bluuebunny/crossref_metadata_2025_split huggingface dataset:
INRICH: interval-based enrichment analysis for genome-wide association studies
Authors: Lee Phil H. , O'Dushlaine Colm , Thomas Brett , Purcell Shaun M. 
Published: April 2012

Abstract
Summary: Here we present INRICH (INterval enRICHment analysis), a pathway-based genome-wide association analysis tool that tests for enriched association signals of predefined gene-sets across independent genomic intervals. INRICH has wide applicability, fast running time and, most importantly, robustness to potential genomic biases and confounding factors. Such factors, including varying gene size and single-nucleotide polymorphism density, linkage disequilibrium within and between genes and overlapping genes with similar annotations, are often not accounted for by existing gene-set enrichment methods. By using a genomic permutation procedure, we generate experiment-wide empirical significance values, corrected for the total number of sets tested, implicitly taking overlap of sets into account. By simulation we confirm a properly controlled type I error rate and reasonable power of INRICH under diverse parameter settings. As a proof of principle, we describe the application of INRICH on the NHGRI GWAS catalog.
Availability: A standalone C++ program, user manual and datasets can be freely downloaded from: http://atgu.mgh.harvard.edu/inrich/.
Contact: shaun@atgu.mgh.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Stability of gene rankings from RNAi screens
Authors: Siebourg Juliane , Merdes Gunter , Misselwitz Benjamin , Hardt Wolf-Dietrich , Beerenwinkel Niko 
Published: April 2012

Abstract
Motivation: Genome-wide RNA interference (RNAi) experiments are becoming a widely used approach for identifying intracellular molecular pathways of specific functions. However, detecting all relevant genes involved in a biological process is challenging, because typically only few samples per gene knock-down are available and readouts tend to be very noisy. We investigate the reliability of top scoring hit lists obtained from RNAi screens, compare the performance of different ranking methods, and propose a new ranking method to improve the reproducibility of gene selection.
Results: The performance of different ranking methods is assessed by the size of the stable sets they produce, i.e. the subsets of genes which are estimated to be re-selected with high probability in independent validation experiments. Using stability selection, we also define a new ranking method, called stability ranking, to improve the stability of any given base ranking method. Ranking methods based on mean, median, t-test and rank-sum test, and their stability-augmented counterparts are compared in simulation studies and on three microscopy image RNAi datasets. We find that the rank-sum test offers the most favorable trade-off between ranking stability and accuracy and that stability ranking improves the reproducibility of all and the accuracy of several ranking methods.
Availability: Stability ranking is freely available as the R/Bioconductor package staRank at http://www.cbg.ethz.ch/software/staRank.
Contact: niko.beerenwinkel@bsse.ethz.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Implicit Substantive Assumptions Underlying the Generalized Event Count Estimator
Authors: Achen Christopher H. 
Published: April 2012

The Generalized Event Count (GEC) estimator (King 1989a) is a statistical model for event counts. Its great attraction is that it provides a general likelihood function for count data, regardless of whether the data come from a Poisson, binomial, or negative binomial distribution. In consequence, it has been used in several recent statistical studies of event counts in the social sciences.Underlying the GEC, however, are unorthodox substantive assumptions about how the event counts have been generated (Amato, this volume). This paper gives some simple examples in which the GEC logic is clearly visible, and it shows how failures of the implicit assumptions can lead to erroneous GEC coefficient estimates and standard errors.
Recantation or Any old ω-sequence would do after all
Authors: BENACERRAF PAUL 
Published: April 2012

Abstract
I once argued (in ‘What Numbers Could Not Be’) that an adequate account of the numbers and our arithmetic practice must satisfy not only the conditions usually recognized to be necessary: (a) identify some w-sequence as the numbers, and (b) correctly characterize the cardinality relation that relates a set to a member of that sequence as its cardinal number—it must also satisfy a third condition: the ‘&lt;’ of the sequence must be recursive. This paper argues that adding this further condition was a mistake—any ω-sequence would do, no matter how undecidable its ‘&lt;’ relation.
A novel and conserved protein AHO‐3 is required for thermotactic plasticity associated with feeding states in Caenorhabditis elegans
Authors: Nishio Nana , Mohri‐Shiomi Akiko , Nishida Yukuo , Hiramatsu Naoya , Kodama‐Namba Eiji , Kimura Kotaro D. , Kuhara Atsushi , Mori Ikue 
Published: April 2012

