bluuebunny/crossref_metadata_2025 huggingface dataset:
Rare variant detection using family-based sequencing analysis
Authors: Peng Gang , Fan Yu , Palculict Timothy B. , Shen Peidong , Ruteshouser E. Cristy , Chi Aung-Kyaw , Davis Ronald W. , Huff Vicki , Scharfe Curt , Wang Wenyi
Published: February 2013

Next-generation sequencing is revolutionizing genomic analysis, but this analysis can be compromised by high rates of missing true variants. To develop a robust statistical method capable of identifying variants that would otherwise not be called, we conducted sequence data simulations and both whole-genome and targeted sequencing data analysis of 28 families. Our method (Family-Based Sequencing Program, FamSeq) integrates Mendelian transmission information and raw sequencing reads. Sequence analysis using FamSeq reduced the number of false negative variants by 14–33% as assessed by HapMap sample genotype confirmation. In a large family affected with Wilms tumor, 84% of variants uniquely identified by FamSeq were confirmed by Sanger sequencing. In children with early-onset neurodevelopmental disorders from 26 families, de novo variant calls in disease candidate genes were corrected by FamSeq as Mendelian variants, and the number of uniquely identified variants in affected individuals increased proportionally as additional family members were included in the analysis. To gain insight into maximizing variant detection, we studied factors impacting actual improvements of family-based calling, including pedigree structure, allele frequency (common vs. rare variants), prior settings of minor allele frequency, sequence signal-to-noise ratio, and coverage depth (
∼
20× to >200×). These data will help guide the design, analysis, and interpretation of family-based sequencing studies to improve the ability to identify new disease-associated genes.
Influence of Stimulus Type on Effects of Flanker, Flanker Position, and Trial Sequence in a Saccadic Eye Movement Task
Authors: Peschke Claudia , Hilgetag Claus C. , Olk Bettina
Published: February 2013

Using the flanker paradigm in a task requiring eye movement responses, we examined how stimulus type (arrows vs. letters) modulated effects of flanker and flanker position. Further, we examined trial sequence effects and the impact of stimulus type on these effects. Participants responded to a central target with a left- or rightward saccade. We reasoned that arrows, being overlearned symbols of direction, are processed with less effort and are therefore linked more easily to a direction and a required response than are letters. The main findings demonstrate that (a) flanker effects were stronger for arrows than for letters, (b) flanker position more strongly modulated the flanker effect for letters than for arrows, and (c) trial sequence effects partly differed between the two stimulus types. We discuss these findings in the context of a more automatic and effortless processing of arrow relative to letter stimuli.
High-speed three-dimensional plasma temperature determination of axially symmetric free-burning arcs
Authors: Bachmann B , Kozakov R , Gött G , Ekkert K , Bachmann J-P , Marques J-L , Schöpp H , Uhrlandt D , Schein J
Published: February 2013

In this paper we introduce an experimental technique that allows for high-speed, three-dimensional determination of electron density and temperature in axially symmetric free-burning arcs. Optical filters with narrow spectral bands of 487.5–488.5 nm and 689–699 nm are utilized to gain two-dimensional spectral information of a free-burning argon tungsten inert gas arc. A setup of mirrors allows one to image identical arc sections of the two spectral bands onto a single camera chip. Two-different Abel inversion algorithms have been developed to reconstruct the original radial distribution of emission coefficients detected with each spectral window and to confirm the results. With the assumption of local thermodynamic equilibrium we calculate emission coefficients as a function of temperature by application of the Saha equation, the ideal gas law, the quasineutral gas condition and the NIST compilation of spectral lines. Ratios of calculated emission coefficients are compared with measured ones yielding local plasma temperatures. In the case of axial symmetry the three-dimensional plasma temperature distributions have been determined at dc currents of 100, 125, 150 and 200 A yielding temperatures up to 20000 K in the hot cathode region. These measurements have been validated by four different techniques utilizing a high-resolution spectrometer at different positions in the plasma. Plasma temperatures show good agreement throughout the different methods. Additionally spatially resolved transient plasma temperatures have been measured of a dc pulsed process employing a high-speed frame rate of 33000 frames per second showing the modulation of the arc isothermals with time and providing information about the sensitivity of the experimental approach.
Regulation of mitophagy by the Gp78 E3 ubiquitin ligase
Authors: Fu Min , St-Pierre Pascal , Shankar Jay , Wang Peter T. C. , Joshi Bharat , Nabi Ivan R.
Published: February 2013

