bluuebunny/crossref_metadata_2025 huggingface dataset:
Meta‐Regression Models and Observational Research
Authors: Bruns Stephan B.
Published: March 2017

Meta‐regression models were originally developed for the synthesis of experimental research where randomization ensures unbiased and consistent estimation of the effect of interest. Most economics research is, however, observational and specification searches may often result in estimates that are biased and inconsistent, for example, due to omitted‐variable biases. We show that if the authors of primary studies search for statistically significant estimates in observational research, meta‐regression models tend to make false‐positive findings of genuine empirical effects. More research is needed to better understand how meta‐regression models need to be specified to help identifying genuine empirical effects in observational research.
Low Wage Returns to Schooling in a Developing Country: Evidence from a Major Policy Reform in Turkey
Authors: Aydemir Abdurrahman , Kirdar Murat G.
Published: March 2017

In this paper, we estimate returns to schooling for young men and women in Turkey using the exogenous and substantial variation in schooling across birth cohorts brought about by the 1997 reform of compulsory schooling within a fuzzy regression discontinuity design. We estimate that the return from an extra year of schooling is about 7–8% for women and an imprecisely estimated 2–2.5% for men. The low level of the estimates for men contrasts starkly with those estimated for other developing countries. We identify several reasons why returns to schooling are low for men and why they are higher for women in our context. In particular, the policy alters the schooling distributions of men and women differently, thus the average causal effect puts a higher weight on the causal effect of schooling at higher grade levels for women than for men.
Genes for resistance to powdery mildew in European barley cultivars registered in the Czech Republic from 2011 to 2015
Authors: Dreiseitl Antonín
Published: March 2017

Barley (Hordeum vulgare) is cultivated on 49.1 million hectares worldwide with 50.2% of the area located in Europe. Powdery mildew, caused by Blumeria graminis f. sp. hordei (Bgh), occurs wherever barley is grown. Cultivar resistance plays an important role in global barley production, especially in parts of Europe where high concentrations of both spring and winter types are grown. The aim of this report was to postulate specific resistance genes in barleys from nine European countries registered in the Czech Republic from 2011 to 2015. Thirty‐five spring cultivars and 27 winter barleys were tested with 56 diverse Bgh isolates. Twenty‐five known resistance genes were postulated, and unknown genes were detected in Sandra, Saturn and Zeppelin. Unidentified specific resistance genes were also present in winter hybrids Hobbit and Wootan. Spring cultivars Arthur and Francin consisted of three and two genotypes, respectively. Resistance gene mlo was present in 26 spring cultivars, and the proportion of cultivars with this gene increased from 62.9% in 2006–2010 to 75.7% in 2011–2015. The gene Mlp1 was identified for the first time in German winter cultivar Saturn. Five spring cultivars registered in Slovakia were included in the tests. All the cultivars that were tested contained one or more specific resistance genes to powdery mildew. Adaptability of the pathogen and possibilities for breeding winter barleys are discussed.
Post‐traumatic Stress Disorder and Antepartum Complications: a Novel Risk Factor for Gestational Diabetes and Preeclampsia
Authors: Shaw Jonathan G. , Asch Steven M. , Katon Jodie G. , Shaw Kate A. , Kimerling Rachel , Frayne Susan M. , Phibbs Ciaran S.
Published: March 2017

Background

Prior work shows that Post‐traumatic Stress Disorder (PTSD) predicts an increased risk of preterm birth, but the causal pathway(s) are uncertain. We evaluate the associations between PTSD and antepartum complications to explore how PTSD's pathophysiology impacts pregnancy.

Methods

This retrospective cohort analysis of all Veterans Health Administration (VA)‐covered deliveries from 2000–12 used the data of VA clinical and administration. Mothers with current PTSD were identified using the ICD‐9 diagnostic codes (i.e. code present during the antepartum year), as were those with historical PTSD. Medical and administrative data were used to identify the relevant obstetric diagnoses, demographics and health, and military deployment history. We used Poisson regression with robust error variance to derive the adjusted relative risk estimates (RR) for the association of PTSD with five clinically relevant antepartum complications [gestational diabetes (GDM), preeclampsia, gestational hypertension, growth restriction, and abruption]. Secondary outcomes included proxies for obstetric complexity (repeat hospitalisation, prolonged delivery hospitalisation, and caesarean delivery).

Results

Of the 15 986 singleton deliveries, 2977 (19%) were in mothers with PTSD diagnoses (1880 (12%) current PTSD). Mothers with the complication GDM were 4.9% and those with preeclampsia were 4.6% of all births. After adjustment, a current PTSD diagnosis (reference = no PTSD) was associated with an increased risk of GDM (RR 1.4, 95% confidence interval (CI) 1.2, 1.7) and preeclampsia (RR 1.3, 95% CI 1.1, 1.6). PTSD also predicted prolonged (>4 day) delivery hospitalisation (RR 1.2, 95% CI 1.01, 1.4), and repeat hospitalisations (RR 1.4, 95% CI 1.2, 1.6), but not caesarean delivery.