Although a large proportion of molecules expressed in the nervous system are conserved from invertebrate to vertebrate, functional properties of such molecules are less characterized. Here, we show that highly conserved hydrolase AHO‐3 acts as a novel regulator of starvation‐induced thermotactic plasticity in Caenorhabditis elegans. As wild‐type animals, aho‐3 mutants migrated to the cultivation temperature on a linear thermal gradient after cultivation at a particular temperature with food. Whereas wild‐type animals cultivated under food‐deprived condition showed dispersed distribution on the gradient, aho‐3 mutants exhibited tendency to migrate toward higher temperature. Such an abnormal behavior was completely rescued by the expression of human homologue of AHO‐3, indicating that the molecular function of AHO‐3 is highly conserved between nematode and human. The behavioral regulation by AHO‐3 requires the N‐terminal cysteine cluster, which ensures the proper subcellular localization of AHO‐3 to sensory endings. Double‐mutant analysis suggested that AHO‐3 acts in the same pathway with ODR‐3, a heterotrimeric G protein alpha subunit. Our results unveiled a novel neural protein in C. elegans, confirming its conserved role in behavioral regulation.
Inhibition of lipid oxidation in anchovy oil (Engraulis encrasicholus) enriched emulsions during refrigerated storage
Authors: Gokoglu Nalan , Topuz Osman Kadir , Buyukbenli Hanife Aydan , Yerlikaya Pinar 
Published: April 2012

SummaryThe aim of this study was to produce a functional emulsion product enriched with anchovy (Engraulis encrasicholus) oil. Tomato and garlic extracts were added to perform oxidative stability. Tomato and garlic extracts were added to avoid oxidative degradation in such a product. The plant extracts delayed the formation of primary and secondary oxidation products. The value of conjugated diens (3.07 ± 0.15) was markedly low in the emulsions containing garlic extract at the end of the storage period. The p–Av values of the emulsions treated with the extracts were significantly (P < 0.01) lower than untreated samples. TBARS formation increased slightly, therewithal statistical difference was not observed in the samples treated with garlic extract during the storage. Strong odour and flavour of the garlic suppressed the odour of fish oil. The panellists preferred the flavour, odour and aroma characteristics of the samples treated with the extracts.
‘Being in it together’: living with a partner receiving deep brain stimulation for advanced Parkinson’s disease – a hermeneutic phenomenological study
Authors: Haahr Anita , Kirkevold Marit , Hall Elisabeth O.C. , Østergaard Karen 
Published: April 2012

haahr a., kirkevold m., hall e.o.c. & østergaard k. (2012) ‘Being in it together’: living with a partner receiving deep brain stimulation for advanced Parkinson’s disease – a hermeneutic phenomenological study. Journal of Advanced Nursing69(2), 338–347. doi: 10.1111/j.1365‐2648.2012.06012.xAbstractAim.  This article is a report of an exploration of the lived experience of being a spouse to a person living with advanced Parkinson’s disease, before and during the first year of deep brain stimulation.Background.  Parkinson’s disease is a chronic progressive neurodegenerative disease. It has a profound impact on the everyday life for patients and spouses. Deep brain stimulation is offered with the aim of reducing symptoms of Parkinson’s disease. The treatment is known to improve quality of life for patients, but little is known of how spouses experience life following their partners’ treatment.Design.  A longitudinal interview study with a hermeneutic phenomenological approach.Method.  Ten spouses were included in the study. Data were gathered in 2007–2008, through qualitative in‐depth interviews with spouses once before and three times during the first year of their partners’ treatment with Deep Brain Stimulation. Data collection and data analysis were influenced by the hermeneutic phenomenological methodology of van Manen.Findings.  The uniting theme ‘Solidarity – the base for joined responsibility and concern’ was the foundation for the relationship between spouses and their partners. Before treatment, the theme ‘Living in partnership’ was dominant. After treatment two dichotomous courses were described ‘A sense of freedom embracing life’ and ‘The challenge of changes and constraint’.Conclusion.  Spouses are deeply involved in their partners’ illness and their experience of life is highly affected by their partners’ illness, both before and after deep brain stimulation. The relationship is founded on solidarity and responsibility, which emphasizes spouses’ need to be informed and involved in the process following Deep Brain Stimulation.
Intensive care unit nurses’ perceptions of patient participation in the acute phase of chronic obstructive pulmonary disease exacerbation: an interview study
Authors: Kvangarsnes Marit , Torheim Henny , Hole Torstein , Öhlund Lennart S. 
Published: April 2012

