bluuebunny/crossref_metadata_2025 huggingface dataset:
Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family
Authors: Young D. F. , Andrejeva J. , Li X. , Inesta-Vaquera F. , Dong C. , Cowling V. H. , Goodbourn S. , Randall R. E.
Published: August 2016

We have previously shown that IFIT1 is primarily responsible for the antiviral action of interferon (IFN) alpha/beta against parainfluenza virus type 5 (PIV5), selectively inhibiting the translation of PIV5 mRNAs. Here we report that while PIV2, PIV5, and mumps virus (MuV) are sensitive to IFIT1, nonrubulavirus members of the paramyxoviridae such as PIV3, Sendai virus (SeV), and canine distemper virus (CDV) are resistant. The IFIT1 sensitivity of PIV5 was not rescued by coinfection with an IFIT1-resistant virus (PIV3), demonstrating that PIV3 does not specifically inhibit the antiviral activity of IFIT1 and that the inhibition of PIV5 mRNAs is regulated bycis-acting elements. We developed anin vitrotranslation system using purified human IFIT1 to further investigate the mechanism of action of IFIT1. While the translations of PIV2, PIV5, and MuV mRNAs were directly inhibited by IFIT1, the translations of PIV3, SeV, and CDV mRNAs were not. Using purified human mRNA-capping enzymes, we show biochemically that efficient inhibition by IFIT1 is dependent upon a 5′ guanosine nucleoside cap (which need not be N7 methylated) and that this sensitivity is partly abrogated by 2′O methylation of the cap 1 ribose. Intriguingly, PIV5 M mRNA, in contrast to NP mRNA, remained sensitive to inhibition by IFIT1 followingin vitro2′O methylation, suggesting that other structural features of mRNAs may influence their sensitivity to IFIT1. Thus, surprisingly, the viral polymerases (which have 2′-O-methyltransferase activity) of rubulaviruses do not protect these viruses from inhibition by IFIT1. Possible biological consequences of this are discussed.

IMPORTANCEParamyxoviruses cause a wide variety of diseases, and yet most of their genes encode structural proteins and proteins involved in their replication cycle. Thus, the amount of genetic information that determines the type of disease that paramyxoviruses cause is relatively small. One factor that will influence disease outcomes is how they interact with innate host cell defenses, including the interferon (IFN) system. Here we show that different paramyxoviruses interact in distinct ways with cells in a preexisting IFN-induced antiviral state. Strikingly, all the rubulaviruses tested were sensitive to the antiviral action of ISG56/IFIT1, while all the other paramyxoviruses tested were resistant. We developed novelin vitrobiochemical assays to investigate the mechanism of action of IFIT1, demonstrating that the mRNAs of rubulaviruses can be directly inhibited by IFIT1 and that this is at least partially because their mRNAs are not correctly methylated.
Avian Leukosis Virus Activation of an Antisense RNA Upstream of
TERT
in B-Cell Lymphomas
Authors: Nehyba Jiri , Malhotra Sanandan , Winans Shelby , O'Hare Thomas H. , Justice James , Beemon Karen
Published: August 2016

Avian leukosis virus (ALV) induces tumors by integrating its proviral DNA into the chicken genome and altering the expression of nearby genes via strong promoter and enhancer elements. Viral integration sites that contribute to oncogenesis are selected in tumor cells. Deep-sequencing analysis of B-cell lymphoma DNA confirmed that the telomerase reverse transcriptase (
TERT
) gene promoter is a common ALV integration target. Twenty-six unique proviral integration sites were mapped between 46 and 3,552 nucleotides (nt) upstream of the
TERT
transcription start site, predominantly in the opposite transcriptional orientation to
TERT
. Transcriptome-sequencing (RNA-seq) analysis of normal bursa revealed a transcribed region upstream of
TERT
in the opposite orientation, suggesting the
TERT
promoter is bidirectional. This transcript appears to be an uncharacterized antisense RNA. We have previously shown that
TERT
expression is upregulated in tumors with integrations in the
TERT
promoter region. We now report that the viral promoter drives the expression of a chimeric transcript containing viral sequences spliced to exons 4 through 7 of this antisense RNA. Clonal expansion of cells with ALV integrations driving overexpression of the
TERT
antisense RNA suggest it may have a role in tumorigenesis.

IMPORTANCE
The data suggest that ALV integrations in the TERT promoter region drive the overexpression of a novel antisense RNA and contribute to the development of lymphomas.
Influenza A Virus Infection in Pigs Attracts Multifunctional and Cross-Reactive T Cells to the Lung
Authors: Talker Stephanie C. , Stadler Maria , Koinig Hanna C. , Mair Kerstin H. , Rodríguez-Gómez Irene M. , Graage Robert , Zell Roland , Dürrwald Ralf , Starick Elke , Harder Timm , Weissenböck Herbert , Lamp Benjamin , Hammer Sabine E. , Ladinig Andrea , Saalmüller Armin , Gerner Wilhelm
Published: August 2016

