bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of levothyroxine sodium treatment on oxidative stress in Hashimoto’s thyroiditis
Authors: Ates Ihsan , Altay Mustafa , Yilmaz Fatma Meric , Topcuoglu Canan , Yilmaz Nisbet , Berker Dilek , Guler Serdar 
Published: March 2016

ObjectiveAlthough several studies reported increased oxidative stress in Hashimoto’s thyroiditis (HT), the effect of levothyroxine treatment on oxidative status is not studied extensively. Therefore, we conducted this study to investigate the effects of levothyroxine replacement on oxidative stress in HT.Design and methodsThirty-six patients recently diagnosed with HT-related hypothyroidism and 36 healthy controls were included in the study. Levothyroxine replacement was started to patients with hypothyroidism, and had been followed-up for 6 months.ResultsMean basal serum total antioxidant status (TAS), total thiol, arylesterase, and paraoxonase 1 (PON1) levels were significantly lower, and serum total oxidant status (TOS) and oxidative stress index (OSI) were significantly higher in the patients with hypothyroid than the controls. In the hypothyroid group serum TAS, total thiol, arylesterase, and PON1 levels increased and serum TOS and OSI levels decreased significantly after levothyroxine treatment. Pretreatment serum TAS, total thiol, PON1, and arylesterase levels were positively correlated with free levothyroxine (fT4) and negatively correlated with thyroid-stimulating hormone (TSH), antithyroid peroxidase (anti-TPO), and antithyroglobulin (anti-TG) levels. Also, pretreatment serum TOS and OSI levels were negatively correlated with fT4levels and positively correlated with TSH, anti-TPO, and anti-TG. We have also found that the fT4and anti-TPO levels are independent predictors of the oxidative stress parameters in stepwise multivariable linear regression analysis.ConclusionThis study suggests that levothyroxine replacement decreases oxidant status and increases antioxidant status following the 6 months of levothyroxine replacement in hypothyroidism that develops in accordance with the HT.
Derivation of a multivariate reference range for pituitary thyrotropin and thyroid hormones: diagnostic efficiency compared with conventional single-reference method
Authors: Hoermann Rudolf , Larisch Rolf , Dietrich Johannes W , Midgley John E M 
Published: March 2016

Although pituitary thyrotropin (TSH) and thyroid hormones are physiologically interrelated, interpretation of measurements is conventionally done separately. Classification of subclinical thyroid dysfunction depends by definition solely on an abnormal TSH. This study examines a composite multivariate approach to disease classification.MethodsBivariate and trivariate reference limits were derived from a thyroid-healthy control group (n=271) and applied to a clinically diverse sample (n=820) from a prospective study, comparing their diagnostic efficiency with the conventional method.ResultsThe following 95% reference limits were derived from the control group: (i) separate reference intervals for TSH, free thyroxine (FT4) and free triiodothyronine (FT3); (ii) bivariate composite reference limits for the logarithmically transformed TSH and FT4, and (iii) trivariate composite reference limits including all three parameters. A multivariate approach converts the “rectangular” or “cuboid” graphical representations of the independent parameters into an ellipse or ellipsoid. When applying these reference limits to the clinical sample, thyroid dysfunctions were classified differently, compared with the separate method, in 6.3 or 12% of all cases by the bivariate or trivariate method respectively. Of the established dysfunctions according to the separate intervals, 26% were reclassified to “euthyroid” by using the bivariate limit. Discrepancies from the laboratory-evaluated reference range were less pronounced.ConclusionsFrequent divergencies between composite multivariate reference limits and a combination of separate univariate reference intervals suggest that statistical analytic techniques may heavily influence thyroid disease classification. This challenges the validity of the conjoined roles of TSH currently employed as both a sensitive screening test and a reliable classification tool for thyroid disease.
El cuerpo maltratado, sinécdoque de la violencia de género en la literatura vasca
Authors: Lasarte Gema 
Published: March 2016