Conclusions

The observed association of PTSD with GDM and preeclampsia is consistent with our nascent understanding of PTSD as a disruptor of neuroendocrine and cardiovascular health.
Inequality of Opportunity in Wages and Consumption in Egypt
Authors: Assaad Ragui , Krafft Caroline , Roemer John , Salehi‐Isfahani Djavad
Published: March 2017

Most explanations of the recent political upheavals in Egypt since 2011 include a reference to rising inequality, but the usual indicators of income inequality in Egypt do not support that inequality was on the rise prior to the uprisings. In this paper we provide measures of inequality of opportunity in wages and consumption for Egypt at different points in time from 1988 to 2012 that shed light on the gap between popular perceptions and measured indices of inequality. Our findings indicate that although measures of inequality of wage income have increased over time in Egypt starting in 1998, the share attributable to circumstances declined steadily throughout the whole period. We attribute this decline to the fact that outcomes for individuals from a middle class background have moved closer to the outcomes of those from a poor background. The outcomes for those from privileged backgrounds remain quite apart from the rest.
Leflunomide for the treatment of trichodysplasia spinulosa in a liver transplant recipient
Authors: Kassar Rawan , Chang Janis , Chan An‐Wen , Lilly Leslie B. , Al Habeeb Ayman , Rotstein Coleman
Published: March 2017

Trichodysplasia spinulosa (TS) is a rare dermatologic complication associated with the immunosuppressive therapy used in solid organ transplantation. The distinctive clinical manifestation of this condition is spiny follicular papules on the face, ears, extremities, and trunk. Histopathologically, abnormally maturing hair follicles with hyperkeratotic material are noted. The condition is produced by the trichodysplasia spinulosa‐associated polyomavirus. Treatment of this condition in the past has entailed a reduction in immunosuppression, topical agents such as cidofovir or retinoids, or oral valganciclovir. Herein, we report a case of generalized TS treated successfully with leflunomide.
Systemic insecticides used in dogs: potential candidates for phlebotomine vector control?
Authors: Gomez Sonia Ares , Picado Albert
Published: March 2017

Zoonotic visceral leishmaniasis (ZVL) is a public health problem endemic in some countries. Current control measures, in particular culling infected dogs, have not reducedZVLincidence in humans. We evaluated the use of five systemic insecticides (spinosad, fluralaner, afoxolaner, sarolaner and moxidectin) currently used in dogs for other purposes (e.g. tick, flea control) in controllingZVLtransmission. The anti‐phlebotomine capacity of these compounds confirmed in experimental studies makes their use inZVLcontrol programmes very promising. Limitations and benefits of using this new control tool are compared to current practices.
Tax-financing of Budget Deficits in LDCs: Re-validation of Laffer Curve Theory
Authors: Okafor Samuel O. , Maduka Olisaemeka D. , Ike Ann N. , Uzoechina Benedict I.
Published: March 2017

Urgent need for quick action to put Nigeria and other developing economies back to the path of economic recovery has almost imposed state of emergency on these economies. Most LDCs are faced with acute shortage of development funds due to recessions accompanying incessant crashes in international financial market. Raising existing tax rates to finance budget deficit in LDCs often generates public debate on pros and cons of such policy option. Study considered Nigeria as typical case of LDCs. Study focused on establishing the effectiveness of tax-financing of budget deficit under Laffer curve theory. Study spanned across 1970-2015. Data were analyzed using ADF, CUSUM, heteroskedasticity, multiple regression, Johansen cointegration and ECM. Results indicate that: (1) Custom and exercise duties, petroleum profit tax and value-added tax contributed significantly to the reduction in budget deficit while company income tax had nonsignificant impact(2)Total government revenue constituted major chunk of planned income for budget deficit financing(3) Deficit financing of capital health expenditure yielded high returns while that of recurrent education expenditure and capital education expenditure was accompanied by low returns (4)Growth and employment generation accelerated deficit financing while private investment decelerated it (5) There were long and short-run relationships among budget deficit, taxes, human capital investment and macroeconomic indicators with significant rate of adjustment of short-run disequilibrium. Study concluded that tax-financing of budget deficit was effective under Laffer curve effect. It was recommended, among others, that LDCs should enlarge their tax bases through inclusion, to finance budget deficit.
Derived Knörrer periodicity and Orlov’s theorem for gauged Landau–Ginzburg models
Authors: Hirano Yuki
Published: March 2017

We prove a Knörrer-periodicity-type equivalence between derived factorization categories of gauged Landau–Ginzburg models, which is an analogy of a theorem proved by Shipman and Isik independently. As an application, we obtain a gauged Landau–Ginzburg version of Orlov’s theorem describing a relationship between categories of graded matrix factorizations and derived categories of hypersurfaces in projective spaces, by combining the above Knörrer periodicity type equivalence and the theory of variations of geometric invariant theory quotients due to Ballard, Favero and Katzarkov.
Vacuum system of positron damping ring for SuperKEKB
Authors: Shibata Kyo , Suetsugu Yusuke , Ishibashi Takuya , Shirai Mitsuru , Terui Shinji , Kanazawa Ken-ichi , Hisamatsu Hiromi
Published: March 2017

To satisfy the requirements of high beam quality for positron injection into the SuperKEKB electron-positron collider, a new damping ring (DR) is constructed in an upgraded injector system. The DR has two arc sections and two straight sections. In the arc sections, the beam pipes have beam position monitor blocks, pumping ports, radio-frequency-shielded bellows, and special connection flanges to fit narrow spaces between closely located magnets. The beam pipes have antechambers on both sides of a beam channel to deal with synchrotron radiation (SR) which irradiates both sides of the beam pipes. The antechambers are also effective in reducing the electron cloud in the beam channel. To remove the heat caused by SR irradiation, a water cooling system is also required in the arc sections. In the straight sections on the other hand, an antechamber structure and a water cooling system are not necessary, and the beam pipes are much simpler than those in the arc sections. Required beam lifetime due to residual gas scattering is longer than 1000 s, and the average pressure should be lower than 1 × 10−5 Pa. Nonevaporable getter (NEG) pumps are mainly used with auxiliary ion pumps, and the average effective pumping speed in the arc sections is approximately 0.013 m3 s−1 m−1 (for CO), just after NEG activation. The material of the beam pipes is aluminum alloy. As additional countermeasures against the electron cloud effect, titanium nitride coating and grooved surfacing are adopted. These reduce the secondary electron yield of the inner surfaces of the beam pipes.
Linear modal stability analysis of bowed-strings
Authors: Debut V. , Antunes J. , Inácio O.
Published: March 2017