Pigs are natural hosts for influenza A viruses and play a critical role in influenza epidemiology. However, little is known about their influenza-evoked T-cell response. We performed a thorough analysis of both the local and systemic T-cell response in influenza virus-infected pigs, addressing kinetics and phenotype as well as multifunctionality (gamma interferon [IFN-γ], tumor necrosis factor alpha [TNF-α], and interleukin-2 [IL-2]) and cross-reactivity. A total of 31 pigs were intratracheally infected with an H1N2 swine influenza A virus (FLUAVsw) and consecutively euthanized. Lungs, tracheobronchial lymph nodes, and blood were sampled during the first 15 days postinfection (p.i.) and at 6 weeks p.i.Ex vivoflow cytometry of lung lymphocytes revealed an increase in proliferating (Ki-67+) CD8+T cells with an early effector phenotype (perforin+CD27+) at day 6 p.i. Low frequencies of influenza virus-specific IFN-γ-producing CD4+and CD8+T cells could be detected in the lung as early as 4 days p.i. On consecutive days, influenza virus-specific CD4+and CD8+T cells produced mainly IFN-γ and/or TNF-α, reaching peak frequencies around day 9 p.i., which were up to 30-fold higher in the lung than in tracheobronchial lymph nodes or blood. At 6 weeks p.i., CD4+and CD8+memory T cells had accumulated in lung tissue. These cells showed diverse cytokine profiles andin vitroreactivity against heterologous influenza virus strains, all of which supports their potential to combat heterologous influenza virus infections in pigs.

IMPORTANCEPigs not only are a suitable large-animal model for human influenza virus infection and vaccine development but also play a central role in the emergence of new pandemic strains. Although promising candidate universal vaccines are tested in pigs and local T cells are the major correlate of heterologous control, detailed and targeted analyses of T-cell responses at the site of infection are scarce. With the present study, we provide the first detailed characterization of magnitude, kinetics, and phenotype of specific T cells recruited to the lungs of influenza virus-infected pigs, and we could demonstrate multifunctionality, cross-reactivity, and memory formation of these cells. This, and ensuing work in the pig, will strengthen the position of this species as a large-animal model for human influenza virus infection and will immediately benefit vaccine development for improved control of influenza virus infections in pigs.
Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives
Authors: Mahar Jackie E. , Nicholson Leila , Eden John-Sebastian , Duchêne Sebastián , Kerr Peter J. , Duckworth Janine , Ward Vernon K. , Holmes Edward C. , Strive Tanja
Published: August 2016

Two closely related caliciviruses cocirculate in Australia: rabbit hemorrhagic disease virus (RHDV) and rabbit calicivirus Australia 1 (RCV-A1). RCV-A1 causes benign enteric infections in the European rabbit (
Oryctolagus cuniculus
) in Australia and New Zealand, while its close relative RHDV causes a highly pathogenic infection of the liver in the same host. The comparison of these viruses provides important information on the nature and trajectory of virulence evolution, particularly as highly virulent strains of RHDV may have evolved from nonpathogenic ancestors such as RCV-A1. To determine the evolution of RCV-A1 we sequenced the full-length genomes of 44 RCV-A1 samples isolated from healthy rabbits and compared key evolutionary parameters to those of its virulent relative, RHDV. Despite their marked differences in pathogenicity and tissue tropism, RCV-A1 and RHDV have evolved in a very similar manner. Both viruses have evolved at broadly similar rates, suggesting that their dynamics are largely shaped by high background mutation rates, and both exhibit occasional recombination and an evolutionary environment dominated by purifying selection. In addition, our comparative analysis revealed that there have been multiple changes in both virulence and tissue tropism in the evolutionary history of these and related viruses. Finally, these new genomic data suggest that either RCV-A1 was introduced into Australia after the introduction of myxoma virus as a biocontrol agent in 1950 or there was drastic reduction of the rabbit population, and hence of RCV-A1 genetic diversity, perhaps coincident with the emergence of myxoma virus.

IMPORTANCE
The comparison of closely related viruses that differ profoundly in propensity to cause disease in their hosts offers a powerful opportunity to reveal the causes of changes in virulence and to study how such changes alter the evolutionary dynamics of these pathogens. Here we describe such a novel comparison involving two closely related RNA viruses that cocirculate in Australia, the highly virulent rabbit hemorrhagic disease virus (RHDV) and the nonpathogenic rabbit calicivirus Australia 1 (RCV-A1). Both viruses infect the European rabbit, but they differ in virulence, tissue tropism, and mechanisms of transmission. Surprisingly, and despite these fundamental differences, RCV-A1 and RHDV have evolved at very similar (high) rates and with strong purifying selection. Furthermore, candidate key mutations were identified that may play a role in virulence and/or tissue tropism and therefore warrant further investigation.
Identification of Residues That Affect Oligomerization and/or Enzymatic Activity of Influenza Virus H5N1 Neuraminidase Proteins
Authors: Dai Meiling , Guo Hongbo , Dortmans Jos C. F. M. , Dekkers Jojanneke , Nordholm Johan , Daniels Robert , van Kuppeveld Frank J. M. , de Vries Erik , de Haan Cornelis A. M.
Published: August 2016

Influenza A virus (IAV) attachment to and release from sialoside receptors is determined by the balance between hemagglutinin (HA) and neuraminidase (NA). The molecular determinants that mediate the specificity and activity of NA are still poorly understood. In this study, we aimed to design the optimal recombinant soluble NA protein to identify residues that affect NA enzymatic activity. To this end, recombinant soluble versions of four different NA proteins from H5N1 viruses were compared with their full-length counterparts. The soluble NA ectodomains were fused to three commonly used tetramerization domains. Our results indicate that the particular oligomerization domain used does not affect the

K
m

value but may affect the specific enzymatic activity. This particularly holds true when the stalk domain is included and for NA ectodomains that display a low intrinsic ability to oligomerize. NA ectodomains extended with a Tetrabrachion domain, which forms a nearly parallel four-helix bundle, better mimicked the enzymatic properties of full-length proteins than when other coiled-coil tetramerization domains were used, which probably distort the stalk domain. Comparison of different NA proteins and mutagenic analysis of recombinant soluble versions thereof resulted in the identification of several residues that affected oligomerization of the NA head domain (position 95) and therefore the specific activity or sialic acid binding affinity (

K
m

value; positions 252 and 347). This study demonstrates the potential of using recombinant soluble NA proteins to reveal determinants of NA assembly and enzymatic activity.