Glycoprotein 78 (Gp78) is a critical E3 ubiquitin ligase in endoplasmic reticulum–associated degradation. Overexpression of Flag-tagged Gp78 (Flag-gp78), but not Flag-gp78 mutated in its RING-finger domain (Flag-RINGmut) with deficient ubiquitin ligase activity, induces mitochondrial fragmentation and ubiquitination and proteasome-dependent degradation of the mitofusin (Mfn) mitochondrial fusion factors Mfn1/Mfn2. After mitochondrial depolarization with carbonyl cyanide m-chlorophenylhydrazone (CCCP), Flag-gp78 induced a threefold loss of depolarized mitochondria and significant loss of the inner mitochondrial protein OxPhosV. Flag-gp78–dependent loss of OxPhosV, but not Mfn1 or Mfn2, was prevented by small interfering RNA (siRNA) knockdown of the autophagy protein Atg5 in CCCP-treated cells. Gp78-induced mitophagy required ubiquitin ligase activity, as it is not observed upon transfection of Flag-RINGmut or cotransfection of Flag-gp78 with ubiquitin mutated at three critical lysine residues (K29, 48, 63R) involved in polyubiquitin chain elongation. Short hairpin RNA knockdown of Gp78 in HT-1080 fibrosarcoma cells increased mitofusin levels and reduced depolarization-induced mitophagy, whereas siRNA knockdown showed that Mfn1, but not Mfn2, was required for Gp78-dependent depolarization-induced mitophagy. Mitochondrial depolarization induced Gp78-dependent expression of the autophagic marker LC3II and recruitment of enhanced green fluorescent protein–LC3 to the Gp78- and calnexin-labeled, mitochondria-associated ER. Finally, Gp78-induced mitophagy is Parkin independent, as it occurs in Parkin-null HeLa cells and upon siRNA-mediated Parkin knockdown in HEK293 cells. This study therefore describes a novel role for the ER-associated Gp78 ubiquitin ligase and the Mfn1 mitochondrial fusion factor in mitophagy.
Similar uptake but different trafficking and escape routes of reovirus virions and infectious subvirion particles imaged in polarized Madin–Darby canine kidney cells
Authors: Boulant Steeve , Stanifer Megan , Kural Comert , Cureton David K. , Massol Ramiro , Nibert Max L. , Kirchhausen Tomas
Published: February 2013

Polarized epithelial cells that line the digestive, respiratory, and genitourinary tracts form a barrier that many viruses must breach to infect their hosts. Current understanding of cell entry by mammalian reovirus (MRV) virions and infectious subvirion particles (ISVPs), generated from MRV virions by extracellular proteolysis in the digestive tract, are mostly derived from in vitro studies with nonpolarized cells. Recent live-cell imaging advances allow us for the first time to visualize events at the apical surface of polarized cells. In this study, we used spinning-disk confocal fluorescence microscopy with high temporal and spatial resolution to follow the uptake and trafficking dynamics of single MRV virions and ISVPs at the apical surface of live polarized Madin–Darby canine kidney cells. Both types of particles were internalized by clathrin-mediated endocytosis, but virions and ISVPs exhibited strikingly different trafficking after uptake. While virions reached early and late endosomes, ISVPs did not and instead escaped the endocytic pathway from an earlier location. This study highlights the broad advantages of using live-cell imaging combined with single-particle tracking for identifying key steps in cell entry by viruses.
Biocontrol of the Reniform Nematode by Bacillus firmus GB-126 and Paecilomyces lilacinus 251 on Cotton
Authors: Castillo Juan D. , Lawrence Kathy S. , Kloepper Joseph W.
Published: February 2013

Due to increased restrictions on the use of chemical nematicides, alternative nematode management strategies, including biocontrol, are needed. The objectives of this study were to evaluate the potential of Bacillus firmus GB-126 and Paecilomyces lilacinus 251 in commercial formulations applied separately or concomitantly to manage Rotylenchulus reniformis in cotton grown under greenhouse, microplot, and field conditions. In the greenhouse, seed treated with B. firmus (1.4 × 107 CFU/seed), an application of P. lilacinus (0.3% vol/vol of water), or the combination of B. firmus and P. lilacinus reduced the number of females, eggs, and vermiforms of R. reniformis (P ≤ 0.02) and increased populations of free-living nematodes (P ≤ 0.01). In microplots and field conditions, populations of R. reniformis vermiforms decreased when exposed to B. firmus and P. lilacinus biocontrol agents at midseason (P ≤ 0.04). Furthermore, stem diameter and free-living nematode numbers increased (P ≤ 0.01) with the combination of B. firmus and P. lilacinus. In the field, numbers of females, eggs, and vermiform life stages at the end of the growing season decreased in the presence of the biocontrol agents applied individually or concomitantly (P ≤ 0.01). Cotton yields from the application of B. firmus GB-126 and P. lilacinus 251 were similar to those from aldicarb, the chemical nematicide standard.
The PredictAD project: development of novel biomarkers and analysis software for early diagnosis of the Alzheimer's disease
Authors: Antila Kari , Lötjönen Jyrki , Thurfjell Lennart , Laine Jarmo , Massimini Marcello , Rueckert Daniel , Zubarev Roman A. , Orešič Matej , van Gils Mark , Mattila Jussi , Hviid Simonsen Anja , Waldemar Gunhild , Soininen Hilkka
Published: February 2013

Alzheimer's disease (AD) is the most common cause of dementia affecting 36 million people worldwide. As the demographic transition in the developed countries progresses towards older population, the worsening ratio of workers per retirees and the growing number of patients with age-related illnesses such as AD will challenge the current healthcare systems and national economies. For these reasons AD has been identified as a health priority, and various methods for diagnosis and many candidates for therapies are under intense research. Even though there is currently no cure for AD, its effects can be managed. Today the significance of early and precise diagnosis of AD is emphasized in order to minimize its irreversible effects on the nervous system. When new drugs and therapies enter the market it is also vital to effectively identify the right candidates to benefit from these. The main objective of the PredictAD project was to find and integrate efficient biomarkers from heterogeneous patient data to make early diagnosis and to monitor the progress of AD in a more efficient, reliable and objective manner. The project focused on discovering biomarkers from biomolecular data, electrophysiological measurements of the brain and structural, functional and molecular brain images. We also designed and built a statistical model and a framework for exploiting these biomarkers with other available patient history and background data. We were able to discover several potential novel biomarker candidates and implement the framework in software. The results are currently used in several research projects, licensed to commercial use and being tested for clinical use in several trials.
Dissection of the factor requirements for spliceosome disassembly and the elucidation of its dissociation products using a purified splicing system
Authors: Fourmann Jean-Baptiste , Schmitzová Jana , Christian Henning , Urlaub Henning , Ficner Ralf , Boon Kum-Loong , Fabrizio Patrizia , Lührmann Reinhard
Published: February 2013