Linearised models are often invoked as a starting point to study complex dynamical systems. Besides their attractive mathematical simplicity, they have a central role for determining the stability properties of static or dynamical states, and can often shed light on the influence of the control parameters on the system dynamical behaviour. While the bowed string dynamics has been thoroughly studied from a number of points of view, mainly by time-domain computer simulations, this paper proposes to explore its dynamical behaviour adopting a linear framework, linearising the friction force near an equilibrium state in steady sliding conditions, and using a modal representation of the string dynamics. Starting from the simplest idealisation of the friction force given by Coulomb's law with a velocity-dependent friction coefficient, the linearised modal equations of the bowed string are presented, and the dynamical changes of the system as a function of the bowing parameters are studied using linear stability analysis. From the computed complex eigenvalues and eigenvectors, several plots of the evolution of the modal frequencies, damping values, and modeshapes with the bowing parameters are produced, as well as stability charts for each system mode. By systematically exploring the influence of the parameters, this approach appears as a preliminary numerical characterisation of the bifurcations of the bowed string dynamics, with the advantage of being very simple compared to sophisticated numerical approaches which demand the regularisation of the nonlinear interaction force. To fix the idea about the potential of the proposed approach, the classic one-degree-of-freedom friction-excited oscillator is first considered, and then the case of the bowed string. Even if the actual stick-slip behaviour is rather far from the linear description adopted here, the results show that essential musical features of bowed string vibrations can be interpreted from this simple approach, at least qualitatively. Notably, the technique provides an instructive and original picture of bowed motions, in terms of groups of well-defined unstable modes, which is physically intuitive to discuss tonal changes observed in real bowed string.
Spatial release from masking based on binaural processing for up to six maskers
Authors: Yost William A.
Published: March 2017

Spatial Release from Masking (SRM) was measured for identification of a female target word spoken in the presence of male masker words. Target words from a single loudspeaker located at midline were presented when two, four, or six masker words were presented either from the same source as the target or from spatially separated masker sources. All masker words were presented from loudspeakers located symmetrically around the centered target source in the front azimuth hemifield. Three masking conditions were employed: speech-in-speech masking (involving both informational and energetic masking), speech-in-noise masking (involving energetic masking), and filtered speech-in-filtered speech masking (involving informational masking). Psychophysical results were summarized as three-point psychometric functions relating proportion of correct word identification to target-to-masker ratio (in decibels) for both the co-located and spatially separated target and masker sources cases. SRM was then calculated by comparing the slopes and intercepts of these functions. SRM decreased as the number of symmetrically placed masker sources increased from two to six. This decrease was independent of the type of masking, with almost no SRM measured for six masker sources. These results suggest that when SRM is dependent primarily on binaural processing, SRM is effectively limited to fewer than six sound sources.
Agrobacterium
delivers VirE2 protein into host cells via clathrin-mediated endocytosis
Authors: Li Xiaoyang , Pan Shen Q.
Published: March 2017

Agrobacterium
type IV secretion system delivers VirE2 into host cells via conserved endocytosis mediated by clathrin adaptor AP2
Canopy near-infrared reflectance and terrestrial photosynthesis
Authors: Badgley Grayson , Field Christopher B. , Berry Joseph A.
Published: March 2017

Quantifying the near-infrared light reflected by plant canopies improves our ability to estimate global photosynthesis.
Nonrainfall water origins and formation mechanisms
Authors: Kaseke Kudzai Farai , Wang Lixin , Seely Mary K.
Published: March 2017

Fog and dew in the Namib Desert have multiple origins and their formation can be differentiated using stable isotopes.
Can flu shots help women get pregnant?
Authors: Leslie Mitch
Published: March 2017

Two trials test whether influenza vaccinations make the body more accepting of IVF embryos.
A conserved NAD
+
binding pocket that regulates protein-protein interactions during aging
Authors: Li Jun , Bonkowski Michael S. , Moniot Sébastien , Zhang Dapeng , Hubbard Basil P. , Ling Alvin J. Y. , Rajman Luis A. , Qin Bo , Lou Zhenkun , Gorbunova Vera , Aravind L. , Steegborn Clemens , Sinclair David A.
Published: March 2017

NAD
+
can influence DNA repair by modulating protein interactions.
Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention
Authors: Tomasetti Cristian , Li Lu , Vogelstein Bert
Published: March 2017

A substantial fraction of mutations in human cancer are attributable to random errors occurring during DNA replication.
A roadmap for rapid decarbonization
Authors: Rockström Johan , Gaffney Owen , Rogelj Joeri , Meinshausen Malte , Nakicenovic Nebojsa , Schellnhuber Hans Joachim
Published: March 2017

Emissions inevitably approach zero with a “carbon law”
How “you” makes meaning
Authors: Orvell Ariana , Kross Ethan , Gelman Susan A.
Published: March 2017

