bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliability and validity of a semi-quantitative FFQ for sodium intake in low-income and low-literacy Brazilian hypertensive subjects
Authors: Ferreira-Sae Maria-Carolina S , Gallani Maria-Cecilia BJ , Nadruz Wilson , Rodrigues Roberta CM , Franchini Kleber G , Cabral Poliana C , Sales Maria Lilian 
Published: May 2009

AbstractObjectiveTo assess the reliability and validity of an FFQ to evaluate dietary patterns of Na consumption among low-income and low-literacy Brazilian hypertensive subjects.DesignThe initial FFQ was submitted to content analysis with the pre-test administered to fifteen subjects. Reliability was evaluated according to the reproducibility criterion, with interviewer administration of the FFQ twice within a 15 d interval. Validity was assessed against a 24 h recall (132 subjects), a 3 d diet record (121 subjects) and a biomarker (24 h urinary Na; 121 subjects). To test the correlation with the biomarker, discretionary salt was added to the FFQ Na values.SettingA large urban teaching hospital in south-eastern Brazil.SubjectsThe study was based on 132 randomly selected subjects (eighty-three women and forty-nine men) aged 18 to 85 years.ResultsKappa coefficients ranged from 0·79 to 0·98, confirming the reproducibility of the FFQ. There was no correlation between urinary Na excretion, the FFQ and the 24 h recall for the general sample, although significant correlations had been observed when methods were summed up (24 h recall + discretionary salt + FFQ; 0·32, P = 0·01). The addition of discretionary salt significantly improved the biomarker-based FFQ validity, with correlation coefficients varying from 0·19 (general sample) to 0·31 (female sub-sample).ConclusionsThe developed FFQ demonstrated satisfactory evidence of validity and reliability and can be used as an important complementary tool for the evaluation of Na intake among Brazilian hypertensive subjects.
Sweets and sugar-sweetened soft drink intake in childhood in relation to adult BMI and overweight. The Cardiovascular Risk in Young Finns Study
Authors: Nissinen Katja , Mikkilä Vera , Männistö Satu , Lahti-Koski Marjaana , Räsänen Leena , Viikari Jorma , Raitakari Olli T 
Published: May 2009

AbstractObjectiveTo investigate the associations of BMI and overweight in adulthood with consumption of sweets and sugar-sweetened soft drinks in childhood and with the change in consumption between childhood and adulthood.DesignLongitudinal 21-year follow-up study of Finnish children and adolescents from childhood to adulthood.SettingThe Cardiovascular Risk in Young Finns Study, comprising participants from both eastern and western Finland.SubjectsBoys (n967) and girls (n1172) aged 3–18 years at baseline in 1980.ResultsThe increase in consumption of sugar-sweetened soft drinks from childhood to adulthood was directly associated with BMI in adulthood in women (b= 0·45,P= 0·0001) but not in men. In women, BMI increased by 0·45 kg/m2for every 10-unit increase per month. Consumption of sweets and sugar-sweetened soft drinks in childhood and adolescence was not associated with BMI in adulthood. The change in consumption of sweets was not associated with BMI in adulthood. The increase in the consumption of sugar-sweetened soft drinks from childhood to adulthood was associated with being overweight (OR = 1·90, 95 % CI 1·38, 2·61) in women, but not in men. No association was found between overweight (BMI ≥ 25 kg/m2) in adulthood and consumption of sweets in childhood or the change in consumption from childhood to adulthood.ConclusionsWe conclude that direct associations exist between adulthood overweight and BMI and an increase in consumption of sugar-sweetened soft drinks in women. Thus sugar-sweetened soft drinks consumption may be important when considering weight management in women.
Unexpectedly high early prevalence of anaemia in 6-month-old breast-fed infants in rural Bangladesh
Authors: Shakur Yaseer A , Choudhury Nuzhat , Ziauddin Hyder SM , Zlotkin Stanley H 
Published: May 2009

