bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of Glycoprotein-Mediated Entry of Severe Fever with Thrombocytopenia Syndrome Virus
Authors: Tani Hideki , Shimojima Masayuki , Fukushi Shuetsu , Yoshikawa Tomoki , Fukuma Aiko , Taniguchi Satoshi , Morikawa Shigeru , Saijo Masayuki
Published: March 2016

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging hemorrhagic fever with a high case fatality rate caused by SFTS virus (SFTSV). Effective vaccines and specific therapies for SFTS are urgently sought, and investigation into virus-host cell interactions is expected to contribute to the development of antiviral strategies. In this study, we have developed a pseudotype vesicular stomatitis virus (VSV) bearing the unmodified Gn/Gc glycoproteins (GPs) of SFTSV (SFTSVpv). We have analyzed the host cell entry of this pseudotype virus and native SFTSV. Both SFTSVpv and SFTSV exhibited high infectivity in various mammalian cell lines. The use of lysosomotropic agents indicated that virus entry occurred via pH-dependent endocytosis. SFTSVpv and SFTSV infectivity was neutralized by serial dilutions of convalescent-phase patient sera. Entry of SFTSVpv and growth of SFTSV were increased in Raji cells expressing not only the C-type lectin dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN) but also DC-SIGN-related (DC-SIGNR) and liver and lymph node sinusoidal endothelial cell C-type lectin (LSECtin). 25-Hydroxycholesterol (25HC), a soluble oxysterol metabolite, inhibited the cell entry of SFTSVpv and the membrane fusion of SFTSV. These results indicate that pH-dependent endocytosis of SFTSVpv and SFTSV is enhanced by attachment to certain C-type lectins. SFTSVpv is an appropriate model for the investigation of SFTSV-GP-mediated cell entry and virus neutralization at lower biosafety levels. Furthermore, 25HC may represent a potential antiviral agent against SFTS.

IMPORTANCE
SFTSV is a recently discovered bunyavirus associated with SFTS, a viral hemorrhagic fever with a high case fatality rate endemic to China, South Korea, and Japan. Because little is known about the characteristics of the envelope protein and entry mechanisms of SFTSV, further studies will be required for the development of a vaccine or effective therapies. In this study, we investigated the mechanism of SFTSV cell entry using SFTSVpv and the native virus. SFTSV can grow in nonsusceptible cell lines in the presence of certain C-type lectins. Moreover, 25HC, an oxysterol metabolite, may represent a potential therapeutic inhibitor of SFTSV infection.
The Large Marseillevirus Explores Different Entry Pathways by Forming Giant Infectious Vesicles
Authors: Arantes Thalita Souza , Rodrigues Rodrigo Araújo Lima , dos Santos Silva Ludmila Karen , Oliveira Graziele Pereira , de Souza Helton Luís , Khalil Jacques Y. B. , de Oliveira Danilo Bretas , Torres Alice Abreu , da Silva Luis Lamberti , Colson Philippe , Kroon Erna Geessien , da Fonseca Flávio Guimarães , Bonjardim Cláudio Antônio , La Scola Bernard , Abrahão Jônatas Santos
Published: March 2016

Triggering the amoebal phagocytosis process is a
sine qua non
condition for most giant viruses to initiate their replication cycle and consequently to promote their progeny formation. It is well known that the amoebal phagocytosis process requires the recognition of particles of >500 nm, and most amoebal giant viruses meet this requirement, such as mimivirus, pandoravirus, pithovirus, and mollivirus. However, in the context of the discovery of amoebal giant viruses in the last decade,
Marseillevirus marseillevirus
(MsV) has drawn our attention, because despite its ability to successfully replicate in
Acanthamoeba
, remarkably it does not fulfill the >500-nm condition, since it presents an ∼250-nm icosahedrally shaped capsid. We deeply investigated the MsV cycle by using a set of methods, including virological, molecular, and microscopic (immunofluorescence, scanning electron microscopy, and transmission electron microscopy) assays. Our results revealed that MsV is able to form giant vesicles containing dozens to thousands of viral particles wrapped by membranes derived from amoebal endoplasmic reticulum. Remarkably, our results strongly suggested that these giant vesicles are able to stimulate amoebal phagocytosis and to trigger the MsV replication cycle by an acidification-independent process. Also, we observed that MsV entry may occur by the phagocytosis of grouped particles (without surrounding membranes) and by an endosome-stimulated pathway triggered by single particles. Taken together, not only do our data deeply describe the main features of MsV replication cycle, but this is the first time, to our knowledge, that the formation of giant infective vesicles related to a DNA virus has been described.

IMPORTANCE
Triggering the amoebal phagocytosis process is a
sine qua non
condition required by most giant viruses to initiate their replication cycle. This process requires the recognition of particles of >500 nm, and many giant viruses meet this requirement. However, MsV is unusual, as despite having particles of ∼250 nm it is able to replicate in
Acanthamoeba
. Our results revealed that MsV is able to form giant vesicles, containing dozens to thousands of viral particles, wrapped in membranes derived from amoebal endoplasmic reticulum. Remarkably, our results strongly suggest that these giant vesicles are able to stimulate phagocytosis using an acidification-independent process. Our work not only describes the main features of the MsV replication cycle but also describes, for the first time to our knowledge, the formation of huge infective vesicles in a large DNA viruses.
Cellular Immune Responses against Simian T-Lymphotropic Virus Type 1 Target Tax in Infected Baboons
Authors: Castro Iris , Giret Teresa M. , Magnani Diogo M. , Maxwell Helen S. , Umland Oliver , Perry Jessica K. , Pecotte Jerilyn K. , Brasky Kathleen M. , Barber Glen N. , Desrosiers Ronald C. , Watkins David I.
Published: March 2016