Linguistically, the generic use of “you” enables people to distance
themselves from negative experiences and to extract some meaning from them.
From chaos to order in active fluids
Authors: Morozov Alexander
Published: March 2017

Random flows in an active fluid become directional under confinement
Tuberculin Skin Testing Boosts Interferon Gamma Responses to DIVA Reagents in Mycobacterium bovis-Infected Cattle
Authors: Jones Gareth J. , Coad Mick , Khatri Bhagwati , Bezos Javier , Parlane Natalie A. , Buddle Bryce M. , Villarreal-Ramos Bernardo , Hewinson R. Glyn , Vordermeier H. Martin
Published: March 2017

Mycobacterium bovis
BCG vaccination sensitizes cattle to bovine tuberculin, which compromises the use of the current bovine tuberculosis (TB) surveillance tests. Although the performance of a blood test (that utilizes antigens expressed by
Mycobacterium bovis
but not by BCG) capable of discriminating infected from vaccinated animals (DIVA interferon gamma test [DIT]) has been evaluated in naturally infected TB field reactors, there is a need to perform similar analysis in a BCG-vaccinated
M. bovis
-infected population. Furthermore, we explored different scenarios under which a DIT may be implemented alongside BCG vaccination: (i) serial testing to resolve potential false-positive skin test results or (ii) a standalone test to replace the single intradermal comparative cervical tuberculin (SICCT) skin test. Our results demonstrated significantly better relative test sensitivity when the DIT was evaluated in a serial test scenario. Direct comparison of pre- and post-skin test blood samples revealed that the SICCT test induced significant boosting of the gamma interferon response in
M. bovis
-infected animals to both the ESAT-6–CFP-10 and Rv3615c peptide cocktails that comprise the DIT, which persisted for the ESAT-6–CFP-10 reagent for at least 14 days. Importantly, no similar boosting effects were observed in noninfected BCG vaccinates, suggesting that DIVA blood testing after a recent skin test would have minimal impact on test specificity.
Comparative Evaluation of Sensititre YeastOne and CLSI M38-A2 Reference Method for Antifungal Susceptibility Testing of Aspergillus spp. against Echinocandins
Authors: Siopi Maria , Pournaras Spyros , Meletiadis Joseph
Published: March 2017

Sensititre YeastOne (YO) panels were assessed for
in vitro
susceptibility testing of echinocandins against 39 isolates of
Aspergillus fumigatus
,
A. flavus
, and
A. terreus
, including two echinocandin-resistant
A. fumigatus
strains, using different inocula (10
3
, 10
4
, and 10
5
CFU/ml), incubation times (16 to 48 h), and endpoints (first blue or purple well) and compared to CLSI M38-A2. The best agreement was found with an inoculum of 10
4
CFU/ml, incubation times of 20 h for
A. flavus
and of 30 h for
A. fumigatus
and
A. terreus
, and reading the first purple well. The reproducibility within ±1 2-fold dilutions was 100% for all three echinocandins. YO color endpoints were 2 to 3 2-fold dilutions lower than CLSI minimum effective concentrations (MECs) of caspofungin and 1 to 2 2-fold dilutions higher than CLSI MECs of micafungin. For anidulafungin, off-scale YO color endpoints were observed. Nevertheless,
A. fumigatus
echinocandin-resistant isolates were detected after 24 h of incubation.
Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus
Authors: Gonzalez-Escalona Narjol , Jolley Keith A. , Reed Elizabeth , Martinez-Urtaza Jaime
Published: March 2017

Vibrio parahaemolyticus
is an important human foodborne pathogen whose transmission is associated with the consumption of contaminated seafood, with a growing number of infections reported over recent years worldwide. A multilocus sequence typing (MLST) database for
V. parahaemolyticus
was created in 2008, and a large number of clones have been identified, causing severe outbreaks worldwide (sequence type 3 [ST3]), recurrent outbreaks in certain regions (e.g., ST36), or spreading to other regions where they are nonendemic (e.g., ST88 or ST189). The current MLST scheme uses sequences of 7 genes to generate an ST, which results in a powerful tool for inferring the population structure of this pathogen, although with limited resolution, especially compared to pulsed-field gel electrophoresis (PFGE). The application of whole-genome sequencing (WGS) has become routine for trace back investigations, with core genome MLST (cgMLST) analysis as one of the most straightforward ways to explore complex genomic data in an epidemiological context. Therefore, there is a need to generate a new, portable, standardized, and more advanced system that provides higher resolution and discriminatory power among
V. parahaemolyticus
strains using WGS data. We sequenced 92
V. parahaemolyticus
genomes and used the genome of strain RIMD 2210633 as a reference (with a total of 4,832 genes) to determine which genes were suitable for establishing a
V. parahaemolyticus
cgMLST scheme. This analysis resulted in the identification of 2,254 suitable core genes for use in the cgMLST scheme. To evaluate the performance of this scheme, we performed a cgMLST analysis of 92 newly sequenced genomes, plus an additional 142 strains with genomes available at NCBI. cgMLST analysis was able to distinguish related and unrelated strains, including those with the same ST, clearly showing its enhanced resolution over conventional MLST analysis. It also distinguished outbreak-related from non-outbreak-related strains within the same ST. The sequences obtained from this work were deposited and are available in the public database (
http://pubmlst.org/vparahaemolyticus
). The application of this cgMLST scheme to the characterization of
V. parahaemolyticus
strains provided by different laboratories from around the world will reveal the global picture of the epidemiology, spread, and evolution of this pathogen and will become a powerful tool for outbreak investigations, allowing for the unambiguous comparison of strains with global coverage.
Analysis of MIC and Disk Diffusion Testing Variables for Gepotidacin and Comparator Agents against Select Bacterial Pathogens
Authors: Koeth L. M. , DiFranco-Fisher J. M. , Scangarella-Oman N. E. , Miller L. A.
Published: March 2017