The spliceosome is a single-turnover enzyme that needs to be dismantled after catalysis to both release the mRNA and recycle small nuclear ribonucleoproteins (snRNPs) for subsequent rounds of pre-mRNA splicing. The RNP remodeling events occurring during spliceosome disassembly are poorly understood, and the composition of the released snRNPs are only roughly known. Using purified components in vitro, we generated post-catalytic spliceosomes that can be dissociated into mRNA and the intron-lariat spliceosome (ILS) by addition of the RNA helicase Prp22 plus ATP and without requiring the step 2 proteins Slu7 and Prp18. Incubation of the isolated ILS with the RNA helicase Prp43 plus Ntr1/Ntr2 and ATP generates defined spliceosomal dissociation products: the intron-lariat, U6 snRNA, a 20–25S U2 snRNP containing SF3a/b, an 18S U5 snRNP, and the “nineteen complex” associated with both the released U2 snRNP and intron-lariat RNA. Our system reproduces the entire ordered disassembly phase of the spliceosome with purified components, which defines the minimum set of agents required for this process. It enabled us to characterize the proteins of the ILS by mass spectrometry and identify the ATPase action of Prp43 as necessary and sufficient for dissociation of the ILS without the involvement of Brr2 ATPase.
Building information modelling (BIM) for sustainable building design
Authors: Wong Kam‐din , Fan Qing
Published: February 2013

Purpose

Because of global environmental concerns, sustainable design has become a mainstream building design goal in recent years. Sustainable development is even more urgent in the light of global climate change. This paper aims to examine the contributions which building information modelling (BIM) can make to the production of sustainable building designs.

Design/methodology/approach

Various research methodologies have been adopted, including literature review, design tool analysis, a case study and structured face‐to‐face interviews. Data collected were synthesized as part of the research process.

Findings

BIM is found to be ideally suited to the delivery of information needed for improved design and building performance. Two most significant benefits of BIM for sustainable building design are: integrated project delivery (IPD) and design optimization. However, there are also barriers to adopting BIM for sustainable design.

Research limitations/implications

This paper does not attempt to address all aspects of BIM functionality because the scope of BIM is very great and the resources of this research were limited.

Practical implications

Successful implementation of BIM is able to eliminate the extra cost of design changes during the subsequent phases of construction process. BIM, therefore, is also capable of enhancing the project delivery culture in future.

Social implications

BIM solutions can contribute to the selection of best solutions to reduce energy and resources consumption. This new technology and the approach also can generate the need of more innovative professionals and job opportunities.

Originality/value

This paper investigates the contribution of BIM to sustainable buildings from the perspective of design performance and improved communication and coordination.
Making the case for “techno‐change alignment”
Authors: Fearon Colm , Manship Sharon , McLaughlin Heather , Jackson Stephen
Published: February 2013

Purpose

The purpose of this paper is to develop “techno‐change alignment” as an approach for evaluating the effectiveness of large‐scale technology‐enabled organisational change, commonly associated with the adoption of enterprise information systems (IS).

Design/methodology/approach

By developing a processual analysis of techno‐change, useful insights are developed concerning techno‐change alignment, within the confines of an enterprise resource planning (ERP) case study. Recent techno‐change literature, emerging ideas on human agency, cultural and social relations are incorporated as part of the evaluation approach taken. The paper also discusses the implications of more recent work on techno‐change and suggests directions for future research.

Findings

In terms of “structural” alignment, the ERP system was chosen because it reflected requirements of the case study in the university/education sector. As part of “strategic and intellectual” alignment, business processes were reviewed, as well as alignment with university aims and strategy goals. “Social and cultural” alignment between different groups of users is paramount for effective integration and re‐embedding of relationships and activities once techno‐change is introduced. Wider implications of processual alignment suggest that bringing users and stakeholders together as human agents for techno‐change within a high priority communication environment is essential for developing effective social relationships.

Originality/value

Given the difficulty of developing usable evaluation mechanisms for techno‐change and complex enterprise information systems, the contribution of this article is the demonstration of an effective interpretative (processual) IS evaluation approach, which the authors refer to as“techno‐change alignment”.
Evidence of lean: a review of international peer‐reviewed journal articles
Authors: Stentoft Arlbjørn Jan , Vagn Freytag Per
Published: February 2013

Purpose

The purpose of this paper is to examine how “lean” is viewed in academic literature and how it is operationalised. The paper also examines how evidence of lean is accounted for in practice.

Design/methodology/approach

This paper discusses a review of 105 international peer‐reviewed journals with the purpose of identifying what has been written about lean. All in all, 154 articles featuring lean in the article title are identified and reviewed.