IMPORTANCE
The IAV HA and NA glycoproteins are important determinants of host tropism and pathogenicity. However, NA is relatively understudied compared to HA. Analysis of soluble versions of these glycoproteins is an attractive way to study their activities, as they are easily purified from cell culture media and applied in downstream assays. In the present study, we analyzed the enzymatic activity of different NA ectodomains with three commonly used tetramerization domains and compared them with full-length NA proteins. By performing a mutagenic analysis, we identified several residues that affected NA assembly, activity, and/or substrate binding. In addition, our results indicate that the design of the recombinant soluble NA protein, including the particular tetramerization domain, is an important determinant for maintaining the enzymatic properties within the head domain. NA ectodomains extended with a Tetrabrachion domain better mimicked the full-length proteins than when the other tetramerization domains were used.
NF-κB and IRF1 Induce Endogenous Retrovirus K Expression via Interferon-Stimulated Response Elements in Its 5′ Long Terminal Repeat
Authors: Manghera Mamneet , Ferguson-Parry Jennifer , Lin Rongtuan , Douville Renée N.
Published: August 2016

Thousands of endogenous retroviruses (ERV), viral fossils of ancient germ line infections, reside within the human genome. Evidence of ERV activity has been observed widely in both health and disease. While this is most often cited as a bystander effect of cell culture or disease states, it is unclear which signals control ERV transcription. Bioinformatic analysis suggests that the viral promoter of endogenous retrovirus K (ERVK) is responsive to inflammatory transcription factors. Here we show that one reason for ERVK upregulation in amyotrophic lateral sclerosis (ALS) is the presence of functional interferon-stimulated response elements (ISREs) in the viral promoter. Transcription factor overexpression assays revealed independent and synergistic upregulation of ERVK by interferon regulatory factor 1 (IRF1) and NF-κB isoforms. Tumor necrosis factor alpha (TNF-α) and LIGHT cytokine treatments of human astrocytes and neurons enhanced ERVK transcription and protein levels through IRF1 and NF-κB binding to the ISREs. We further show that in ALS brain tissue, neuronal ERVK reactivation is associated with the nuclear translocation of IRF1 and NF-κB isoforms p50 and p65. ERVK overexpression can cause motor neuron pathology in murine models. Our results implicate neuroinflammation as a key trigger of ERVK provirus reactivation in ALS. These molecular mechanisms may also extend to the pathobiology of other ERVK-associated inflammatory diseases, such as cancers, HIV infection, rheumatoid arthritis, and schizophrenia.

IMPORTANCEIt has been well established that inflammatory signaling pathways in ALS converge at NF-κB to promote neuronal damage. Our findings suggest that inflammation-driven IRF1 and NF-κB activity promotes ERVK reactivation in neurons of the motor cortex in ALS. Thus, quenching ERVK activity through antiretroviral or immunomodulatory regimens may hinder virus-mediated neuropathology and improve the symptoms of ALS or other ERVK-associated diseases.
A Phenotypically Silent
vanB2
Operon Carried on a Tn
1549
-Like Element in Clostridium difficile
Authors: Knight Daniel R. , Androga Grace O. , Ballard Susan A. , Howden Benjamin P. , Riley Thomas V.
Published: August 2016

In an era when the development of new antimicrobial drugs is slow, vancomycin remains the preferred antimicrobial therapy for
Clostridium difficile
infection (CDI), the most important health care-related infection in the world today. The emergence of resistance to vancomycin would have significant consequences in relation to treating patients with CDI. In this paper, we describe for the first time a complete set of vancomycin resistance genes in
C. difficile
. The genes were very similar to genes found in vancomycin-resistant enterococci (VRE) that were associated with the emergence and global dissemination of this organism. Fortunately, the
C. difficile
strain did not show any reduced susceptibility to vancomycin
in vitro
(MIC, 1 mg/liter), possibly because of a small difference in one gene. However, this observation signals that we may be very close to seeing a fully vancomycin-resistant strain of
C. difficile
.
Comparison of the NBM 200 non-invasive haemoglobin sensor with Sahli's haemometer among adolescent girls in rural India
Authors: Ahankari A S , Dixit J V , Fogarty A W , Tata L J , Myles P R
Published: August 2016

Objective

The study objective was to compare haemoglobin (Hb) measurements between the NBM 200 (non-invasive Hb sensor) and Sahli's haemometer in adolescent girls in a rural Indian setting.

Methods

Participants included girls aged between 13 and 17 years from 34 villages in Tuljapur and Lohara blocks of Osmanabad district, Maharashtra, India. Hb measurements from the non-invasive sensor (NBM 200) were compared with measurements obtained from Sahli's haemometer using the Bland-Altman plot, Spearman correlation coefficient, sensitivity, specificity and area under the receiver operating characteristic curve analysis (AUROC).