This study was conducted to determine the effect of testing parameters on the
in vitro
activity of gepotidacin, a new triazaacenaphthylene antibacterial agent for the treatment of conventional and biothreat pathogens. CLSI methods, and variations of those methods, were used to test 10
Staphylococcus aureus
, 10
Streptococcus pneumoniae
, 10
Haemophilus influenzae
, and 5
Escherichia coli
isolates by MIC and 30
S. aureus
, 15
S. pneumoniae
, and 15
S. pyogenes
isolates by disk diffusion (DD) methods. Levofloxacin and linezolid were tested as comparator agents for MIC and DD methods, respectively. Broth microdilution (BMD), macrodilution (MD), and agar dilution (AD) methods were compared. Variations in media, temperature, incubation time, CO
2
level, and inoculum concentration were tested by all methods, and variations in pH, calcium, magnesium, zinc, potassium, thymidine, and polysorbate 80 levels were tested by BMD and DD. The addition of albumin, serum, and lung surfactant was studied by BMD. The variables that impacted the results the most were high inoculum and pH 5.5 (no growth of
H. influenzae
and
S. pneumoniae
by BMD). Gepotidacin AD MIC levels were increased and disk zone diameters were decreased for all species in 10% CO
2
incubation. The following variables had a minimal effect on gepotidacin results: pH, agar method, atmospheric condition, temperature, and addition of serum and albumin for broth methods. There were also some slight differences in gepotidacin disk results between disk manufacturers and some agar types and also with potassium and thymidine for
S. pneumoniae
. For all other variations, gepotidacin MIC and disk results were considered comparable to reference results.
Evaluation of bioMérieux's Dissociated Vidas Lyme IgM II and IgG II as a First-Tier Diagnostic Assay for Lyme Disease
Authors: Molins Claudia R. , Delorey Mark J. , Replogle Adam , Sexton Christopher , Schriefer Martin E.
Published: March 2017

The recommended laboratory diagnostic approach for Lyme disease is a standard two-tiered testing (STTT) algorithm where the first tier is typically an enzyme immunoassay (EIA) that if positive or equivocal is reflexed to Western immunoblotting as the second tier. bioMérieux manufactures one of the most commonly used first-tier EIAs in the United States, the combined IgM/IgG Vidas test (LYT). Recently, bioMérieux launched its dissociated first-tier tests, the Vidas Lyme IgM II (LYM) and IgG II (LYG) EIAs, which use purified recombinant test antigens and a different algorithm than STTT. The dissociated LYM/LYG EIAs were evaluated against the combined LYT EIA using samples from 471 well-characterized Lyme patients and controls. Statistical analyses were conducted to assess the performance of these EIAs as first-tier tests and when used in two-tiered algorithms, including a modified two-tiered testing (MTTT) approach where the second-tier test was a C6 EIA. Similar sensitivities and specificities were obtained for the two testing strategies (LYT versus LYM/LYG) when used as first-tier tests (sensitivity, 83 to 85%; specificity, 85 to 88%) with an observed agreement of 80%. Sensitivities of 68 to 69% and 76 to 77% and specificities of 97% and 98 to 99% resulted when the two EIA strategies were followed by Western immunoblotting and when used in an MTTT, respectively. The MTTT approach resulted in significantly higher sensitivities than did STTT. Overall, the LYM/LYG EIAs performed equivalently to the LYT EIA in test-to-test comparisons or as first-tier assays in STTT or MTTT with few exceptions.
Evaluation of the bioNexia Legionella Test, Including Impact of Incubation Time Extension, for Detection of Legionella pneumophila Serogroup 1 Antigen in Urine
Authors: Badoux Paul , Euser Sjoerd M. , Bruin Jacob P. , Mulder Patrick P. G. , Yzerman Ed P. F.
Published: March 2017

In this study, we compared the bioNexia test (bioMérieux, Marcy-l'Étoile, France), a new immunochromatographic assay for the detection of
Legionella pneumophila
serogroup 1 in urine, with the BinaxNOW urinary antigen test (Alere, Waltham, Massachusetts, USA). After 15 min of incubation (in accordance with the manufacturers' instructions), the sensitivities and specificities were, respectively, 76.5% and 97.2% for the bioNexia test and 87.1% and 100% for the BinaxNOW test. After a prolonged incubation time of 60 min, the sensitivities and specificities increased to, respectively, 89.4% and 97.2% for the bioNexia test and 91.8% and 100% for the BinaxNOW test. When the tests were read after 15 min, the concentration of discrepant urine samples increased the sensitivities to 94.1% for both tests. In conclusion, we found that although the bioNexia test showed lower sensitivity for the detection of
L. pneumophila
antigen in nonconcentrated urine compared to the BinaxNOW test, a prolonged incubation time as well as the use of concentrated samples showed comparable sensitivities for both tests.
Loss of the Human Cytomegalovirus US16 Protein Abrogates Virus Entry into Endothelial and Epithelial Cells by Reducing the Virion Content of the Pentamer
Authors: Luganini Anna , Cavaletto Noemi , Raimondo Stefania , Geuna Stefano , Gribaudo Giorgio
Published: March 2017

