bluuebunny/crossref_metadata_2025 huggingface dataset:
Nest trampling and ground nesting birds: Quantifying temporal and spatial overlap between cattle activity and breeding redshank
Authors: Sharps Elwyn , Smart Jennifer , Mason Lucy R. , Jones Kate , Skov Martin W. , Garbutt Angus , Hiddink Jan G.
Published: July 2017

Conservation grazing for breeding birds needs to balance the positive effects on vegetation structure and negative effects of nest trampling. In the UK, populations of Common redshank Tringa totanus breeding on saltmarshes declined by >50% between 1985 and 2011. These declines have been linked to changes in grazing management. The highest breeding densities of redshank on saltmarshes are found in lightly grazed areas. Conservation initiatives have encouraged low‐intensity grazing at <1 cattle/ha, but even these levels of grazing can result in high levels of nest trampling. If livestock distribution is not spatially or temporally homogenous but concentrated where and when redshank breed, rates of nest trampling may be much higher than expected based on livestock density alone. By GPS tracking cattle on saltmarshes and monitoring trampling of dummy nests, this study quantified (i) the spatial and temporal distribution of cattle in relation to the distribution of redshank nesting habitats and (ii) trampling rates of dummy nests. The distribution of livestock was highly variable depending on both time in the season and the saltmarsh under study, with cattle using between 3% and 42% of the saltmarsh extent and spending most their time on higher elevation habitat within 500 m of the sea wall, but moving further onto the saltmarsh as the season progressed. Breeding redshank also nest on these higher elevation zones, and this breeding coincides with the early period of grazing. Probability of nest trampling was correlated to livestock density and was up to six times higher in the areas where redshank breed. This overlap in both space and time of the habitat use of cattle and redshank means that the trampling probability of a nest can be much higher than would be expected based on standard measures of cattle density. Synthesis and applications: Because saltmarsh grazing is required to maintain a favorable vegetation structure for redshank breeding, grazing management should aim to keep livestock away from redshank nesting habitat between mid‐April and mid‐July when nests are active, through delaying the onset of grazing or introducing a rotational grazing system.
High body mass index is a predictor of left ventricular reverse remodelling in heart failure with reduced ejection fraction
Authors: Cescau Arthur , Van Aelst Lucas N.L. , Baudet Mathilde , Cohen Solal Alain , Logeart Damien
Published: July 2017

Aims

Structural and functional left ventricular alterations can occur in heart failure (HF), referred to as left ventricular reverse remodelling (LVRR). This study aimed to define novel predictors of LVRR besides well‐known effects of medical and device therapy.

Methods and results

From echographic database, we included 295 patients with both left ventricular ejection fraction (LVEF) ≤45% and indexed left ventricular end‐diastolic diameter ≥33 mm/m2 and who had at least two echocardiographic exams with a delay between 3 and 12 months. LVRR was defined as the combination of (i) normalization of LVEF (LVEF ≥50%) or increase in LVEF ≥10% and (ii) a decrease in indexed left ventricular end‐diastolic diameter ≥10%. Clinical follow‐up was also obtained. LVRR occurred in 53 (18%) patients. Patients in the LVRR group were more likely to present with de novo HF (75% vs. 42%), had lower LVEF and left ventricular end‐diastolic volumes at index examination, yet a higher body mass index (BMI) than non‐LVRR patients. Obesity was observed in 25% of LVRR patients vs. 14% in others. In multivariate analyses, BMI (per each 1 kg/m2 increase) emerged as a predictor of LVRR: odds ratio 1.10 (95% confidence interval 1.02–1.19) after adjustment to other predictors of LVRR. During a mean follow‐up of 37 months, 32% of patients had a major adverse cardiac event; de novo HF, age, and LVEF were associated with major adverse cardiac event.

Conclusions

We identified significant relationship between high BMI and LVRR. This intriguing novel finding deserves further study.
Identifying the Cause of Voltage and Fill Factor Losses in Perovskite Solar Cells by Using Luminescence Measurements
Authors: Wu Nandi , Wu Yiliang , Walter Daniel , Shen Heping , Duong The , Grant Dale , Barugkin Chog , Fu Xiao , Peng Jun , White Thomas , Catchpole Kylie , Weber Klaus
Published: July 2017

The open‐circuit voltage (VOC) and fill factor are key performance parameters of solar cells, and understanding the underlying mechanisms that limit these parameters in real devices is critical to their optimization. Device modeling is combined with luminescence and cell current–voltage (I–V) measurements to show that carrier transport limitations within the cell can significantly reduce the cell voltage around the maximum power point as well as, under certain conditions, at VOC. An important consequence is that the cell terminal voltage cannot be assumed a priori to be only limited by parasitic recombination. It is demonstrated that luminescence‐based measurements can be used to reconstruct cell I–V curves with removal of any transport limitation effects, which allows the contribution of recombination, shunt resistance, and series resistance on the fill factor to be clarified. Such luminescence‐based measurements allow the contactless characterization of cells and cell precursor structures, and should prove highly valuable as a diagnostic tool for the development of new cell structures and large‐area cells.
A Joint Analysis of Asthma Affection Status and IgE Levels in Multiple Data Sets Collected for Asthma
Authors: Markianos Kyriacos , Carlson Scott , Gibbs Mark , Kruglyak Leonid
Published: July 2017

