bluuebunny/crossref_metadata_2025_split huggingface dataset:
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes
Authors: Wheeler Nicole E. , Barquist Lars , Kingsley Robert A. , Gardner Paul P. 
Published: July 2015

AbstractMotivationNext generation sequencing technologies have provided us with a wealth of information on genetic variation, but predicting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics.ResultsWe present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation inSalmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms.AvailabilityA program implementing DBS for pairwise genome comparisons is freely available at:https://github.com/UCanCompBio/deltaBS.Contactnicole.wheeler@pg.canterbury.ac.nz,lars.barquist@uni-wuerzburg.deSupplementary informationSupplementary data are available at BioRxiv online.
metaCCA: Summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis
Authors: Cichonska Anna , Rousu Juho , Marttinen Pekka , Kangas Antti J , Soininen Pasi , Lehtimäki Terho , Raitakari Olli T , Järvelin Marjo-Riitta , Salomaa Veikko , Ala-Korpela Mika , Ripatti Samuli , Pirinen Matti 
Published: July 2015

AbstractA dominant approach to genetic association studies is to perform univariate tests between genotype-phenotype pairs. However, analysing related traits together increases statistical power, and certain complex associations become detectable only when several variants are tested jointly. Currently, modest sample sizes of individual cohorts and restricted availability of individual-level genotype-phenotype data across the cohorts limit conducting multivariate tests.We introducemetaCCA, a computational framework for summary statistics-based analysis of a single or multiple studies that allows multivariate representation of both genotype and phenotype. It extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.Multivariate meta-analysis of two Finnish studies of nuclear magnetic resonance metabolomics bymetaCCA, using standard univariate output from the program SNPTEST, shows an excellent agreement with the pooled individual-level analysis of original data. Motivated by strong multivariate signals in the lipid genes tested, we envision that multivariate association testing usingmetaCCAhas a great potential to provide novel insights from already published summary statistics from high-throughput phenotyping technologies.Code is available athttps://github.com/aalto-ics-kepaco.
Lonely are the brave
Authors: Khilay Snéha 
Published: July 2015

Purpose
– Highlights the notion of a dominant organizational culture and examines what can happen when this conflicts with an individual employee’s set of beliefs.

Design/methodology/approach
– Provides examples of employees who have challenged the dominant culture in their organization and considers some of the outcomes.

Findings
– Investigates how people get caught up in the “need-to-be-liked” syndrome and behave in a manner that causes discomfort, yet continue to do so while occasionally losing sight of strongly held values or perspectives.

Practical implications
– Tells the stories of individuals who, although their fight for justice involved difficulties and emotional grief, had to take responsibility and focus on the outcome they wanted, basically to continue their personal and professional lives with their heads held high.

Originality/value
– Recounts cases of individuals who have faced adversity in their work because of them voicing their differences, raising concerns and being treated in a negative manner as a result.
Do native and invasive plants differ in their interactions with arbuscular mycorrhizal fungi? A meta‐analysis
Authors: Bunn Rebecca A. , Ramsey Philip W. , Lekberg Ylva 
Published: July 2015

Summary

Divergent hypotheses have been proposed that suggest plant invasions either enhance or degrade the mutualism between plants and arbuscular mycorrhizal (AM) fungi, but their relative support remains unknown.

We conducted a meta‐analysis using 67 publications, involving 70 native and 55 invasive plant species to assess support for the enhanced mutualism hypothesis, the degraded mutualism hypothesis and an alternative hypothesis that factors other than invasive status (such as plant functional group) better predict AM function following invasion. We used multiple measurements to test these hypotheses: AM fungal colonization, growth responses to AM fungi and AM fungal‐mediated shifts in competitive interactions among native and invasive plants. Additionally, we assessed whether invasive plants alter AM associations in native plants and whether native and invasive plants host different AM fungal abundances and communities.