Results

Paired measurements from both methods were obtained from 766 adolescent girls (N=766). Hb levels estimated by Sahli's haemometer ranged from 5.0 to 14.0 g/dL (mean 10.1 g/dL, SD 1.41), whereas measurements obtained from the NBM 200 ranged from 9.5 to 15.2 g/dL (mean 12.8 g/dL, SD 1.42). The Bland-Altman analysis indicated a mean difference of −2.70 g/dL (95% CI −2.84 to −2.55) demonstrating an overestimation of Hb measurement by the NBM 200 compared with the Sahli's haemometer measurements. The NBM 200 showed low sensitivity (23.6%) and moderate specificity (61.8%) for the diagnosis of anaemia. The AUROC score was 0.43 indicating an underestimation of anaemia in our study population by the NBM 200.

Conclusions

Hb measurements obtained from the NBM 200 were consistently higher leading to an underestimation of prevalence of anaemia compared with Sahli's haemometer estimates among adolescent girls in India.
Impact of an SMS advice programme on maternal and newborn health in rural China: study protocol for a quasi-randomised controlled trial
Authors: Su Yanfang , Yuan Changzheng , Zhou Zhongliang , Heitner Jesse , Campbell Benjamin
Published: August 2016

Introduction

Expectant mothers in low-income and middle-income countries often lack access to vital information about pregnancy, preparation for birth and best practices when caring for their newborn. Innovative solutions are needed to bridge this knowledge gap and dramatically improve maternal and neonatal health in these settings. This study aims to evaluate the impact of an innovative text messaging intervention on maternal and neonatal health outcomes.

Methods and analysis

This study offers expectant mothers in rural China a package of free short messages via cell phone regarding pregnancy and childbirth. These messages are tailored to each mother's gestational week. It is hypothesised that delivering these short advice messages to pregnant women can improve maternal and newborn health. The study uses factorial quasi-randomisation to compare psychological, behavioural and health outcomes between 4 groups: 2 groups receiving different sets of short message interventions (ie, good household prenatal practices and healthcare seeking), a group receiving both interventions and a control group. Treatment assignment occurs at the individual level. The primary outcome is newborn health, measured by appropriateness of weight for gestational age. Secondary outcomes include severe neonatal and maternal morbidity as well as psychological and behavioural measures. This study has enrolled pregnant women who attend county maternal and child health centres for their prenatal visits.

Discussion

This pilot is the first large-scale effort to build a comprehensive evidence base on the impact of prenatal text messages via cell phone on maternal and newborn health outcomes in China. The study has broad implications for public health policy in China and the implementation of mobile health interventions in low-resource settings around the world.

Ethics

This study was approved by the Ethics Committee of the School of Medicine at Xi'an Jiaotong University on 18 January 2013.

Trial registration number

NCT02037087; Pre-results.
Cancer symptom scale preferences: does one size fit all?
Authors: Jeter Kirby , Blackwell Siobhan , Burke Lucy , Joyce David , Moran Catherine , Conway Emma Victoria , Cremen Iseult , O'Connor Brenda , Ui Dhuibhir Pauline , Walsh Declan
Published: August 2016

Objectives

Patients with advanced cancer do not report all symptoms, so assessment is best done systematically. However, for such patients, completion rates of some symptom instruments are <50%. Symptoms can be quantified by various scales including the Categorical Response Scale (CRS), Numerical Rating Scale (NRS) and Visual Analogue Scale (VAS). Patient preferences for CRS, NRS and VAS in symptom assessment and their clinical utility in 3 cancer symptoms: pain, tiredness and appetite loss were determined.

Methods

A prospective survey was conducted involving cancer admissions to a 36-bed palliative care unit.

Results

100 inpatients were recruited, aged 38–93 years (x̅ =71 years; SD=11.6), with median Eastern Cooperative Oncology Group (ECOG) scores of 2 (range 0–4). VAS was the least preferred measure. 52% of patients choose the same scale for all 3 symptoms and 44% for 2, with 4% choosing a different individual scale per symptom. There was moderate agreement between participant scale preference and observer determined ease of scale completion (loss of appetite: κ=0.36; pain: κ=0.49; tiredness: κ=0.45). Participants preferred CRS for appetite loss (48%) and tiredness (40%) and NRS for pain (44%).

Conclusions

VAS was the least favoured scale and should be used cautiously in this population. Most participants had a scale preference with high intrapatient consistency between scales. CRS was preferred for appetite loss and tiredness and NRS for pain. Consideration should be given to individualised cancer symptom assessment according to patient scale preference.
Establishing an injury indicator for severe paediatric injury
Authors: Pike Ian , Khalil Mina , Yanchar Natalie L , Tamim Hala , Nathens Avery B , Macpherson Alison K
Published: August 2016

Background

Routinely gathered injury data, such as hospitalisations, may be subject to variation from sources other than injury incidence. There is a need for an indicator that defines severe injury, which may be less vulnerable to fluctuations due to changes in care policies. The purpose of this study was to identify International Classification of Diseases-10 codes associated with severe paediatric injuries and to specify and validate a severe paediatric injury indicator.