We present a joint linkage analysis of eight data sets collected for asthma. Three of the data sets are full genome scans, while the remaining five concentrate on a 40‐cM region on chromosome 5. We perform the analysis using one qualitative and one quantitative phenotype: asthma status and IgE level. Considering all data sets simultaneously, we do not find evidence for linkage to asthma affection status beyond the level expected to occur by chance twice per genome scan. In contrast, we observe significant linkage to IgE level on chromosome 6. © 2001 Wiley‐Liss, Inc.
Multilocus Linkage Analysis of the German Asthma Data
Authors: Zandi Peter P. , Klein Alison P. , Addington Anjene Musick , Hetmanski Jacqueline B. , Roberts Linda , Pella Rita , Shrestha Sadeep , Shaw Cheng-Kuang , Kiat Heng Chew , Langefeld Carl D. , Beaty Terri H.
Published: July 2017

We analyzed data from the German Asthma Genetics Group with three methods that utilize pedigree‐specific nonparametric linkage scores to facilitate the search for multiple independent and interacting susceptibility loci. The three methods included a conditional analysis, logistic regression, and neural networks. Although there were differences, the three methods identified many of the same susceptibility loci. The most consistent evidence was provided for loci on chromosomes 1, 2, 6, 9, and 15. Both the conditional and the logistic regression analyses suggested an epistatic relationship between loci on chromosomes 2 and 9. The logistic regression analysis further revealed evidence for locus heterogeneity between loci on chromosomes 6 and 15. Finally, the neural network analysis identified a potential locus on chromosome 17 that was not identified in the other analyses. © 2001 Wiley‐Liss, Inc.
The Importance of Connections: Joining Components of the Hutterite Pedigree
Authors: Chapman N.H. , Leutenegger A.-L. , Badzioch M.D. , Bogdan M. , Conlon E.M. , Daw E.W. , Gagnon F. , Li N. , Maia J.M. , Wijsman E.M. , Thompson E.A.
Published: July 2017

We analyzed a quantitative trait (serum IgE levels), and a binary trait (asthma), in four Hutterite sub‐pedigrees. A genome screen for asthma was performed using GENEHUNTER, and interesting regions were followed up using extended pedigrees and the FASTLINK package. Markov chain Monte Carlo (MCMC) methods were used to assess haplotype sharing among affected individuals (MORGAN/AUTOZYG), and to perform a combined oligogenic segregation and linkage analysis (LOKI) for log10(IgE). We found evidence for at least two susceptibility loci for asthma on chromosome 5, and a QTL for log10(IgE) on chromosome 1. Our analyses demonstrate that using the most complete pedigree structure possible is advisable, with attention to the possibility of heterogeneity among subunits of a very large pedigree. © 2001 Wiley‐Liss, Inc.
Pedigree Selection and Tests of Linkage in a Hutterite Asthma Pedigree
Authors: Greenwood Celia M.T. , Bureau Alexandre , Loredo-Osti J Concepción , Roslin Nicole M. , Crumley M. Joyce , Brewer Carl G. , Fujiwara T. Mary , Goldstein Darlene R. , Morgan Kenneth
Published: July 2017

We explored methods for kinship and linkage analysis in a Hutterite pedigree comprising 1,544 individuals, 72 of whom were diagnosed with asthma. Subpedigrees were selected by (a) identifying nuclear families containing asthmatics, (b) identifying couples with many asthmatic descendants in an ad hoc manner, and (c) finding the most recent common ancestors of all asthmatics. Markov chain Monte Carlo (MCMC) methods were used to estimate allele sharing in the larger subpedigrees and transmission/disequilibrium tests were performed on nuclear families. On chromosome 5q near the cytokine cluster, modest evidence for linkage to asthma was obtained. Using MCMC, we were able to evaluate the evidence for linkage in complex subpedigrees of several hundred individuals, and hence, incorporate some of the co‐ancestry of this founder population. © 2001 Wiley‐Liss, Inc.
Marker Selection by Akaike Information Criterion and Bayesian Information Criterion
Authors: Li Wentian , Nyholt Dale R.
Published: July 2017

We carried out a discriminant analysis with identity by descent (IBD) at each marker as inputs, and the sib pair type (affected‐affected versus affected‐unaffected) as the output. Using simple logistic regression for this discriminant analysis, we illustrate the importance of comparing models with different number of parameters. Such model comparisons are best carried out using either the Akaike information criterion (AIC) or the Bayesian information criterion (BIC). When AIC (or BIC) stepwise variable selection was applied to the German Asthma data set, a group of markers were selected which provide the best fit to the data (assuming an additive effect). Interestingly, these 25–26 markers were not identical to those with the highest (in magnitude) single‐locus lod scores. © 2001 Wiley‐Liss, Inc.
Family‐Based Association Tests for Qualitative and Quantitative Traits Using Single‐Nucleotide Polymorphism and Microsatellite Data
Authors: Wilk Jemma B. , Volcjak Jeannine S. , Myers Richard H. , Maher Nancy E. , Knowlton Beth A. , Heard-Costa Nancy L. , Demissie Serkalem , Cupples L. Adrienne , DeStefano Anita L.
Published: July 2017