AbstractObjectiveTo determine the prevalence of anaemia and maternal and infant factors associated with Hb values in infants at 6 months of age in rural Bangladesh.DesignInfants (born to mothers supplemented with Fe–folic acid from mid-pregnancy) were visited at birth and 6 months of age. Mothers’ anthropometric status, and infants’ birth weight, gestational age at birth, weight and Hb concentration at 6 months were measured. Household socio-economic and demographic data, infant feeding practices and health status were collected using a pre-tested structured questionnaire.SettingRural Bangladesh.SubjectsFour hundred and two infants.ResultsFor the total cohort (n402), the range of anaemia prevalence values was from 30·6 % using a cut-off value of Hb < 95 g/l to 71·9 % using a value of Hb < 110 g/l. Birth weight and month of birth were the only factors positively associated with infant Hb in a linear regression model (P= 0·008 and 0·011, respectively).ConclusionsThere was an unexpectedly high prevalence of anaemia in infants at 6 months of age, before the assumed period of vulnerability. Hb at this age tended to be higher in those with higher birth weight. We also found a season effect on Hb, as it tended to be higher as the study progressed. The high prevalence of anaemia at such an early age needs to be addressed to minimize the disease’s long-term consequences.
Acceptability and use of iron and iron-alloy cooking pots: implications for anaemia control programmes
Authors: Tripp Katherine , MacKeith Nancy , Woodruff Bradley A , Talley Leisel , Mselle Laurent , Mirghani Zahra , Abdalla Fathia , Bhatia Rita , Seal Andrew J 
Published: May 2009

AbstractObjectiveTo evaluate the acceptability of iron and iron-alloy cooking pots prior to an intervention trial and to investigate factors affecting retention and use.DesignPre-trial research was conducted on five types of iron and iron-alloy pots using focus group discussions and a laboratory evaluation of Fe transfer during cooking was undertaken. Usage and retention during the subsequent intervention trial were investigated using focus group discussions and market monitoring.SettingThree refugee camps in western Tanzania.SubjectsRefugee health workers were selected for pre-trial research. Mothers of children aged 6–59 months participated in the investigation of retention and use.ResultsPre-trial research indicated that the stainless steel pot would be the only acceptable type for use in this population due to excessive rusting and/or the high weight of other types. Cooking three typical refugee dishes in stainless steel pots led to an increase in Fe content of 3·2 to 17·1 mg/100 g food (P < 0·001). During the trial, the acceptability of the stainless steel pots was lower than expected owing to difficulties with using, cleaning and their utility for other purposes. Households also continued to use their pre-existing pots, and stainless steel pots were sold to increase household income.ConclusionsPre-trial research led to the selection of a stainless steel pot that met basic acceptability criteria. The relatively low usage reported during the trial highlights the limitations of using high-value iron-alloy cooking pots as an intervention in populations where poverty and the availability of other pots may lead to selling.
CP-logic: A language of causal probabilistic events and its relation to logic programming
Authors: VENNEKENS JOOST , DENECKER MARC , BRUYNOOGHE MAURICE 
Published: May 2009

AbstractThis paper develops a logical language for representing probabilistic causal laws. Our interest in such a language is two-fold. First, it can be motivated as a fundamental study of the representation of causal knowledge. Causality has an inherent dynamic aspect, which has been studied at the semantical level by Shafer in his framework of probability trees. In such a dynamic context, where the evolution of a domain over time is considered, the idea of a causal law as something which guides this evolution is quite natural. In our formalization, a set of probabilistic causal laws can be used to represent a class of probability trees in a concise, flexible and modular way. In this way, our work extends Shafer's by offering a convenient logical representation for his semantical objects. Second, this language also has relevance for the area of probabilistic logic programming. In particular, we prove that the formal semantics of a theory in our language can be equivalently defined as a probability distribution over the well-founded models of certain logic programs, rendering it formally quite similar to existing languages such as ICL or PRISM. Because we can motivate and explain our language in a completely self-contained way as a representation of probabilistic causal laws, this provides a new way of explaining the intuitions behind such probabilistic logic programs: we can say precisely which knowledge such a program expresses, in terms that are equally understandable by a non-logician. Moreover, we also obtain an additional piece of knowledge representation methodology for probabilistic logic programs, by showing how they can express probabilistic causal laws.
Fuzzy linguistic logic programming and its applications
Authors: LE VAN HUNG , LIU FEI , TRAN DINH KHANG 
Published: May 2009

