bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sodium iron EDTA and ascorbic acid, but not polyphenol oxidase treatment, counteract the strong inhibitory effect of polyphenols from brown sorghum on the absorption of fortification iron in young women
Authors: Cercamondi Colin I. , Egli Ines M. , Zeder Christophe , Hurrell Richard F. 
Published: August 2013

In addition to phytate, polyphenols (PP) might contribute to low Fe bioavailability from sorghum-based foods. To investigate the inhibitory effects of sorghum PP on Fe absorption and the potential enhancing effects of ascorbic acid (AA), NaFeEDTA and the PP oxidase enzyme laccase, we carried out three Fe absorption studies in fifty young women consuming dephytinised Fe-fortified test meals based on white and brown sorghum varieties with different PP concentrations. Fe absorption was measured as the incorporation of stable Fe isotopes into erythrocytes. In study 1, Fe absorption from meals with 17 mg PP (8·5 %) was higher than that from meals with 73 mg PP (3·2 %) and 167 mg PP (2·7 %;P< 0·001). Fe absorption from meals containing 73 and 167 mg PP did not differ (P= 0·9). In study 2, Fe absorption from NaFeEDTA-fortified meals (167 mg PP) was higher than that from the same meals fortified with FeSO4(4·6v.2·7 %;P< 0·001), but still it was lower than that from FeSO4-fortified meals with 17 mg PP (10·7 %;P< 0·001). In study 3, laccase treatment decreased the levels of PP from 167 to 42 mg, but it did not improve absorption compared with that from meals with 167 mg PP (4·8v.4·6 %;P= 0·4), whereas adding AA increased absorption to 13·6 % (P< 0·001). These findings suggest that PP from brown sorghum contribute to low Fe bioavailability from sorghum foods and that AA and, to a lesser extent, NaFeEDTA, but not laccase, have the potential to overcome the inhibitory effect of PP and improve Fe absorption from sorghum foods.
An Early Silurian ‘Herefordshire’ myodocope ostracod from Greenland and its palaeoecological and palaeobiogeographical significance
Authors: PERRIER VINCENT , SIVETER DAVID J. , WILLIAMS MARK , LANE PHILIP D. 
Published: August 2013

AbstractHere we record the occurrence of a new species of the Herefordshire Lagerstätte ostracod genusPaulinefrom the Lower Silurian (upper Telychian) of North Greenland.Pauline nivisissp. nov. was recovered from a limestone boulder (Pentamerus Bjerge Formation) collected south of Kap Schuchert, Washington Land. It is reasonable to transpose the palaeobiology known from the HerefordshirePauline avibella– body, limbs including swimming antennae, lateral eyes, gills and alimentary system – into the carapace of the Greenland species, which represents the oldest cylindroleberidid myodocopid and almost the oldest known myodocope, and is the first record of a Herefordshire Lagerstätte genus from outside the Welsh Borderland locality. Morphological, sedimentological and faunal evidence suggest that the Greenland species was nektobenthic. This is compatible with the notion that ostracods (specifically myodocopids) did not invade the water column until later in the Silurian, in the Wenlock and Ludlow epochs.Paulineis an Early Silurian link between ‘Baltic-British’ and North Laurentian ostracod faunas, endorsing the idea that the UK and Greenland were in close geographical proximity, near a remnant Iapetus Ocean, during late Llandovery time.
Tonsil tie simulator
Authors: Duodu J , Lesser T H J 
Published: August 2013

AbstractBackground:The surgical trainee has to acquire surgical skills in an era of reduced training hours and greater demands for efficient use of operating theatre time. Many surgical specialties are utilising model and simulation-based training to provide safe, low-pressure training opportunities for today's trainee.Method and results:This paper describes a simple, relatively inexpensive tonsillectomy model that enables the practice of tonsil removal and ligation of bleeding vessels. The model is beneficial for the patient, trainee and trainer.Conclusion:The pseudo mouth and active bleeding components of this model provide the trainee with a relatively inexpensive, realistic model with which to gain confidence and competence in the skill of ligating tonsillar blood vessels with a tonsil tie.
Prevalence and molecular epidemiology of Staphylococcus aureus in Swedish nursing homes – as revealed in the SHADES study
Authors: STARK L. , OLOFSSON M. , LÖFGREN S. , MÖLSTAD S. , LINDGREN P.-E. , MATUSSEK A. 
Published: August 2013