The human cytomegalovirus (HCMV) US12 gene family encodes a group of predicted seven-transmembrane proteins whose functions have yet to be established. While inactivation of individual US12 members in laboratory strains of HCMV does not affect viral replication in fibroblasts, disruption of the US16 gene in the low-passage-number TR strain prevents viral growth in endothelial and epithelial cells. In these cells, the US16-null viruses fail to express immediate early (IE), early (E), and late (L) viral proteins due to a defect which occurs prior to IE gene expression. Here, we show that this defective phenotype is a direct consequence of deficiencies in the entry of US16-null viruses in these cell types due to an impact on the gH/gL/UL128/UL130/UL131A (pentamer) complex. Indeed, viral particles released from fibroblasts infected with US16-null viruses were defective for the pentamer, thus preventing entry during infections of endothelial and epithelial cells. A link between pUS16 and the pentamer was further supported by the colocalization of pUS16 and pentamer proteins within the cytoplasmic viral assembly compartment (cVAC) of infected fibroblasts. Deletion of the C-terminal tail of pUS16 reproduced the defective growth phenotype and alteration of virion composition as US16-null viruses. However, the pentamer assembly and trafficking to the cVAC were not affected by the lack of the C terminus of pUS16. Coimmunoprecipitation results then indicated that US16 interacts with pUL130 but not with the mature pentamer or gH/gL/gO. Together, these results suggest that pUS16 contributes to the tropism of HCMV by influencing the content of the pentamer into virions.

IMPORTANCE
Human cytomegalovirus (HCMV) is major pathogen in newborns and immunocompromised individuals. A hallmark of HCMV pathogenesis is its ability to productively replicate in an exceptionally broad range of target cells. The virus infects a variety of cell types by exploiting different forms of the envelope glycoprotein gH/gL hetero-oligomers, which allow entry into many cell types through different pathways. For example, incorporation of the pentameric gH/gL/UL128/UL130/UL131A complex into virions is a prerequisite for infection of endothelial and epithelial cells. Here, we show that the absence of US16, a thus far uncharacterized HCMV multitransmembrane protein, abrogates virus entry into endothelial and epithelial cells and that this defect is due to the lack of adequate amounts of the pentameric complex in extracellular viral particles. Our study suggests pUS16 as a novel viral regulatory protein important for shaping virion composition in a manner that influences HCMV cell tropism.
Feline Immunodeficiency Virus Evolutionarily Acquires Two Proteins, Vif and Protease, Capable of Antagonizing Feline APOBEC3
Authors: Yoshikawa Rokusuke , Takeuchi Junko S. , Yamada Eri , Nakano Yusuke , Misawa Naoko , Kimura Yuichi , Ren Fengrong , Miyazawa Takayuki , Koyanagi Yoshio , Sato Kei
Published: March 2017

The interplay between viral and host proteins has been well studied to elucidate virus-host interactions and their relevance to virulence. Mammalian genes encode apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins, which act as intrinsic restriction factors against lentiviruses. To overcome APOBEC3-mediated antiviral actions, lentiviruses have evolutionarily acquired an accessory protein, viral infectivity factor (Vif), and Vif degrades host APOBEC3 proteins via a ubiquitin/proteasome-dependent pathway. Although the Vif-APOBEC3 interaction and its evolutionary significance, particularly those of primate lentiviruses (including HIV) and primates (including humans), have been well investigated, those of nonprimate lentiviruses and nonprimates are poorly understood. Moreover, the factors that determine lentiviral pathogenicity remain unclear. Here, we focus on feline immunodeficiency virus (FIV), a pathogenic lentivirus in domestic cats, and the interaction between FIV Vif and feline APOBEC3 in terms of viral virulence and evolution. We reveal the significantly reduced diversity of FIV subtype B compared to that of other subtypes, which may associate with the low pathogenicity of this subtype. We also demonstrate that FIV subtype B Vif is less active with regard to feline APOBEC3 degradation. More intriguingly, we further reveal that FIV protease cleaves feline APOBEC3 in released virions. Taken together, our findings provide evidence that a lentivirus encodes two types of anti-APOBEC3 factors, Vif and viral protease.

IMPORTANCE
During the history of mammalian evolution, mammals coevolved with retroviruses, including lentiviruses. All pathogenic lentiviruses, excluding equine infectious anemia virus, have acquired the
vif
gene via evolution to combat APOBEC3 proteins, which are intrinsic restriction factors against exogenous lentiviruses. Here we demonstrate that FIV, a pathogenic lentivirus in domestic cats, antagonizes feline APOBEC3 proteins by both Vif and a viral protease. Furthermore, the Vif proteins of an FIV subtype (subtype B) have attenuated their anti-APOBEC3 activity through evolution. Our findings can be a clue to elucidate the complicated evolutionary processes by which lentiviruses adapt to mammals.
Recombinant Modified Vaccinia Virus Ankara Generating Ebola Virus-Like Particles
Authors: Schweneker Marc , Laimbacher Andrea S. , Zimmer Gert , Wagner Susanne , Schraner Elisabeth M. , Wolferstätter Michael , Klingenberg Marieken , Dirmeier Ulrike , Steigerwald Robin , Lauterbach Henning , Hochrein Hubertus , Chaplin Paul , Suter Mark , Hausmann Jürgen
Published: March 2017