Arbuscular mycorrhizal fungal colonization (%) and average growth responses did not differ between native and invasive plants. However, growth responses (±) were dampened among invasive plants, and the positive correlation between AM fungal colonization and growth response in native plants was absent in invasive plants. Rather than plant invasive status, plant functional group was a significant explanatory factor; forbs were generally more colonized and exhibited positive growth responses (when grown alone and in competition), whereas grass responses were neutral to negative.

Arbuscular mycorrhizal fungal abundance (measured by percentage colonization, extraradical hyphal and spore densities, as well as neutral lipid fatty acid and glomalin concentrations) did not differ between native and invasive plants, but invasive plants hosted different AM fungal communities in 78% of studies. AM fungal colonization of native plants was lower when grown with, or after, invasive plants, likely due to the prevalence of non‐mycorrhizal plants in studies of neighbour and legacy effects.

Synthesis. Neither the degraded nor the enhanced mutualism hypothesis was supported, suggesting that invasions do not select for directional shifts in AM associations. Instead, our results indicate that AM fungi are most likely to influence invasion trajectories when native and invasive plants belong to different functional groups.
Freshwater protists do not go with the flow: population structure in Gonyostomum semen independent of connectivity among lakes
Authors: Sassenhagen Ingrid , Sefbom Josefin , Säll Torbjörn , Godhe Anna , Rengefors Karin 
Published: July 2015

SummaryMany recent studies have found genetically differentiated populations in microorganisms despite potentially high dispersal. We designed a study to specifically examine the importance of physical dispersal barriers, i.e. geographic distance and lack of hydrological connectivity, in restricting gene flow and enhancing divergence in limnic microorganisms. We focused on the nuisance microalga Gonyostomum semen, which has recently expanded in Northern Europe and differentiated into genetically distinct populations. G. semen was sampled from six lakes distributed in two adjacent watersheds, which thereby comprised, both connected and non‐connected lakes. The individual isolates were genotyped by amplified fragment length polymorphism. Several lake populations were differentiated from each other, but connectivity within watersheds could not explain the observed population genetic pattern. However, isolation by distance was moderate and might limit the gene flow among distant populations. In addition, we found low, but significant linkage disequilibrium, which indicates regular sexual recombination in this species, despite its high degree of asexual reproduction. Therefore, we conclude that the genetic properties of microalgae with occasional sexual reproduction essentially mirror regularly recombining species. Furthermore, the data indicated bottlenecks supporting the hypothesized recent range expansion of this species.
The Politics of Parliamentary Strengthening
Authors: Power Greg 
Published: July 2015

AbstractParliament's International Development Committee made a powerful case this year that DFID should put more money into parliamentary strengthening in developing countries. Arguing that parliaments were central to tackling corruption, improving economic development and building stable political settlements, they recommended that parliaments should be at the ‘heart of DFID's governance work’. The report, though, also touched on wider issues of how DFID commissions and monitors its political programmes, suggesting fundamental changes to both. DFID recognises these challenges, and offered either full or partial agreement with most of the recommendations. The challenge that remains, though, is moving from the rhetoric of ‘engaging with politics’ to a much improved form of political and parliamentary programming.
‘M‐apping’ sleep? Trends and transformations in the digital age
Authors: Williams Simon J. , Coveney Catherine , Meadows Robert 
Published: July 2015

AbstractThis article critically explores recent trends and transformations in the monitoring and management of sleep in the digital age, taking as its focus the advent of new digital technologies to trace and track the ‘sleep of ourselves’ far away from the conventional sleep laboratory or clinic. Our argument is situated dually in the history of sleep science and medicine on the one hand, and the rise of new digital forms of so‐called self‐tracking and mobile health (m‐Health) on the other hand. While the recent history of sleep science and medicine may rightly we suggest, in Kroker's terms, be characterised as a concern with the ‘sleep of others’, a new chapter in this story may well be dawning through the advent of these smart new mobile tools and technologies for mapping, or ‘m‐apping’ as we term it, the ‘sleep of ourselves’ in the digital age. The problems and prospects this holds are then critically considered – through the interrelated themes of selfhood, sociality and governance – and some preliminary conclusions ventured in this new digital domain.
Combination of Face Regions in Forensic Scenarios
Authors: Tome Pedro , Fierrez Julian , Vera‐Rodriguez Ruben , Ortega‐Garcia Javier 
Published: July 2015

