bluuebunny/crossref_metadata_2025_split huggingface dataset:
Periodontal therapy decreases serum levels of adipocyte fatty acid‐binding protein in systemically healthy subjects: a pilot clinical trial
Authors: Li X. , Tse H. F. , Yiu K. H. , Zhang C. , Jin L. J. 
Published: October 2012

Background and ObjectiveAdipocyte fatty acid‐binding protein (A‐FABP) is expressed in adipocytes, macrophages and microvascular endothelial cells, and it plays a central role in inflammation, atherosclerosis and metabolic responses. This pilot study investigated the effect of nonsurgical periodontal therapy on the serum levels of A‐FABP in subjects with chronic periodontitis.Material and MethodsA pilot clinical trial was conducted in 24 otherwise healthy Chinese subjects with moderate to severe chronic periodontitis. The treatment group (n = 12) received nonsurgical periodontal therapy immediately, whereas in the control group (n = 12) the treatment was delayed for 3 months. The serum levels of A‐FABP were measured by ELISAs. Other inflammatory and endothelial biomarkers and periodontal conditions were evaluated at baseline and at the 3‐month follow‐up appointment.ResultsA‐FABP levels decreased significantly in the treatment group compared with the control group (treatment effect: −1.7 ng/mL; 95% confidence interval: −2.8 to −0.6; p = 0.003). The treatment also significantly improved periodontal conditions but had no significant effect on other biomarkers. In the multivariable regression model, the change in the percentage of sites with detectable plaque was significantly associated with the change in the level of A‐FABP (beta: 0.04, 95% confidence interval: 0.01–0.06, p = 0.004).ConclusionWithin the limitations of this pilot study, the current findings suggest that treatment of periodontitis may significantly decrease the serum levels of A‐FABP. Further longitudinal study with a large sample size is warranted to confirm this finding and elaborate the relevant clinical implications.
Sleep‐Wake profiles in patients with primary biliary cirrhosis
Authors: Montagnese Sara , Nsemi Letizia M. , Cazzagon Nora , Facchini Silvia , Costa Laura , Bergasa Nora V. , Amodio Piero , Floreani Annarosa 
Published: October 2012

AbstractBackgroundImpaired sleep quality and daytime sleepiness have been described in patients with primary biliary cirrhosis (PBC). However, no information is available on their sleep timing/diurnal preference.AimsTo evaluate such variables and determine their relationship with sleep quality, fatigue, pruritus and quality of life.MethodsSeventy‐four patients with PBC (58 ± 12 years), 79 healthy volunteers (56 ± 8 years) and 60 patients with cirrhosis (58 ± 12 years) underwent formal assessment of sleep quality/timing, diurnal preference and daytime sleepiness. Patients with PBC also underwent assessment of fatigue, quality of life and the daytime course of sleepiness/pruritus.ResultsSleep timing was significantly delayed in both patients with PBC and with cirrhosis, compared to healthy volunteers (sleep onset time: 23:18 ± 01:00 vs. 23:30 ± 01:00 vs. 22:54 ± 00:54 hours, respectively; P < 0.05). In patients with PBC, delayed sleep timing was associated with impaired sleep quality (P < 0.05). Sleepiness showed a physiological daily rhythm, with early afternoon/evening peaks. Pruritus was absent in the morning and increased over the afternoon/evening hours. Both the daytime course of pruritus and sleepiness changed in relation to diurnal preference. Patients with PBC and significant pruritus (upper quartile) had prolonged sleep latency (39 ± 37 vs. 21 ± 23 min, P = 0.05) and earlier wake‐up times (5.9 ± 0.8 vs. 6.7 ± 0.9 min, P < 0.05). Significant correlations were observed between sleep timing and quality of life.ConclusionsPatients with PBC exhibited a delay in sleep timing that was associated with impaired sleep quality/quality of life. In addition, an interplay was observed between diurnal preference and the daytime course of pruritus/sleepiness.
Liver transplantation for overlap syndromes of autoimmune liver diseases
Authors: Bhanji Rahima A. , Mason Andrew L. , Girgis Safwat , Montano‐Loza Aldo J. 
Published: October 2012