kvangarsnes m., torheim h., hole t. & öhlund l.s. (2012) Intensive care unit nurses’ perceptions of patient participation in the acute phase of chronic obstructive pulmonary disease exacerbation: an interview study. Journal of Advanced Nursing69(2), 425–434. doi: 10.1111/j.1365‐2648.2012.06021.xAbstractAim.  To report a study conducted to explore intensive care unit nurses’ perceptions of patient participation in the acute phase of chronic obstructive pulmonary disease exacerbation.Background.  An acute exacerbation is a life‐threatening situation, which patients often consider to be extremely frightening. Healthcare personnel exercise considerable power in this situation, which challenges general professional notions of patient participation.Design.  Critical discourse analysis.Methods.  In the autumn of 2009, three focus group interviews with experienced intensive care nurses were conducted at two hospitals in western Norway. Two groups had six participants each, and one group had five (N = 17). The transcribed interviews were analysed by means of critical discourse analysis.Findings.  The intensive care nurses said that an exacerbation is often an extreme situation in which healthcare personnel are exercising a high degree of control and power over patients. Patient participation during exacerbation often takes the form of non‐involvement. The participating nurses attached great importance to taking a sensitive approach when meeting patients. The nurses experienced challenging ethical dilemmas.Conclusion.  This study shows that patient participation should not be understood in universal terms, but rather in relation to a specific setting and the interactions that occur in this setting. Healthcare personnel must develop skill, understanding, and competence to meet these challenging ethical dilemmas. A collaborative inter‐professional approach between physicians and nurses is needed to meet the patients’ demand for involvement.
A Bayesian analysis of gene flow from crops to their wild relatives: cultivated (Lactuca sativa L.) and prickly lettuce (L. serriola L.) and the recent expansion of L. serriola in Europe
Authors: UWIMANA BRIGITTE , D’ANDREA LUIGI , FELBER FRANÇOIS , HOOFTMAN DANNY A. P. , Den NIJS HANS C. M. , SMULDERS MARINUS J. M. , VISSER RICHARD G. F. , Van De WIEL CLEMENS C. M. 
Published: April 2012

AbstractInterspecific gene flow can lead to the formation of hybrid populations that have a competitive advantage over the parental populations, even for hybrids from a cross between crops and wild relatives. Wild prickly lettuce (Lactuca serriola) has recently expanded in Europe and hybridization with the related crop species (cultivated lettuce, L. sativa) has been hypothesized as one of the mechanisms behind this expansion. In a basically selfing species, such as lettuce, assessing hybridization in natural populations may not be straightforward. Therefore, we analysed a uniquely large data set of plants genotyped with SSR (simple sequence repeat) markers with two programs for Bayesian population genetic analysis, STRUCTURE and NewHybrids. The data set comprised 7738 plants, including a complete genebank collection, which provided a wide coverage of cultivated germplasm and a fair coverage of wild accessions, and a set of wild populations recently sampled across Europe. STRUCTURE analysis inferred the occurrence of hybrids at a level of 7% across Europe. NewHybrids indicated these hybrids to be advanced selfed generations of a hybridization event or of one backcross after such an event, which is according to expectations for a basically selfing species. These advanced selfed generations could not be detected effectively with crop‐specific alleles. In the northern part of Europe, where the expansion of L. serriola took place, the fewest putative hybrids were found. Therefore, we conclude that other mechanisms than crop/wild gene flow, such as an increase in disturbed habitats and/or climate warming, are more likely explanations for this expansion.
Population size and major valleys explain microsatellite variation better than taxonomic units for caribou in western Canada
Authors: SERROUYA ROBERT , PAETKAU DAVID , McLELLAN BRUCE N. , BOUTIN STAN , CAMPBELL MITCH , JENKINS DEBORAH A. 
Published: April 2012