AbstractThis article presents an experimental analysis of the combination of different regions of the human face on various forensic scenarios to generate scientific knowledge useful for the forensic experts. Three scenarios of interest at different distances are considered comparing mugshot and CCTV face images using MORPH and SC face databases. One of the main findings is that inner facial regions combine better in mugshot and close CCTV scenarios and outer facial regions combine better in far CCTV scenarios. This means, that depending of the acquisition distance, the discriminative power of the facial regions change, having in some cases better performance than the full face. This effect can be exploited by considering the fusion of facial regions which results in a very significant improvement of the discriminative performance compared to just using the full face.
Development of Titanium Dioxide (TiO2) Nanocoatings on Food Contact Surfaces and Method to Evaluate Their Durability and Photocatalytic Bactericidal Property
Authors: Yemmireddy Veerachandra K. , Farrell Glenn D. , Hung Yen‐Con 
Published: July 2015

AbstractTitanium dioxide (TiO2) is a well‐known photocatalyst for its excellent bactericidal property under UVA light. The purpose of this study was to develop physically stable TiO2 coatings on food contact surfaces using different binding agents and develop methods to evaluate their durability and microbicidal property. Several types of organic and inorganic binders such as polyvinyl alcohol, polyethylene glycol, polyurethane, polycrylic, sodium and potassium silicates, shellac resin, and other commercial binders were used at 1:1 to 1:16 nanoparticle to binder weight ratios to develop a formulation for TiO2 coating on stainless steel surfaces. Among the tested binders, polyurethane, polycrylic, and shellac resin were found to be physically more stable when used in TiO2 coating at 1:4 to 1:16 weight ratio. The physical stability of TiO2 coatings was determined using adhesion strength and scratch hardness tests by following standard ASTM procedures. Further, wear resistance of the coatings was evaluated based on a simulated cleaning procedure used in food processing environments. TiO2 coating with polyurethane at a 1:8 nanoparticle to binder weight ratio showed the highest scratch hardness (1.08 GPa) followed by coating with polycrylic (0.68 GPa) and shellac (0.14 GPa) binders. Three different techniques, namely direct spreading, glass cover‐slip, and indented coupon were compared to determine the photocatalytic bactericidal property of TiO2 coatings against Escherichia coli 0157:H7 at 2 mW/cm2 UVA light intensity. Under the tested conditions, the indented coupon technique was found to be the most appropriate method to determine the bactericidal property of TiO2 coatings and showed a reduction of 3.5 log CFU/cm2 in 2 h.
Preparation of High‐Grade Powders from Tomato Paste Using a Vacuum Foam Drying Method
Authors: Sramek Martin , Schweiggert Ralf Martin , van Kampen Andreas , Carle Reinhold , Kohlus Reinhard 
Published: July 2015