Using the Genetic Analysis Workshop 12 simulated data, we contrasted results for association tests in nuclear families and extended pedigrees using single‐nucleotide polymorphism (SNP) data, and we compared results for different trait definitions, for outbred and isolate populations, and for SNP and microsatellite data. SNPs in major genes 1 and 6 were analyzed using transmission disequilibrium testing (TDT) [Spielman et al., Am J Hum Genet 52:506–16, 1993], sibship disequilibrium testing (SDT) [Horvath and Laird, Am J Hum Genet 63:1886–97, 1998], family‐based association testing (FBAT) [Horvath et al., Eur J Hum Genet 9:301–6, 2001], and a chi‐square analysis of founders. TDT and SDT were applied in a sample of independent nuclear families, while FBAT was applied in extended pedigrees. SNPs and microsatellites were analyzed with dichotomous and quantitative trait definitions using FBAT in the isolate and outbred populations. The results of the TDT, SDT, and FBAT analyses are comparable using SNP data to identify the disease gene. However, these tests of association were not helpful in discriminating between functional and non‐functional SNPs in disequilibrium. SNP data were able to identify association with affection status in a gene that influences the liability directly (MG6), but did not perform as well when assessing association with affection status in a gene that influences the outcome only through a quantitative trait (MGI). Association with MGI was observed using the SNP data when the outcome was defined quantitatively. Microsatellite data were relatively unsuccessful in identifying association with the markers in the region of a major gene. The magnitude of the associations between SNPs and the dichotomous or quantitative trait definitions were similar in the outbred and isolated populations. © 2001 Wiley‐Liss, Inc.
The Single‐Nucleotide Polymorphism Lottery: How Useful are a Few Common SNPs in Identifying Disease‐Associated Alleles?
Authors: Barton Anne , Chapman Philip , Myerscough Anne , Pinel Tracy , Davies Nick , Worthington Jane , John Sally
Published: July 2017

It has been proposed that using association analysis of single nucleotide polymorphism (SNP) markers in candidate genes may be more successful in identifying disease susceptibility genes for complex diseases. Finding all the SNPs within a candidate gene and genotyping a large case‐control cohort is a resource‐intensive process. As linkage disequilibrium extends across small regions of the genome, the expectation is that a few common anonymous SNPs will be sufficient to detect functional disease‐associated alleles. The aim of this investigation was to compare the ability of a number of family‐ and population‐based association methods to identify known susceptibility loci using the Genetic Analysis Workshop 12 simulated data set. As expected, case‐control methods were more likely to detect association with individual SNPs but family‐based haplotyping methods appeared better able to localize the position of functional polymorphism. © 2001 Wiley‐Liss, Inc.
Using Single Nucleotide Polymorphisms to Investigate Association Between a Candidate Gene and Disease
Authors: Saunders Catherine L. , Crockford Gillian P. , Bishop D. Timothy , Barrett Jennifer H.
Published: July 2017

A range of study designs, using unrelated or family controls, were used to investigate the pattern of association with disease of single nucleotide polymorphisms (SNPs) within candidate gene 1 (simulated data). Strong evidence of disease association at the functional locus was detected using all study designs, and in the “general” but not the “isolated” population the functional polymorphism displayed considerably higher association than surrounding SNPs. There was much variation in the strength of association of SNPs with disease, up to 70% of which was explained by SNP allele frequency and distance from the functional polymorphism. Some common polymorphisms very close to the functional locus however showed no association with disease. Analysis of short haplotypes of SNPs reduced but did not totally remove this feature. © 2001 Wiley‐Liss, Inc.
Exploiting Linkage Disequilibrium in Population Isolates
Authors: Culverhouse Robert , Lin Jennifer , Liu Kuang-Yu , Suarez Brian K.
Published: July 2017

A comparison of haplotype frequencies between unrelated cases and controls from population isolates identifies a strong signal for the presence/absence of the discrete phenotype in an interval on chromosome 6 bounded by markers 34 and 35. We define a dissimilarity index, D, which is sensitive to differences in allele distributions and differences in the patterns of linkage disequilibrium between cases and controls. We describe two statistical methods to utilize D: a method appropriate for a single moderately sized sample and a sequential approach appropriate for multiple small independent samples. © 2001 Wiley‐Liss, Inc.
Analysis of Single Nucleotide Polymorphisms in Candidate Genes Using the Pedigree Disequilibrium Test
Authors: Hardy Sarah W. , Weir Bruce S. , Kaplan Norman L. , Martin Eden R.
Published: July 2017

The pedigree disequilibrium test (PDT) has been proposed recently as a test for association in general pedigrees [Martin et al., Am J Hum Genet 67:146–54, 2000]. The Genetic Analysis Workshop (GAW) 12 simulated data, with many extended pedigrees, is an example the type of data to which the PDT is ideally suited. In replicate 42 from the general population the PDT correctly identifies candidate genes 1, 2, and 6 as containing single nucleotide polymorphisms (SNPs) that arc significantly associated with the disease. We also applied the truncated product method (TPM) [Zaykin et al., Genet Epidemiol, in press] to combine p‐values in overlapping windows across the genes. Our results show that the TPM is helpful in identifying significant SNPs as well as removing spurious false positives. Our results indicate that, using the PDT, functional disease‐associated SNPs can be successfully identified with a dense map of moderately polymorphic SNPs. © 2001 Wiley‐Liss, Inc.
A New Nonparametric Linkage Statistic for Mapping Both Qualitative and Quantitative Trait Loci
Authors: Camp Nicola J. , Gutin Alexander , Abkevich Victor , Farnham James M. , Cannon-Albright Lisa , Thomas Alun
Published: July 2017