There are currently 5 million to 10 million human T-lymphotropic virus type 1 (HTLV-1)-infected people, and many of them will develop severe complications resulting from this infection. A vaccine is urgently needed in areas where HTLV-1 is endemic. Many vaccines are best tested in nonhuman primate animal models. As a first step in designing an effective HTLV-1 vaccine, we defined the CD8
+
and CD4
+
T cell response against simian T-lymphotropic virus type 1 (STLV-1), a virus closely related to HTLV-1, in olive baboons (
Papio
anubis
). Consistent with persistent antigenic exposure, we observed that STLV-1-specific CD8
+
T cells displayed an effector memory phenotype and usually expressed CD107a, gamma interferon (IFN-γ), and tumor necrosis factor alpha (TNF-α). To assess the viral targets of the cellular immune response in STLV-1-infected animals, we used intracellular cytokine staining to detect responses against overlapping peptides covering the entire STLV-1 proteome. Our results show that, similarly to humans, the baboon CD8
+
T cell response narrowly targeted the Tax protein. Our findings suggest that the STLV-1-infected baboon model may recapitulate some of the important aspects of the human response against HTLV-1 and could be an important tool for the development of immune-based therapy and prophylaxis.

IMPORTANCE
HTLV-1 infection can lead to many different and often fatal conditions. A vaccine deployed in areas of high prevalence might reduce the incidence of HTLV-1-induced disease. Unfortunately, there are very few animal models of HTLV-1 infection useful for testing vaccine approaches. Here we describe cellular immune responses in baboons against a closely related virus, STLV-1. We show for the first time that the immune response against STLV-1 in naturally infected baboons is largely directed against the Tax protein. Similar findings in humans and the sequence similarity between the human and baboon viruses suggest that the STLV-1-infected baboon model might be useful for developing a vaccine against HTLV-1.
Internal Proteins of the Procapsid and Mature Capsids of Herpes Simplex Virus 1 Mapped by Bubblegram Imaging
Authors: Wu Weimin , Newcomb William W. , Cheng Naiqian , Aksyuk Anastasia , Winkler Dennis C. , Steven Alasdair C.
Published: March 2016

The herpes simplex virus 1 (HSV-1) capsid is a huge assembly, ∼1,250 Å in diameter, and is composed of thousands of protein subunits with a combined mass of ∼200 MDa, housing a 100-MDa genome. First, a procapsid is formed through coassembly of the surface shell with an inner scaffolding shell; then the procapsid matures via a major structural transformation, triggered by limited proteolysis of the scaffolding proteins. Three mature capsids are found in the nuclei of infected cells. A capsids are empty, B capsids retain a shrunken scaffolding shell, and C capsids—which develop into infectious virions—are filled with DNA and ostensibly have expelled the scaffolding shell. The possible presence of other internal proteins in C capsids has been moot as, in cryo-electron microscopy (cryo-EM), they would be camouflaged by the surrounding DNA. We have used bubblegram imaging to map internal proteins in all four capsids, aided by the discovery that the scaffolding protein is exceptionally prone to radiation-induced bubbling. We confirmed that this protein forms thick-walled inner shells in the procapsid and the B capsid. C capsids generate two classes of bubbles: one occupies positions beneath the vertices of the icosahedral surface shell, and the other is distributed throughout its interior. A likely candidate is the viral protease. A subpopulation of C capsids bubbles particularly profusely and may represent particles in which expulsion of scaffold and DNA packaging are incomplete. Based on the procapsid structure, we propose that the axial channels of hexameric capsomers afford the pathway via which the scaffolding protein is expelled.

IMPORTANCE
In addition to DNA, capsids of tailed bacteriophages and their distant relatives, herpesviruses, contain internal proteins. These proteins are often essential for infectivity but are difficult to locate within the virion. A novel adaptation of cryo-EM based on detecting gas bubbles generated by radiation damage was used to localize internal proteins of HSV-1, yielding insights into how capsid maturation is regulated. The scaffolding protein, which forms inner shells in the procapsid and B capsid, is exceptionally bubbling-prone. In the mature DNA-filled C capsid, a previously undetected protein was found to underlie the icosahedral vertices: this is tentatively assigned as a storage form of the viral protease. We also observed a capsid species that appears to contain substantial amounts of scaffolding protein as well as DNA, suggesting that DNA packaging and expulsion of the scaffolding protein are coupled processes.
Biomechanical characteristics of head injuries from falls in children younger than 48 months
Authors: Hughes Jonathon , Maguire Sabine , Jones Michael , Theobald Peter , Kemp Alison
Published: March 2016

Background

A fall-height threshold is important when evaluating the likelihood of structural head injury or abusive head trauma. This study investigates witnessed falls to correlate the fall characteristics with the extent of injury.

Method

Case–control study of children aged ≤48 months who attended one hospital following a fall from <3 m (10 ft), comparing cases who sustained a skull fracture or intracranial injury (ICI) with controls, who had minor head injuries. Characteristics included: the mechanism of injury, surface of impact, site of impact to the head and fall height.