Findings

Lean has moved from application only in production to being used in other sectors, such as the public and service sectors. Most contributions are still found in production and supply chain journals, however, and few contributions discuss the basis of lean or provide a clear definition of the meaning of lean. The literature review indicates that there is a low level of operationalisation of the concept of lean, making the concept seem unclear and vague. About one‐third of the reviewed articles apply a toolbox view on lean; and, in general, the positive effect of lean is documented in only a few of the articles reviewed.

Research limitations/implications

Only those articles published in international, peer‐reviewed journals are examined. Discussion of lean, however, might be found in other sources, such as textbooks, conference proceedings and PhD dissertations.

Practical implications

Due to the indistinct definitions of lean that were discovered, one should use the concept of lean with care. It is especially important to specify the conditions and to describe the intentions of usage.

Originality/value

This paper is the first comprehensive literature review with regard to lean and evidence in relationship to definitions of and assumptions about lean.
Capital structure – does ownership structure matter? Theory and Indian evidence
Authors: Ganguli Santanu K.
Published: February 2013

Purpose

Based on the agency theory, the purpose of this paper is to theoretically argue and empirically investigate how ownership structure impacts the capital structure of the listed mid‐cap companies in India and whether the capital structure as exogenous variable has a role in determining ownership structure as well.

Design/methodology/approach

Simultaneity between capital structure and ownership structure is checked through Hausman specification test on endogeneity. Fixed effect panel regression model is used to analyze five years of data (2005‐2009) on the sample units, to find the relation between leverage and ownership structure after controlling for profitability, risk, tangibility, growth and size.

Findings

Empirical results on Indian firms suggest that the ownership structure does impact capital structure but not the vice versa. Consistent with theoretical prediction empirical results reveal that the leverage is positively related to concentrated shareholding and has a negative relation with diffuseness of shareholding after controlling for profitability, risk, tangibility, growth and size. The findings are consistent with “managerial entrenchment hypothesis” and “pecking order theory” of capital structure.

Practical implications

The findings of the paper will enable the practitioners and analysts to understand as to why, in the bank and financial institution‐dominated debt financing system in India, leverage is closely associated with concentrated ownership pattern and why retained earning is a preferred vehicle of financing for the firms with diffused shareholding.

Originality/value

The results of the study enrich the literature on capital structure, agency cost and corporate governance issues in several ways.
Making health and wellbeing boards a success: engaging providers
Authors: Mumford Bill
Published: February 2013

Purpose

The aim of this paper is to bring attention to the current level of engagement of care service provider organisations with shadow health and wellbeing boards. The paper argues that full engagement of provider organisations will improve the effective working of the future health and wellbeing boards; both in the creation of good commissioning strategies and in their subsequent implementation.

Design/methodology/approach

A survey of Voluntary Organisations Disability Group (VODG) members was undertaken, and analysed alongside other reports of progress in implementation.

Findings

Currently there is a very low level of engagement of provider organisations. A notable exception is in Coventry which is an exemplar for good engagement: a case study is provided.

Originality/value

This is new knowledge. Also, a connection is made between emerging government policy on market facilitation in social care and its implications for health and wellbeing boards.
Making Cities Resilient: from awareness to implementation
Authors: Molin Valdés Helena , Amaratunga Dilanthi , Haigh Richard
Published: February 2013

Purpose

The purpose of this paper is to provide an update of the United Nations International Strategy for Disaster Reduction (UNISDR) campaign on Making Cities Resilient.

Design/methodology/approach

An opinion piece written by the Director a.i. of UNISDR and the Editors of the International Journal of Disaster Resilience in the Built Environment.

Findings

The campaign will continue and the focus will shift to more implementation support, city‐to‐city learning and cooperation, local action planning and monitoring of progress in cities.

Originality/value

Continued advocacy will seek to commit more cities and increase the support by national governments to support city resilience and local capacities.
Resolution of adefovir‐related nephrotoxicity by adefovir dose‐reduction in patients with chronic hepatitis B
Authors: Hartono J. L. , Aung M. O. , Dan Y. Y. , Gowans M. , Lim K. , Lee Y. M. , Lee G. H. , Low H. C. , Tan P. S. , Thwin M. A. , Soon C. , Chiu L.‐L. , Khoo M. J. , Koay E. , Lim S. G.
Published: February 2013

Background

Chronic hepatitis B patients (CHB) treated with adefovir were followed up to evaluate nephrotoxicity and its outcome.

Aim

To assess the incidence of renal dysfunction during adefovir therapy in Asian patients and factors associated with it, and evaluate strategies to improve adefovir‐related renal dysfunction and their impact on viral suppression.

Methods

Chronic hepatitis B clinic patients from a tertiary hospital on adefovir treatment, with their clinical and laboratory parameters were extracted from the hospital electronic clinical database in an observational study design. Patients were excluded if they had liver/renal transplant, baseline renal impairment or were on dialysis. Adefovir‐related renal dysfunction was defined as adefovir‐related abnormal serum creatinine (ARASC) > 125 μmol/L (males), >90 μmol/L (females); adefovir‐related abnormal GFR <60 mL/min; and adefovir‐related increased serum creatinine >0.5 mg/dL, without other known causes of nephrotoxicity.