AbstractIdentifying conservation units below the species level is becoming increasingly important, particularly when limited resources necessitate prioritization for conservation among such units. This problem is exemplified with caribou, a mammal with a circum‐Arctic distribution that is exposed to a broad spectrum of ecological conditions, but is also declining in many parts of its range. We used microsatellite markers to evaluate the suitability of existing intra‐specific taxonomic designations to act as population units for conservation and contrasted this with landscape features that were independent of taxonomy. We also quantified the relationship between genetic differentiation and subpopulation size, a factor that has been under‐represented in landscape genetic research. Our data set included three subspecies and three ecotypes of caribou that varied in population size by five orders of magnitude. Our results indicated that genetic structure did not correspond to existing taxonomic designation, particularly at the level of ecotype. Instead, we found that major valleys and population size were the strongest factors associated with substructure. There was a negative exponential relationship between population size and FST between pairs of adjacent subpopulations, suggesting that genetic drift was the mechanism causing the structure among the smallest subpopulations. A genetic assignment test revealed that movement among subpopulations was a fraction of the level needed to stabilize smaller subpopulations, indicating little chance for demographic rescue. Such results may be broadly applicable to landscape genetic studies, because population size and corresponding rates of drift have the potential to confound interpretations of landscape effects on population structure.
Reprogramming of carbon metabolism by the transcriptional activators AcuK and AcuM in Aspergillus nidulans
Authors: Suzuki Yumi , Murray Sandra L. , Wong Koon Ho , Davis Meryl A. , Hynes Michael J. 
Published: April 2012

SummaryThe ability of fungi to use carbon sources metabolized via the TCA cycle requires gluconeogenesis. In Aspergillus nidulans the AcuK and AcuM transcription factors regulate the expression of the gluconeogenic genes acuF, encoding phosphoenolpyruvate carboxykinase, and acuG, encoding fructose‐1,6‐bisphosphatase. Expressed proteins containing the AcuK/AcuM N‐terminal DNA‐binding domains bind together in vitro to motifs containing repeats of CGG separated by seven bases (CCGN7CCG) and the functionality of these sequences was verified in vivo by acuF–lacZ reporter studies. Chromatin immunoprecipitation analysis showed inter‐dependent DNA binding of the proteins to the promoters of gluconeogenic genes in vivo independent of the carbon source. Deletion of the mdhC gene encoding a cytoplasmic/peroxisomal malate dehydrogenase showed that this activity is not essential for gluconeogenesis and indicated that induction of AcuK/AcuM regulated genes might result from malate accumulation. Deletion of the gene for the alternative oxidase did not affect growth on gluconeogenic carbon sources; however, expression was absolutely dependent on AcuK and AcuM. Orthologues of AcuK and AcuM, are present in a wide range of fungal taxa and the CCGN7CCG motif is present in the 5′ of many genes involved in gluconeogenesis indicating a fundamental role for these transcription factors in reprogramming fungal carbon metabolism.
Street‐level workers’ criteria for identifying indigents to be exempted from user fees in Burkina Faso
Authors: Ridde V. , Sombie I. 
Published: April 2012