Results

Forty-seven children had a skull fracture or ICI, while 416 children had minor head injuries. The mean fall height for minor head injuries was significantly lower than that causing skull fracture/ICI (p<0.001). No skull fracture/ICI was recorded in children who fell <0.6 m (2 ft), based on the height of the head centre of gravity. Skull fractures/ICI were more likely in children aged ≤12 months (p<0.001) from impacts to the temporal/parietal or occipital region (p<0.001), impacts onto wood (p=0.004) and falls from a carer's arms, particularly when on stairs (p<0.001). No significant difference was reported between the mean fall heights of children who had a simple skull fracture (n=17) versus those who had a complex fracture or ICI (n=30).

Conclusions

An infant is more likely to sustain a skull fracture/ICI from a fall above a 0.6 m (2 ft) threshold, based on the height of the head centre of gravity, or with a parietal/temporal or occipital impact. These variables should be recorded when evaluating the likelihood of skull fracture/ICI.
A randomised controlled trial of a code-word enuresis alarm
Authors: Caldwell Patrina H Y , Sureshkumar Premala , Kerr Marianne I , Hamilton Sana , Teixeira-Pinto Armando , Macaskill Petra , Craig Jonathan C
Published: March 2016

Objective

To compare a novel code-word alarm with a commercially available wireless alarm for treating enuresis.

Setting

A tertiary paediatric centre.

Patients

Children aged 6–18 with at least 3 wet nights per week in the previous 6 months referred by doctors.

Outcomes

Primary outcome: the proportion who achieved a full response (14 consecutive dry nights) by 16 weeks. Secondary outcomes: change in frequency of wetting, duration of alarm training, percentage of wet nights that the child woke to the alarm, adherence to treatment, adverse events and satisfaction with treatment.

Results

Of the 353 participants, 176 were assigned to the code-word alarm and 177 to control. At 16 weeks, 54% (95% CI 47% to 61%) in the experimental group and 47% (95% CI 40% to 55%) in the control group had achieved a full response (p=0.22), with 74% and 66%, respectively, attaining a 50% or more reduction in wetting frequency (p=0.14). The experimental group woke more often than the control group (median percentage of waking 88% vs 77%, p=0.003) and had a greater reduction in wet nights (median reduction of 10 vs 9 nights per fortnight). Fewer in the experimental group discontinued therapy before achieving a full response (27% vs 37% discontinued, p=0.04). There were no significant differences in relapse rates at 6 months, adverse events or satisfaction between the two alarms.

Conclusions

Although the code-word alarm increased waking, no difference in full response rates was demonstrated between the two alarms.

Trial registration number

ACTRN12609000070235.
Validation of two algorithms for managing children with a non-blanching rash
Authors: Riordan F Andrew I , Jones Laura , Clark Julia
Published: March 2016

Background

Paediatricians are concerned that children who present with a non-blanching rash (NBR) may have meningococcal disease (MCD). Two algorithms have been devised to help identify which children with an NBR have MCD.

Aim

To evaluate the NBR algorithms’ ability to identify children with MCD.

Methods

The Newcastle-Birmingham-Liverpool (NBL) algorithm was applied retrospectively to three cohorts of children who had presented with NBRs. This algorithm was also piloted in four hospitals, and then used prospectively for 12 months in one hospital. The National Institute for Health and Care Excellence (NICE) algorithm was validated retrospectively using data from all cohorts.

Results

The cohorts included 625 children, 145 (23%) of whom had confirmed or probable MCD. Paediatricians empirically treated 324 (52%) children with antibiotics. The NBL algorithm identified all children with MCD and suggested treatment for a further 86 children (sensitivity 100%, specificity 82%). One child with MCD did not receive immediate antibiotic treatment, despite this being suggested by the algorithm. The NICE algorithm suggested 382 children (61%) who should be treated with antibiotics. This included 141 of the 145 children with MCD (sensitivity 97%, specificity 50%).

Conclusions

These algorithms may help paediatricians identify children with MCD who present with NBRs. The NBL algorithm may be more specific than the NICE algorithm as it includes fewer features suggesting MCD. The only significant delay in treatment of MCD occurred when the algorithms were not followed.
Atypical patterns of cardiac involvement in Fabry disease
Authors: Coughlan J J , Elkholy K , O'Brien J , Kiernan T
Published: March 2016

A 58-year-old woman was referred to our cardiology service with chest pain, exertional dyspnoea and palpitations on a background of known Fabry disease diagnosed with genetic testing in 1994. ECG showed sinus rhythm, shortened PR interval, widespread t wave inversion, q waves in the lateral leads and left ventricular hypertrophy (LVH). Coronary angiogram showed only mild atheroma. Transthoracic echocardiogram showed anterolateral LVH and reduced left ventricular cavity size in keeping with Fabry cardiomyopathy. Cardiac MRI demonstrated asymmetric hypertrophy with evidence of diffuse myocardial fibrosis in the maximally hypertrophied segments from base to apex with late gadolinium enhancement in the anterior and anteroseptal walls. This was quite an atypical appearance for Fabry cardiomyopathy. This case highlights the heterogeneity of patterns of cardiac involvement that may be associated with this rare X-linked lysosomal disorder.
Seroprevalence and factors associated with equine herpesvirus type 1 and 4 in Spanish Purebred horses in Spain
Authors: Cruz F. , Fores P. , Mughini‐Gras L. , Ireland J. , Moreno M. A. , Newton J. R.
Published: March 2016