Methods

Two data sets that included the ISS and the survival risk ratio were used to produce a list of diagnoses to define severe paediatric injury. The list was sent to trauma surgeons who classified each code as severe enough or not severe enough to require care in a trauma centre. The indicator was fully specified, then validated by using a different data set to validate the codes in a real-world situation.

Results

Sixty diagnoses were identified as representing severe paediatric injury. Following specification, the indicator was applied to an existing comprehensive data set of paediatric injuries. The decline in hospitalisation of paediatric injuries was significantly steeper for severe than non-severe injuries, suggesting that factors related to the decline in this trauma subset are unlikely to be related to changes in access or other components of trauma care delivery.

Conclusions

This indicator can be used for the evaluation of trends in severe paediatric trauma and will help identify populations at risk. This research may inform policies and procedures for referrals of severe childhood injury to appropriate levels of care.
Towards a structure of feeling: abjection and allegories of disease in science fiction ‘mutation’ films
Authors: Pheasant-Kelly Frances
Published: August 2016

This article considers differences between the representation of mutation in science fiction films from the 1950s and the present, and identifies distinctive changes over this time period, both in relation to the narrative causes of genetic disruption and in the aesthetics of its visual display. Discerning an increasingly abject quality to science fiction mutations from the 1970s onwards—as a progressive tendency to view the physically opened body, one that has a seemingly fluid interior–exterior reversal, or one that is almost beyond recognition as humanoid—the article connects a propensity for disgust to the corresponding socio-cultural and political zeitgeist. Specifically, it suggests that such imagery is tied to a more expansive ‘structure of feeling’, proposed by Raymond Williams and emergent since the 1970s, but gathering momentum in later decades, that reflects an ‘opening up’ of society in all its visual, socio-cultural and political configurations. Expressly, it parallels a change from a repressive, patriarchal society that constructed medicine as infallible and male doctors as omnipotent to one that is generally more liberated, transparent and equitable. Engaging theoretically with the concept of a ‘structure of feeling’, and critically with scientific, cinematic and cultural discourses, two post-1970s’ ‘mutation’ films,The Fly(1986) andDistrict 9(2009), are considered in relation to their pre-1970s’ predecessors, and their aesthetics related to the perceptions and articulations of the medical profession at their respective historic moments, locating such instances within a broader medico-political canvas.
Feline lost: making microchipping compulsory for domestic cats
Authors: Roberts M.
Published: August 2016

The independent nature of cats means that they are more likely to become lost or injured than dogs. Maggie Roberts believes that microchipping of cats should be compulsory in the UK as is the case with dogs.
Similar substrate oxidation rates in concentric and eccentric cycling matched for aerobic power output
Authors: Isacco Laurie , Ritter Ophélie , Tordi Nicolas , Laroche Davy , Degano Bruno , Bouhaddi Malika , Rakobowchuk Mark , Mourot Laurent
Published: August 2016

This study investigated substrate oxidation in concentric and eccentric cycling matched for aerobic power output in the postprandial state. Energy expenditure, respiratory exchange ratio, and fat and carbohydrate oxidation rates were measured at rest and after 15, 30, and 45 min of eccentric and concentric cycling in 12 men. Absolute and relative aerobic power output and energy expenditure were similar during concentric and eccentric exercise. No effect of exercise modality was observed for substrate metabolism.
Experimental study of a naturally weathered stiff clay
Authors: Mandaglio Maria Clorinda , Moraci Nicola , Rosone Marco , Farulla Camillo Airò
Published: August 2016

Studying the shear strength of a naturally weathered clay is important to understand rain-induced slope failures in weathered soils. However, experimental studies on naturally weathered soils are limited. The paper focuses on the laboratory experimental investigation carried out to analyse the shear strength of a naturally weathered stiff clay that can be found in unsaturated conditions in situ. This has an important practical relevance in the evaluation of the stability conditions of natural slopes at clay outcrops. Different experimental techniques of suction measurement were used to obtain the soil-water retention curve of the clay over a wide range of suctions. Scanning electronic microscope (SEM) observations and results of mercury intrusion porosimetry (MIP) tests are also presented to highlight the considerable fabric arrangement modifications at the microstructural level induced by wetting–drying processes. Moreover, isotropic consolidated drained triaxial compression tests on undisturbed and reconstituted saturated specimens and controlled-suction triaxial compression tests on unsaturated undisturbed specimens were carried out. The test results allowed examination of the saturated mechanical behaviour of clay and comparison of the mechanical behaviour of the saturated material with that in an unsaturated condition.
Suggesting Alternative Scenarios Using Use Case Specification Patterns for Requirement Completeness
Authors: Ko Deokyoon , Park Sooyong , Kim Yourim , Park Soojin , Kim Suntae
Published: August 2016

Completeness in software requirements specification is one of the key factors for successful software development. For specifying software requirements, scenario-based approach is broadly used, comprising a basic flow regarding the successful use of the system, and alternative flows describing abnormal or less frequent interactions of the system. However, alternative flows tend to be frequently missed in many cases, because of the relative lower significance rather than the basic flow, which eventually have an influence on achieving the completeness of software requirements. In order to address the issue, we propose an approach for automatically recommending alternative flows from a basic flow by extracting the essential use case patterns based on the occurrence patterns of the agents and measuring the verb similarity between the main verbs of each scenario. In order to validate our approach, we apply it to three industrial case studies, and show comprehensiveness of the suggested alternative flows and synergic effectiveness for inexperienced developers.
Supporting Semantic Concept Retrieval with Negative Correlations in a Multimedia Big Data Mining System
Authors: Yan Yilin , Shyu Mei-Ling , Zhu Qiusha
Published: August 2016