SUMMARYKnowledge of carriage and population dynamics of Staphylococcus aureus is crucial for infection risk assessment and to reveal transmission patterns of strains. We report the prevalence and molecular epidemiology of S. aureus in elderly people (n = 290) living in nursing homes in three cities in the south of Sweden. The overall carriage prevalence rate was 48% when results from nares (31%) and throat (34%) samples were combined. Common spa types were equally distributed but a frequent type, t160, was found only in one of the regions. Carriage of different spa types was detected in 23% of individuals and antimicrobial resistance rates were higher in S. aureus isolates from those carrying more than one spa type. Five of the 21 individuals who carried different spa types were colonized simultaneously with resistant and non-resistant strains. Seventeen per cent of the individuals carried S. aureus of the same spa type on all occasions. Methicillin resistance was not detected. In conclusion we found a high prevalence of S. aureus in this elderly population with a high rate of dual colonization with different spa types. We also found signs of institutional spread of one strain.
Campylobacteriosis in returning travellers and potential secondary transmission of exotic strains
Authors: MUGHINI-GRAS L. , SMID J. H. , WAGENAAR J. A. , DE BOER A. , HAVELAAR A. H. , FRIESEMA I. H. M. , FRENCH N. P. , GRAZIANI C. , BUSANI L. , VAN PELT W. 
Published: August 2013

SUMMARYMultilocus sequence types (STs) were determined for 232 and 737Campylobacter jejuni/coliisolates from Dutch travellers and domestically acquired cases, respectively. Putative risk factors for travel-related campylobacteriosis, and for domestically acquired campylobacteriosis caused by exotic STs (putatively carried by returning travellers), were investigated. Travelling to Asia, Africa, Latin America and the Caribbean, and Southern Europe significantly increased the risk of acquiring campylobacteriosis compared to travelling within Western Europe. Besides eating chicken, using antacids, and having chronic enteropathies, we identified eating vegetable salad outside Europe, drinking bottled water in high-risk destinations, and handling/eating undercooked pork as possible risk factors for travel-related campylobacteriosis. Factors associated with domestically acquired campylobacteriosis caused by exotic STs involved predominantly person-to-person contacts around popular holiday periods. We concluded that putative determinants of travel-related campylobacteriosis differ from those of domestically acquired infections and that returning travellers may carry several exotic strains that might subsequently spread to domestic populations even through limited person-to-person transmission.
Augmentative transcranial direct current stimulation (tDCS) in poor responder depressed patients: a follow-up study
Authors: Dell'Osso Bernardo , Dobrea Cristina , Arici Chiara , Benatti Beatrice , Ferrucci Roberta , Vergari Maurizio , Priori Alberto , Altamura A. Carlo 
Published: August 2013

ObjectivesTranscranial direct current stimulation (tDCS) is a non-invasive neurostimulation technique that has received increasing interest in the area of mood disorders over the last several years. While acute, double-blind, sham-controlled studies have already reported positive findings in terms of efficacy and safety for tDCS, follow-up data are lacking. This need prompted the present follow-up study, which assesses post-acute effects of tDCS (no maintenance stimulation was performed), in the mid-term, in a sample of major depressives.MethodsAfter completing an acute, open trial of tDCS, 23 outpatients with either major depressive disorder or bipolar disorder entered a naturalistic follow-up (T1) with clinical evaluations at one week (T2), 1 month (T3), and 3 months (T4). A quantitative analysis of Hamilton Depression Rating Scale (HAM-D), Montgomery–Asberg Depression Rating Scale (MADRS), and Young Mania Rating Scale (YMRS) total scores, through repeated measures analysis of variance (ANOVA) (T1–T4) and pairedt-test for comparing specific time points (T1–T2, T2–T3, and T3–T4), was performed. In addition, a qualitative analysis on the basis of treatment response and remission (HAM-D) was performed.ResultsEven though a progressive reduction of follow-up completers was observed from T2 to T4 (95.6% at T2, 65.2% at T3, and 47.8% at T4), the antidepressant effects of acute tDCS persisted over 3 months in almost half of the sample. Of note, no post-acute side effects emerged during the follow-up observation. The most frequent causes of drop-out from this study included major modifications in therapeutic regimen (30%) and poor adherence to follow-up visits (17%).ConclusionsIn this mid-term, open, follow-up study, tDCS showed mixed results. Further controlled studies are urgently needed to assess its effects beyond the acute phase.
A conceptual framework for improving well-being in people with a diagnosis of psychosis
Authors: Schrank B. , Riches S. , Bird V. , Murray J. , Tylee A. , Slade M. 
Published: August 2013

