON RUTILE (110) SURFACE
Authors: CASTILLO DARWIN , ONTANEDA JORGE , STASHANS ARVIDS
Published: February 2014

Density functional theory (DFT) and generalized gradient approximation (GGA) have been employed to study adsorption geometry and electronic properties of the system consisting of rutile (110) surface and dopamine molecule. Hubbard U-like term is included to consider more adequately 3d electrons of Ti atoms. Results indicate that dopamine adsorption takes place in a bidentate geometry by forming strong bonds between two molecular oxygens and two titaniums situated on the surface. Geometry changes of molecular atoms, as well as those constituting upmost layer of the surface has been discussed in detail. Reduction in the band-gap width due to the adsorption has been found implying potential interest of the system for light-harvesting solar cells.
Optimizations of inductively coupled plasma etching and design for sensing window of Mach–Zehnder interferometer sensor in polymer technology
Authors: Yang Tianfu , Wang Tianjiao , Zheng Chuantao , Wang Xibin , Zhang Daming
Published: February 2014

The inductively coupled plasma etching parameters for fabricating sensing windows of integrated Mach–Zehnder interferometer sensor based on polymers are systematically investigated. Under the optimum etching condition, we fabricate an improved sensing waveguide with three sensing surfaces, whose sensitivity can be enhanced by a factor of 3.5 in theory. Through precisely controlling the etching time, low propagation loss and high hydrophilicity are both achieved in the etched sensing waveguide. This optimizing approach along with rapid response and stable operation has rendered the MZI waveguide sensor more competent to practical requirements of RI sensing and biochemical sensing.
Dielectric, multiferroic properties and resistance modulation of Ta-doped Bi0.97Ba0.03FeO3 ceramics
Authors: Wang X. , Wang S. Y. , Liu W. F. , Guo F. , Xi X. J. , Wang H. J. , Li D. J.
Published: February 2014

Single phase Bi 0.97 Ba 0.03 Fe 1-x Ta x O 3 ceramics with x = 0, 0.01, 0.03, 0.05 were synthesized by modified rapid sintering process method. The formation of rhombohedral perovskite-like structure was confirmed by X-ray diffraction investigation for all the samples. Dielectric and leakage current measurements indicated that the content of the oxygen vacancy in the samples decreased as a function of the substitution of Ta 5+ ions. A distinct threshold switching behavior was observed in the leakage current density. The impedance measurements suggested that the grain effect made a major contribution to the resistance. The changes in dielectric, multiferroic properties and resistance modulation of the Ta 5+ and Ba 2+ co-doped BiFeO 3 ceramics could have a huge potential for material application.
The coherence of boson–fermion mixed system
Authors: Wang Ji-Guo , Xue Ju-Kui
Published: February 2014

In this paper, we investigate the quantum coherence of Bose–Fermi mixtures of ultracold dipolar particles trapped in a three-site Bose–Fermi–Hubbard model. We show that the interplay between the boson–boson on-site interaction, boson–fermion on-site interaction, and boson–fermion inter-site dipole–dipole interaction (DDI) results in interesting coherence characters. When boson–boson on-site interaction is present, the resonance character of coherence against both boson–fermion DDI and boson–fermion on-site interaction emerges, the coherence of the system can be enhanced at certain values of boson–fermion on-site interaction and boson–fermion DDI. DDI of fermion–fermion affects the coherence weak and the phase coherence decreases monotonically for all the values of fermion–fermion DDI. The obtained coherent characters are further confirmed within the variational analyzing of the ground state energy.
ROTO-TRANSLATIONAL EFFECTS ON DEFLECTION OF LIGHT AND PARTICLE BY MOVING KERR BLACK HOLE
Authors: HE G. , LIN W.
Published: February 2014