Equine herpesvirus type 1 (EHV‐1) and type 4 (EHV‐4) have a worldwide distribution and cause respiratory disease, abortion, neonatal death and myeloencephalopathy in susceptible horses. Given the scarcity of serological EHV‐1/EHV‐4 data in Spain, the objective of this cross‐sectional study was to estimate the seroprevalence of EHV‐1/EHV‐4 and to identify potential horse‐level and stud farm‐level factors associated with EHV‐1/EHV‐4 in the breeding Spanish Purebred (SP) horse population in central Spain. Serum samples from 334 SP unvaccinated horses, collected between September 2011 and November 2013 at 30 stud farms, were tested using a commercially available EHV‐1/EHV‐4 antibody ELISA and seroneutralisation as the World Organisation for Animal Health reference confirmation test. Data on factors putatively associated with seropositivity to EHV‐1/EHV‐4 were collected via a questionnaire and examined using logistic regression analysis. EHV‐1/EHV‐4 seroprevalence in the SP breeding population in central Spain, standardised for the sex distribution of the reference horse population, was 53.9 per cent (95 per cent confidence interval 44.0 per cent to 63.8 per cent). Increasing age, southern location of the stud farm, temperate climate during the summer, and a smaller surface area used for breeding activities in the farm were associated with increased odds for EHV‐1/EHV‐4 seropositivity, whereas EHV‐1/EHV‐4 vaccination of other resident horses and separation of breeding mares from youngsters were protective factors.
Effects of dietary conjugated linoleic acid on cytotoxicity of peripheral blood lymphocytes in piglets
Authors: Liu Yongxiang , Liu Yanli , Qiu Rongchao , Jiang Dongfeng
Published: March 2016

The aim of this study was to investigate the effects of dietary conjugated linoleic acid (CLA) on the cytotoxicity of peripheral blood lymphocytes in piglets. A total of forty 21-d-old Duroc × Large White × Landrace weaned piglets were randomly allocated into two treatment groups and fed with control diet or 2% CLA diet for 6 weeks. Dietary CLA significantly increased the number of peripheral blood CD8+ T lymphocytes (P < 0.05). Compared with the control group, cytotoxicity, perforin, and granzyme B mRNA expression of peripheral blood lymphocytes in piglets from the CLA-supplementation group increased by 29.98% (P < 0.01), 32.87% (P < 0.01), and 43.36% (P < 0.05), respectively. The piglets on the CLA diet had higher mRNA expression of Lck and Fyn in peripheral blood lymphocytes (P < 0.05). The content of C16:0 significantly increased in piglets from the dietary CLA-supplementation group (P < 0.05), whereas the content of C18:1 significantly decreased (P < 0.05). The CLA content of peripheral blood lymphocytes in piglets in the CLA diet group ranged up to 0.24% (P < 0.01). These results suggest that dietary CLA enhanced cytotoxicity of peripheral blood lymphocytes perhaps through changing its fatty acid composition.
Adult lifetime reproductive value in fish depends on size and fecundity type
Authors: Tsoukali Stavroula , Olsson Karin H. , Visser André W. , MacKenzie Brian R.
Published: March 2016

In a stable population, the adult lifetime reproductive value must be balanced against early life survival. Although delaying maturity may increase fecundity, it also reduces survival. Larger size at maturity therefore not only allows for higher fecundity, but requires it. Using simple arguments from life history, we derive a direct proportionality relationship between the adult lifetime reproductive value and weight at maturation and find that this relationship is consistent with empirical evidence from 28 stocks and species of bony fish from temperate–boreal environments. However, the expected proportionality falls off if mortality increases to include fishing. Furthermore, we find that the fecundity type (determinate or indeterminate) affects the predicted adult reproductive value, which is significantly (10-fold) higher for an indeterminate spawner than for a determinate spawner of the same weight. These differences may relate to trade-offs in the adult life history traits and (or) to seasonality in the spawning environment, with subsequent consequences for early life stage survivorship.
Parata hard red spring wheat
Authors: Spaner D. , Iqbal M. , Navabi A. , Strenzke K. , Beres B.
Published: March 2016

Parata is a hard red spring wheat developed at the University of Alberta. In three years of testing in the Parkland Cooperative Registration Test, Parata was higher yielding (P < 0.05) than AC Splendor (5.9 %) and CDC Teal (4.1 %) but similar to CDC Osler and AAC Connery. Parata matured earlier than CDC Teal, CDC Osler and AAC Connery and 1.6 days later than AC Splendor. Parata was shorter than all checks except AAC Connery and exhibited lodging resistance better than AC Splendor and CDC Osler. Test weight of Parata was greater than all checks by at least 1 kg hL−1, while seed mass was within the range of the check cultivars. Parata was rated resistant to the prevalent races of stem and stripe rust in three years of testing. It was rated R/MR in two years and MS in one year for leaf rust; and was I in two years and S in one year for common bunt. The FHB disease indices for Parata ranged from MS (1 rating) to MR in six station years. Three years of end-use quality evaluation has indicated that Parata is acceptable for the CWRS class, with improvements especially in flour yield and flour ash.
Heavy metal concentration in soil in the tailing dam vicinity of an old gold mine in Johannesburg, South Africa
Authors: Olobatoke R.Y. , Mathuthu M.
Published: March 2016