Results

A total of 271/383 adefovir‐treated patients were suitable for analysis and 33(12%) patients developed abnormal serum creatinine. Cumulative increase in proportion of patients with ARASC was 33.8% and GFR ≤60 mL/min was 38.3% by 6 years, while serum creatinine increase ≥0.5 mg/dL was 21.48% by 5 years. Using multivariate analysis, the only independent baseline predictor of ARASC was GFR ≤76.1 mL/min. Patients who had ARASC had similar levels of viral suppression to those who did not have ARASC. Those who had ARASC either continued adefovir (24%), switched therapy (24%) or had adefovir dose reduction (52%). ARASC resolved and GFR normalised in almost all patients after either switching therapy or reducing adefovir dose, with no difference between the two strategies (P = 0.737). Those with adefovir dose reduction had no significant increase in HBV DNA (P = 0.170).

Conclusions

Adefovir‐related renal dysfunction occurred in a significant number of adefovir‐treated patients, but reduction of the dose led to renal improvement without compromising treatment efficacy.
Degradation of Archaeological Wood Under Freezing and Thawing Conditions—Effects of Permafrost and Climate Change
Authors: Matthiesen H. , Jensen J. B. , Gregory D. , Hollesen J. , Elberling B.
Published: February 2013

The degradation of archaeological wood at freezing and thawing temperatures is studied at the site of Qajaa in West Greenland through a combination of environmental monitoring, measurement of oxygen consumption and microscopy of wood samples. Permanently frozen wood is still very well preserved after 2–4000 years, while wood samples that thaw every summer show attack by soft rot and an average density loss of 0.1 g cm–3 (corresponding to 25% of the dry mass) over the past 27 years. Future increases in temperature may increase the decay rate significantly (Q10 = 4.2 at 0–10°C) but the effects on site depend on local hydrology.
The Mother‐Citizen and the Working Girl: First‐Wave Feminist Citizenship Claims in Canada and Discursive Opportunities for Twenty‐First Century Childcare Policy
Authors: Hallgrimsdottir Helga K. , Benoit Cecilia , Phillips Rachel
Published: February 2013

L'État providence Canadien est déséquilibré: leader mondial dans certains domaines de l'investissement social—plus particulièrement en soins de santé et enseignement supérieur—il traîne dans d'autres domaines de la dépense d'aide sociale, y compris les politiques de garde d'enfants. Nous constatons qu'aujourd'hui la résistance dans la plupart des régions du Canada à la politique de garde d'enfants universel a des racines historiques profondes. Elle est de fait intégré dans le cadre même du bien‐être social canadien: le contrat de citoyenneté sociale. Nous employons une approche de “bas en haut” sur l'état du bien‐être en nous concentrant sur la façon dont les acteurs collectifs, en particulier, les féministes de la première vague et leurs contemporains au sein des organisations du mouvement ouvrier, ont encadrées et caractérisé la citoyenneté sociale féminine; Nous constatons que l'exclusion de l'adhésion des femmes employées tronque les possibilités discursives par lesquelles des revendications pour des provisions universelles de bien‐être sociale pourraient être apportées.

Canada's welfare state is lopsided: while leading the world in some areas of social investment—most notably health care and higher education—it is a laggard in other areas of social welfare spending, including childcare policies. We find that policy resistance to universal childcare in most regions of Canada today has deep historical roots and is, indeed, embedded into the very framework of the Canadian welfare state: the social citizenship contract. We employ a “bottom‐up” perspective on the welfare state focusing on how collective actors, in particular, first‐wave feminists and their contemporaries within labor movement organizations, framed and characterized female social citizenship in ways that excluded employed women from full membership and, in this, truncated discursive opportunities by which claims for universal welfare state provisions could be made.
Preparation, Characterization, and Thermophysical Properties of (La0.95Sr0.05)2Ce2O6.95 Ceramic for Thermal Barrier Coatings
Authors: Zhang Hong‐Song , Lv Jian‐Guo , Li Gang , Chen Xiao‐Ge , Wang Xin‐Li
Published: February 2013

The La2Ce2O7 powder doped with Sr was synthesized by sol‐gel method in this study and its dense bulk samples were also prepared by pressureless‐sintered at 1600°C for 10 h. Its phase composition, microstructure, and thermophysical property were investigated. Results reveal that pure (La0.95Sr0.05)2Ce2O6.95 with single fluorite structure was successfully synthesized. Microstructure of bulk sample is dense. Its thermal expansion coefficient is higher than that of Y2O3‐stabilized ZrO2 (YSZ) and its thermal conductivity is lower than that of YSZ. These results show that (La0.95Sr0.05)2Ce2O6.95 ceramic can be explored as the candidate material for thermal barrier coatings.
Assessment of capsule endoscopy scoring index, clinical disease activity, and C‐reactive protein in small bowel Crohn's disease
Authors: Yang Li , Ge Zhi‐Zheng , Gao Yun‐Jie , Li Xiao‐Bo , Dai Jun , Zhang Yao , Xue Han‐Bing , Zhao Yun‐Jia
Published: February 2013

Background and Study Aims

Small bowel Crohn's disease (SBCD) patients are frequently assessed by capsule endoscopy (CE), which enables direct visualization of small bowel mucosal abnormalities; however, the correlations between CE scoring index (CESI), C‐reactive protein (CRP), and disease activity indices remain undefined. We aimed to determine correlations between the CESI, clinical disease activity indices, and CRP in SBCD patients.