Velocity effects in first-order Schwarzschild deflection of light and particles have been explored in the previous literature. In this paper, we investigate the roto-translational-motion induced deflection by one moving Kerr black hole with an arbitrary, but constant speed. It is shown that the coupling between the effects of the rotation and the translational motion always exists for both light and particles. The contribution of the roto-translational deflection to the total bending angle is discussed in detail. This ratio takes upper limit for light and it decreases monotonically with increasing translational velocity for a massive particle. For a given translational velocity of black hole, this ratio increases with the particle's velocity. In addition, the post-Newtonian dynamics of the photon and particle is also presented.
2013 update of the discoveries of nuclides
Authors: Thoennessen M.
Published: February 2014

The 2013 update of the discovery of nuclide project is presented. Details of the 12 new nuclides observed for the first time in 2013 are described. In addition, the discovery of266Db has been included and the previous assignments of six other nuclides were changed. Overview tables of where and how nuclides were discovered have also been updated and are discussed.
GPUfs
Authors: Silberstein Mark , Ford Bryan , Keidar Idit , Witchel Emmett
Published: February 2014

As GPU hardware becomes increasingly general-purpose, it is quickly outgrowing the traditional, constrained GPU-as-coprocessor programming model. This article advocates for extending standard operating system services and abstractions to GPUs in order to facilitate program development and enable harmonious integration of GPUs in computing systems. As an example, we describe the design and implementation of GPUFs, a software layer which provides operating system support for accessing host files directly from GPU programs. GPUFs provides a POSIX-like API, exploits GPU parallelism for efficiency, and optimizes GPU file access by extending the host CPU's buffer cache into GPU memory. Our experiments, based on a set of real benchmarks adapted to use our file system, demonstrate the feasibility and benefits of the GPUFs approach. For example, a self-contained GPU program that searches for a set of strings throughout the Linux kernel source tree runs over seven times faster than on an eight-core CPU.
Towards runtime adaptation in AUTOSAR
Authors: Zeller Marc , Prehofer Christian , Krefft Daniel , Weiss Gereon
Published: February 2014

In many industrial application domains networked embedded systems realize safety-critical applications. In such systems, adapting the software distribution at runtime can be used to optimize system configurations, to add new features or to handle failure cases. The main objective of this paper is to devise a flexible and efficient solution for runtime adaptation in AUTOSAR, which requires minimal changes to the current architecture. We elaborate the main challenges for extending AUTOSAR and argue that small changes in the architecture and design process are feasible and effective for this purpose. Our work is validated by a proof of concept implementation.
Fair bandwidth sharing among virtual machines in a multi-criticality scope
Authors: Groesbrink Stefan , Almeida Luis , de Sousa Mario , Petters Stefan M.
Published: February 2014

System virtualization's consolidation in separated virtual machines provides a reasonable way to integrate formerly distinct systems into a single mixed-criticality multi-core system. We propose an adaptive resource management scheme for virtualization-based systems that have to be certified. Periodic servers and the elastic task model combine analyzability at design time with adaptability at runtime. A mode change or the enabling/disabling of tasks trigger a resource redistribution, which guarantees that a specified minimum is always allocated and obtains a fair distribution of spare capacity among the virtual machines. The partitioned scheduling and the assignment of static priorities ease certification. The scheme has the potential to improve the resource utilization and support adaptive and self-optimizing applications with strongly varying execution times.
Fault-tolerant hierarchical real-time scheduling with backup partitions on single processor
Authors: Jin Hyun-Wook
Published: February 2014

The resource partitioning has been suggested to provide efficient composition of multi-threaded real-time applications. Partitioning can provide reliable and flexible software upgrade as partitions are strongly isolated in terms of resources. However, there are always possibility of experiencing software faults while operating on a real plant. To avoid entering a hazardous state due to a partition that is yet to be fully verified, we can deploy a backup partition that may implement inefficient algorithms or limited features but is verified with respect to reliability. The backup partition performs failover to carry out missions of the corresponding primary partition when a software fault is detected. There have been significant researches for fault-tolerant real-time scheduling but considerations for partitioned systems have not been studied. In this paper, we extend the resource model for hierarchical real-time scheduling to support primary and backup partitions. Our model can support context-dependent and context-independent tasks in the backup partition efficiently. In addition, we provide the schedulability analysis for suggested model.
On the conceptual design of a dynamic component model for reconfigurable AUTOSAR systems
Authors: Axelsson Jakob , Kobetski Avenir
Published: February 2014