Soil contamination with heavy metals is a serious concern to food production and human health. The present study was conducted to evaluate the impact of tailings from an old mining site on heavy metal contamination of soil. Using a GPS to map out different sites around the tailing dam, soil samples were taken from under grassland at the different sites, at depths of 15 cm and 1 m, using a shovel and handheld auger. The samples were prepared, acid digested, and analyzed for a multi-element suite by inductively coupled plasma atomic emission spectrometry. Results showed heavy metal concentration in the order of Cr > Zn > As > Mn > Cu > Pb > Ni > Sr > Hg. Most of the soil samples contained high concentration of As (13.46–234.6 mg kg−1). Soil concentrations of As, Hg, Cr, and Mn also decreased with distance from the dump material. Single contamination index of each pollutant, calculated according to the South African Soil Quality Standards revealed very high and medium pollution grades for As (index = 7.39) and Cr (index = 2.16), respectively. Arsenic is a metal associated with gold ore and soil pollution by such metals can make it infertile and unsuitable for plants.
Vertex algebras associated to the affine Lie algebras of abelian polynomial current algebras
Authors: Yang Jinwei
Published: March 2016

We construct a family of vertex algebras associated to the affine Lie algebra of polynomial current algebras of finite-dimensional abelian Lie algebras, along with their modules and logarithmic modules. These vertex algebras and their (logarithmic) modules are strongly [Formula: see text]-graded and quasi-conformal. We then show that matrix elements of products and iterates of logarithmic intertwining operators among these logarithmic modules satisfy certain systems of differential equations. Using these systems of differential equations, we verify the convergence and extension property needed in the logarithmic tensor category theory developed by Huang, Lepowsky and Zhang.
Monte Carlo estimation of the number of tatami tilings
Authors: Kimura Kenji , Higuchi Saburo
Published: March 2016

Motivated by the way Japanese tatami mats are placed on the floor, we consider domino tilings with a constraint and estimate the number of such tilings of plane regions. We map the system onto a monomer-dimer model with a novel local interaction on the dual lattice. We make use of a variant of the Hamiltonian replica exchange Monte Carlo method where data for ferromagnetic and anti-ferromagnetic models are combined to make a single family of histograms. The properties of the density of states is studied beyond exact enumeration and combinatorial methods. The logarithm of the number of the tilings is linear in the boundary length of the region for all the regions studied.
Electron mobility limited by scattering from threading dislocation lines within gallium nitride
Authors: Mohammad Alavi Seyed , Bagani Erfan
Published: March 2016

Theoretical as well as experimental studies in the literature suggest that defect sites associated with the threading dislocation lines within [Formula: see text]-type gallium nitride (GaN) act to trap free electrons from the bulk of this semiconductor material. As a result, the core of the threading dislocation lines become negatively charged. The charge accumulated along the core of a threading dislocation line should be screened by a charge of opposite polarity and equal in absolute value per unit length along the dislocation line. In the present work, we model this screened charge buildup along the threading dislocation lines by two concentric space-charge cylinders. Quantum mechanical theory of scattering in cylindrical coordinates is then employed in order to numerically compute the electron mobility limited by scattering from the charged threading dislocation lines. The dependence of the computed electron mobility on the dislocation line density and on the amount of charge accumulated per unit length along the core of the dislocation lines is also investigated in this work. Our computed electron mobility results are compared with results from existing calculations of the GaN dislocation scattering limited electron mobility in the literature.
Fluctuation-induced dielectric permittivity in the isotropic phase of cholesteric liquid crystals
Authors: Mukherjee Prabir K. , Das Asok K.
Published: March 2016

The temperature and pressure dependence of the static dielectric permittivity in the isotropic phase of the isotropic to cholesteric phase transition is calculated using Landau–de Gennes’s fluctuation theory, allowing spatial variation of the orientational order parameter. A comparison is made with experimental data available in the isotropic phase of the isotropic to cholesteric phase transition.
On the Stability of Feature Selection Methods in Software Quality Prediction: An Empirical Investigation
Authors: Wang Huanjing , Khoshgoftaar Taghi M. , Seliya Naeem
Published: March 2016

Software quality modeling is the process of using software metrics from previous iterations of development to locate potentially faulty modules in current under-development code. This has become an important part of the software development process, allowing practitioners to focus development efforts where they are most needed. One difficulty encountered in software quality modeling is the problem of high dimensionality, where the number of available software metrics is too large for a classifier to work well. In this case, many of the metrics may be redundant or irrelevant to defect prediction results, thereby selecting a subset of software metrics that are the best predictors becomes important. This process is called feature (metric) selection. There are three major forms of feature selection: filter-based feature rankers, which uses statistical measures to assign a score to each feature and present the user with a ranked list; filter-based feature subset evaluation, which uses statistical measures on feature subsets to find the best feature subset; and wrapper-based subset selection, which builds classification models using different subsets to find the one which maximizes performance. Software practitioners are interested in which feature selection methods are best at providing the most stable feature subset in the face of changes to the data (here, the addition or removal of instances). In this study we select feature subsets using fifteen feature selection methods and then use our newly proposed Average Pairwise Tanimoto Index (APTI) to evaluate the stability of the feature selection methods. We evaluate the stability of feature selection methods on a pair of subsamples generated by our fixed-overlap partitions algorithm. Four different levels of overlap are considered in this study. 13 software metric datasets from two real-world software projects are used in this study. Results demonstrate that ReliefF (RF) is the most stable feature selection method and wrapper based feature subset selection shows least stability. In addition, as the overlap of partitions increased, the stability of the feature selection strategies increased.
Aggregating Data Sampling with Feature Subset Selection to Address Skewed Software Defect Data
Authors: Gao Kehan , Khoshgoftaar Taghi M. , Napolitano Amri
Published: March 2016