AbstractBackground/AimsThe term overlap syndrome describes variant forms of autoimmune hepatitis (AIH) that present in combination with either characteristics of primary biliary cirrhosis (PBC), or primary sclerosing cholangitis (PSC). This study analysed the outcomes and evidence of recurrent liver disease after liver transplantation in patients with overlap syndromes compared with patients transplanted for single autoimmune liver disease.MethodsWe evaluated 231 adult patients who received a liver transplant as a result of autoimmune liver diseases; including 103 with PBC, 84 with PSC, 32 with AIH and 12 with overlap syndrome (7 AIH‐PBC and 5 AIH‐PSC).ResultsPatients with overlap syndromes had a higher probability of recurrence than patients with a single autoimmune liver disease (5 years: 53% vs. 17%; 10 years 69% vs. 29%, P = 0.001). Furthermore, median time for recurrence in overlap syndrome was shorter when compared with patients with single autoimmune liver disease (67 ± 20 vs. 172 ± 9 months, P = 0.001). The diagnosis of overlap syndrome was independently associated with a higher risk to develop recurrent disease than patients transplanted with a single disease (HR 3.39, P = 0.007). Median graft survival for overlap syndrome was 123 ± 16 months and 180 ± 8 months in patients with single autoimmune liver diseases (P = 0.9), and median patient survival for overlap syndrome was 135 ± 13 months and 193 ± 8 months in patients with single autoimmune liver disease (P = 0.6).ConclusionsPatients that received an allograft for end‐stage liver disease secondary to overlap syndrome had a higher rate of disease recurrence when compared with transplant recipients with single autoimmune liver disorders, but the overall survival was comparable.
Non‐IBD immunological diseases are a risk factor for reduced survival in PSC
Authors: Rupp Christian , Mummelthei Anne , Sauer Peter , Weiss Karl H. , Schirmacher Peter , Stiehl Adolf , Stremmel Wolfgang , Gotthardt Daniel N. 
Published: October 2012

AbstractBackgroundPrimary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease. It is known to be associated with immunological diseases (IDs), such as inflammatory bowel disease (IBD) and autoimmune hepatitis (AIH).AimWe evaluated the presence of IDs besides IBD and AIH in a cohort of PSC patients, and its association with clinical outcome.MethodsThis is a prospective cohort study of 195 PSC patients that were evaluated over the period 1987–2010 in our tertiary care centre. The presence of ID was determined using a retrospective chart review. IDs were subclassified into autoimmune disease (AID) and immune‐mediated inflammatory disease (IMID), according to current guidelines.ResultsTwenty‐seven of 195 (13.8%) PSC patients had at least one additional ID other than IBD (70%) or AIH (5%). The most frequent AIDs were autoimmune thyroiditis (2.6%) and diabetes mellitus type 1 (2.1%). The most frequent IMIDs were psoriasis (3.6%) and sarcoidosis (2.1%). After more than 20 years of follow‐up, concomitant IDs represent an independent risk factor for reduced transplantation‐free survival in patients with PSC (mean: 8.9 years vs. 16.3 years, P = 0.012). Further subgroup analysis revealed a significantly reduced survival especially in patients with concomitant IMID (P = 0.017).ConclusionPatients with concomitant IDs, especially IMID, are a clinically important subgroup of PSC patients. This significant phenotype warrants further genetic and immunological studies.
When gender matters: new insights into the relationships between social systems and the genetic structure of human populations
Authors: Destro Bisol Giovanni , Capocasa Marco , Anagnostou Paolo 
Published: October 2012