The automotive industry has recently developed the embedded software standard AUTOSAR, which is now being introduced widely in production vehicles. The standard structures the application into reusable components that can be deployed in a specific vehicle using a configuration scheme. However, this configuration takes place at design time, with no provision for dynamically installing components to reconfigure the system. In this paper, we present the conceptual design of a dynamic component model that extends an AUTOSAR based control unit with the possibility to add plug-in components that execute on a virtual machine. This concept is intended to give benefits in terms of much shorter deployment time for new functions, even into vehicles that have already been produced. Further, it creates opportunities for vehicles to take part in federated embedded systems together with other products. It also opens up a market for third-party developers, and fosters open innovation in an ecosystem around the automotive software business.
Reconfigurable industrial process monitoring using the CHROMOSOME middleware
Authors: Sommer Stephan , Geisinger Michael , Buckl Christian , Bauer Gerd , Knoll Alois
Published: February 2014

In all areas of industrial production and construction, companies have to implement processes with increasing complexity and reliability to satisfy their customer's needs with respect to product quality and continuity. Fulfilling these requirements means to employ continuous process monitoring and documentation without increasing production cost significantly even in case of subsequent reorganization of the production facility. The Multifunk research project focuses on the development and integration of features into the CHROMOSOME middleware to provide the basis for an intelligent, self-adapting process monitoring framework for production quality assurance. The key features of the framework are self-organization and self-configuration based on meta information in combination with industry standard protocols to guarantee an easy integration into industrial processes. The CHROMOSOME middleware is used on top of smart sensor platform MST2012 that has been developed in the course of the research project to tie established analog sensors to the digital process monitoring world. The contribution of this paper is a flexible, self-adaptive embedded middleware in combination with a smart sensor gateway for industrial process monitoring.
CS Ed Week 2013
Authors: Alvarado Christine
Published: February 2014

As advertised in the October 2013 edition of the Bulletin, this year's CS Ed Week encouraged everyone to host an "Hour of Code" event, in which educators hosted (at least) an hour of CS instruction to any audience they chose. SIGCSE members responded to the call enthusiastically. Here is just a sampling of the many great Hour of Code events that were put on.
SIGCSE 2014 preview
Authors: Nagel Kris , Dougherty JD
Published: February 2014

"Leveraging Computing to Change Education!" SIGCSE 2014 brings professionals from around the world together to present education research and practical experience reports in the form of papers, panels, workshops, and other informal sessions. The 45th Annual SIGCSE Technical Symposium on Computer Science Education will be held in Atlanta, Georgia, March 5--8, 2014 at the Hyatt Regency Hotel.
Study of a Conformational Equilibrium of Lisinopril by HPLC, NMR, and DFT
Authors: Bouabdallah Sondes , Ben Dhia Med Thaieb , Driss Med Rida
Published: February 2014

The isomerization of lisinopril has been investigated using chromatographic, NMR spectroscopic, and theoretical calculations. The NMR data, particularly the NOEDIFF experiments, show that the major species that was eluted first is thetransform. The proportion was 77% and 23% for thetransandcis, respectively. The thermodynamic parameters (ΔH,ΔS, andΔG) were determined by varying the temperature in the NMR experiments. The interpretations of the experimental data were further supported by DFT/B3LYP calculations.
Disjointness Preserving and Functional Type Disjointness Preserving Operators
Authors: Moorthy C. Ganesa , Ramasamy C. T.
Published: February 2014

A new concept called functional type disjointness preserving operators is introduced and structure of disjointness preserving and functional type disjointness preserving operators on some function spaces are analysed.
Regulation of NAMPT in Human Gingival Fibroblasts and Biopsies
Authors: Damanaki Anna , Nokhbehsaim Marjan , Eick Sigrun , Götz Werner , Winter Jochen , Wahl Gerhard , Jäger Andreas , Jepsen Søren , Deschner James
Published: February 2014

