bluuebunny/crossref_metadata_2025_split huggingface dataset:
The direction of the difference between Canadian and American erythrocyte folate concentrations is dependent on the assay method employed: a comparison of the Canadian Health Measures Survey and National Health and Nutrition Examination Survey
Authors: Colapinto Cynthia K. , Tremblay Mark S. , Aufreiter Susanne , Bushnik Tracey , Pfeiffer Christine M. , O'Connor Deborah L. 
Published: October 2014

Fortification of select grain products with folic acid and periconceptional supplementation recommendations in Canada and the USA have improved folate status, and have been associated with a reduced risk of neural tube defects. In the present study, we aimed to conduct a comparison of erythrocyte folate concentrations from the 2007–9 Canadian Health Measures Survey (CHMS) and the 2007–8 US National Health and Nutrition Examination Survey (NHANES). Erythrocyte folate concentration was assessed in participants aged 6–79 years (CHMS,n5248; NHANES,n7070). To account for different folate assays employed – Immulite 2000 immunoassay (CHMS) and microbiological assay (NHANES) – a conversion equation was generated (n152 adults) to adjust the CHMS data.tTests were used to examine country differences. Median Canadian erythrocyte folate concentrations (method-adjusted) were lower than those of Americans (988 and 1100 nmol/l, respectively), but unadjusted median Canadian erythrocyte folate concentrations were higher (1250 nmol/l). The upper 95 % CI boundary of the method-adjusted Canadian erythrocyte folate distribution overlapped that of the American erythrocyte folate concentrations, while the lower 95 % CI boundary of the method-adjusted Canadian erythrocyte folate data was below the American distribution. In summary, the fact that erythrocyte folate concentrations were either higher or lower in Canadians compared with Americans, depending on whether an adjustment was made to account for assay differences, suggests that caution must be exercised in evaluating erythrocyte folate data from different countries because analytical methods are not readily comparable. Furthermore, we cannot unequivocally conclude that there are true differences in erythrocyte folate concentrations between the Canadian and American populations in the post-fortification era.
Co-feeding transmission in Lyme disease pathogens
Authors: VOORDOUW MAARTEN J. 
Published: October 2014

SUMMARYThis review examines the phenomenon of co-feeding transmission in tick-borne pathogens. This mode of transmission is critical for the epidemiology of several tick-borne viruses but its importance forBorrelia burgdorferi sensu lato, the causative agents of Lyme borreliosis, is still controversial. The molecular mechanisms and ecological factors that facilitate co-feeding transmission are therefore examined with particular emphasis onBorreliapathogens. Comparison of climate, tick ecology and experimental infection work suggests that co-feeding transmission is more important in European than North American systems of Lyme borreliosis, which potentially explains why this topic has gained more traction in the former continent than the latter. While new theory shows that co-feeding transmission makes a modest contribution toBorreliafitness, recent experimental work has revealed new ecological contexts where natural selection might favour co-feeding transmission. In particular, co-feeding transmission might confer a fitness advantage in the Darwinian competition among strains in mixed infections. Future studies should investigate the ecological conditions that favour the evolution of this fascinating mode of transmission in tick-borne pathogens.
Selection for protection from insolation results in the visual isolation of Yellow-eyed Penguin Megadyptes antipodes nests
Authors: CLARK RYAN D. , MATHIEU RENAUD , SEDDON PHILIP J. 
Published: October 2014