AbstractThe paper introduces fuzzy linguistic logic programming, which is a combination of fuzzy logic programming, introduced by P. Vojtáš, and hedge algebras in order to facilitate the representation and reasoning on human knowledge expressed in natural languages. In fuzzy linguistic logic programming, truth values are linguistic ones, e.g., VeryTrue, VeryProbablyTrue and LittleFalse, taken from a hedge algebra of a linguistic truth variable, and linguistic hedges (modifiers) can be used as unary connectives in formulae. This is motivated by the fact that humans reason mostly in terms of linguistic terms rather than in terms of numbers, and linguistic hedges are often used in natural languages to express different levels of emphasis. The paper presents: (a) the language of fuzzy linguistic logic programming; (b) a declarative semantics in terms of Herbrand interpretations and models; (c) a procedural semantics which directly manipulates linguistic terms to compute a lower bound to the truth value of a query, and proves its soundness; (d) a fixpoint semantics of logic programs, and based on it, proves the completeness of the procedural semantics; (e) several applications of fuzzy linguistic logic programming; and (f) an idea of implementing a system to execute fuzzy linguistic logic programs.
Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria
Authors: Penn Kevin , Jenkins Caroline , Nett Markus , Udwary Daniel W , Gontang Erin A , McGlinchey Ryan P , Foster Brian , Lapidus Alla , Podell Sheila , Allen Eric E , Moore Bradley S , Jensen Paul R 
Published: May 2009

AbstractGenomic islands have been shown to harbor functional traits that differentiate ecologically distinct populations of environmental bacteria. A comparative analysis of the complete genome sequences of the marine Actinobacteria Salinispora tropica and Salinispora arenicola reveals that 75% of the species-specific genes are located in 21 genomic islands. These islands are enriched in genes associated with secondary metabolite biosynthesis providing evidence that secondary metabolism is linked to functional adaptation. Secondary metabolism accounts for 8.8% and 10.9% of the genes in the S. tropica and S. arenicola genomes, respectively, and represents the major functional category of annotated genes that differentiates the two species. Genomic islands harbor all 25 of the species-specific biosynthetic pathways, the majority of which occur in S. arenicola and may contribute to the cosmopolitan distribution of this species. Genome evolution is dominated by gene duplication and acquisition, which in the case of secondary metabolism provide immediate opportunities for the production of new bioactive products. Evidence that secondary metabolic pathways are exchanged horizontally, coupled with earlier evidence for fixation among globally distributed populations, supports a functional role and suggests that the acquisition of natural product biosynthetic gene clusters represents a previously unrecognized force driving bacterial diversification. Species-specific differences observed in clustered regularly interspaced short palindromic repeat sequences suggest that S. arenicola may possess a higher level of phage immunity, whereas a highly duplicated family of polymorphic membrane proteins provides evidence for a new mechanism of marine adaptation in Gram-positive bacteria.
Efficient exact motif discovery
Authors: Marschall Tobias , Rahmann Sven 
Published: May 2009