AbstractWe present a rapid and gentle drying method for the production of high‐grade tomato powders from double concentrated tomato paste, comparing results with powders obtained by foam mat air drying and freeze dried powders. The principle of this method consists of drying tomato paste in foamed state at low temperatures in vacuum. The formulations were dried at temperatures of 50, 60, and 70 °C and vacuum of 200 mbar. Foam stability was affected by low serum viscosity and the presence of solid particles in tomato paste. Consequently, serum viscosity was increased by maltodextrin addition, yielding optimum stability at tomato paste:maltodextrin ratio of 2.4:1 (w/w) in dry matter. Material foamability was improved by addition of 0.5% (w/w, fresh weight) egg white. Because of solid particles in tomato paste, foam air filling had to be limited to critical air volume fraction of Φ = 0.7. The paste was first pre‐foamed to Φ = 0.2 and subsequently expanded in vacuo. After drying to a moisture content of 5.6% to 7.5% wet base (w.b.), the materials obtained were in glassy state. Qualities of the resulting powders were compared with those produced by freeze and air drying. Total color changes were the least after vacuum drying, whereas air drying resulted in noticeable color changes. Vacuum foam drying at 50 °C led to insignificant carotenoid losses, being equivalent to the time‐consuming freeze drying method. In contrast, air drying caused lycopene and β‐carotene losses of 18% to 33% and 14% to 19% respectively. Thus, vacuum foam drying enables production of high‐grade tomato powders being qualitatively similar to powders obtained by freeze drying.
Notes on farm‐retail price transmission and marketing margin behavior
Authors: Kinnucan Henry W. , Zhang Dengjun 
Published: July 2015

AbstractPerfect farm‐retail price transmission sometimes is taken to mean an elasticity of price transmission (EPT) equal to 1. We show that this definition is inconsistent with Gardner's (1975) model. We also show that the absolute marketing margin (defined as the difference between the retail price and farm price) responds differently to shifts in retail demand, input supply, and technical change in the marketers’ production function than does the relative marketing margin (defined as the ratio of the retail price to the farm price). The empirical implications of these results are discussed in some detail.
Occupational skin disease in Victoria, Australia
Authors: Cahill Jennifer L , Williams Jason D , Matheson Melanie C , Palmer Amanda M , Burgess John A , Dharmage Shyamali C , Nixon Rosemary L 
Published: July 2015

AbstractObjectivesTo describe the characteristics of patients with occupational skin disease (OSD) in a tertiary referral clinic in Victoria, Australia.MethodsA retrospective review was conducted of records from patients seen at the Occupational Dermatology Clinic in Melbourne, Australia between 1 January 1993 and 31 December 2010.ResultsOf the 2894 people assessed in the clinic during the 18‐year period, 44% were women and 56% were men. In all, 2177 (75%) were diagnosed with occupational skin disease (OSD). Of the patients with a work‐related skin condition, 45% (n = 979) were considered to be atopic. The most common diagnosis in those with OSD was irritant contact dermatitis (ICD) (44%), followed by allergic contact dermatitis (33%) and endogenous eczema (11%). Women were significantly more likely to have soaps and detergents (P < 0.001) and water/wet work (P < 0.001) as causes of their ICD than men. Men were significantly more likely to have oils and coolants (P < 0.001) and solvent exposures (P < 0.001) as causes of their ICD. Occupational groups with the highest incidence of OSD were the hair and beauty professions (70 per 100 000), followed by machine and plant operators (38 per 100 000) and health‐care workers (21 per 100 000).ConclusionWe confirm the importance of occupational contact dermatitis as the most common cause of OSD, with ICD being the most common diagnosis. There are differences in the causes of ICD between our group of male and female workers. For the first time in Australia, rates of OSD in certain industries have been calculated.
Tree pollen allergens—an update from a molecular perspective
Authors: Asam C. , Hofer H. , Wolf M. , Aglas L. , Wallner M. 
Published: July 2015