AbstractObjectives  Universal healthcare coverage cannot be achieved in Africa as long as the indigent, the poorest, are unable to access healthcare systems. This study was carried out in Burkina Faso to obtain street‐level workers’ perspectives on what criteria should be used to select indigents to be exempted from user fees.Methods  Two group consensus techniques were used (Delphi and Concept Mapping). The participants were nurses (CM; n = 24), midwives (CM; n = 23) from a rural district and Social Action agents (CM; n = 31) and healthcare workers (Delphi n = 23) in training at two national schools.Results  Altogether, 446 criteria were proposed. The nurses put forward criteria related to being ill without support and being a victim of society. The midwives focused more on the disabled poor and those who were ill and unsupported. The healthcare workers in training mentioned disabled persons and the elderly with no family support. The Social Action agents spoke about vulnerability related to illness or disability and the fact of being excluded or being a disaster victim.Conclusions  These criteria proposed by street‐level workers add to other studies conducted in Burkina Faso and should help the State to improve indigents’ access to care.
Acquired patch‐type blue nevus with overlying vitiligo: a case report
Authors: Wang Peng , Cheng Yan , Yang Hanjun , Ran Yuping 
Published: April 2012

AbstractBackground  Blue nevi are a group of congenital and acquired dermal melanocytoses characterized by a blue‐gray appearance on the skin. The common blue nevus and cellular blue nevus are the most common subtypes. Patch‐type blue nevus is rather rare.Observations  We describe a 77‐year‐old Chinese male with a 6 × 8‐cm non‐palpable blue patch overlaid by a depigmented patch on the back of the left scalp. Histological examination of the blue‐gray patch showed numerous spindled and elongated bipolar dendritic melanocytes in the upper reticular dermis and an absence of epidermal melanocytes. Immunohistochemically, these dendritic melanocytes were positive for S‐100 and HMB‐45. A diagnosis of a patch‐type blue nevus with overlying vitiligo was made after the biopsy.Conclusions  The patient presents an unusual manifestation of patch‐type blue nevi with overlying vitiligo. To the best of our knowledge, these features have not been previously described.
Prevalence survey of dermatological conditions in mountainous north India
Authors: Grills Nathan , Grills Claire , Spelman Tim , Stoove Mark , Hellard Margaret , El‐Hayek Carol , Singh Rajesh 
Published: April 2012

AbstractBackground Dermatological conditions account for a substantial proportion of the global burden of disease in low and middle income countries (Bickers D, Lim H, Margolis D, et al. The burden of skin diseases: 2004. A joint project of the American Academy of Dermatology Association and the Society for Investigative Dermatology. J Am Acad Dermatol 2006; 55: 490–500) and place major pressures on primary healthcare centers (Satimia F, McBride S, Leppard B. Prevalence of skin disease in rural Tanzania and factors influencing the choice of health care, modern or traditional. Arch Dermatol 1998; 134: 1363–1366). In mountainous North India, where limited resources are available for skin care, no dermatological data exists on prevalence, treatment patterns, or associations. The study aimed to measure prevalence and treatment of dermatological conditions and associated factors in Uttarakhand so to inform delivery of dermatological care and prevention programs in India.Methods Single stage cluster randomized sampling generated seven cluster units or villages. Household members (n = 1275) from each cluster were interviewed, and where possible, examined and offered treatment.Results Dermatological conditions were prevalent (45.3%), with 33% being of infectious etiology. Atopic dermatitis (9.2%), scabies (4.4%), tinea corporis (4.1%), and pityriasis alba (3.6%) were most prevalent. Multivariate analysis showed that cohabitation with animals (OR = 1.62, 95% CI‐1.35, 1.95) was a predictor of any skin diseases. A health practitioner was not consulted in 64.7% of dermatological conditions, and where consulted, approximately 69% received inappropriate or ineffective treatments. Excessive spending on dermatological care was commonplace. Limitations associated with cross‐sectional cluster methodology included the underrepresentation of seasonal conditions and conditions of short duration. Caste proved difficult to randomize across clusters given villages were often composed according to caste.Conclusion These results demonstrate a high prevalence of dermatological conditions and a pattern of conditions somewhat distinctive to this mountainous area of North India. These findings will assist development of appropriate and cost‐effective dermatological services in these mountainous regions.