Background.Well-being is important for people with severe mental illness, such as psychosis. So far, no clear concept of well-being exists for this client group. A recent systematic review and narrative synthesis developed a static framework of well-being components. The present study aims to validate the static framework and to illuminate the processes by which well-being is experienced by people with psychosis.Methods.Semi-structured interviews were conducted with 23 service users with psychosis exploring their experience of well-being. Thematic analysis was used to analyse the data employing techniques taken from grounded theory to enhance the rigour of the analysis. Respondent validation was undertaken with 13 of the 23 participants.Results.Three superordinate categories of well-being were identified: current sense of self; transition to enhanced sense of self and enhanced sense of self. In the dynamic process of improving well-being the current sense of self undergoes a transition to an enhanced sense of self. The four factors influencing the transition are consistent with the static framework of well-being, hence validating the static framework. In addition, we identified three determinants of current sense of self and seven indicators of enhanced sense of self, which represent the achievement of improved well-being.Conclusions.This study provides an empirically defensible framework for understanding well-being in terms of determinants, influences and indicators. The influences are targets for interventions to improve well-being, and the indicators are outcome domains to assess the effectiveness of services in supporting well-being.
Physical impairments of monitoring trails in all optical transparent networks
Authors: Hosszu Éva , Moghaddam Ehsan Sarvghad , Tapolcai János , Mazroa Dániel 
Published: August 2013

In recent years, following the deployment of wavelength division multiplexing networks, fault detection and localisation has become a challenging issue in networks with high reliability. Optical layer monitoring schemes based on monitoring trails (m ‐trail) are considered an efficient way to localise a single fault unambiguously in all‐optical networks. In spite of the extensive work on the m ‐trail concept, the issue has not been validated from the feasibility point of view. Previous works on the m ‐trail monitoring scheme have focused mainly on algorithm design for minimising the number of monitors, however, none of them have observed that length limitations should be considered as well. The authors investigate the physical constraints of launching m ‐trails, mainly focusing on the maximum length that each m ‐trail may have and describe an algorithm that solves the length constrained m ‐trail formulation problem. Numerous simulations were implemented in a physical layer simulator for observing qualitative parameters in different m ‐trail lengths. The authors propose 15 000 km as a length limit for each m ‐trail for out‐of‐band monitoring. Finally, an algorithmic solution is provided for monitoring trail design problem satisfying these physical constraints.
Population-genomic insights into the evolutionary origin and fate of obligately asexualDaphnia pulex
Authors: Tucker Abraham E. , Ackerman Matthew S. , Eads Brian D. , Xu Sen , Lynch Michael 
Published: August 2013

SignificanceDrawing from whole-genome sequences of multiple genotypes, this study documents the molecular-genetic consequences of the loss of recombination in a microcrustacean, demonstrating that loss of heterozygosity via gene conversion-like processes is a dramatically more powerful force than accumulation of new mutations.
Língua de Preto, the Basic Variety at the root of West African Portuguese Creoles
Authors: Kihm Alain , Rouge Jean-Louis 
Published: August 2013