Patients and Methods

A prospective study was conducted between October 2008 and February 2011 on 58 established SBCD patients and suspected patients who received a definitive SBCD diagnosis during study. Patients underwent complete CE and were scored according to the CESI and Harvey–Bradshaw index (HBI). Statistical correlation among CESI, HBI, and CRP was assessed.

Results

Weak, but significant, correlations were found between CESI and HBI (r = 0.4, P < 0.01). The correlation between CESI and CRP was moderate (r = 0.58, P < 0.01). The median CRP value was significantly higher in patients with moderate to severe CESI compared with the mild group (22.60 ± 16.79 mg/L vs 11.88 ± 8.39 mg/L, P < 0.01). Changes between baseline and follow‐up CESI failed to correlate with the delta‐HBI or delta‐CRP (both, P > 0.05).

Conclusions

In this cohort of SBCD patients, clinical disease activity index was not reliable predictors of mucosal inflammation. CRP, however, might be a useful inflammatory marker for evaluating the moderate to severe CE activity in SBCD patients. Furthermore, therapy‐induced clinical and biological improvement was not associated with repair of SBCD mucosal lesions.
THE CONTINUOUS WAVELET TRANSFORM: MOVING BEYOND UNI‐ AND BIVARIATE ANALYSIS
Authors: Aguiar‐Conraria Luís , Soares Maria Joana
Published: February 2013

A body of work using the continuous wavelet transform has been growing. We provide a self‐contained summary on its most relevant theoretical results, describe how such transforms can be implemented in practice, and generalize the concept of simple coherency to partial wavelet coherency and multiple wavelet coherency, moving beyond bivariate analysis. We also describe a family of wavelets, which emerges as an alternative to the popular Morlet wavelet, the generalized Morse wavelets. A user‐friendly toolbox, with examples, is attached to this paper.
The association between polyploidy and clonal reproduction in diploid and tetraploidChamerion angustifolium
Authors: Baldwin Sarah J. , Husband Brian C.
Published: February 2013

Clonal reproduction is associated with the incidence of polyploidy in flowering plants. This pattern may arise through selection for increased clonality in polyploids compared to diploids to reduce mixed‐ploidy mating. Here, we test whether clonal reproduction is greater in tetraploid than diploid populations of the mixed‐ploidy plant,Chamerion angustifolium,through an analysis of the size and spatial distribution of clones in natural populations usingAFLPgenotyping and a comparison of root bud production in a greenhouse study. Natural tetraploid populations (N = 5) had significantly moreAFLPgenotypes ( = 10.8) than diploid populations ( = 6.0). Tetraploid populations tended to have fewer ramets per genotype and fewer genotypes with >1 ramet. In a spatial autocorrelation analysis, ramets within genotypes were more spatially aggregated in diploid populations than in tetraploid populations. In the greenhouse, tetraploids allocated 90.4% more dry mass to root buds than diploids, but tetraploids produced no more root buds and 44% fewer root buds per unit root mass than diploids. Our results indicate that clonal reproduction is significant in most populations, but tetraploid populations are not more clonal than diploids, nor are their clones more spatially aggregated. As a result, tetraploids may be less sheltered from mixed‐ploidy mating and diploids more exposed to inbreeding, the balance of which could influence the establishment of tetraploids in diploid populations.
Sucrose functions as a signal involved in the regulation of strawberry fruit development and ripening
Authors: Jia Haifeng , Wang Yuanhua , Sun Mingzhu , Li Bingbing , Han Yu , Zhao Yanxia , Li Xingliang , Ding Ning , Li Chen , Ji Wenlong , Jia Wensuo
Published: February 2013

Fleshy fruits are classically divided into climacteric and nonclimacteric types. It has long been thought that the ripening of climacteric and nonclimacteric fruits is regulated by ethylene and abscisic acid (ABA), respectively. Here, we report that sucrose functions as a signal in the ripening of strawberry (Fragaria × ananassa), a nonclimacteric fruit.

Pharmacological experiments, as well as gain‐ and loss‐of‐function studies, were performed to demonstrate the critical role of sucrose in the regulation of fruit ripening.

Fruit growth and development were closely correlated with a change in sucrose content. Exogenous sucrose and its nonmetabolizable analog, turanose, induced ABA accumulation in fruit and accelerated dramatically fruit ripening. A set of sucrose transporters, FaSUT1–7, was identified and characterized, among which FaSUT1 was found to be a major component responsible for sucrose accumulation during fruit development. RNA interference‐induced silencing of FaSUT1 led to a decrease in both sucrose and ABA content, and arrested fruit ripening. By contrast, overexpression of FaSUT1 led to an increase in both sucrose and ABA content, and accelerated fruit ripening.

In conclusion, this study demonstrates that sucrose is an important signal in the regulation of strawberry fruit ripening.
The reliability of online information regarding orthognathic surgery available to the public
Authors: Cobb R.J. , Scotton W.J.
Published: February 2013

Objective

The purpose of this study is to assess the quality of online information regarding orthognathic surgery using common internet searches.

Methods

Five common search engines were queried using the string ‘orthognathic surgery OR jaw osteotomy OR surgical orthodontics’. The first 30 sites revealed by each search engine were reviewed and the content quality of the following components was assessed by two independent reviewers: indications, surgical procedure, complications, post‐operative healing and long term outcome. Components were scored 0 to 2 depending on whether topics were addressed and if in accordance with current accepted practice patterns.