Defect prediction is an important process activity frequently used for improving the quality and reliability of software products. Defect prediction results provide a list of fault-prone modules which are necessary in helping project managers better utilize valuable project resources. In the software quality modeling process, high dimensionality and class imbalance are the two potential problems that may exist in data repositories. In this study, we investigate three data preprocessing approaches, in which feature selection is combined with data sampling, to overcome these problems in the context of software quality estimation. These three approaches are: Approach 1 — sampling performed prior to feature selection, but retaining the unsampled data instances; Approach 2 — sampling performed prior to feature selection, retaining the sampled data instances; and Approach 3 — sampling performed after feature selection. A comparative investigation is presented for evaluating the three approaches. In the experiments, we employed three sampling methods (random undersampling, random oversampling, and synthetic minority oversampling), each combined with a filter-based feature subset selection technique called correlation-based feature selection. We built the defect prediction models using five common classification algorithms. The case study was based on software metrics and defect data collected from multiple releases of a real-world software system. The results demonstrated that the type of sampling methods used in data preprocessing significantly affected the performance of the combination approaches. It was found that when the random undersampling technique was used, Approach 1 performed better than the other two approaches. However, when the feature selection technique was used in conjunction with an oversampling method (random oversampling or synthetic minority oversampling), we strongly recommended Approach 3.
WORST-CASE PORTFOLIO OPTIMIZATION IN A MARKET WITH BUBBLES
Authors: BELAK CHRISTOPH , CHRISTENSEN SÖREN , MENKENS OLAF
Published: March 2016

We investigate a utility maximization problem in the presence of asset price bubbles. At random times, the investor receives warnings that a bubble has formed in the market which may lead to a crash in the risky asset. We propose a regime-switching model for the warnings and we make no assumptions about the distribution of the timing and the size of the crashes. Instead, we assume that the investor takes a worst-case perspective towards their impacts, i.e. the investor maximizes her expected utility under the worst-case crash scenario. We characterize the value function by a system of Hamilton–Jacobi–Bellman equations and derive a coupled system of ordinary differential equations for the optimal strategies. Numerical examples are provided.
On fixed point sets of wavelet induced isomorphisms and frame induced monomorphisms
Authors: Srivastava Swati , Yadav G. C. S.
Published: March 2016

In this paper, we study fixed point sets of wavelet induced isomorphisms for symmetric wavelet sets. Also, introducing the notion of frame induced monomorphism for a frame wavelet set, as a generalization of the wavelet induced isomorphism for a wavelet set, we provide a construction of frame wavelet sets in [Formula: see text]. We also study fixed point sets of these maps.
Groups with Finitely Many Homomorphic Images of Finite Rank
Authors: de Giovanni Francesco , Russo Alessio
Published: March 2016

A group is called a Černikov group if it is abelian-by-finite and satisfies the minimal condition on subgroups. A new characterization of Černikov groups is given here, by proving that in a suitable large class of generalised soluble groups they coincide with the groups having only finitely many homomorphic images of finite rank (up to isomorphisms) and admitting an ascending normal series whose factors have finite rank.
t-Singular Linear Spaces
Authors: Guo Jun , Li Fenggao , Wang Kaishun
Published: March 2016

As a generalization of singular linear spaces, we introduce the concept of t-singular linear spaces, make some anzahl formulas of subspaces, and determine the suborbits of t-singular linear groups.
Generators of Simple Modular Lie Superalgebras
Authors: Tang Liming , Liu Wende
Published: March 2016

Let X be one of the finite-dimensional graded simple Lie superalgebras of Cartan type W, S, H, K, HO, KO, SHO or SKO over an algebraically closed field of characteristic p > 3. In this paper we prove that X can be generated by one element except the ones of type W, HO, KO or SKO in certain exceptional cases in which X can be generated by two elements. As a subsidiary result, we prove that certain classical Lie superalgebras or their relatives can be generated by one or two elements.
Fabrication of Superior Au–Ag Composites Surface-Enhanced Raman Scattering Active Substrates Based on One-Step Method of Chemical Etching
Authors: Zhang Li , Fang Jinghuai , Wang Chaonan , Xu Tian , Jin Yonglong
Published: March 2016

Bimetallic silver–gold composites are currently among the most studied substrates for detection based on surface-enhanced Raman scattering (SERS). Here, we developed Au–Ag composite films as high sensitivity, large-scale, chemically stable and reproducible SERS substrates. Au–Ag composite films were fabricated by chemical etching of Ag–Au alloy leaves with HAuCl4 aqueous solutions. Along with galvanic replacement reaction and dealloying, films with distinct microstructural features exhibit dramatic improvement in the SERS intensity. Especially, the Au–Ag composite films with legible nano-ridges fabricated by alloy leaves of 9 carat present the strongest SERS enhancement. The superior SERS enhancement is attributed to the confluence effect of enhanced local surface plasmon fields and electromagnetic coupling within nanogaps, sharp edges and corners. In addition, results showed that features of the films mightily depend on the initial proportions of Ag–Au alloys.
High Frequency Decay Parameter (Kappa) for Ahar–Varzaghan Double Earthquakes, Iran (MW 6.5 & 6.3)
Authors: Samaei Meghdad , Miyajima Masakatsu , Yazdani Azad , Jaafari Farhad
Published: March 2016