Língua de Preto
falar Guiné

In the first part of the study (sections 1–4), we substantiate our claim that such literary representations are indeed reliable renditions of the linguistic medium African slaves in Portugal actually used in their interactions with the white population and among themselves. We propose a historical scenario to account for the ‘return’ of LdP to Africa, i.e. Senegambia, where it soon became the lingua franca of trade between Portuguese expatriates and the local populations. From this lingua franca, creoles subsequently arose.
In the second part (sections 5–11), we propose an extensive outline of LdP grammar such as we are able to retrieve from the corpus. Comparisons with present-day WAPCs are attempted.
We conclude (sections 12–13) that the availability of such historical testimonies indeed gives us the exceptional opportunity of gaining some first-hand knowledge of the transitional medium that necessarily separates a lexifier language from ‘its’ creole(s). The fact that this transitional medium, we think, looks much more like a BV than a destructured jargon lends support to the assumption that untutored L2 acquisition by adults played a crucial role in creole formation.
The transparency of creoles
Authors: Leufkens Sterre 
Published: August 2013

In this article I propose that creoles are relatively transparent compared to their source languages. This means that they display more one-to-one relations between meaning and form. Transparency should be distinguished from the concepts of simplicity, ease of acquisition, and regularity. Definitions of these notions are given and it is shown how they have been mixed up in earlier literature.
The transparency of creoles is explained as a result of language contact. When people speaking radically different languages communicate, they tend to use maximally intelligible forms, i.e. transparent forms. The repeated selection of transparent over opaque forms will lead to the formation of a relatively transparent language. Hence, creoles are predicted to be either as transparent as or more transparent than their source languages.
An empirical study is performed to test this prediction. The transparency of four contact languages and their sub- and superstrates is measured by checking them on a list of non-transparent features. It turns out that they all exhibit opaque structures, but that there is a striking absence of so called form-based forms: linguistic elements and rules that are not motivated pragmatically or semantically. This indicates that such ‘empty’ forms are lost during intense language contact.
On the non-creole basis for Afro-Bolivian Spanish
Authors: Sessarego Sandro 
Published: August 2013

This article provides a sociohistorical and linguistic account for the development of Afro-Bolivian Spanish (ABS), an Afro-Hispanic vernacular spoken in Los Yungas, Department of La Paz, Bolivia. Previous research has indicated that ABS might be the descendent of an Afro-Hispanic pidgin (Lipski 2008), which first creolized in colonial times and eventually decreolized due to contact with Spanish after the Bolivian Land Reform of 1952.
The present study argues that ABS was probably never a creole, but rather a language relatively close to Spanish from its inception. The basis on which this claim is built consists of sociodemographic and linguistic data. The findings strongly indicate that the historical conditions for a creole language to emerge were not in place in Bolivia for the period under analysis (15th–19th century).
Vulnerability of Primary Care Organizations to the National Health Service Reform in England
Authors: Iparraguirre José , Gentry Tom , Peña Diego 
Published: August 2013

AbstractWe study how ready or vulnerable each Primary Care Organization (PCO) in England was in 2010 to the National Health Service reforms announced in the Government white paper Equity and Excellence: Liberating the NHS, later enacted by the Health and Social Care Act 2012. We define vulnerability as a combination of latent variables and present a novel methodological approach to measuring organizational and wider impacts of health policy reforms. Areas with higher concentrations of older people were not correlated with vulnerability except where there was also deprivation. This contrasts with wide‐spread qualitative and quantitative evidence of sub‐optimal care of older people within the health service. This suggests there may be an over‐reliance on using activity, which was proportionately higher in the least vulnerable areas, to determine funding and quality markers rather than outcomes. A risk of the reform process could be a negative impact on deprived areas which appear to be financially less secure and more likely to have long‐established health inequalities.
A Turing test for artificial expression data
Authors: Maier Robert , Zimmer Ralf , Küffner Robert 
Published: August 2013