With the extensive use of smart devices and blooming popularity of social media websites such as Flickr, YouTube, Twitter, and Facebook, we have witnessed an explosion of multimedia data. The amount of data nowadays is formidable without effective big data technologies. It is well-acknowledged that multimedia high-level semantic concept mining and retrieval has become an important research topic; while the semantic gap (i.e., the gap between the low-level features and high-level concepts) makes it even more challenging. To address these challenges, it requires the joint research efforts from both big data mining and multimedia areas. In particular, the correlations among the classes can provide important context cues to help bridge the semantic gap. However, correlation discovery is computationally expensive due to the huge amount of data. In this paper, a novel multimedia big data mining system based on the MapReduce framework is proposed to discover negative correlations for semantic concept mining and retrieval. Furthermore, the proposed multimedia big data mining system consists of a big data processing platform with Mesos for efficient resource management and with Cassandra for handling data across multiple data centers. Experimental results on the TRECVID benchmark datasets demonstrate the feasibility and the effectiveness of the proposed multimedia big data mining system with negative correlation discovery for semantic concept mining and retrieval.
Shared Memory Multicore MicroBlaze System with SMP Linux Support
Authors: Matthews Eric , Shannon Lesley , Fedorova Alexandra
Published: August 2016

In this work, we present PolyBlaze, a scalable and configurable multicore platform for FPGA-based embedded systems and systems research. PolyBlaze is an extension of the MicroBlaze soft processor, leveraging the configurability of the MicroBlaze and bringing it into the multicore era with Linux Symmetric Multi-Processor (SMP) support. This work details the hardware modifications required for the MicroBlaze processor and its software stack to enable fully validated SMP operations, including atomic operation support, shared interrupts and timers, and exception handling. New in this work, we present a scalable and flexible memory hierarchy optimized for Field Programmable Gate Arrays (FPGAs), which manages atomic operations and provides support for future flexible memory hierarchies and heterogeneous systems. Also new is an in-depth analysis of key performance characteristics, including memory bandwidth, latency, and resource usage. For all system configurations, bandwidth is found to scale linearly with the addition of processor cores until the memory interface is saturated. Additionally, average memory latency remains constant until the memory interface is saturated; after which, it scales linearly with each additional processor core.
White matter and cognition: making the connection
Authors: Filley Christopher M. , Fields R. Douglas
Published: August 2016

Whereas the cerebral cortex has long been regarded by neuroscientists as the major locus of cognitive function, the white matter of the brain is increasingly recognized as equally critical for cognition. White matter comprises half of the brain, has expanded more than gray matter in evolution, and forms an indispensable component of distributed neural networks that subserve neurobehavioral operations. White matter tracts mediate the essential connectivity by which human behavior is organized, working in concert with gray matter to enable the extraordinary repertoire of human cognitive capacities. In this review, we present evidence from behavioral neurology that white matter lesions regularly disturb cognition, consider the role of white matter in the physiology of distributed neural networks, develop the hypothesis that white matter dysfunction is relevant to neurodegenerative disorders, including Alzheimer's disease and the newly described entity chronic traumatic encephalopathy, and discuss emerging concepts regarding the prevention and treatment of cognitive dysfunction associated with white matter disorders. Investigation of the role of white matter in cognition has yielded many valuable insights and promises to expand understanding of normal brain structure and function, improve the treatment of many neurobehavioral disorders, and disclose new opportunities for research on many challenging problems facing medicine and society.
Negative News: Cl−and HCO3−in the Vascular Wall
Authors: Boedtkjer Ebbe , Matchkov Vladimir V. , Boedtkjer Donna M. B. , Aalkjaer Christian
Published: August 2016

Cl−and HCO3−are the most prevalent membrane-permeable anions in the intra- and extracellular spaces of the vascular wall. Outwardly directed electrochemical gradients for Cl−and HCO3−permit anion channel opening to depolarize vascular smooth muscle and endothelial cells. Transporters and channels for Cl−and HCO3−also modify vascular contractility and structure independently of membrane potential. Transport of HCO3−regulates intracellular pH and thereby modifies the activity of enzymes, ion channels, and receptors. There is also evidence that Cl−and HCO3−transport proteins affect gene expression and protein trafficking. Considering the extensive implications of Cl−and HCO3−in the vascular wall, it is critical to understand how these ions are transported under physiological conditions and how disturbances in their transport can contribute to disease development. Recently, sensing mechanisms for Cl−and HCO3−have been identified in the vascular wall where they modify ion transport and vasomotor function, for instance, during metabolic disturbances. This review discusses current evidence that transport (e.g., via NKCC1, NBCn1, Ca2+-activated Cl−channels, volume-regulated anion channels, and CFTR) and sensing (e.g., via WNK and RPTPγ) of Cl−and HCO3−influence cardiovascular health and disease.
Strategic Lean Organizational Design: Towards Lean World-Small World Configurations through Discrete Dynamic Organizational Motifs
Authors: Villalba-Diez Javier , Ordieres-Meré Joaquín B.
Published: August 2016