Este artículo analiza dos novelas de autoría femenina: Tango Urdina, de Aitziber Etxeberria, que trata especificamente sobre el maltrato, y Aulki Jokoa, de Uxue Alberdi, que aborda el tema de la violencia sufrida por las mujeres en tiempos de guerra. Estas dos novelas se han puesto en comparación con otras tres novelas contemporáneas de autoría masculina: Zoaz infernura, laztana, de Anjel Lertzundi; Zureak egin du, de Iñaki Friera, y Golgota, de Xabier Montoya. Las dos primeras tienen como eje temático los malos tratos y la última incorpora el tema de la violencia ejercida contra las mujeres en las contiendas bélicas.
Detecting and Quantifying Changing Selection Intensities from Time-Sampled Polymorphism Data
Authors: Shim Hyunjin , Laurent Stefan , Matuszewski Sebastian , Foll Matthieu , Jensen Jeffrey D 
Published: March 2016

AbstractDuring his well-known debate with Fisher regarding the phenotypic dataset of Panaxia dominula, Wright suggested fluctuating selection as a potential explanation for the observed change in allele frequencies. This model has since been invoked in a number of analyses, with the focus of discussion centering mainly on random or oscillatory fluctuations of selection intensities. Here, we present a novel method to consider nonrandom changes in selection intensities using Wright-Fisher approximate Bayesian (ABC)-based approaches, in order to detect and evaluate a change in selection strength from time-sampled data. This novel method jointly estimates the position of a change point as well as the strength of both corresponding selection coefficients (and dominance for diploid cases) from the allele trajectory. The simulation studies of this method reveal the combinations of parameter ranges and input values that optimize performance, thus indicating optimal experimental design strategies. We apply this approach to both the historical dataset of P. dominula in order to shed light on this historical debate, as well as to whole-genome time-serial data from influenza virus in order to identify sites with changing selection intensities in response to drug treatment.
Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174
Authors: Baker Christopher W , Miller Craig R , Thaweethai Tanayott , Yuan Jeffrey , Baker Meghan Hollibaugh , Joyce Paul , Weinreich Daniel M 
Published: March 2016

Abstract
Researchers in evolutionary genetics recently have recognized an exciting opportunity in decomposing beneficial mutations into their proximal, mechanistic determinants. The application of methods and concepts from molecular biology and life history theory to studies of lytic bacteriophages (phages) has allowed them to understand how natural selection sees mutations influencing life history. This work motivated the research presented here, in which we explored whether, under consistent experimental conditions, small differences in the genome of bacteriophage φX174 could lead to altered life history phenotypes among a panel of eight genetically distinct clones. We assessed the clones’ phenotypes by applying a novel statistical framework to the results of a serially sampled parallel infection assay, in which we simultaneously inoculated each of a large number of replicate host volumes with ∼1 phage particle. We sequentially plated the volumes over the course of infection and counted the plaques that formed after incubation. These counts served as a proxy for the number of phage particles in a single volume as a function of time. From repeated assays, we inferred significant, genetically determined heterogeneity in lysis time and burst size, including lysis time variance. These findings are interesting in light of the genetic and phenotypic constraints on the single-protein lysis mechanism of φX174. We speculate briefly on the mechanisms underlying our results, and we discuss the potential importance of lysis time variance in viral evolution.
The Genetic Linkage Map of the Medicinal Mushroom Agaricus subrufescens Reveals Highly Conserved Macrosynteny with the Congeneric Species Agaricus bisporus
Authors: Foulongne-Oriol Marie , Rocha de Brito Manuela , Cabannes Delphine , Clément Aurélien , Spataro Cathy , Moinard Magalie , Dias Eustáquio Souza , Callac Philippe , Savoie Jean-Michel 
Published: March 2016

Abstract
Comparative linkage mapping can rapidly facilitate the transfer of genetic information from model species to orphan species. This macrosynteny analysis approach has been extensively used in plant species, but few example are available in fungi, and even fewer in mushroom crop species. Among the latter, the Agaricus genus comprises the most cultivable or potentially cultivable species. Agaricus bisporus, the button mushroom, is the model for edible and cultivable mushrooms. We have developed the first genetic linkage map for the basidiomycete A. subrufescens, an emerging mushroom crop known for its therapeutic properties and potential medicinal applications. The map includes 202 markers distributed over 16 linkage groups (LG), and covers a total length of 1701 cM, with an average marker spacing of 8.2 cM. Using 96 homologous loci, we also demonstrated the high level of macrosynteny with the genome of A. bisporus. The 13 main LG of A. subrufescens were syntenic to the 13 A. bisporus chromosomes. A disrupted synteny was observed for the three remaining A. subrufescens LG. Electronic mapping of a collection of A. subrufescens expressed sequence tags on A. bisporus genome showed that the homologous loci were evenly spread, with the exception of a few local hot or cold spots of homology. Our results were discussed in the light of Agaricus species evolution process. The map provides a framework for future genetic or genomic studies of the medicinal mushroom A. subrufescens.
Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data
Authors: Sanjak Jaleal S , Long Anthony D , Thornton Kevin R 
Published: March 2016