Due to its important effects on the ecological dynamics and the genetic structure of species, biologists have long been interested in gender‐biased dispersal, a condition where one gender is more prone to move from the natal site. More recently, this topic has attracted a great attention from human evolutionary geneticists. Considering the close relations between residential rules and social structure, gender‐biased dispersal is, in fact, regarded as an important case study concerning the effects of socio‐cultural factors on human genetic variation. It all started with the seminal paper by Mark Seielstad, Erich Minch and Luigi Luca Cavalli Sforza from Stanford University (Seielstad et al. 1998). They observed a larger differentiation for Y‐chromosome than mitochondrial DNA between extant human populations, purportedly a consequence of the prevalence of long‐term patrilocality in human societies. Subsequent studies, however, have highlighted the need to consider geographically close and culturally homogeneous groups, disentangle signals due to different peopling events and obtain unbiased estimates of genetic diversity. In this issue of Molecular Ecology, not only do Marks et al. (2012) adopt an experimental design which addresses these concerns, but they also take a further and important step forward by integrating the genetic analysis of two distant populations, the Basotho and Spanish, with data regarding migration rates and matrimonial distances. Using both empirical evidence and simulations, the authors show that female‐biased migration due to patrilocality might shape the genetic structure of human populations only at short ranges and under substantial differences in migration rates between genders. Providing a quantitative framework for future studies of the effects of residential rules on the human genome, this study paves the way for further developments in the field. On a wider perspective, Marks et al.'s work demonstrates the power of approaches which integrate biological, cultural and demographic lines of evidence in the study of relations between social and genetic structures of human populations.
Localizing FST outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation‐with‐gene‐flow
Authors: Via Sara , Conte Gina , Mason‐Foley Casey , Mills Kelly 
Published: October 2012

AbstractPopulations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence‐with‐gene‐flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing FST outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis that between‐population recombination and gene exchange are reduced over large ‘divergence hitchhiking’ (DH) regions. As expected under divergence hitchhiking, our map confirms that QTL and divergent markers cluster together in multiple large genomic regions. Under divergence hitchhiking, the nonoutlier markers within these regions should show signs of reduced gene exchange relative to nonoutlier markers in genomic regions where ongoing gene flow is expected. We use this predicted difference among nonoutliers to perform a critical test of divergence hitchhiking. Results show that nonoutlier markers within clusters of FST outliers and QTL resolve the genetic population structure of the two host races nearly as well as the outliers themselves, while nonoutliers outside DH regions reveal no population structure, as expected if they experience more gene flow. These results provide clear evidence for divergence hitchhiking, a mechanism that may dramatically facilitate the process of speciation‐with‐gene‐flow. They also show the power of integrating genome scans with genetic analyses of the phenotypic traits involved in local adaptation and population divergence.
Genome‐wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
Authors: Wagner Catherine E. , Keller Irene , Wittwer Samuel , Selz Oliver M. , Mwaiko Salome , Greuter Lucie , Sivasundar Arjun , Seehausen Ole 
Published: October 2012

AbstractAlthough population genomic studies using next generation sequencing (NGS) data are becoming increasingly common, studies focusing on phylogenetic inference using these data are in their infancy. Here, we use NGS data generated from reduced representation genomic libraries of restriction‐site‐associated DNA (RAD) markers to infer phylogenetic relationships among 16 species of cichlid fishes from a single rocky island community within Lake Victoria's cichlid adaptive radiation. Previous attempts at sequence‐based phylogenetic analyses in Victoria cichlids have shown extensive sharing of genetic variation among species and no resolution of species or higher‐level relationships. These patterns have generally been attributed to the very recent origin (<15 000 years) of the radiation, and ongoing hybridization between species. We show that as we increase the amount of sequence data used in phylogenetic analyses, we produce phylogenetic trees with unprecedented resolution for this group. In trees derived from our largest data supermatrices (3 to >5.8 million base pairs in width), species are reciprocally monophyletic with high bootstrap support, and the majority of internal branches on the tree have high support. Given the difficulty of the phylogenetic problem that the Lake Victoria cichlid adaptive radiation represents, these results are striking. The strict interpretation of the topologies we present here warrants caution because many questions remain about phylogenetic inference with very large genomic data set and because we can with the current analysis not distinguish between effects of shared ancestry and post‐speciation gene flow. However, these results provide the first conclusive evidence for the monophyly of species in the Lake Victoria cichlid radiation and demonstrate the power that NGS data sets hold to resolve even the most difficult of phylogenetic challenges.
The extreme disjunction between Beringia and Europe in Ranunculus glacialis s. l. (Ranunculaceae) does not coincide with the deepest genetic split – a story of the importance of temperate mountain ranges in arctic–alpine phylogeography
Authors: Ronikier M. , Schneeweiss G. M. , Schönswetter P. 
Published: October 2012