SummaryThe concealed and widely dispersed nests of the rare and endangered Yellow-eyed Penguin Megadyptes antipodes, or “hoiho”, have been considered to reflect an essential requirement for the visual isolation of nest sites from conspecifics. However, this may be a consequence of selection for habitat features that provide protection from insolation, thereby minimising the risk of heat stress. To help improve the understanding of hoiho nesting requirements and the effectiveness of habitat restoration, we aimed to determine whether visual isolation from conspecifics or protection from insolation is the primary driver of hoiho nest site selection. We compared the mean maximum distance of visibility and the mean percentage insolation cover of active nests with randomly sampled unused sites in flax Phormium tenax and Hebe elliptica coastal scrub at Boulder Beach, and in coastal forest at Hinahina Cove, New Zealand, 2006–2007. Results of univariate tests and the evaluation of logistic regression models suggested that the amount of insolation cover was more important than visibility for hoiho nest site selection, particularly in flax and scrub. In addition, Spearman's correlations indicated that decreasing insolation cover significantly increased the visibility of nests in the forest habitat, and had a similar effect on inter-nest distance in flax. We infer that hoiho nest site selection and distribution are influenced primarily by the location and density of micro-habitat features (particularly within 1 m of the ground) that provide optimal protection from insolation, possibly along with other important features such as a firm backing structure. Strong selection for these features results in the typical but non-essential visual isolation of nest sites from conspecifics. Restoration of nesting habitats with a relatively high density and diversity of vegetation and solid structures within 1 m of the ground may eventually provide an optimal availability and quality of suitable nest sites.
Effects of hunting management on Mediterranean farmland birds
Authors: CARO JESÚS , DELIBES-MATEOS MIGUEL , ESTRADA ALBA , BORRALHO RUI , GORDINHO LUÍS , REINO LUÍS , BEJA PEDRO , ARROYO BEATRIZ 
Published: October 2014

SummaryHunting and its associated management have significant costs and benefits for biodiversity conservation, which makes this socio-economic activity highly controversial at both international and regional levels. We investigated relationships between management for small game species (mainly Red-legged PartridgesAlectoris rufaand rabbitsOryctolagus cuniculus) and both abundance and richness of farmland and scrubland songbirds, raptors and ground-nesting birds, and on the abundance of three species of conservation concern (Little BustardTetrax tetrax, Eurasian Thick-kneeBurhinus oedicnemusand Montagu’s HarrierCircus pygargus) in southern Portugal farmland. We compared 12 game estates and 12 matching areas with similar sizes and land uses but no game management. Richness and abundance were estimated from fixed point counts, and were related to game regime (managed or unmanaged), habitat characteristics and census period. Our results showed that game management was associated, albeit weakly, with higher abundance of raptors and ground-nesting birds, but no relationship (either positive or negative) was found for other guilds and species. Habitat was generally the most important factor explaining bird species richness and abundance. Our results suggest possibilities for promoting management systems that could maximize both hunting sustainability and conservation value of managed areas, particularly when management helps to improve or maintain beneficial habitats or practices for farmland birds.
Array comparative genomic hybridisation testing in CHD
Authors: Hightower Hannah B. , Robin Nathaniel H. , Mikhail Fady M. , Ambalavanan Namasivayam 
Published: October 2014

AbstractBackground: CHD is the leading cause of mortality due to birth defects. Array comparative genomic hybridisation (aCGH) detects submicroscopic copy number changes and may improve identification of the genetic basis of CHD. Methods: This is a retrospective analysis of 1252 patients from a regional referral centre who had undergone aCGH. Of the patients, 173 had CHD. A whole-genome custom-designed oligonucleotide array with >44,000 probes was used to detect copy number changes. Results: Of the 1252 patients, 335 (26.76%) had abnormal aCGH results. Of the 173 patients with CHD, 50 (28.9%) had abnormal aCGH results versus 284 (26.3%) of 1079 non-cardiac patients. There were six patients with CHD who had well-described syndromes such as Wolf–Hirschhorn, trisomy 13, DiGeorge, and Williams. Of the patients with CHD, those with left-sided heart disease had the highest proportion (14/31; 45.13%) of abnormal aCGH results, followed by those with conotruncal heart disease (10/29; 34.48%), endocardial cushion defects (13/50; 26%), complex/other heart disease (12/52; 23.08%), and patent ductus arteriosus (1/11; 9.09%). Conclusions: Patients with CHD are at a substantial risk of having microdeletions and microduplications. The incidence of abnormalities on aCGH analysis is higher than identified with karyotype, and identification of copy number changes may help identify the genetic basis of the specific heart defects. However, aCGH may not have a significant diagnostic yield in those with isolated CHD. Further research using larger data sets may help identify candidate genes associated with CHD.
Neuroplastizität und Lernen im Alter
Authors: Pinter Daniela , Weiss Elisabeth M. , Papousek Ilona , Fink Andreas 
Published: October 2014