AbstractGenome-wide association studies (GWAS) have associated many single variants with complex disease, yet the better part of heritable complex disease risk remains unexplained. Analytical tools designed to work under specific population genetic models are needed. Rare variants are increasingly shown to be important in human complex disease, but most existing GWAS data do not cover rare variants. Explicit population genetic models predict that genes contributing to complex traits and experiencing recurrent, unconditionally deleterious, mutation will harbor multiple rare, causative mutations of subtle effect. It is difficult to identify genes harboring rare variants of large effect that contribute to complex disease risk via the single marker association tests typically used in GWAS. Gene/region-based association tests may have the power detect associations by combining information from multiple markers, but have yielded limited success in practice. This is partially because many methods have not been widely applied. Here, we empirically demonstrate the utility of a procedure based on the rank truncated product (RTP) method, filtered to reduce the effects of linkage disequilibrium. We apply the procedure to the Wellcome Trust Case Control Consortium (WTCCC) data set, and uncover previously unidentified associations, some of which have been replicated in much larger studies. We show that, in the absence of significant rare variant coverage, RTP based methods still have the power to detect associated genes. We recommend that RTP-based methods be applied to all existing GWAS data to maximize the usefulness of those data. For this, we provide efficient software implementing our procedure.
Sequence of the Gonium pectorale Mating Locus Reveals a Complex and Dynamic History of Changes in Volvocine Algal Mating Haplotypes
Authors: Hamaji Takashi , Mogi Yuko , Ferris Patrick J , Mori Toshiyuki , Miyagishima Shinya , Kabeya Yukihiro , Nishimura Yoshiki , Toyoda Atsushi , Noguchi Hideki , Fujiyama Asao , Olson Bradley J S C , Marriage Tara N , Nishii Ichiro , Umen James G , Nozaki Hisayoshi 
Published: March 2016

Abstract
Sex-determining regions (SDRs) or mating-type (MT) loci in two sequenced volvocine algal species, Chlamydomonas reinhardtii and Volvox carteri, exhibit major differences in size, structure, gene content, and gametolog differentiation. Understanding the origin of these differences requires investigation of MT loci from related species. Here, we determined the sequences of the minus and plus MT haplotypes of the isogamous 16-celled volvocine alga, Gonium pectorale, which is more closely related to the multicellular V. carteri than to C. reinhardtii. Compared to C. reinhardtii MT, G. pectorale MT is moderately larger in size, and has a less complex structure, with only two major syntenic blocs of collinear gametologs. However, the gametolog content of G. pectorale MT has more overlap with that of V. carteri MT than with C. reinhardtii MT, while the allelic divergence between gametologs in G. pectorale is even lower than that in C. reinhardtii. Three key sex-related genes are conserved in G. pectorale MT: GpMID and GpMTD1 in MT–, and GpFUS1 in MT+. GpFUS1 protein exhibited specific localization at the plus-gametic mating structure, indicating a conserved function in fertilization. Our results suggest that the G. pectorale–V. carteri common ancestral MT experienced at least one major reformation after the split from C. reinhardtii, and that the V. carteri ancestral MT underwent a subsequent expansion and loss of recombination after the divergence from G. pectorale. These data begin to polarize important changes that occurred in volvocine MT loci, and highlight the potential for discontinuous and dynamic evolution in SDRs.
A HAND2 Loss-of-Function Mutation Causes Familial Ventricular Septal Defect and Pulmonary Stenosis
Authors: Sun Yu-Min , Wang Jun , Qiu Xing-Biao , Yuan Fang , Li Ruo-Gu , Xu Ying-Jia , Qu Xin-Kai , Shi Hong-Yu , Hou Xu-Min , Huang Ri-Tai , Xue Song , Yang Yi-Qing 
Published: March 2016