Organizations face strong international competition in the global market arena in achieving strategic goals such as high quality of product or service at lower cost while increasing their ability to respond quickly to requirements of the market. These challenges concern strategically designing organizations that can meet global challenges and specialize locally to meet performance constraints. After introducing the concept of organizational functional and structural motifs as small organizational building block, our findings suggest the hypothesis that a strategic organizational design (SOD) approach to meet these challenges involves maximizing the number and diversity of functional motifs, while minimizing the repertoire of structural motifs. By detecting characteristic structural motifs, we provide organizational leaders with specific Lean SOD solutions with which to meet local and global challenges simultaneously. As a matter of application, we show the implementation of such an SOD approach in nine US hospitals that form one large health care holding.
A Novel Hybrid Method for Short-Term Power Load Forecasting
Authors: Yuansheng Huang , Shenhai Huang , Jiayin Song
Published: August 2016

Influenced by many uncertain and random factors, nonstationary, nonlinearity, and time-variety appear in power load series, which is difficult to forecast accurately. Aiming at locating these issues of power load forecasting, an innovative hybrid method is proposed to forecast power load in this paper. Firstly, ensemble empirical mode decomposition (EEMD) is used to decompose the power load series into a series of independent intrinsic mode functions (IMFs) and a residual term. Secondly, genetic algorithm (GA) is then applied to determine the best weights of each IMF and the residual term named ensemble empirical mode decomposition based on weight (WEEMD). Thirdly, least square support vector machine (LSSVM) and nonparametric generalized autoregressive conditional heteroscedasticity (NPGARCH) are employed to forecast the subseries, respectively, based on the characteristics of power load series. Finally, the forecasted power load of each component is summed as the final forecasted result of power load. Compared with other methods, the forecasting results of this proposed model applied to the electricity market of Pennsylvania-New Jersey-Maryland (PJM) indicate that the proposed model outperforms other models.
Association between IgG4 Autoantibody and Complement Abnormalities in Systemic Lupus Erythematosus
Authors: Pan Qingjun , Guo Linjie , Wu Jing , Cai Jun , Liao Huanjin , Lan Qiaofen , Peng Yanxia , He Yiming , Liu Hua-feng
Published: August 2016

In order to investigate the association between IgG4 autoantibody and complement abnormalities in systemic lupus erythematosus (SLE), 72 newly diagnosed SLE patients, 67 rheumatoid arthritis (RA) patients, and 41 healthy normals were employed. Serum levels of antinuclear IgG4 and IgG4-specific IgM-rheumatoid factor (RF) were measured, and the correlations between serum levels of antinuclear IgG4 and several clinical parameters were analyzed. Also, the levels of IgG subclasses, C1q, and C3 deposition in lupus nephritis (LN) were detected. The results showed that serum levels of antinuclear IgG4 were higher in SLE patients relative to healthy normals (P<0.01). Serum levels of antinuclear IgG4 in SLE patients were positively correlated with serum levels of total IgG4, albumin, and C3 (r=0.61,P<0.05;r=0.40,P<0.05; andr=0.54,P<0.05, resp.) and negatively correlated with 24-hour urinary protein (r=0.49,P<0.05). Serum levels of IgG4-specific IgM-RF were higher in RA patients than in SLE patients (P<0.001). Also, the ratio of the deposition score for IgG4/(IgG1 + IgG2 + IgG3 + IgG4) was negatively correlated with the score for C1q and C3 deposition in LN (r=0.34,P<0.05;r=0.51,P<0.01, resp.). In summary, the IgG4 autoantibody may dampen the inflammatory response in SLE, thus maybe providing a novel therapeutic target for SLE.
Crystalline Coating and Its Influence on the Water Transport in Concrete
Authors: Reiterman Pavel , Pazderka Jiri
Published: August 2016

The presented paper deals with an experimental study of the efficiency of surface coating treatment based on secondary crystallization as an additional protection of the subsurface concrete structure loaded by moisture or ground water pressure. The aim of the experimental program was the evaluation of the depth impact of the crystalline coating and the assessment of the reliability of construction joints performed on models simulating real conditions of the concrete structure. The evolution of the secondary crystallizing process was monitored using the water absorption test carried out at different depths of the samples. The coefficient of adsorption decreased to 60% of the reference mixture for a surface layer of up to 40 mm at 28 days and to 50% at 180 days after the coating’s application. Furthermore, the electrical resistivity method was applied with respect to the nature of measurement and the low accessibility of real subsurface concrete structures. The results of moisture measurement at a depth of 180–190 mm from the surface treated with a crystalline coating showed an essential decrease in moisture content percentage in comparison with untreated specimens (measured 125 days after the coating’s application).
The Immune System in Tissue Environments Regaining Homeostasis after Injury: Is “Inflammation” Always Inflammation?
Authors: Kulkarni Onkar P. , Lichtnekert Julia , Anders Hans-Joachim , Mulay Shrikant R.
Published: August 2016

Inflammation is a response to infections or tissue injuries. Inflammation was once defined by clinical signs, later by the presence of leukocytes, and nowadays by expression of “proinflammatory” cytokines and chemokines. But leukocytes and cytokines often have rather anti-inflammatory, proregenerative, and homeostatic effects. Is there a need to redefine “inflammation”? In this review, we discuss the functions of “inflammatory” mediators/regulators of the innate immune system that determine tissue environments to fulfill the need of the tissue while regaining homeostasis after injury.
The Evaluation of Financing Efficiency of China’s Stock Market
Authors: Dong Ji-chang , Zhu Lin-lin , Wang Bing , Dong Zhi , Li Xiu-ting
Published: August 2016