There are currently no approved therapeutics or vaccines to treat or protect against the severe hemorrhagic fever and death caused by Ebola virus (EBOV). Ebola virus-like particles (EBOV VLPs) consisting of the matrix protein VP40, the glycoprotein (GP), and the nucleoprotein (NP) are highly immunogenic and protective in nonhuman primates against Ebola virus disease (EVD). We have constructed a modified vaccinia virus Ankara-Bavarian Nordic (MVA-BN) recombinant coexpressing VP40 and GP of EBOV Mayinga and the NP of Taï Forest virus (TAFV) (MVA-BN-EBOV-VLP) to launch noninfectious EBOV VLPs as a second vaccine modality in the MVA-BN-EBOV-VLP-vaccinated organism. Human cells infected with either MVA-BN-EBOV-VLP or MVA-BN-EBOV-GP showed comparable GP expression levels and transport of complex N-glycosylated GP to the cell surface. Human cells infected with MVA-BN-EBOV-VLP produced large amounts of EBOV VLPs that were decorated with GP spikes but excluded the poxviral membrane protein B5, thus resembling authentic EBOV particles. The heterologous TAFV NP enhanced EBOV VP40-driven VLP formation with efficiency similar to that of the homologous EBOV NP in a transient-expression assay, and both NPs were incorporated into EBOV VLPs. EBOV GP-specific CD8 T cell responses were comparable between MVA-BN-EBOV-VLP- and MVA-BN-EBOV-GP-immunized mice. The levels of EBOV GP-specific neutralizing and binding antibodies, as well as GP-specific IgG1/IgG2a ratios induced by the two constructs, in mice were also similar, raising the question whether the quality rather than the quantity of the GP-specific antibody response might be altered by an EBOV VLP-generating MVA recombinant.

IMPORTANCE
The recent outbreak of Ebola virus (EBOV), claiming more than 11,000 lives, has underscored the need to advance the development of safe and effective filovirus vaccines. Virus-like particles (VLPs), as well as recombinant viral vectors, have proved to be promising vaccine candidates. Modified vaccinia virus Ankara-Bavarian Nordic (MVA-BN) is a safe and immunogenic vaccine vector with a large capacity to accommodate multiple foreign genes. In this study, we combined the advantages of VLPs and the MVA platform by generating a recombinant MVA-BN-EBOV-VLP that would produce noninfectious EBOV VLPs in the vaccinated individual. Our results show that human cells infected with MVA-BN-EBOV-VLP indeed formed and released EBOV VLPs, thus producing a highly authentic immunogen. MVA-BN-EBOV-VLP efficiently induced EBOV-specific humoral and cellular immune responses in vaccinated mice. These results are the basis for future advancements, e.g., by including antigens from various filoviral species to develop multivalent VLP-producing MVA-based filovirus vaccines.
Stoichiometric homeostasis: a test to predict tundra vascular plant species and community-level responses to climate change
Authors: Gu Qian , Zamin Tara J. , Grogan Paul
Published: March 2017

Climate change is having profound influences on Arctic tundra plant composition, community dynamics, and ecosystem processes. Stoichiometric homeostasis (H), the degree to which a plant maintains its internal nutrient concentrations independent of nutrient variations in its environment, may be a useful approach to predict the impacts of these influences. In this case study, we used fertilization manipulation data to calculate homeostasis indices based on nitrogen (HN), phosphorus (HP), and nitrogen to phosphorus ratios (HN:P) of aboveground tissues for seven common tundra vascular species belonging to three growth forms. We then analyzed species H relationships with dominance, spatial stability, and responsiveness to various experimental manipulations. Each of the H indices was correlated amongst tissue types within each species and was generally highest in ericoid mycorrhizal host species and lowest in the ectomycorrhizal birch. Species HP and HN:P were consistently positively correlated with aboveground biomass within the controls and across all manipulations. Furthermore, these same species were spatially stable across experimentally warmed field plots. Stoichiometric homeostasis theory has been successful in predicting grassland community dynamics. This first test of its applicability across a variety of Arctic plant growth forms highlights its considerable potential in predicting tundra plant community structure and responses to environmental change.
Influence of stress and water content on air permeability of intact loess
Authors: Chen Cunli , Zhang Dengfei , Zhang Jie
Published: March 2017

Air permeability is one of the key parameters in performing consolidation analysis of unsaturated soil. Few data are available regarding the air permeability for intact loess under different applied stresses. The work reported in this paper evaluated the air permeability at isotropic stress using data obtained from laboratory investigations for intact loess. Air permeability tests were performed on specimens of intact loess at various water contents and isotropic stresses. Stress remarkably affected air permeability as a function of both liquid saturation and volumetric air content. There were all unique relationships not only between relative air permeability and liquid saturation as well as relative volumetric air content, but also between air permeability and modified air saturation for different stresses. The relative air permeability against liquid saturation could be well described by the Parker–van Genuchten–Mulaem (P-vG-M) model in terms of total liquid saturation. The relationship between relative air permeability and relative volumetric air content could be more conveniently expressed by the reference point power law (RPL) model, using the reference point values at natural water content rather than that at air-dried water content. Compared with the other two models, the proposed modified air saturation power law (MAPL) model was more appropriate to predict the air permeability.
Experimental addition of cover lowers the perception of danger and increases reproduction in meadow voles (Microtus pennsylvanicus)
Authors: Dehn M.M. , Ydenberg R.C. , Dill L.M.
Published: March 2017