Trotz des Zitates „was Hänschen nicht lernt, lernt Hans nimmermehr“, ist man niemals zu alt um Neues zu lernen und diese Lernprozesse bewirken bis ins hohe Alter sowohl strukturelle, als auch funktionelle Veränderungen des Gehirns. Neuronale Plastizität beschreibt Veränderungen der Gehirnstruktur und/oder Funktion in Abhängigkeit von Veränderungen im Verhalten, in der Umwelt und in neuronalen Prozessen. Solche Veränderungen können adaptiv (z. B. durch Lernen) oder „restorativ“ (z. B. nach einem Schlaganfall) auftreten und finden ein Leben lang statt.Das erwachsene Gehirn ist bemerkenswert formbar, aber im Vergleich zu Kindern scheint es für Erwachsene oft schwieriger Neues zu erlernen. Aber auch im Alter ist das Erlernen neuer Fähigkeiten bzw. eine körperliche oder kognitive Leistungssteigerung möglich. Insbesondere zugrundeliegende Veränderungen auf struktureller (Hippocampusvolumen) und funktioneller Ebene (Steigerung der Effizienz) dieser Lernprozesse werden in dieser Übersichtsarbeit exemplarisch dargestellt.Der folgende Beitrag liefert einen selektiven Überblick über die Veränderungen im Gehirn während wir altern und stellt Möglichkeiten dar, wie erfolgreiches (Gehirn-) Altern gefördert werden kann. Sowohl eine erhöhte physische, als auch geistige Aktivität ermöglicht Leistungssteigerungen in spezifischen, geübten Bereichen und scheint förderlich für gesundes Gehirnaltern. Allerdings scheitert häufig der Transfer dieser Leistungsverbesserungen auf den Alltag. Die Förderung kreativer Denkprozesse, also der Fähigkeit konventionelle Muster des Denkens zu verlassen und Neues/Originelles zu generieren könnte eine Option bieten Transfereffekte zu erleichtern. Allerdings fehlen aktuell systematische, empirische Untersuchungen im Bereich der Kreativitätsförderung im höheren Alter.
Alternative meiotic chromatid segregation in the holocentric plant Luzula elegans
Authors: Heckmann Stefan , Jankowska Maja , Schubert Veit , Kumke Katrin , Ma Wei , Houben Andreas 
Published: October 2014

AbstractHolocentric chromosomes occur in a number of independent eukaryotic lineages. They form holokinetic kinetochores along the entire poleward chromatid surfaces, and owing to this alternative chromosome structure, species with holocentric chromosomes cannot use the two-step loss of cohesion during meiosis typical for monocentric chromosomes. Here we show that the plant Luzula elegans maintains a holocentric chromosome architecture and behaviour throughout meiosis, and in contrast to monopolar sister centromere orientation, the unfused holokinetic sister centromeres behave as two distinct functional units during meiosis I, resulting in sister chromatid separation. Homologous non-sister chromatids remain terminally linked after metaphase I, by satellite DNA-enriched chromatin threads, until metaphase II. They then separate at anaphase II. Thus, an inverted sequence of meiotic sister chromatid segregation occurs. This alternative meiotic process is most likely one possible adaptation to handle a holocentric chromosome architecture and behaviour during meiosis.
Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice
Authors: Yang Wanneng , Guo Zilong , Huang Chenglong , Duan Lingfeng , Chen Guoxing , Jiang Ni , Fang Wei , Feng Hui , Xie Weibo , Lian Xingming , Wang Gongwei , Luo Qingming , Zhang Qifa , Liu Qian , Xiong Lizhong 
Published: October 2014