Results

Of the 150 links, 138 were accessible. Fifty‐two per cent were orientated for laypeople. Sixty‐six per cent had an affiliation with a medical institution or professional organisation. Authors were mainly maxillofacial surgeons, orthodontists (56%) or unspecified (33%). High scoring content components included indications and surgical procedure. Poorly scoring components included complications and long‐term outcome. Virtually, none of the websites were accredited by a healthcare website accreditation organisation.

Conclusions

Online information available to the public regarding orthognathic surgery is generally of poor quality. Certain critical aspects of the surgical process are often overlooked by websites.
Erupted rootless type III dense in dente (dilated odontoma) masquerading as peripheral gingival pathosis
Authors: Ide F. , Ito Y. , Muramatsu T. , Saito I. , Mishima K.
Published: February 2013

Dense in dente, also known as dense invaginatus or dilated odontoma, is a developed malformed tooth and usually does not pose a diagnostic challenge. Described here is a unique case in which a rootless type III dense in dente (dilated odontoma) between the lower deciduous molars in a 2‐year‐old girl emerged through the gingiva mimicking a peripheral developing odontoma. At the time of examination, neither anchored in bone nor associated with an underlying un‐erupted tooth. The small size, the superficial position in the growing mandible, the absence of the overlying bone and the physiologic eruptive movement of the neighbouring teeth may predispose the present rootless dense in dente to erupt in the gingiva.
Aquaporin Trafficking in Plant Cells: An Emerging Membrane‐Protein Model
Authors: Luu Doan‐Trung , Maurel Christophe
Published: February 2013

Aquaporins (AQPs) are channel proteins that facilitate the transport of water and small solutes across biological membranes. In plants, AQPs exhibit a high multiplicity of isoforms in relation to a high diversity of sub‐cellular localizations, at the plasma membrane (PM) and in various intracellular compartments. Some members also exhibit a dual localization in distinct cell compartments, whereas others show polarized or domain‐specific expression at the PM or tonoplast, respectively. A diversity of mechanisms controlling the routing of newly synthesized AQPs towards their destination membranes and involving diacidic motifs, phosphorylation or tetramer assembly is being uncovered. Recent approaches using single particle tracking, fluorescence correlation spectroscopy and fluorescence recovery after photobleaching have, in combination with pharmacological interference, stressed the peculiarities of AQP sub‐cellular dynamics in environmentally challenging conditions. A role for clathrin and sterol‐rich domains in cell surface dynamics and endocytosis of PM AQPs was uncovered. These recent advances provide deep insights into the cellular mechanisms of water transport regulation in plants. They also point to AQPs as an emerging model for studying the sub‐cellular dynamics of plant membrane proteins.
Fruit Flies Medicate Offspring After Seeing Parasites
Authors: Kacsoh Balint Z. , Lynch Zachary R. , Mortimer Nathan T. , Schlenke Todd A.
Published: February 2013

Mother Knows Best

Fruit flies feed on decomposing fruit, a food source rich in alcohol, and thus have evolved a high alcohol tolerance not shared by many other species. High levels of ingested alcohol protect fly larvae against parasitic wasp larvae.

Kacsoh
et al.

(p.
947
) show that this therapeutic use of alcohol to combat a parasite has an intergenerational component. When fly mothers were permitted to see parasitic wasps, they preferentially laid their eggs on substrates containing high alcohol levels as a way to medicate their offspring against potential infection.
The Aerosol Nucleation Puzzle
Authors: Andreae Meinrat O.
Published: February 2013

Field studies in a boreal forest and laboratory experiments reveal how atmospheric aerosols are formed from gas molecules.

[Also see Report by

Kulmala
et al.

]
Congress Tries Again to Head Off Looming Helium Crisis
Authors: Cho Adrian
Published: February 2013

A bill has been introduced in Congress that would prevent an acute but wholly self-inflicted shortage of helium from striking later this year.
How Sweet It Is: Genes Show How Bacteria Colonized Human Teeth
Authors: Gibbons Ann
Published: February 2013

New genetic studies show that when humans invented farming, cavity-causing microbes that had lurked at low levels bloomed on their teeth, and left the modern mouth a depauperate ecosystem.
Mycobacterium bovis DNA Detection in Colostrum as a Potential Indicator of Vaccination Effectiveness against Bovine Tuberculosis
Authors: Herrera-Rodríguez Sara E. , Gordiano-Hidalgo María Alejandra , López-Rincón Gonzálo , Bojorquez-Narváez Luis , Padilla-Ramírez Francisco Javier , Pereira-Suárez Ana Laura , Flores-Valdez Mario Alberto , Estrada-Chávez Ciro
Published: February 2013