AbstractCongenital heart disease (CHD) is the most common developmental abnormality, and is the leading noninfectious cause of mortality in neonates. Increasing evidence demonstrates that genetic defects play an important role in the pathogenesis of CHD. However, CHD exhibits substantial heterogeneity, and the genetic determinants for CHD remain unknown in the overwhelming majority of cases. In the current study, the coding exons and flanking introns of the HAND2 gene, which encodes a basic helix-loop-helix transcription factor essential for normal cardiovascular development, were sequenced in 192 unrelated patients with CHD, and a novel heterozygous mutation, p.S65I, was identified in a patient with congenital ventricular septal defect (VSD). Genetic analysis of the index patient’s pedigree revealed that the mutation was present in all seven affected family members available, but absent in the 13 unaffected family members examined. Besides, in addition to VSD, five of the proband’s close relatives also had pulmonary stenosis (PS), and the proband’s son also had double outlet right ventricle (DORV). The missense mutation, which altered an evolutionarily conserved amino acid, was absent in 300 unrelated, ethnically matched healthy individuals. Biological analyses using a dual-luciferase reporter assay system showed that the mutant HAND2 was associated with significantly diminished transcriptional activity. Furthermore, the mutation abolished the synergistic activation between HAND2 and GATA4, as well as NKX2.5—two other cardiac core transcriptional factors that have been causally linked to CHD. These findings indicate that HAND2 loss-of-function mutation contributes to human CHD, perhaps via its interaction with GATA4 and NKX2.5.
Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species
Authors: Jung Paul P , Sigwalt Anastasie , Ohnuki Shinsuke , de Montigny Jacky , Ohya Yoshikazu , Schacherer Joseph 
Published: March 2016

Abstract
It is now clear that the exploration of the genetic and phenotypic diversity of nonmodel species greatly improves our knowledge in biology. In this context, we recently launched a population genomic analysis of the protoploid yeast Lachancea kluyveri (formerly Saccharomyces kluyveri), highlighting a broad genetic diversity (π = 17 × 10−3) compared to the yeast model organism, S. cerevisiae (π = 4 × 10−3). Here, we sought to generate a comprehensive view of the phenotypic diversity in this species. In total, 27 natural L. kluyveri isolates were subjected to trait profiling using the following independent approaches: (i) analyzing growth in 55 growth conditions and (ii) investigating 501 morphological changes at the cellular level. Despite higher genetic diversity, the fitness variance observed in L. kluyveri is lower than that in S. cerevisiae. However, morphological features show an opposite trend. In addition, there is no correlation between the origins (ecological or geographical) of the isolate and the phenotypic patterns, demonstrating that trait variation follows neither population history nor source environment in L. kluyveri. Finally, pairwise comparisons between growth rate correlation and genetic diversity show a clear decrease in phenotypic variability linked to genome variation increase, whereas no such a trend was identified for morphological changes. Overall, this study reveals for the first time the phenotypic diversity of a distantly related species to S. cerevisiae. Given its genetic properties, L. kluyveri might be useful in further linkage mapping analyses of complex traits, and could ultimately provide a better insight into the evolution of the genotype–phenotype relationship across yeast species.
Latitudinal Clines of the Human Vitamin D Receptor and Skin Color Genes
Authors: Tiosano Dov , Audi Laura , Climer Sharlee , Zhang Weixiong , Templeton Alan R , Fernández-Cancio Monica , Gershoni-Baruch Ruth , Sánchez-Muro José Miguel , El Kholy Mohamed , Hochberg Zèev 
Published: March 2016

AbstractThe well-documented latitudinal clines of genes affecting human skin color presumably arise from the need for protection from intense ultraviolet radiation (UVR) vs. the need to use UVR for vitamin D synthesis. Sampling 751 subjects from a broad range of latitudes and skin colors, we investigated possible multilocus correlated adaptation of skin color genes with the vitamin D receptor gene (VDR), using a vector correlation metric and network method called BlocBuster. We discovered two multilocus networks involving VDR promoter and skin color genes that display strong latitudinal clines as multilocus networks, even though many of their single gene components do not. Considered one by one, the VDR components of these networks show diverse patterns: no cline, a weak declining latitudinal cline outside of Africa, and a strong in- vs. out-of-Africa frequency pattern. We confirmed these results with independent data from HapMap. Standard linkage disequilibrium analyses did not detect these networks. We applied BlocBuster across the entire genome, showing that our networks are significant outliers for interchromosomal disequilibrium that overlap with environmental variation relevant to the genes’ functions. These results suggest that these multilocus correlations most likely arose from a combination of parallel selective responses to a common environmental variable and coadaptation, given the known Mendelian epistasis among VDR and the skin color genes.
Embryonal Control of Yellow Seed Coat Locus ECY1 Is Related to Alanine and Phenylalanine Metabolism in the Seed Embryo of Brassica napus
Authors: Wang Fulin , He Jiewang , Shi Jianghua , Zheng Tao , Xu Fei , Wu Guanting , Liu Renhu , Liu Shengyi 
Published: March 2016