Adipokines, such as nicotinamide phosphoribosyltransferase (NAMPT), are molecules, which are produced in adipose tissue. Recent studies suggest that NAMPT might also be produced in the tooth-supporting tissues, that is, periodontium, which also includes the gingiva. The aim of this study was to examine if and under what conditions NAMPT is produced in gingival fibroblasts and biopsies from healthy and inflamed gingiva. Gingival fibroblasts produced constitutively NAMPT, and this synthesis was significantly increased by interleukin-1βand the oral bacteriaP. gingivalisandF. nucleatum. Inhibition of the MEK1/2 and NFκB pathways abrogated the stimulatory effects ofF. nucleatumon NAMPT. Furthermore, the expression and protein levels of NAMPT were significantly enhanced in gingival biopsies from patients with periodontitis, a chronic inflammatory infectious disease of the periodontium, as compared to gingiva from periodontally healthy individuals. In summary, the present study provides original evidence that gingival fibroblasts produce NAMPT and that this synthesis is increased under inflammatory and infectious conditions. Local synthesis of NAMPT in the inflamed gingiva may contribute to the enhanced gingival and serum levels of NAMPT, as observed in periodontitis patients. Moreover, local production of NAMPT by gingival fibroblasts may represent a possible mechanism whereby periodontitis may impact on systemic diseases.
Nociceptive Neurons Differentially Express Fast and Slow T-Type Ca2+Currents in Different Types of Diabetic Neuropathy
Authors: Khomula Eugen V. , Borisyuk Anya L. , Viatchenko-Karpinski Viacheslav Y. , Briede Andrea , Belan Pavel V. , Voitenko Nana V.
Published: February 2014

T-type Ca2+channels are known as important participants of nociception and their remodeling contributes to diabetes-induced alterations of pain sensation. In this work we have established that about 30% of rat nonpeptidergic thermal C-type nociceptive (NTCN) neurons of segments L4–L6 express a slow T-type Ca2+current (T-current) while a fast T-current is expressed in the other 70% of these neurons. Streptozotocin-induced diabetes in young rats resulted in thermal hyperalgesia, hypoalgesia, or normalgesia 5-6 weeks after the induction. Our results show that NTCN neurons obtained from hyperalgesic animals do not express the slow T-current. Meanwhile, the fraction of neurons expressing the slow T-current did not significantly change in the hypo- and normalgesic diabetic groups. Moreover, the peak current density of fast T-current was significantly increased only in the neurons of hyperalgesic group. In contrast, the peak current density of slow T-current was significantly decreased in the hypo- and normalgesic groups. Experimental diabetes also resulted in a depolarizing shift of steady-state inactivation of fast T-current in the hyperalgesic group and slow T-current in the hypo- and normalgesic groups. We suggest that the observed changes may contribute to expression of different types of peripheral diabetic neuropathy occurring during the development of diabetes mellitus.
Blood Lead Levels and Health Problems of Lead Acid Battery Workers in Bangladesh
Authors: Ahmad Sk. Akhtar , Khan Manzurul Haque , Khandker Salamat , Sarwar A. F. M. , Yasmin Nahid , Faruquee M. H. , Yasmin Rabeya
Published: February 2014