Abstract
Motivation: The motif discovery problem consists of finding over-represented patterns in a collection of biosequences. It is one of the classical sequence analysis problems, but still has not been satisfactorily solved in an exact and efficient manner. This is partly due to the large number of possibilities of defining the motif search space and the notion of over-representation. Even for well-defined formalizations, the problem is frequently solved in an ad hoc manner with heuristics that do not guarantee to find the best motif.
Results: We show how to solve the motif discovery problem (almost) exactly on a practically relevant space of IUPAC generalized string patterns, using the p-value with respect to an i.i.d. model or a Markov model as the measure of over-representation. In particular, (i) we use a highly accurate compound Poisson approximation for the null distribution of the number of motif occurrences. We show how to compute the exact clump size distribution using a recently introduced device called probabilistic arithmetic automaton (PAA). (ii) We define two p-value scores for over-representation, the first one based on the total number of motif occurrences, the second one based on the number of sequences in a collection with at least one occurrence. (iii) We describe an algorithm to discover the optimal pattern with respect to either of the scores. The method exploits monotonicity properties of the compound Poisson approximation and is by orders of magnitude faster than exhaustive enumeration of IUPAC strings (11.8 h compared with an extrapolated runtime of 4.8 years). (iv) We justify the use of the proposed scores for motif discovery by showing our method to outperform other motif discovery algorithms (e.g. MEME, Weeder) on benchmark datasets. We also propose new motifs on Mycobacterium tuberculosis.
Availability and Implementation: The method has been implemented in Java. It can be obtained from http://ls11-www.cs.tu-dortmund.de/people/marschal/paa_md/
Contact: tobias.marschall@tu-dortmund.de; sven.rahmann@tu-dortmund.de
Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum
Authors: Huang Yang , Wuchty Stefan , Ferdig Michael T. , Przytycka Teresa M. 
Published: May 2009

Abstract
Motivation: Analysis of expression quantitative trait loci (eQTL) significantly contributes to the determination of gene regulation programs. However, the discovery and analysis of associations of gene expression levels and their underlying sequence polymorphisms continue to pose many challenges. Methods are limited in their ability to illuminate the full structure of the eQTL data. Most rely on an exhaustive, genome scale search that considers all possible locus–gene pairs and tests the linkage between each locus and gene.
Result: To analyze eQTLs in a more comprehensive and efficient way, we developed the Graph based eQTL Decomposition method (GeD) that allows us to model genotype and expression data using an eQTL association graph. Through graph-based heuristics, GeD identifies dense subgraphs in the eQTL association graph. By identifying eQTL association cliques that expose the hidden structure of genotype and expression data, GeD effectively filters out most locus–gene pairs that are unlikely to have significant linkage. We apply GeD on eQTL data from Plasmodium falciparum, the human malaria parasite, and show that GeD reveals the structure of the relationship between all loci and all genes on a whole genome level. Furthermore, GeD allows us to uncover additional eQTLs with lower FDR, providing an important complement to traditional eQTL analysis methods.
Contact: przytyck@ncbi.nlm.nih.gov
Identifying novel constrained elements by exploiting biased substitution patterns
Authors: Garber Manuel , Guttman Mitchell , Clamp Michele , Zody Michael C. , Friedman Nir , Xie Xiaohui 
Published: May 2009

AbstractMotivation: Comparing the genomes from closely related species provides a powerful tool to identify functional elements in a reference genome. Many methods have been developed to identify conserved sequences across species; however, existing methods only model conservation as a decrease in the rate of mutation and have ignored selection acting on the pattern of mutations.Results: We present a new approach that takes advantage of deeply sequenced clades to identify evolutionary selection by uncovering not only signatures of rate-based conservation but also substitution patterns characteristic of sequence undergoing natural selection. We describe a new statistical method for modeling biased nucleotide substitutions, a learning algorithm for inferring site-specific substitution biases directly from sequence alignments and a hidden Markov model for detecting constrained elements characterized by biased substitutions. We show that the new approach can identify significantly more degenerate constrained sequences than rate-based methods. Applying it to the ENCODE regions, we identify as much as 10.2% of these regions are under selection.Availability: The algorithms are implemented in a Java software package, called SiPhy, freely available at http://www.broadinstitute.org/science/software/.Contact: xhx@ics.uci.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Ontology quality assurance through analysis of term transformations
Authors: Verspoor Karin , Dvorkin Daniel , Cohen K. Bretonnel , Hunter Lawrence 
Published: May 2009