Financing is the main way for listed companies to obtain funds in China, and it is the “reservoir” which can guarantee enterprises to operate continuously. Financing efficiency can be used to measure the efficiency in using enterprises’ own funds, and it is one of the main indicators which are concerned by the stakeholders of listed companies. This paper mainly researches on the impact of equity financing on the financing efficiency of listed companies as a whole and selects 300 listed companies in the Shanghai and Shenzhen Stock Exchange as decision-making units. Then this paper analyzes the financial data of sample companies in 2008–2014. Finally, it can be concluded that the financing efficiency of listed companies in China is generally low, and the total factor productivity in the stock market continued to decline between 2003 and 2005 and then rose rapidly.
Preparation of Porous MnO@C Core-Shell Nanowires as Anodes for Lithium-Ion Batteries
Authors: Chen Shouhui , Chen Yaqin , Zhou Rihui , Wu Jiafeng , Song Yonggui , Li Ping , Song Yonghai , Wang Li
Published: August 2016

Porous MnO@C core-shell nanowires were prepared via a simple and facile method. The morphologies, the phase purity, the mass contents, and the BET surface area of the composite were characterized by SEM, XRD, TGA, and N2adsorption test, respectively. When the composite served as an anode for lithium-ion batteries, it showed superior electrochemical performances. The MnO@C composite presented a reversible capacity of 448.1 mAh g−1after 100 cycles at the current rate of 200 mA g−1.
Modeling of Flow Stress of 2026 Al Alloy under Hot Compression
Authors: Xiao Zheng-bing , Huang Yuan-chun , Liu Yu
Published: August 2016

In order to investigate the workability and to optimize the hot forming parameters for 2026 Al alloy, hot compression tests were performed in the temperature range of 350~450°C with strain rates of 0.01~10 s−1and 60% deformation degree on a Gleeble-1500 thermosimulation machine. The true stress-strain curves obtained exhibit that the stress increases dramatically at small strains and then moves forward to a steady state, showing dynamic flow softening. Meanwhile, on the basis of Arrhenius equation, a constitutive equation on the flow stress, temperature, and strain rate was proposed. Yet, the values of the predicated stress from the equation and the true stress differ by as much as 50.10%. Given the intricate impact of precipitation of the second phases on the strength of 2026 Al alloy, the introduction of a revised equation with the reinforcement of temperature was carried out, fitting well with the experiment data at peak stresses. What is more, both pictures obtained by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were compatible with all the inferences.
Prevalence and Scanning Electron Microscopic Identification of Anoplocephalid Cestodes among Small Ruminants in Senegal
Authors: Ndom Mallé , Diop Gora , Quilichini Yann , Yanagida Tetsuya , Ba Cheikh Tidiane , Marchand Bernard
Published: August 2016

This study was undertaken to determine the prevalence of anoplocephalid cestodes in sheep and goats in Senegal. Intestines of 462 sheep and 48 goats were examined; 47.4% of sheep and 6.2% of goats were infected. The species identified and their prevalence were, among sheep,Avitellina centripunctata38.7%,Moniezia expansa15.4%,Stilesia globipunctata16.7%, andThysaniezia ovilla0.4%. Among goats, they wereM. expansa6.2% andT. ovilla2.1%. The prevalence of all species was not statistically different between dry and rainy seasons. The infections were single or multiple. Indeed, 56.2% of sheep were infected by a single species, 37.4% by two species, and 6.4% by three species. For goats, 66.7% were infected byM. expansaand 33.3% by bothM. expansaandT. ovilla. Scanning electron microscopic (SEM) observations of tapeworms show the general diagnosis characters of these species.
Adaptive Sliding Mode Control of Generator Excitation System with Output Constraints
Authors: Sun Liying
Published: August 2016

A nonlinear excitation controller for the uncertain parameters and external disturbances is designed by using the backstepping method and sliding mode control theory. In the design process, nonlinear features are retained completely with no linear technique used here. Compared with the excitation controllers designed via conventional linearization, the newly designed one has superiorities in strong robustness to external disturbances, good adaptive ability to variation of system parameters, super transient performance, and the ability to assure preset constraints. Simulation results prove the validity and stability of the controller.
Cutaneous Metastases of the Synchronous Primary Endometrial and Bilateral Ovarian Cancer: An Infrequent Presentation and Literature Review
Authors: Kanyilmaz Gul , Aktan Meryem , Koc Mehmet , Findik Siddika
Published: August 2016

There are limited data about the cutaneous metastases of gynecological malignancies in the literature. Based on this limited number of studies, cutaneous metastases from gynecological malignancies are uncommon occurrences. Cutaneous metastases from the synchronous endometrioid carcinoma of the uterine corpus and bilateral ovaries arising from endometriosis are extremely rare. Herein, we report a 51-year-old woman with FIGO Stage 1A Grade 1 endometrial endometrioid-type adenocarcinoma and synchronous bilateral Stage 1B ovarian endometrioid-type adenocarcinoma who presented 34 months following total abdominal hysterectomy and bilateral salpingo-oophorectomy with skin metastases. After the patient underwent an excisional biopsy, we applied a palliative radiotherapy. The patient received the combination therapy with cisplatin and doxorubicin after the completion of radiotherapy but the disease evolution was rapidly fatal and the patient died 4 months after her admission to our department due to widely disseminated disease.