Introduction. Use of lead acid battery (LAB) in Bangladesh has risen with sharp rise of motor vehicles. As result, manufacture of LAB is increasing. Most of the lead used by these industries comes from recycling of LAB. Workers in LAB industry are at risk of exposure lead and thus development of lead toxicity.Objective. The objective of this study was to measure the blood lead concentration and to assess the magnitude of health problems attributable to lead toxicity among the LAB manufacturing workers.Methods. A cross-sectional study was conducted among the workers of LAB manufacturing industries located in Dhaka city.Result. Mean blood lead level (BLL) among the workers was found to be high. They were found to be suffering from a number of illnesses attributable to lead toxicity. The common illnesses were frequent headache, numbness of the limbs, colic pain, nausea, tremor, and lead line on the gum. High BLL was also found to be related to hypertension and anemia of the workers.Conclusion. High BLL and illnesses attributable to lead toxicity were prevalent amongst workers of the LAB manufacturing industries, and this requires attention especially in terms of occupational hygiene and safety.
TRAP1 Regulates Proliferation, Mitochondrial Function, and Has Prognostic Significance in NSCLC
Authors: Agorreta Jackeline , Hu Jianting , Liu Dongxia , Delia Domenico , Turley Helen , Ferguson David JP. , Iborra Francisco , Pajares María J. , Larrayoz Marta , Zudaire Isabel , Pio Ruben , Montuenga Luis M. , Harris Adrian L. , Gatter Kevin , Pezzella Francesco
Published: February 2014

The TNF receptor-associated protein 1 (TRAP1) is a mitochondrial HSP that has been related to drug resistance and protection from apoptosis in colorectal and prostate cancer. Here, the effect of TRAP1 ablation on cell proliferation, survival, apoptosis, and mitochondrial function was determined in non–small cell lung cancer (NSCLC). In addition, the prognostic value of TRAP1 was evaluated in patients with NSCLC. These results demonstrate that TRAP1 knockdown reduces cell growth and clonogenic cell survival. Moreover, TRAP1 downregulation impairs mitochondrial functions such as ATP production and mitochondrial membrane potential as measured by TMRM (tetramethylrhodamine methylester) uptake, but it does not affect mitochondrial density or mitochondrial morphology. The effect of TRAP1 silencing on apoptosis, analyzed by flow cytometry and immunoblot expression (cleaved PARP, caspase-9, and caspase-3) was cell line and context dependent. Finally, the prognostic potential of TRAP1 expression in NSCLC was ascertained via immunohistochemical analysis which revealed that high TRAP1 expression was associated with increased risk of disease recurrence (univariate analysis, P = 0.008; multivariate analysis, HR: 2.554; 95% confidence interval, 1.085–6.012; P = 0.03). In conclusion, these results demonstrate that TRAP1 impacts the viability of NSCLC cells, and that its expression is prognostic in NSCLC.

Implications: TRAP1 controls NSCLC proliferation, apoptosis, and mitochondrial function, and its status has prognostic potential in NSCLC. Mol Cancer Res; 12(5); 660–9. ©2014 AACR.
Echocardiography-Derived Tricuspid Regurgitant Jet Velocity Is an Important Marker for the Progression of Sickle-Cell Disease
Authors: Upadhya Bharathi , Stacey Richard Brandon , Ntim William , Knovich Mary Ann , Pu Min
Published: February 2014

Background: Although echocardiography-derived tricuspid regurgitant jet velocity (TRV) is associated with increased mortality in sickle-cell disease (SCD), it is unclear whether increased TRV is a marker of multiorgan disease due to systemic vasculopathy or related to increased pulmonary artery systolic pressure with episodes of multiple acute chest syndrome (ACS). Methods: Our study analyzed 148 consecutive patients with transthoracic echocardiography with TRV data, who came to our adult SCD Clinic at the Wake Forest Baptist Medical Center. For our analysis, we took TRV ≥2.5 m/s as elevated. Patients were followed on average for 9 years. Results: TRV ≥3 m/s was significantly associated with increased mortality (p < 0.001), thromboembolism (p < 0.001), hospitalization for ACS (p < 0.001), supraventricular arrhythmia (p = 0.028), right ventricular (RV) dilation, decreased hemoglobin and increased creatinine. Patients with a progressive increase in TRV during follow-up had increased mortality (36.7 vs. 8.6%, p = 0.007) and increased ACS (45 vs. 5.7%, p < 0.001). Death was independently associated with TRV ≥3 m/s (p = 0.023), ACS (p = 0.001) and increased RV basal diameter (p = 0.003). Conclusions: TRV is an important global marker for the severity and progression of SCD, and carries a significant prognostic implication.
Effects of AST-120 on Blood Concentrations of Protein-Bound Uremic Toxins and Biomarkers of Cardiovascular Risk in Chronic Dialysis Patients
Authors: Lee Chien-Te , Hsu Chung-Yao , Tain You-Lin , Ng Hwee-Yeong , Cheng Ben-Chong , Yang Chih-Chau , Wu Chien-Hsing , Chiou Terry Ting-Yu , Lee Yueh-Ting , Liao Shang-Chih
Published: February 2014