Abstract
Motivation: The lack of reliable, comprehensive gold standards complicates the development of many bioinformatics tools, particularly for the analysis of expression data and biological networks. Simulation approaches can provide provisional gold standards, such as regulatory networks, for the assessment of network inference methods. However, this just defers the problem, as it is difficult to assess how closely simulators emulate the properties of real data.
Results: In analogy to Turing’s test discriminating humans and computers based on responses to questions, we systematically compare real and artificial systems based on their gene expression output. Different expression data analysis techniques such as clustering are applied to both types of datasets. We define and extract distributions of properties from the results, for instance, distributions of cluster quality measures or transcription factor activity patterns. Distributions of properties are represented as histograms to enable the comparison of artificial and real datasets. We examine three frequently used simulators that generate expression data from parameterized regulatory networks. We identify features distinguishing real from artificial datasets that suggest how simulators could be adapted to better emulate real datasets and, thus, become more suitable for the evaluation of data analysis tools.
Availability: See http://www2.bio.ifi.lmu.de/∼kueffner/attfad/ and the supplement for precomputed analyses; other compendia can be analyzed via the CRAN package attfad. The full datasets can be obtained from http://www2.bio.ifi.lmu.de/∼kueffner/attfad/data.tar.gz.
Contact: robert.kueffner@bio.ifi.lmu.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Incorporating prior knowledge into Gene Network Study
Authors: Wang Zixing , Xu Wenlong , San Lucas F. Anthony , Liu Yin 
Published: August 2013

AbstractMotivation: A major goal in genomic research is to identify genes that may jointly influence a biological response. From many years of intensive biomedical research, a large body of biological knowledge, or pathway information, has accumulated in available databases. There is a strong interest in leveraging these pathways to improve the statistical power and interpretability in studying gene networks associated with complex phenotypes. This prior information is a valuable complement to large-scale genomic data such as gene expression data generated from microarrays. However, it is a non-trivial task to effectively integrate available biological knowledge into gene expression data when reconstructing gene networks.Results: In this article, we developed and applied a Lasso method from a Bayesian perspective, a method we call prior Lasso (pLasso), for the reconstruction of gene networks. In this method, we partition edges between genes into two subsets: one subset of edges is present in known pathways, whereas the other has no prior information associated. Our method assigns different prior distributions to each subset according to a modified Bayesian information criterion that incorporates prior knowledge on both the network structure and the pathway information. Simulation studies have indicated that the method is more effective in recovering the underlying network than a traditional Lasso method that does not use the prior information. We applied pLasso to microarray gene expression datasets, where we used information from the Pathway Commons (PC) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) as prior information for the network reconstruction, and successfully identified network hub genes associated with clinical outcome in cancer patients.Availability: The source code is available at http://nba.uth.tmc.edu/homepage/liu/pLasso.Contact: Yin.Liu@uth.tmc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions
Authors: Shugay Mikhail , Ortiz de Mendíbil Iñigo , Vizmanos José L. , Novo Francisco J. 
Published: August 2013

Abstract
Motivation: Gene fusions resulting from chromosomal aberrations are an important cause of cancer. The complexity of genomic changes in certain cancer types has hampered the identification of gene fusions by molecular cytogenetic methods, especially in carcinomas. This is changing with the advent of next-generation sequencing, which is detecting a substantial number of new fusion transcripts in individual cancer genomes. However, this poses the challenge of identifying those fusions with greater oncogenic potential amid a background of ‘passenger’ fusion sequences.
Results: In the present work, we have used some recently identified genomic hallmarks of oncogenic fusion genes to develop a pipeline for the classification of fusion sequences, namely, Oncofuse. The pipeline predicts the oncogenic potential of novel fusion genes, calculating the probability that a fusion sequence behaves as ‘driver’ of the oncogenic process based on features present in known oncogenic fusions. Cross-validation and extensive validation tests on independent datasets suggest a robust behavior with good precision and recall rates. We believe that Oncofuse could become a useful tool to guide experimental validation studies of novel fusion sequences found during next-generation sequencing analysis of cancer transcriptomes.
Availability and implementation: Oncofuse is a naive Bayes Network Classifier trained and tested using Weka machine learning package. The pipeline is executed by running a Java/Groovy script, available for download at www.unav.es/genetica/oncofuse.html.
Contact: fnovo@unav.es
Supplementary information: Supplementary data are available at Bioinformatics online.