AbstractEven as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits.
Suppressing qubit dephasing using real-time Hamiltonian estimation
Authors: Shulman M. D. , Harvey S. P. , Nichol J. M. , Bartlett S. D. , Doherty A. C. , Umansky V. , Yacoby A. 
Published: October 2014

AbstractUnwanted interaction between a quantum system and its fluctuating environment leads to decoherence and is the primary obstacle to establishing a scalable quantum information processing architecture. Strategies such as environmental and materials engineering, quantum error correction and dynamical decoupling can mitigate decoherence, but generally increase experimental complexity. Here we improve coherence in a qubit using real-time Hamiltonian parameter estimation. Using a rapidly converging Bayesian approach, we precisely measure the splitting in a singlet-triplet spin qubit faster than the surrounding nuclear bath fluctuates. We continuously adjust qubit control parameters based on this information, thereby improving the inhomogenously broadened coherence time "Equation missing" from tens of nanoseconds to >2 μs. Because the technique demonstrated here is compatible with arbitrary qubit operations, it is a natural complement to quantum error correction and can be used to improve the performance of a wide variety of qubits in both meteorological and quantum information processing applications.
Efficient generation of knock-in transgenic zebrafish carrying reporter/driver genes by CRISPR/Cas9-mediated genome engineering
Authors: Kimura Yukiko , Hisano Yu , Kawahara Atsuo , Higashijima Shin-ichi 
Published: October 2014

AbstractThe type II bacterial CRISPR/Cas9 system is rapidly becoming popular for genome-engineering due to its simplicity, flexibility and high efficiency. Recently, targeted knock-in of a long DNA fragment via homology-independent DNA repair has been achieved in zebrafish using CRISPR/Cas9 system. This raised the possibility that knock-in transgenic zebrafish could be efficiently generated using CRISPR/Cas9. However, how widely this method can be applied for the targeting integration of foreign genes into endogenous genomic loci is unclear. Here, we report efficient generation of knock-in transgenic zebrafish that have cell-type specific Gal4 or reporter gene expression. A donor plasmid containing a heat-shock promoter was co-injected with a short guide RNA (sgRNA) targeted for genome digestion, a sgRNA targeted for donor plasmid digestion and Cas9 mRNA. We have succeeded in establishing stable knock-in transgenic fish with several different constructs for 4 genetic loci at a frequency being exceeding 25%. Due to its simplicity, design flexibility and high efficiency, we propose that CRISPR/Cas9-mediated knock-in will become a standard method for the generation transgenic zebrafish.
Log-odds sequence logos
Authors: Yu Yi-Kuo , Capra John A. , Stojmirović Aleksandar , Landsman David , Altschul Stephen F. 
Published: October 2014

Abstract
Motivation: DNA and protein patterns are usefully represented by sequence logos. However, the methods for logo generation in common use lack a proper statistical basis, and are non-optimal for recognizing functionally relevant alignment columns.
Results: We redefine the information at a logo position as a per-observation multiple alignment log-odds score. Such scores are positive or negative, depending on whether a column’s observations are better explained as arising from relatedness or chance. Within this framework, we propose distinct normalized maximum likelihood and Bayesian measures of column information. We illustrate these measures on High Mobility Group B (HMGB) box proteins and a dataset of enzyme alignments. Particularly in the context of protein alignments, our measures improve the discrimination of biologically relevant positions.
Availability and implementation: Our new measures are implemented in an open-source Web-based logo generation program, which is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/index.html . A stand-alone version of the program is also available from this site.
Contact: altschul@ncbi.nlm.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Co-Existence in the Fields? GM, Organic, and Conventional Food Crops
Authors: Thies Janice E. 
Published: October 2014