Background: Removal of protein-bound uremic toxins by dialysis therapy is limited. The effect of oral adsorbent AST-120 in chronic dialysis patients has rarely been investigated. Methods: AST-120 was administered 6.0 g/day for 3 months in 69 chronic dialysis patients. The blood concentrations of indoxyl sulfate, p-cresol sulfate and biomarkers of cardiovascular risk were determined before and after AST-120 treatment. Results: AST-120 significantly decreased both the total and free forms of indoxyl sulfate and p-cresol sulfate ranging from 21.9 to 58.3%. There were significant simultaneous changes of the soluble tumor necrosis factor-like weak inducer of apoptosis (sTWEAK, 24% increase), malondialdehyde (14% decrease) and interleukin-6 (19% decrease). A significant association between the decrease of indoxyl sulfate and changes of sTWEAK and interleukin-6 was noted. Conclusions: AST-120 effectively decreased indoxyl sulfate and p-cresol sulfate levels in both total and free forms. AST-120 also improved the profile of cardiovascular biomarkers.
‘Residence Is Not Home' Is a Particular Type of Delusion Associated with Cognitive Decline of Alzheimer's Disease
Authors: Nakatsuka Masahiro , Meguro Kenichi , Nakamura Kei , Akanuma Kyoko , Yamaguchi Satoshi
Published: February 2014

Background: Although delusion is one of the common symptoms of Alzheimer's disease (AD), the association between cognitive deficits and delusions remains unclear. Considering the heterogeneity of delusion, the correlation may depend upon the type of the delusion. Methods: 142 consecutive first-visit AD outpatients of the Tajiri Clinic (Osaki, Miyagi, Japan) were enrolled in the study. Psychological data included the Mini-Mental State Examination (MMSE), the Cognitive Abilities Screening Instrument (CASI) and the Frequency-Weighted Behavioral Pathology in Alzheimer's Disease Rating Scale (BEHAVE-AD-FW). Correlations to cognitive deficits for each category of delusional content were evaluated. Results: More severe delusion of ‘residence is not home' was significantly correlated with a lower total MMSE score and poorer orientation as assessed with the CASI. This type of delusion also correlated to activity disturbances and was weakly associated with affective disturbances. Conclusion: Our findings suggest that the ‘residence is not home' delusion is a particular symptom that has a cognitive background, particularly disorientation, and should be discriminated from other delusional phenomena. We should cope with delusions specifying what types of delusions are present since the content of delusions may critically mark the symptomatology of AD. For this purpose, the BEHAVE-AD-FW may be suitable.
Reversal of Cognitive Dysfunction by Total Removal of a Large Lateral Ventricle Meningioma: A Case Report with Neuropsychological Assessments
Authors: Kashiwazaki Daina , Takaiwa Akiko , Nagai Shoichi , Akioka Naoki , Kurosaki Kunikazu , Noguchi Kyo , Kuwayama Naoya , Kuroda Satoshi
Published: February 2014

Although cognitive impairment is one of the major symptoms of ventricular tumors, few studies have reported the details of cognitive impairment before and after their surgical removal. The expected effects on cognitive function should also be considered when choosing a surgical approach. We report the case of a large lateral ventricle meningioma in which cognitive impairment was detected on detailed neuropsychological examinations. The tumor was totally removed through the right superior temporal gyrus. Postoperative neuropsychological assessment revealed the reversal of cognitive impairment. As cognitive impairment is complex and easily overlooked, it is important to precisely assess neuropsychological function in patients with large brain tumors.