We describe an alternative nonparametric linkage (NPL) statistic to that of Kruglyak et al. [Am. J. Hum. Genet. 58:1347–63, 1996] that can be used with qualitative phenotypes, and is easily extended for use with quantitative phenotypes. We analyzed the Genetic Analysis Workshop 12 simulated isolated population data, replicate 1, using two phenotypes; affected status (AFF) a dichotomous phenotype and quantitative trait Q5, which was chosen since it was the most strongly associated with AFF. One false positive significant NPL score was observed for the AFF phenotype. For Q5 a single region on chromosome 1 reached genome‐wide significance. The peak of this signal was for marker D01G137 at 135.1 cM with a quantitative trait locus (QTL)‐NPL score of 4.19. The nearest marker to the true location of the major gene (MG5 at 137.1 cM) was D01G139 at position 135.8 cM, where the QTL‐NPL score was still high at 4.08. © 2001 Wiley‐Liss, Inc.
Does Simultaneous Consideration of Multiple Regions Improve Disease Gene Localization?
Authors: Biernacka Joanna , Lewinger Juan Pablo , Chan Viann , Bull Shelley B.
Published: July 2017

Improvement in localization of disease susceptibility genes by simultaneous consideration of multiple interacting loci was assessed using the Genetic Analysis Workshop 12 simulated data. Evidence of linkage at primary loci was used to weight families for analyses at secondary loci. To identify regions linked to disease susceptibility genes, parametric and allele‐sharing genome scans were performed in the extended pedigrees and nuclear families, respectively. The position of the peak allele‐sharing lod was used as the estimate of a disease gene location. In weighted analyses, the positions where the greatest lod increases occurred were taken as alternative estimates of the gene locations. Variability of the location estimates of disease genes given by the unweighted and weighted analyses was compared. Similar analyses were carried out using true disease loci to determine weights. Weighted analyses did not in general improve the localization of disease genes in this data set, even with a large sample of 1,928 nuclear families, due to the features of the underlying additive liability threshold model. © 2001 Wiley‐Liss, Inc.
Linkage Analysis of Genetic Analysis Workshop 12 Simulated Data Based on Affected Individuals Only
Authors: Cordell Heather J. , Dudbridge Frank
Published: July 2017

A variety of allele‐sharing methods was used to assess linkage to disease for a whole‐genome screen in each of ten replicates from the Genetic Analysis Workshop 12 simulated data. Analysis of each replicate produced many false positive results in addition to a few “true” positives. Conditioning on the strongest initial linkage and reanalyzing using a variety of conditional methods did not improve the power for detection or help discriminate between true and false positive signals. © 2001 Wiley‐Liss, Inc.
Covariates in Linkage Analysis Using Sibling and Cousin Pairs
Authors: Saccone Nancy L. , Rochberg Nan , Neuman Rosalind J. , Rice John P.
Published: July 2017

Using simulated data from GAW 12, problem 2, we further develop a novel technique to detect and use significant covariates in linkage analysis. The method, first introduced by Rice et al. [Genet Epidemiol 17(Suppl. 1):S691–5, 19991, uses logistic regression to model perturbation in sharing as a function of covariate levels. The original method allows use of all sib pairs (concordant affected, concordant unaffected, and discordant). Here we extend this method to include cousin pairs in analysis. © 2001 Wiley‐Liss, Inc.
Multipoint Linkage Analysis Under Heterogeneity: Incorporation of Parametric and Nonparametric Approaches
Authors: Chiu Yen-Feng , Addington Anjene Musick , Beaty Terri H. , Klein Alison P. , Liang Kung-Yee
Published: July 2017

Using a recently developed multipoint parametric method, which tests for linkage in the presence of heterogeneity, we performed a genome‐wide search for linkage using the German asthma data. Both dominant and recessive models were assumed in this parametric approach. Identity‐by‐descent (IBD) sharing for affected sibs was also calculated to help identify an appropriate genetic model and localize the trait locus. The strongest evidence for linkage was on chromosome 6 (p‐value=0.00006) under the dominant model with heterogeneity. Using both linkage and IBD sharing information for D6S422 (36.55 cM) on chromosome 6, we conducted exploratory analyses to locate additional trait loci that might explain the linkage heterogeneity. We found evidence of heterogeneity between D6S422 and D11S4111 based on a test of association (p‐value = 0.0015). © 2001 Wiley‐Liss, Inc.
Exploring Haplotype Sharing Methods in General and Isolated Populations to Detect Gene(s) of a Complex Genetic Trait
Authors: Beckmann Lars , Fischer Christine , Deck Klaus-Georg , Nolte Ilja M. , te Meerman Gerard , Chang-Claude Jenny
Published: July 2017

We applied a new haplotype sharing method to the simulated Genetic Analysis Workshop 12 data for both isolated and general populations without knowledge of the disease model, using affection status as phenotype and three different sample sizes. The highest peak for the mean sharing of the haplotypes was found in the isolated population for the markers D06G034 and D06G035, which flank the candidate genes located on chromosome 6, with ‐log10(p) values of 2.9 and 7.0 in the moderate and large study samples, respectively. The whole genome screen detected three further loci with ‐log10(p) values of 3.0, which turned out to be false positives. None of the true gene loci were detected in the general population even in the largest sample. The test of linkage disequilibrium based on excess haplotype sharing over the linkage equilibrium expectation revealed z‐values one order of magnitude higher in the isolated than in the general population. This approach appears to be promising for mapping genes of complex diseases depending on population characteristics. © 2001 Wiley, Liss, Inc.
Genome Scan of Complex Traits by Haplotype Sharing Correlation
Authors: Qian Dajun , Thomas Duncan C.
Published: July 2017