Predation danger is pervasive for small mammals and is expected to select strongly for behavioural tactics that reduce the risk. In particular, since it may be considered a cost of reproduction, predation danger is expected to affect the level of reproductive effort. We test this hypothesis in a population of meadow voles (Microtus pennsylvanicus (Ord, 1815)) under seminatural conditions in field enclosures. We manipulated the voles’ perception of predation danger by adjusting the available cover and measured giving up density (GUD) in food patches to verify that the perception of danger differed between high- and low-cover treatments. Treatments did not differ in actual predation rate, in vole density, or in the quantity or quality of food. During the experiments, we measured indices of vole reproductive effort including activity (electronic detectors), foraging intensity (fecal plates), and the number of young produced (livetrapping). Voles in the high-cover (lower danger) treatments were more active, foraged more, and produced 85% more young per female per trap period than voles in the low-cover (higher danger) treatment. We briefly discuss the population consequences of this adaptive behavioural flexibility.
Action principles for hydro- and thermo-dynamics
Authors: Fronsdal Christian
Published: March 2017

For all its brilliant success stories, theoretical physics is actually in a lamentable state. The best way to highlight the situation and at the same time point out that it is not difficult to do better — using action principles — is to present several examples.
Peakompactons: Peaked compact nonlinear waves
Authors: Christov Ivan C. , Kress Tyler , Saxena Avadh
Published: March 2017

This paper is meant as an accessible introduction to/tutorial on the analytical construction and numerical simulation of a class of nonstandard solitary waves termed peakompactons. These peaked compactly supported waves arise as solutions to nonlinear evolution equations from a hierarchy of nonlinearly dispersive Korteweg–de Vries-type models. Peakompactons, like the now-well-known compactons and unlike the soliton solutions of the Korteweg–de Vries equation, have finite support, i.e., they are of finite wavelength. However, unlike compactons, peakompactons are also peaked, i.e., a higher spatial derivative suffers a jump discontinuity at the wave’s crest. Here, we construct such solutions exactly by reducing the governing partial differential equation to a nonlinear ordinary differential equation and employing a phase-plane analysis. A simple, but reliable, finite-difference scheme is also designed and tested for the simulation of collisions of peakompactons. In addition to the peakompacton class of solutions, the general physical features of the so-called [Formula: see text] hierarchy of nonlinearly dispersive Korteweg–de Vries-type models are discussed as well.
Early time evolution of a localized nonlinear excitation in the β-FPUT chain
Authors: Kashyap Rahul , Westley Alexandra , Datta Amitava , Sen Surajit
Published: March 2017

We present the detailed dynamics of the particles in the [Formula: see text]-Fermi–Pasta–Ulam–Tsingou (FPUT) chain after the initiation of a localized nonlinear excitation (LNE) by squeezing a central bond in the monodispersed chain at time [Formula: see text] = 0 while all other particles remain in their original relaxed positions. In the absence of phonons in the system, the LNE appears to initiate its relaxation process by symmetrically emitting two very weak solitary waves. The next stage involves the spreading of the LNE and the formation of nonsolitary wave-like objects to broaden the excitation region until a stage is reached when many weak solitary wave-like objects can be emitted as the system begins its journey to quasi-equilibrium and then to equilibrium. In addition to being of fundamental interest, these systems may be realized using cantilever systems and could well hold the key to constructing the next generation of broadband energy harvesting systems.
Study on the effects of Ga-2N high co-doping and preferred orientation on the stability, bandgap and absorption spectrum of ZnO
Authors: Hou Qing-Yu , Li Wen-Cai , Qu Ling-Feng , Zhao Chun-Wang
Published: March 2017

Currently, the stability and visible light properties of Ga-2N co-doped ZnO systems have been studied extensively by experimental analysis and theoretical calculations. However, previous theoretical calculations arbitrarily assigned Ga- and 2N-doped sites in ZnO. In addition, the most stable and possible doping orientations of doped systems have not been fully and systematically considered. Therefore, in this paper, the electron structure and absorption spectra of the unit cells of doped and pure systems were calculated by first-principles plane-wave ultrasoft pseudopotential with the GGA[Formula: see text]U method. Calculations were performed for pure ZnO, Ga-2N supercells heavily co-doped with Zn[Formula: see text]Ga[Formula: see text]O[Formula: see text]N[Formula: see text] ([Formula: see text], [Formula: see text]) under different co-doping orientations and conditions, and the Zn[Formula: see text]GaN2O[Formula: see text] interstitial model. The results indicated that under different orientations and constant Ga-2N co-doping concentrations, the systems co-doped with Ga-N atoms vertically oriented to the [Formula: see text]-axis and with another N atom located in the nearest-neighboring site exhibited higher stability over the others, thus lowering formation energy and facilitating doping. Moreover, Ga-interstitial- and 2N-co-doped ZnO systems easily formed chemical compounds. Increasing co-doping concentration while the co-doping method remained constant decreased doped system volume and lowered formation energies. Meantime, co-doped systems were more stable and doping was facilitated. The bandgap was also narrower and red shifting of the absorption spectrum was more significant. These results agreed with previously reported experimental results. In addition, the absorption spectra of Ga-interstitial- and 2N-co-doped ZnO both blue shifted in the UV region compared with that of the pure ZnO system.
Laws of large numbers for q-dependent random variables and nonextensive statistical mechanics
Authors: Trindade Marco A. S.
Published: March 2017

In this work, we prove a weak law and a strong law of large numbers through the concept of [Formula: see text]-product for dependent random variables, in the context of nonextensive statistical mechanics. Applications for the consistency of estimators are presented and connections with stochastic processes are discussed.