The high frequency decay parameter, kappa and its variations in distance is evaluated using 114 three component strong motion records from two strong events in Northwestern Iran. We show that in classical method of estimating kappa, the results are very sensitive to the choices of [Formula: see text] (where spectrum starts to fall) and [Formula: see text] (where spectrum reaches the noise floor) and automated procedures for estimating kappa are likely to lead to a biased estimation. For the present database, we found an obvious concavity in dependency of kappa on distance. The kappa values in distance were regressed to a trilinear shape for which the first line has a zero slope. Based on this trilinear shape the zero distance kappa are 0.043 and 0.026 for horizontal and vertical components, respectively.
Bi-Directional Pseudo-Acceleration Response Spectra
Authors: Ruangrassamee Anat , Palasri Chitti , Lukkunaprasit Panitan
Published: March 2016

In seismic design, excitations are usually considered separately in two perpendicular directions of structures. In fact, the two components of ground motions occur simultaneously. This paper clarifies the effects of bi-directional excitations on structures and proposes the response spectra called “bi-directional pseudo-acceleration response spectra”. A simplified analytical model of a two-degree-of-freedom system was employed. The effect of directivity of ground motions was taken into account by applying strong motion records in all directions. The analytical results were presented in the form of the acceleration ratio response spectrum defined as the bi-directional pseudo-acceleration response spectrum normalized by a pseudo-acceleration response spectrum.
Optical clearing mechanisms characterization in muscle
Authors: Oliveira Luís , Carvalho M. Inês , Nogueira Elisabete , Tuchin Valery V.
Published: March 2016

Optical immersion clearing is a technique that has been widely studied for more than two decades and that is used to originate a temporary transparency effect in biological tissues. If applied in cooperation with clinical methods it provides optimization of diagnosis and treatment procedures. This technique turns biological tissues more transparent through two main mechanisms — tissue dehydration and refractive index (RI) matching between tissue components. Such matching is obtained by partial replacement of interstitial water by a biocompatible agent that presents higher RI and it can be completely reversible by natural rehydration in vivo or by assisted rehydration in ex vivo tissues. Experimental data to characterize and discriminate between the two mechanisms and to find new ones are necessary. Using a simple method, based on collimated transmittance and thickness measurements made from muscle samples under treatment, we have estimated the diffusion properties of glucose, ethylene glycol (EG) and water that were used to perform such characterization and discrimination. Comparing these properties with data from literature that characterize their diffusion in water we have observed that muscle cell membrane permeability limits agent and water diffusion in the muscle. The same experimental data has allowed to calculate the optical clearing (OC) efficiency and make an interpretation of the internal changes that occurred in muscle during the treatments. The same methodology can now be used to perform similar studies with other agents and in other tissues in order to solve engineering problems at design of inexpensive and robust technologies for a considerable improvement of optical tomographic techniques with better contrast and in-depth imaging.
New sufficient conditions for contractively widely more generalized hybrid mappings to have a fixed point
Authors: Kawasaki Toshiharu
Published: March 2016

Hasegawa, Kawasaki and Kobayashi [Fixed point theorems for contractively widely more generalized hybrid mappings in metric spaces, to appear in Linear and Nonlinear Anal.] introduced the concept of contractively widely more generalized hybrid mappings in a metric space. On the other hand, Bogin [A generalization of a fixed point theorem of Goebel, Kirk and Shimi, Canad. Math. Bull. 19 (1976) 7–12] showed a fixed point theorem. However, Bogin’s result is not included in our results. In this paper, we consider new sufficient conditions as to cover the Bogin’s fixed point theorem for contractively widely more generalized hybrid mappings to have a fixed point.
THE EFFECT OF DEVELOPMENT ON THE CLIMATE SENSITIVITY OF ELECTRICITY DEMAND IN INDIA
Authors: GUPTA ESHITA
Published: March 2016

The climate sensitivity of electricity demand in India is likely to be highly sensitive to growth in income. Thus, both intensive and extensive adjustments in cooling and heating will play an important role in determining future climate change impacts on electricity demand. This paper utilizes a national level panel dataset of 28 Indian states for the period 2005–2009. The preferred estimates indicate that climate change will increase electricity demand by 6.7% with 4% p.a. GDP growth and 8.5% with 6% p.a. GDP growth in 2030 over the reference scenario of no climate change. This reflects the fact that the estimated marginal effect of a hotter climate is greater when income is higher. Over 50% of the climate change impacts will be due to extensive adjustments as the current penetration of space conditioning equipments such as air conditioners is very low.
China’s Strategic Foreign Initiatives Under Xi Jinping
Authors: Baviera Aileen S. P.
Published: March 2016