AbstractA central tenet in a free society is the freedom to choose how to conduct one’s life and manage one’s property, with the responsibility to see that these same freedoms are ensured for others. Considerable effort must be expended to enable freedom of choice among a population, particularly in contentious circumstances, and especially in open systems, such as agriculture. The emergence of conventional agriculture, which relies on the heavy use of synthetic, agrochemical inputs required that concessions/compromises be made, largely by organic farmers, to enable conventional and organic agriculture to co-exist. The advent of genetically modified (GM) crops presents unique co-existence issues, particularly in light of the natural ability of transgenic organisms to hybridize, reproduce, and spread in the environment. Means by which the integrity of organic, conventional and GM farming systems might be assured in order to preserve and ensure farmer and consumer choice is discussed.
What is theory for?
Authors: Johnson Matthew H. 
Published: October 2014

AbstractThis chapter is deliberately very simple. It should be read as an introduction, a first step, into the more complex issues discussed elsewhere in this Handbook. It defines theory, and discusses theory’s relationship to practice. It sees theory not as good or as bad, but simply as necessary. It examines the case both for and against explicit reflection on theory, and the case both for and against the existence of specifically archaeological theory. In conclusion, the chapter argues for theory as part of a wider project of learning about the world.
Art and the Literary
Authors: Fraser Hilary 
Published: October 2014

Abstract
This essay explores the creative dialogue between practices of writing, reading, and viewing in the Victorian period evident from the proliferation of new or greatly enhanced intermedial forms: illustrated books and magazines; narrative and genre paintings; pictures with accompanying texts; the portrait as an experimental literary form; fiction about art; ekphrastic poetry; and the new genre of art literature. It asks, what were the historical conditions for this extraordinary syncopation of word and image, writing and seeing? How do we understand the dynamically transformative contexts (a vastly expanding periodical press, new and diversified exhibition cultures, widening opportunities for travel) within which such visual/textual hybrids and doublings were produced and consumed, and in what ways were they constitutive of modernity? The chapter reflects upon ‘visuality’ as a nineteenth-century coinage, and the concept of ‘translation’ between media, discussing work by Frederic Leighton, Dante Gabriel Rossetti, John Ruskin, Walter Pater, and Oscar Wilde.
News Media Creation and Recreation of the Spiritual-But-Not-Religious
Authors: Drescher Elizabeth 
Published: October 2014

Abstract
This article explores news media coverage of the spiritual-but-not-religious (SBNR) population in the United States in the context of spirituality and religion. It considers how the phrase “spiritual but not religious” came into the popular lexicon before describing the demographics of the SBNR population. It then traces the development of the SBNR population from the 1980s by focusing on news reporting in national print media such as Newsweek, Time, the New York Times, the Washington Post, and the Los Angeles Times as well as online news sources such as the Huffington Post. The article also considers the relationship between Baby Boomers and the SBNR population, along with the SBNR’s political role in relation to issues of religious pluralism, identity, and tolerance following the 9/11 terrorist attacks. Finally, it discusses media representations of the SBNR as a reflection of America’s changing religious and spiritual character.
Religion in the Balkan Wars
Authors: Perica Vjekoslav 
Published: October 2014

Abstract
This article examines the roles of the Serbian Orthodox Church, the Catholic Church in Croatia, and the Islamic religious authority of Bosnia and Herzegovina in the 1991–1995 war inWestern Balkans. Religion in this case has been instrumental as a factor for galvanizing conflict and rationalizing its outcomes. The article also notes religious activities aimed at preventing violence and healing postconflict societies. The public influence of these religions began during the collapse of socialist Yugoslavia. Through the war and afterward, religions continued rebuilding resources and increasing influence. Traditional religion was blended with the new national ideologies carried out by ethnic nationalist parties allied with the ethnic majority churches established as state religions. Two decades after the Balkan war, the growing influence of these religions in public sphere coincides with the post-Yugoslav new ethnic nations’ failures in state building and democratic transition.