AbstractIt is estimated that pollen allergies affect approximately 40% of allergic individuals. In general, tree pollen allergies are mainly elicited by allergenic trees belonging to the orders Fagales, Lamiales, Proteales, and Pinales. Over 25 years ago, the gene encoding the major birch pollen allergen Bet v 1 was the first such gene to be cloned and its product characterized. Since that time, 53 tree pollen allergens have been identified and acknowledged by the WHO/IUIS allergen nomenclature subcommittee. Molecule‐based profiling of allergic sensitization has helped to elucidate the immunological connections of allergen cross‐reactivity, whereas advances in biochemistry have revealed structural and functional aspects of allergenic proteins. In this review, we provide a comprehensive overview of the present knowledge of the molecular aspects of tree pollen allergens. We analyze the geographic distribution of allergenic trees, discuss factors pivotal for allergic sensitization, and describe the role of tree pollen panallergens. Novel allergenic tree species as well as tree pollen allergens are continually being identified, making research in this field highly competitive and instrumental for clinical applications.
Randomized controlled trial of probiotics after colonoscopy
Authors: D'Souza Basil , Slack Timothy , Wong Shing W. , Lam Francis , Muhlmann Mark , Koestenbauer Jakob , Dark Jonathan , Newstead Graham 
Published: July 2015

AbstractBackgroundUp to 20% of patients have ongoing abdominal symptoms at day 2 and beyond following colonoscopy. It was hypothesized that some of these symptoms are related to alterations in gut microbiota secondary to bowel preparation and would improve with probiotics compared with placebo.MethodsPatients were given either a probiotic or placebo capsule in the days following colonoscopy. Colonoscopy was performed with air insufflation. The probiotic capsule contained the strains Lactobacillus acidophilus NCFM and Bifidobacterium lactis Bi‐07. Patients recorded their symptoms at 1 h, 1, 2, 4, 7 and 14 days post colonoscopy and returned results once their symptoms had resolved. The primary outcomes used were the length of days to resolution of bloating, abdominal pain and altered bowel function post colonoscopy.ResultsA total of 320 patients were randomized. After loss to follow‐up and withdrawal, 133 patients were analysed in the probiotic group and 126 in the placebo group. Patients having probiotic had a lower number of pain days following colonoscopy, 1.99 versus 2.78 days (P < 0.033). There was no significant difference in bloating or return to normal bowel habit days (P = 0.139 and 0.265 respectively). Subgroup analysis revealed that patients with pre‐existing abdominal pain benefited from probiotics in number of pain days, 2.16 versus 4.08 (P = 0.0498).ConclusionOur study has shown a significant reduction in the duration of pain days post colonoscopy in patients taking probiotic compared with placebo. No significant effect was seen in terms of return to normal bowel function or bloating post colonoscopy.
Failures in risk assessment and risk management for cosmetic preservatives in Europe and the impact on public health
Authors: Schwensen Jakob F. , White Ian R. , Thyssen Jacob P. , Menné Torkil , Johansen Jeanne D. 
Published: July 2015

SummaryBackgroundIn view of the current and unprecedented increase in contact allergy to methylisothiazolinone (MI), we characterized and evaluated two recent epidemics of contact allergy to preservatives used in cosmetic products to address failures in risk assessment and risk management.ObjectiveTo evaluate temporal trends of preservative contact allergy.MethodsThe study population included consecutive patch tested eczema patients seen at a university hospital between 1985 and 2013. A total of 23 138 patients were investigated for a contact allergy.ResultsThe overall prevalence of contact allergy to at least one preservative increased significantly over the study period, from 6.7% in 1985 to 11.8% in 2013 (p < 0.001). Importantly, the preservatives methyldibromo glutaronitrile and MI rapidly resulted in high sensitization prevalence rates, which reached epidemic proportions. Although the proportion of patients with current clinical disease attributable to methyldibromo glutaronitrile contact allergy decreased significantly following the ban on its use in cosmetic products (p < 0.001), the sudden and high proportion of current sensitization to MI requires immediate attention (p < 0.001).ConclusionsThe introduction of new preservatives in Europe with inadequate pre‐market risk assessment has rapidly increased the overall burden of cutaneous disease caused by preservatives. We suggest that the cosmetic industry has a responsibility to react faster and replace troublesome preservatives when a preservative contact allergy epidemic is recognized, but the European Commission has the ultimate responsibility for failures in risk management after new, major sensitizing preservatives are introduced onto the market.