We introduce a haplotype‐sharing correlation in founder haplotypes for use in genome scanning. The method evaluates the correlation between phenotype similarity and haplotype similarity at each candidate location. When applied to Genetic Analysis Workshop 12 simulated data for disease status, age at onset, and quantitative traits Q1–Q5, we found highly significant signals near four simulated disease loci in genome scans using microsatellite marker data and highly significant gene effects in three casual genes using sequence data. © 2001 Wiley‐Liss, Inc.
Combined Multipoint Analysis of Multiple Asthma Data Sets Based on the Posterior Probability of Linkage
Authors: Wang Kai , Huang Jian , Logue Mark , Vieland Veronica
Published: July 2017

In the presence of multiple data sets, an important issue is how to best measure the overall evidence for linkage across data sets. Previously, we advocated the use of the posterior probability of linkage (PPL) for this purpose [Vieland, Am J Hum Genet 63:947–54, 1998; Wang et al., Ann Hum Genet 64:533–53, 2000; Vieland et al., Hum Hered 51:199–208, 2001]. In this paper, we propose a critical modification of our earlier two‐point PPL in order to handle multiple‐point calculations. The proposed modification is then applied to the genome‐screen data sets and the COAG chromosome 5 data sets provided by GAW 12. We find linkage signals at location (in the order of the strength of the signal) 45 cM on chromosome 6, 23 cM on chromosome 20, and 30 cM on chromosome 1. No linkage signal is found on chromosome 5. © 2001 Wiley‐Liss, Inc.
Use of Variable Marker Density, Principal Components, and Neural Networks in the Dissection of Disease Etiology
Authors: Pankratz Nathan , Kirkwood Sandra C. , Flury Leah , Koller Daniel L. , Foroud Tatiana
Published: July 2017

Several approaches were taken to identify the loci contributing to the quantitative and qualitative phenotypes in the Genetic Analysis Workshop 12 simulated data set. To identify possible quantitative trait loci (QTL), the quantitative traits were analyzed using SOLAR. The four replicates identified as the “best replicates” by the simulators, 42, 25, 33, and 38, were analyzed separately. Each of the five quantitative phenotypes was analyzed individually in the four replicates. To increase the power to detect QTL with pleiotropic effects, principal component analysis was performed and one new multivariate phenotype was estimated. In each instance, after performing a 10‐cM genome screen, fine mapping was completed in the initially identified linked regions to further evaluate the evidence for linkage. This approach of initially performing a coarse marker screen followed by analyses using much higher marker density successfully identified all the QTL playing a role in the quantitative phenotypes. The principal component phenotype did not substantially improve the power of QTL detection or localization. A neural network approach was utilized to identify loci contributing to disease status. The neural network technique identified the strongest gene influencing disease status as well as a locus contributing to quantitative traits 3 and 4; however, the inputs that contributed the greatest information were markers not in QTL regions. © 2001 Wiley‐Liss, Inc.
Comparison of Likelihood Approaches for Combined Segregation and Linkage Analysis of a Complex Disease and a Candidate Gene Marker Under Different Ascertainment Schemes
Authors: Martinez Maria , Goldstein Alisa M. , O'Connell Jeffrey R.
Published: July 2017

We compared two joint likelihood approaches, with complete (L1) or without (L2) linkage disequilibrium, under different ascertainment schemes, for the genetic analysis of the disease trait and marker gene 1 in replicate 42. Joint likelihoods were computed without a correction for the selection scheme. For the different sampling schemes we have explored, our results suggest that L1 is a more powerful approach than L2 to detect major gene and covariatc effects as well as to identify accurately gene×covariate interaction effects in a common and complex disease such as the Genetic Analysis Workshop 12 MG6 simulated trait. © 2001 Wiley‐Liss, Inc.
Does Accounting for Mitochondrial Genetic Variation Improve the Fit of Genetic Models?
Authors: Czerwinski Stefan A. , Williams Jeff T. , Demerath Ellen W. , Towne Bradford , Siervogel Roger M. , Blangero John
Published: July 2017

We describe a simple variance component model for estimating the effect of mitochondrial DNA (mtDNA) inheritance on quantitative trait variation. The model is applied to quantitative trait Q5 in the simulated general population data from Genetic Analysis Workshop (GAW) 12. Although the mitochondrial effect on Q5 is small (5.3%) and the power of the method to detect the effect is correspondingly low, analysis over the available population replicates demonstrates that the effect of maternal relatedness can be detected and estimated accurately. © 2001 Wiley‐Liss, Inc.
Linkage Analysis of Quantitative Traits in Randomly Ascertained Pedigrees: Comparison of Penetrance‐Based and Variance Component Analysis
Authors: Göring Harald H.H. , Williams Jeff T. , Blangero John
Published: July 2017

Penetrance‐based linkage analysis and variance component linkage analysis are two methods that are widely used to localize genes influencing quantitative traits. Using computer programs PAP and SOLAR as representative software implementations, we have conducted an empirical comparison of both methods' power to map quantitative trait loci in extended, randomly ascertained pedigrees, using simulated data. Two‐point linkage analyses were conducted on several quantitative traits of different genetic and environmental etiology using both programs, and the lod scores were compared. The two methods appear to have similar power when the underlying quantitative trait locus is diallelic, with one or the other method being slightly more powerful depending on the characteristics of the quantitative trait and the quantitative trait locus. In the case of a multiallelic quantitative trait locus, however, the variance component approach has much greater power. These findings suggest that one should give careful thought to the likely allelic architecture of the quantitative trait to be analyzed when choosing between these two analytical approaches. It may be the case in general that linkage methods which explicitly or implicitly rely on the assumption of a diallelic trait locus fare poorly when this assumption is incorrect. © 2001 Wiley‐Liss, Inc.
Detecting Genotype × Age Interaction
Authors: Almasy Laura , Towne Bradford , Peterson Charles , Blangero John
Published: July 2017