This article provides a summary of China’s new strategic foreign initiatives under Xi Jinping’s leadership. These initiatives include the “One Belt, One Road” proposal, the establishment of the Asian Infrastructure Investment Bank, and calls for a “New Asian Security Concept” as well as for “a new type of major power relations.” In a localized Southeast Asian context, they are operationalized, as projects under the so-called 21st Century Maritime Silk Road proposal, a “[Formula: see text] cooperation framework for China-Southeast Asia relations,” and the so-called “dual track” approach to the management of the South China Sea disputes. These initiatives are expected to provide a favorable external environment for the attainment of the “Chinese dream” and to pave the way for China to emerge into a position of global power and leadership. The article mainly focuses on what these initiatives may be signaling to China’s neighbors, and the subsequent implications for Southeast Asia and its relations with China. There are, for instance, some doubts as to whether China can be a reliable provider of security and stability as public goods in its own region if China itself is a key party in the territorial contentions and power rivalries that could be likely causes of conflict. The fact that China is still trying to defend primordial territorial and cultural-ideational interests, settle historical scores, and find an effective model for its domestic politics and governance that will serve its increasingly globalized economy, indicates that China may not be ready yet to make the sacrifices and compromises that will be required of regional — let alone global — leadership.
The carboxyl-terminally truncated kidney anion exchanger 1 R901X dRTA mutant is unstable at the plasma membrane
Authors: Almomani Ensaf , Lashhab Rawad , Alexander R. Todd , Cordat Emmanuelle
Published: March 2016

Mutations in the SLC4A1 gene coding for kidney anion exchanger 1 (kAE1) cause distal renal tubular acidosis (dRTA). We investigated the fate of the most common truncated dominant dRTA mutant kAE1 R901X. In renal epithelial cells, we found that kAE1 R901X is less abundant than kAE1 wild-type (WT) at the plasma membrane. Although kAE1 WT and kAE1 R901X have similar half-lives, the decreased abundance of kAE1 R901X at the surface is due to an increased endocytosis rate and a decreased recycling rate of endocytosed proteins. We propose that, in polarized renal epithelial cells, the apically mistargeted kAE1 R901X mutant is endocytosed faster than kAE1 WT and its recycling to the basolateral membrane is delayed. This resets the equilibrium, such that kAE1 R901X resides predominantly in an endomembrane compartment, thereby likely participating in development of dRTA disease.
Alternatively activated macrophages exhibit an anticalcifying activity dependent on extracellular ATP/pyrophosphate metabolism
Authors: Villa-Bellosta Ricardo , Hamczyk Magda R. , Andrés Vicente
Published: March 2016

Calcium-phosphate deposition (CPD) in atherosclerotic lesions, which begins in middle age and increases with aging, is a major independent predictor of future cardiovascular disease morbi-mortality. Remodeling of atherosclerotic vessels during aging is regulated in part by intimal macrophages, which can polarize to phenotypically distinct populations with distinct functions. This study tested the hypothesis that classically activated macrophages (M1φs) and alternatively activated macrophages (M2φs) differently affect vascular smooth muscle cell (VSMC) calcification and investigated the underlying mechanisms. We analyzed mouse VSMC-macrophage cocultures using a transwell system. Coculture of VSMCs with M2φs significantly reduced CPD, but coculture with M1φs had no effect. The anticalcific effect of M2φs was associated with elevated amounts of extracellular ATP and pyrophosphate (PPi), two potent inhibitors of CPD, and was lost upon forced hydrolysis of these metabolites. In M2φs and VSMC-M2φs cocultures, analysis of the ectoenzymes that regulate extracellular ATP/PPi metabolism revealed increased mRNA expression and activity of ectoenzyme nucleotide pyrophosphatase/phosphodiesterase-1, which synthesizes PPi from ATP, without changes in tissue-nonspecific alkaline phosphatase, which hydrolyzes PPi. In conclusion, increased accumulation of extracellular ATP and PPi by alternatively activated mouse M2φs inhibits CPD. These results reveal novel mechanisms underlying macrophage-dependent control of intimal calcification.
Metaplasticity in human primary somatosensory cortex: effects on physiology and tactile perception
Authors: Jones Christina B. , Lulic Tea , Bailey Aaron Z. , Mackenzie Tanner N. , Mi Yi Qun , Tommerdahl Mark , Nelson Aimee J.
Published: March 2016

Theta-burst stimulation (TBS) over human primary motor cortex evokes plasticity and metaplasticity, the latter contributing to the homeostatic balance of excitation and inhibition. Our knowledge of TBS-induced effects on primary somatosensory cortex (SI) is limited, and it is unknown whether TBS induces metaplasticity within human SI. Sixteen right-handed participants (6 females, mean age 23 yr) received two TBS protocols [continuous TBS (cTBS) and intermittent TBS (iTBS)] delivered in six different combinations over SI in separate sessions. TBS protocols were delivered at 30 Hz and were as follows: a single cTBS protocol, a single iTBS protocol, cTBS followed by cTBS, iTBS followed by iTBS, cTBS followed by iTBS, and iTBS followed by cTBS. Measures included the amplitudes of the first and second somatosensory evoked potentials (SEPs) via median nerve stimulation, their paired-pulse ratio (PPR), and temporal order judgment (TOJ). Dependent measures were obtained before TBS and at 5, 25, 50, and 90 min following stimulation. Results indicate similar effects following cTBS and iTBS; increased amplitudes of the second SEP and PPR without amplitude changes to SEP 1, and impairments in TOJ. Metaplasticity was observed such that TOJ impairments following a single cTBS protocol were abolished following consecutive cTBS protocols. Additionally, consecutive iTBS protocols altered the time course of effects when compared with a single iTBS protocol. In conclusion, 30-Hz cTBS and iTBS protocols delivered in isolation induce effects consistent with a TBS-induced reduction in intracortical inhibition within SI. Furthermore, cTBS- and iTBS-induced metaplasticity appear to follow homeostatic and nonhomeostatic rules, respectively.