Abstract
Motivation: It is important for the quality of biological ontologies that similar concepts be expressed consistently, or univocally. Univocality is relevant for the usability of the ontology for humans, as well as for computational tools that rely on regularity in the structure of terms. However, in practice terms are not always expressed consistently, and we must develop methods for identifying terms that are not univocal so that they can be corrected.
Results: We developed an automated transformation-based clustering methodology for detecting terms that use different linguistic conventions for expressing similar semantics. These term sets represent occurrences of univocality violations. Our method was able to identify 67 examples of univocality violations in the Gene Ontology.
Availability: The identified univocality violations are available upon request. We are preparing a release of an open source version of the software to be available at http://bionlp.sourceforge.net.
Contact: karin.verspoor@ucdenver.edu
Inference of locus-specific ancestry in closely related populations
Authors: Paşaniuc Bogdan , Sankararaman Sriram , Kimmel Gad , Halperin Eran 
Published: May 2009

AbstractA characterization of the genetic variation of recently admixed populations may reveal historical population events, and is useful for the detection of single nucleotide polymorphisms (SNPs) associated with diseases through association studies and admixture mapping. Inference of locus-specific ancestry is key to our understanding of the genetic variation of such populations. While a number of methods for the inference of locus-specific ancestry are accurate when the ancestral populations are quite distant (e.g. African–Americans), current methods incur a large error rate when inferring the locus-specific ancestry in admixed populations where the ancestral populations are closely related (e.g. Americans of European descent).Results: In this work, we extend previous methods for the inference of locus-specific ancestry by the incorporation of a refined model of recombination events. We present an efficient dynamic programming algorithm to infer the locus-specific ancestries in this model, resulting in a method that attains improved accuracies; the improvement is most significant when the ancestral populations are closely related. An evaluation on a wide range of scenarios, including admixtures of the 52 population groups from the Human Genome Diversity Project demonstrates that locus-specific ancestry can indeed be accurately inferred in these admixtures using our method. Finally, we demonstrate that imputation methods can be improved by the incorporation of locus-specific ancestry, when applied to admixed populations.Availability: The implementation of the WINPOP model is available as part of the LAMP package at http://lamp.icsi.berkeley.edu/lampContact: heran@icsi.berkeley.edu
IsoRankN: spectral methods for global alignment of multiple protein networks
Authors: Liao Chung-Shou , Lu Kanghao , Baym Michael , Singh Rohit , Berger Bonnie 
Published: May 2009

Abstract
Motivation: With the increasing availability of large protein–protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is further delineated into two sub-problems: local alignment, to find small conserved motifs across networks, and global alignment, which attempts to find a best mapping between all nodes of the two networks. In this article, our aim is to improve upon existing global alignment results. Better network alignment will enable, among other things, more accurate identification of functional orthologs across species.
Results: We introduce IsoRankN (IsoRank-Nibble) a global multiple-network alignment tool based on spectral clustering on the induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment in coverage and consistency on multiple alignments of the five available eukaryotic networks. Being based on spectral methods, IsoRankN is both error tolerant and computationally efficient.
Availability: Our software is available freely for non-commercial purposes on request from: http://isorank.csail.mit.edu/
Contact: bab@mit.edu
Family classification without domain chaining
Authors: Joseph Jacob M. , Durand Dannie 
Published: May 2009

Abstract
Motivation: Classification of gene and protein sequences into homologous families, i.e. sets of sequences that share common ancestry, is an essential step in comparative genomic analyses. This is typically achieved by construction of a sequence homology network, followed by clustering to identify dense subgraphs corresponding to families. Accurate classification of single domain families is now within reach due to major algorithmic advances in remote homology detection and graph clustering. However, classification of multidomain families remains a significant challenge. The presence of the same domain in sequences that do not share common ancestry introduces false edges in the homology network that link unrelated families and stymy clustering algorithms.
Results: Here, we investigate a network-rewiring strategy designed to eliminate edges due to promiscuous domains. We show that this strategy can reduce noise in and restore structure to artificial networks with simulated noise, as well as to the yeast genome homology network. We further evaluate this approach on a hand-curated set of multidomain sequences in mouse and human, and demonstrate that classification using the rewired network delivers dramatic improvement in Precision and Recall, compared with current methods. Families in our test set exhibit a broad range of domain architectures and sequence conservation, demonstrating that our method is flexible, robust and suitable for high-throughput, automated processing of heterogeneous, genome-scale data.
contact: jacobmj@cmu.edu