This paper explores several extensions to the variance component method, which incorporate genotype × age interaction effects. We evaluate the performance of these methods for detecting genotype × age interaction in quantitative genetic analyses of a quantitative trait (Q4), contrasting this with false positive detection rates obtained from a phenotype influenced by the same genes but without genotype × age interaction effects (Q3). We then assess the impact on linkage power and false positive rate of allowing a QTL‐specific genotype × age interaction in linkage analysis of these same traits. © 2001 Wiley‐Liss, Inc.
Modeling Age×Major Gene Interaction by a Variance Component Approach
Authors: Shete Sanjay S. , Chen Jianfang , Zhou Xiaojun , Amos Christopher I.
Published: July 2017

The variance component method has become popular for linkage analysis due to its computational simplicity and generally high power. In this paper we model phenotypic variability of an individual as a mixed effects model in which both the major gene as well as the polygene effects interact with age. We applied the proposed model to the simulated data of Genetic Analysis Workshop 12. We considered the quantitative trait, Q4, in the outbred population. Two major genes influence this trait, each interacting with age independently. Consequently, trait variability is a function of age and also there is interaction of major gene effects with age. By using our model we were able to detect interaction between the major gene effects and age for this trait. © 2001 Wiley‐Liss, Inc.
Multivariate properties of extreme precipitation events in the Pearl River basin, China: Magnitude, frequency, timing, and related causes
Authors: Duan Limin , Zheng Jiangyu , Li Wei , Liu Tingxi , Luo Yanyun
Published: July 2017

Daily precipitation/temperature data collected at 74 weather stations across the Pearl River basin of China (PRBC), for the years 1952–2013, were used to analyse extreme precipitation (EP) processes at annual and seasonal scales in terms of precipitation magnitude, occurrence rates, and timing. Peak‐over‐threshold sampling, modified Mann‐Kendall trend tests, and Poisson regression model were utilized in this study. Causes driving the observed statistical behaviours of EP were investigated, focusing particularly on the impacts of temperature change and the El Niño–Southern Oscillation (ENSO). EP events, which occur mainly during April and September, are most frequent in June. At an annual scale, they are subject to relatively even interannual distributions during the wet season. Significant trends were observed in the magnitude, frequency, and timing of EP events during the dry seasons, although no such trends were seen during the wet seasons. Seasonal shifts in EP can easily trigger sudden flood or drought events and warming temperatures, and ENSO events also have significant impacts on EP processes across the PRBC, as reflected by their increased magnitude and frequency in the western PRBC and decreased precipitation magnitudes in the eastern PRBC during ENSO periods. These results provide important evidence of regional hydrological responses to global climate changes in terms of EP regimes in tropical and subtropical zones.
Utility of 2‐Acetyl Benzofuran for the Synthesis of New Heterocycles as Potential Anticancer Agents
Authors: Abdel‐Aziem Anhar
Published: July 2017

A novel series of benzofuran derivatives containing thiazole, thiadiazine, and pyridotriazolopyrimidine were synthesized starting from 1‐(benzofuran‐2‐yl)‐3‐(1H–indol‐3‐yl)prop‐2‐en‐1‐one. Also, triazolopyrimidine derivatives were prepared from the reaction of 2‐acetylbenzofuran and pyrazole‐4‐carbaldehyde with 2‐thiobarbutyric acid and reaction of the product with hydrazonoyl halides. The structures of the newly synthesized compounds were elucidated on the basis of elemental analyses, spectral data, and alternative synthetic routes whenever possible. Anticancer activity against 60 different human tumor cell lines representing leukemia, melanoma, and cancers of the lung, colon, brain, ovary, breast, prostate, and kidney was validated by the U.S. National Cancer Institute using a two‐stage process. The results revealed that pyrazoline‐1‐thiocarbohydrazide 4b, triazolopyrimidine 20d, and pyrimidine thione 25 have promising antitumor activity against most cell lines.
Adaptable Access for Naphthaquinone Annulation: Bioactivity and Molecular Modeling Evaluations
Authors: Hamama Wafaa S. , Hassanien Alaa El‐Din E. , Zoorob Hanafi H.
Published: July 2017

A series of nitrogenous compounds containing 1,4‐naphhoquinone moiety such as lawsone, benzo[g]quinolone‐5,10‐diones, benzo[g]quinazoline‐5,10‐diones, and benzo[b] naphthodiazepine‐6,11‐diones analogs was synthesized by reaction of Lawsone (1) with different reagents. The structures of produced compounds were confirmed by variable spectra analysis. The molecular structures of the obtained molecules were studied. The products exhibited potent antioxidant and antitumor activities.
The color of cancer: Margin guidance for oral cancer resection using elastic scattering spectroscopy
Authors: Grillone Gregory A. , Wang Zimmern , Krisciunas Gintas P. , Tsai Angela C. , Kannabiran Vishnu R. , Pistey Robert W. , Zhao Qing , Rodriguez‐Diaz Eladio , A'Amar Ousama M. , Bigio Irving J.
Published: July 2017

Objectives/Hypothesis

To evaluate the usefulness of elastic scattering spectroscopy (ESS) as a diagnostic adjunct to frozen section analysis in patients with diagnosed squamous cell carcinoma of the oral cavity.

Study Design

Prospective analytic study.