Abstract
Seed coat color is determined by the type of pigment deposited in the seed coat cells. It is related to important agronomic traits of seeds such as seed dormancy, longevity, oil content, protein content and fiber content. In Brassica napus, inheritance of seed coat color is related to maternal effects and pollen effects (xenia effects). In this research we isolated a mutation of yellow seeded B. napus controlled by a single Mendelian locus, which is named Embryonal Control of Yellow seed coat 1 (Ecy1). Microscopy of transverse sections of the mature seed show that pigment is deposited only in the outer layer of the seed coat. Using Illumina Hisequation 2000 sequencing technology, a total of 12 GB clean data, 116× coverage of coding sequences of B. napus, was achieved from seeds 26 d after pollination (DAP). It was assembled into 172,238 independent transcripts, and 55,637 unigenes. A total of 139 orthologous genes of Arabidopsis transparent testa (TT) genes were mapped in silico to 19 chromosomes of B. napus. Only 49 of the TT orthologous genes are transcribed in seeds. However transcription of all orthologs was independent of embryonal control of seed coat color. Only 55 genes were found to be differentially expressed between brown seeds and the yellow mutant. Of these 55, 50 were upregulated and five were downregulated in yellow seeds as compared to their brown counterparts. By KEGG classification, 14 metabolic pathways were significantly enriched. Of these, five pathways: phenylpropanoid biosynthesis, cyanoamino acid metabolism, plant hormone signal transduction, metabolic pathways, and biosynthesis of secondary metabolites, were related with seed coat pigmentation. Free amino acid quantification showed that Ala and Phe were present at higher levels in the embryos of yellow seeds as compared to those of brown seeds. This increase was not observed in the seed coat. Moreover, the excess amount of free Ala was exactly twice that of Phe in the embryo. The pigment substrate chalcone is synthesized from two molecules of Ala and one molecule of Phe. The correlation between accumulation of Ala and Phe, and disappearance of pigment in the yellow seeded mutant, suggests that embryonal control of seed coat color is related with Phe and Ala metabolism in the embryo of B. napus.
Staufen Negatively Modulates MicroRNA Activity in Caenorhabditis elegans
Authors: Ren Zhiji , Veksler-Lublinsky Isana , Morrissey David , Ambros Victor 
Published: March 2016

Abstract
The double-stranded RNA-binding protein Staufen has been implicated in various posttranscriptional gene regulatory processes. Here, we demonstrate that the Caenorhabditis elegans homolog of Staufen, STAU-1, functionally interacts with microRNAs. Loss-of-function mutations of stau-1 significantly suppress phenotypes of let-7 family microRNA mutants, a hypomorphic allele of dicer, and a lsy-6 microRNA partial loss-of-function mutant. Furthermore, STAU-1 modulates the activity of lin-14, a target of lin-4 and let-7 family microRNAs, and this modulation is abolished when the 3′ untranslated region of lin-14 is removed. Deep sequencing of small RNA cDNA libraries reveals no dramatic change in the levels of microRNAs or other small RNA populations between wild-type and stau-1 mutants, with the exception of certain endogenous siRNAs in the WAGO pathway. The modulation of microRNA activity by STAU-1 does not seem to be associated with the previously reported enhanced exogenous RNAi (Eri) phenotype of stau-1 mutants, since eri-1 exhibits the opposite effect on microRNA activity. Altogether, our results suggest that STAU-1 negatively modulates microRNA activity downstream of microRNA biogenesis, possibly by competing with microRNAs for binding on the 3′ untranslated region of target mRNAs.