Bovine tuberculosis (bTB) remains a problem on many dairy farms in Mexico, as well as a public health risk. We previously found a high frequency ofMycobacterium bovisDNA in colostrum from dairy cows using a nested PCR to detectmpb70. Since there are no reliablein vivotests to determine the effectiveness of boosterMycobacterium bovisBCG vaccination against bTB, in this work we monitoredM. bovisDNA in colostrum by using this nested PCR. In order to decrease the risk of adverse reactions in animals likely containing viableM. bovis, a single application of BCG and a subunit vaccine (EEP-1) formulated withM. bovisculture filtrate proteins (CFP) and a copolymer as the adjuvant was performed in tuberculin skin test-negative cattle (TST−), while TST reactor animals (TST+) received EEP-1 only. Booster immunization using EEP-1 was applied to both groups, 2 months after primary vaccination to whole herds and 12 months later to lactating cows. Colostrum samples were collected from 6 farms where the cows were vaccinated over a 12-month period postvaccination and, for comparison, from one control farm where the cows were not vaccinated with comparable bTB prevalence. We observed an inverse relationship between the frequency ofM. bovisDNA detection and time postvaccination at the first (P< 0.001) and second (P< 0.0001) 6-month periods. Additionally, the concentration of gamma interferon (IFN-γ) was higher inmpb70PCR-positive colostrum samples (P= 0.0003). These results suggest thatM. bovisDNA frequency in colostrum could be a potentially useful biomarker for bTB vaccine efficacy on commercial dairy farms.
Genetic Screen of a Mutant Poxvirus Library Identifies an Ankyrin Repeat Protein Involved in Blocking Induction of Avian Type I Interferon
Authors: Laidlaw Stephen M. , Robey Rebecca , Davies Marc , Giotis Efstathios S. , Ross Craig , Buttigieg Karen , Goodbourn Stephen , Skinner Michael A.
Published: February 2013

Mammalian poxviruses, including vaccinia virus (VACV), have evolved multiple mechanisms to evade the host type I interferon (IFN) responses at different levels, with viral proteins targeting IFN induction, signaling, and antiviral effector functions. Avian poxviruses (avipoxviruses), which have been developed as recombinant vaccine vectors for permissive (i.e., poultry) and nonpermissive (i.e., mammals, including humans) species, encode no obvious equivalents of any of these proteins. We show that fowlpox virus (FWPV) fails to induce chicken beta IFN (ChIFN2) and is able to block its induction by transfected poly(I·C), an analog of cytoplasmic double-stranded RNA (dsRNA). A broad-scale loss-of-function genetic screen was used to find FWPV-encoded modulators of poly(I·C)-mediated ChIFN2 induction. It identified
fpv012
, a member of a family of poxvirus genes highly expanded in the avipoxviruses (31 in FWPV; 51 in canarypox virus [CNPV], representing 15% of the total gene complement), encoding proteins containing N-terminal ankyrin repeats (ANKs) and C-terminal F-box-like motifs. Under ectopic expression, the first ANK of
fpv012
is dispensable for inhibitory activity and the CNPV ortholog is also able to inhibit induction of ChIFN2. FWPV defective in
fpv012
replicates well in culture and barely induces ChIFN2 during infection, suggesting that other factors are involved in blocking IFN induction and resisting the antiviral effectors. Nevertheless, unlike parental and revertant viruses, the mutants induce moderate levels of expression of interferon-stimulated genes (ISGs), suggesting either that there is sufficient ChIFN2 expression to partially induce the ISGs or the involvement of alternative, IFN-independent pathways that are also normally blocked by
fpv012
.
Top 10 practical lessons learned from physical activity interventions in overweight and obese children and adolescents
Authors: Alberga Angela S. , Medd Emily R. , Adamo Kristi B. , Goldfield Gary S. , Prud'homme Denis , Kenny Glen P. , Sigal Ronald J.
Published: February 2013

Physical activity (PA) interventions targeting overweight and obese children and adolescents have shown only modest success, and dropout is an area of concern. Proper design and implementation of a PA intervention is critical for maximizing adherence and thus increasing the overall health benefits from PA participation. We propose practical advice based on our collective clinical trial experience with support from the literature on best practices related to PA interventions in overweight and obese children and adolescents. The top 10 lessons learned are (i) PA setting–context is important; (ii) choice of fitness trainer matters; (iii) physical activities should be varied and fun; (iv) the role of the parent–guardian should be considered; (v) individual physical and psychosocial characteristics should be accounted for; (vi) realistic goals should be set; (vii) regular reminders should be offered; (viii) a multidisciplinary approach should be taken; (ix) barriers should be identified early and a plan to overcome them developed; and (x) the right message should be communicated: specifically, what's in it for them? The recommendations in this paper can be used in other pediatric PA programs, physical education settings, and public health programs, with the hope of decreasing attrition and increasing the benefits of PA participation to promote health in children and adolescents.
UNDERSTANDING SMALL BUSINESS SCAMS
Authors: SCHAPER MICHAEL T. , WEBER PAUL
Published: February 2013

This paper provides an overview of the current state of knowledge about small business scams. A scam is a form of dishonest action, based upon an invitation to participate in an activity. Victims are encouraged, mislead or induced to voluntarily interact with the perpetrator, and ultimately to willingly surrender over money, information or other valuable resources. Common forms of scams directed towards small business include phishing, false business valuations and sales, fake overpayments, false directory and advertisement listings, bust-outs, blowing, cramming, advance fee fraud and misleading self-employment projects. The limited research evidence available to date suggests that small enterprises are particularly vulnerable to these types of criminal activity, are less inclined to report such events, are likely to be subject to repeat attacks, and are particularly susceptible to online scams. This occurs because small businesses often lack the in-house skills, resources and reporting arrangements needed to effectively detect and prevent scams. The paper also briefly examines the entrepreneurial nature of scammers, and explores some of the emergent literature on the psychology of small business scams that may explain scam propensity. Strategies for combating and avoiding scams are discussed, as are suggestions for future research directions in the area.