Methods

Subjects for this single institution, institutional review board–approved study were recruited from among patients undergoing surgical resection for squamous cell cancer of the oral cavity. A portable ESS device with a contact fiberoptic probe was used to obtain spectral signals. Four to 10 spectral readings were obtained on each subject from various sites including gross tumor and normal‐appearing mucosa in the surgical margin. Each reading was correlated with the histopathologic findings of biopsies taken from the exact location of the spectral readings. A diagnostic algorithm based on multidimensional pattern recognition/machine learning was developed. Sensitivity and specificity, error rate, and area under the curve were used as performance metrics for tests involving classification between disease and nondisease classes.

Results

Thirty‐four (34) subjects were enrolled in the study. One hundred seventy‐six spectral data point/biopsy specimen pairs were available for analysis. ESS distinguished normal from abnormal tissue, with a sensitivity ranging from 84% to 100% and specificity ranging from 71% to 89%, depending on how the cutoff between normal and abnormal tissue was defined (i.e., mild, moderate, or severe dysplasia). There were statistically significant differences in

malignancy scores between histologically normal tissue and invasive cancer and between noninflamed tissue and inflamed tissue.

Conclusions

This is the first study to evaluate the effectiveness of ESS in guiding mucosal resection margins in oral cavity cancer. ESS provides fast, real‐time assessment of tissue without the need for pathology expertise. ESS appears to be effective in distinguishing between normal mucosa and invasive cancer and between “normal” tissue (histologically normal and mild dysplasia) and “abnormal” tissue (severe dysplasia and carcinoma in situ) that might require further margin resection. Further studies, however, are needed with a larger sample size to validate these findings and to determine the effectiveness of ESS in distinguishing visibly and histologically normal tissue from visibly normal but histologically abnormal tissue.

Level of Evidence

NA Laryngoscope, 127:S1–S9, 2017
How to Outgrow Your Native Neighbour? Belowground Changes under Native Shrubs at an Early Stage of Invasion
Authors: Ulm Florian , Jacinto João , Cruz Cristina , Máguas Cristina
Published: July 2017

While it is acknowledged that invasive species are a global driver of land degradation, their effects are often only noticed when the invasion has been going on for a while. However, early stage processes must play a fundamental role in plant establishment until invasive plants are able to outgrow the native vegetation. In ten plots of 100 m2 each, we tested the hypothesis that belowground properties are associated with early invasion processes aboveground. We examined the early stage of invasion by a woody legume (Acacia longifolia), growing in the canopy of native dune shrubs (Corema album) as a model system in oligotrophic primary dunes in southern Portugal. Biomass under canopies of invaded and non‐invaded C. album shrubs as well as organic matter (OM) distribution in various soil fractions was measured. In accordance with our hypothesis, A. longifolia presence was related to increased C. album foliar δ15N, a proxy for nitrogen derived from the invasive legume. Under invaded canopies, root and rhizosphere biomass were higher, as was OM in the silt‐clay fraction. Also, δ15N of the OM in the silt‐clay fraction under invaded canopies was enriched, while δ13C was depleted. Finally, we found that the ratio between OM in the biotic versus soil compartment could be a good early indicator for invasion. These findings suggest that even when aboveground invasion pressure on the system is low, it is imperative for ecosystem conservation to remove young plants, as they might alter soil functioning already at an early stage of invasion. Copyright © 2017 John Wiley & Sons, Ltd.
Preliminary estimates of the contribution of Arctic nitrogen fixation to the global nitrogen budget
Authors: Sipler Rachel E. , Gong Donglai , Baer Steven E. , Sanderson Marta P. , Roberts Quinn N. , Mulholland Margaret R. , Bronk Deborah A.
Published: July 2017

Dinitrogen (N2) fixation is the source of all biologically available nitrogen on earth, and its presence or absence impacts net primary production and global biogeochemical cycles. Here, we report rates of 3.5–17.2 nmol N L−1 d−1 in the ice‐free coastal Alaskan Arctic to show that N2 fixation in the Arctic Ocean may be an important source of nitrogen to a seasonally nitrogen‐limited system. If widespread in surface waters over ice‐free shelves throughout the Arctic, N2 fixation could contribute up to 3.5 Tg N yr−1 to the Arctic nitrogen budget. At these rates, N2 fixation occurring in ice‐free summer waters would offset up to 27.1% of the Arctic denitrification deficit and contribute an additional 2.7% to N2 fixation globally, making it an important consideration in the current debate of whether nitrogen in the global ocean is in steady state. Additional investigations of high‐latitude marine diazotrophic physiology are required to refine these N2 fixation estimates.
Oral administration of Grifola frondosa polysaccharides improves memory impairment in aged rats via antioxidant action
Authors: Chen Zhaoxia , Tang Yanan , Liu Along , Jin Xiaobao , Zhu Jiayong , Lu Xuemei
Published: July 2017

Scope

Grifola frondosa is an edible/medicinal mushroom with great nutritional value and bioactivity. The present study was performed to evaluate the beneficial effect of polysaccharides isolated from Grifola frondosa on memory impairment in aged rats.

Methods and results

20‐month‐old rats were gavaged with Grifola frondosa polysaccharides (GFP) for 8 weeks. Morris Water Maze test revealed that GFP administration significantly improved memory impairment in aged rats. GFP supply was also found to attenuate age‐associated changes of brain histology and ultrastructure observed by light microscopy and transmission electron microscopy. Moreover, the increase of total antioxidant capacity (T‐AOC), glutathione peroxidase (GPx) activity, superoxide dismutase (SOD) activity, catalase (CAT) activity, as well as the decreased nitric oxide (NO) and malondialdehyde (MDA) levels, were consistent with the behavioral results.

Conclusion

These findings indicated that oral administration of GFP could improve memory impairment via antioxidant action, and dietary supplementation with GFP may provide potential benefits on brain aging.
Z‐scores for fetal left atrial size and left atrium–descending aorta distance in fetuses with isolated total anomalous pulmonary venous connection
Authors: Mao Yan Kai , Zhao Bo Wen , Zheng Feng Hua , Wang Bei , Peng Xiao Hui , Chen Ran , Pan Mei
Published: July 2017

Objectives

To construct Z‐score reference ranges for fetal left atrial (LA) size and left atrium–descending aorta distance (LDD or ‘post‐LA distance’) at 20 to 40 weeks' gestation and to compare these parameters between fetuses with isolated total anomalous pulmonary venous connection (TAPVC) and normal fetuses.

Methods

Three hundred thirty‐three normal singleton fetuses from 20 to 40 weeks' gestation were enrolled in a prospective cross‐sectional study. Six cardiovascular dimensions were obtained by two‐dimensional echocardiography. Z‐score reference ranges of these measurements were determined against gestational age (GA) and fetal biometric variables, using regression analysis of the mean and standard deviation. Also, we reviewed fetal echocardiograms from ten fetuses with postnatal diagnosis of isolated TAPVC and made the measurements on archived images. Subsequently, all parameters were compared between the normal and TAPVC groups.

Results

A simple linear regression model was the best description of the mean and standard deviation of most variables in normal cases, with the exception of the mean LDD based on GA, which was best fitted by a quadratic regression. Fetuses with TAPVC had significantly lower LA size Z‐scores [80% (8/10) of which were under −2] and increased LDD Z‐scores [100% (10/10) of which were greater than 2]. Using an LDD Z‐score of >2.22 was both highly sensitive (100%) and specific (98.5%) for distinguishing between TAPVC and normal hearts.

Conclusion

Normal data and Z‐scores of fetal LA size and LDD were provided against GA and fetal biometry. This could be useful for quantitative assessment of fetal TAPVC. Increased post‐LA distance and decreased LA size may be markers for the prenatal diagnosis of TAPVC. © 2017 John Wiley & Sons, Ltd.
Eco‐friendly produced lightweight structural graphene/polyamide 12 nanocomposite: Mechanical performance and the controlling microstructural mechanisms
Authors: Adel Marwa , El‐Shazly Ossama , El‐Wahidy El‐Wahidy F. , El‐Maghraby Azza , Mohamed Marwa A.A.
Published: July 2017

The present study explores the potential use of graphene nanoplatelets (GL‐GNPs), synthesized from glucose through a new chemical approach that is facile, economical, and eco‐friendly alternative to the conventional Hummer's method, as a nanoreinforcement in polymers for the production of light‐weight structural polymer nanocomposites. Understanding the interface character of GL‐GNPs/Polyamide 12 (PA12) nanocomposites with various nanofiller loadings and how this affects their tensile behavior, are focal points of interest. Results reveal that enhancements in polymer stiffness and strength are superior at low GL‐GNPs content than higher contents. This is attributed to higher degree of GL‐GNPs exfoliation and increased polymer phase crystallinity. Interestingly, abundant small/imperfect PA12 crystallites have grown on the GL‐GNPs surface, strongly interlinking thus the polymer and graphene phases within nanocomposites. The intensity of such crystallites in interface region is the determinant of the nanocomposites' Young's modulus, assessed at small applied tensile stress. While the GL‐GNPs‐PA12 interfacial bonding is the determinant of yield and ultimate strengths, estimated at medium and high stress levels. Overall, the 1 wt% GL‐GNPs/PA12 nanocomposite is considered the optimum. Its low density and good mechanical performance among the previously developed graphene/Polyamide nanocomposites, propose promising future for GL‐GNPs‐based nanocomposites as ecofriendly and cost‐effective lightweight structural material. POLYM. ENG. SCI., 58:1201–1212, 2018. © 2017 Society of Plastics Engineers
Substituent‐Controlled Selective and Sensitive Potential Optical Fluoride Sensors Based on Salicylidene Schiff Base Derivatives
Authors: Patil Sagar K. , Das Dipanwita
Published: July 2017

A series of colorimetric chemosensors 2‐((anthracen‐9‐ylmethylene)hydrazonomethyl)phenol (1) and its derivatives with electron donating (–tBu, 2) and withdrawing groups (–Cl, 3) have been synthesized for selective colorimetric ion sensing. Receptor 1 exhibits ability to colorimetric recognition of F− ions in aqueous environment without any interference of other anions revealed in UV‐vis study. Remarkable substituents effect has been observed in selective sensing as receptors 1 and 2 are exclusive colorimetric sensor for F− ion only while probe 3 senses selectively F−, AcO− and H2PO4− ions. A significant red shift (>90 nm) in intra‐ligand charge transfer (ICT) band have been observed after F− ion addition in probes 1 and 2 results distinct color change visible by naked eyes. Proton transfer mechanism has been revealed by absorption and 1H NMR titration study. In case of 1 and 2, two‐step processes have been observed, namely, formation of hydrogen‐bonded complex [LH⋅⋅⋅F]− between receptor and F− followed by F− induced deprotonation of the complex to form L− and FHF−. In contrast, for 3, simple Brönsted acid‐base reaction has been observed. The F− selectivity is demonstrated to be finely tuned by electron push‐pull effect of the substituents on the ortho/para positions of phenyl ring. The excellent selectivity and sensitivity of 1 for F− over AcO− and H2PO4− is ascribed to the fitness in acidity of its phenolic O−H group.