AbstractThe arctic–alpine Ranunculus glacialis s. l. is distributed in high‐mountain ranges of temperate Europe and in the North, where it displays an extreme disjunction between the North Atlantic Arctic and Beringia. Based on comprehensive sampling and employing plastid and nuclear marker systems, we (i) test whether the European/Beringian disjunction correlates with the main evolutionary diversification, (ii) reconstruct the phylogeographic history in the Arctic and in temperate mountains and (iii) assess the susceptibility of arctic and mountain populations to climate change. Both data sets revealed several well‐defined lineages, mostly with a coherent geographic distribution. The deepest evolutionary split did not coincide with the European/Beringian disjunction but occurred within the Alps. The Beringian lineage and North Atlantic Arctic populations, which reached their current distribution via rapid postglacial colonization, show connections to two divergent pools of Central European populations. Thus, immigration into the Arctic probably occurred at least twice. The presence of a rare cpDNA lineage related to Beringia in the Carpathians supports the role of these mountains as a stepping stone between temperate Europe and the non‐European Arctic, and as an important area of high‐mountain biodiversity. The temperate and arctic ranges presented contrasting phylogeographic histories: a largely static distribution in the former and rapid latitudinal spread in the latter. The persistence of ancient lineages with a strictly regional distribution suggests that the ability of R. glacialis to survive repeated climatic changes within southern mountain ranges is greater than what recently was predicted for alpine plants from climatic envelope modelling.
Consequences of a poecilogonous life history for genetic structure in coastal populations of the polychaete Streblospio benedicti
Authors: Zakas Christina , Wares John P. 
Published: October 2012

AbstractIn many species, alternative developmental pathways lead to the production of two distinct phenotypes, promoting the evolution of morphological novelty and diversification. Offspring type in marine invertebrates influences transport time by ocean currents, which dictate dispersal potential and gene flow, and thus has sweeping evolutionary effects on the potential for local adaptation and on rates of speciation, extinction and molecular evolution. Here, we use the polychaete Streblospio benedicti to investigate the effects of dimorphic offspring type on gene flow and genetic structure in coastal populations. We use 84 single nucleotide polymorphism (SNP) markers for this species to assay populations on the East and West Coasts of the United States. Using these markers, we found that in their native East Coast distribution, populations of S. benedicti have high‐population genetic structure, but this structure is associated primarily with geographic separation rather than developmental differences. Interestingly, very little genetic differentiation is recovered between individuals of different development types when they occur in the same or nearby populations, further supporting that this is a true case of poecilogony. In addition, we were able to demonstrate that the recently introduced (~100 ya) West Coast populations probably originated from a lecithotrophic population near Delaware.
The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps
Authors: Mosca E. , Eckert A. J. , Di Pierro E. A. , Rocchini D. , La Porta Nicola , Belletti P. , Neale D. B. 
Published: October 2012

AbstractClimate is one of the most important drivers of local adaptation in forest tree species. Standing levels of genetic diversity and structure within and among natural populations of forest trees are determined by the interplay between climatic heterogeneity and the balance between selection and gene flow. To investigate this interplay, single nucleotide polymorphisms (SNPs) were genotyped in 24 to 37 populations from four subalpine conifers, Abies alba Mill., Larix decidua Mill., Pinus cembra L. and Pinus mugo Turra, across their natural ranges in the Italian Alps and Apennines. Patterns of population structure were apparent using a Bayesian clustering program, STRUCTURE, which identified three to five genetic groups per species. Geographical correlates with these patterns, however, were only apparent for P. cembra. Multivariate environmental variables [i.e. principal components (PCs)] were subsequently tested for association with SNPs using a Bayesian generalized linear mixed model. The majority of the SNPs, ranging from six in L. decidua to 18 in P. mugo, were associated with PC1, corresponding to winter precipitation and seasonal minimum temperature. In A. alba, four SNPs were associated with PC2, corresponding to the seasonal minimum temperature. Functional annotation of those genes with the orthologs in Arabidopsis revealed several genes involved in abiotic stress response. This study provides a detailed assessment of population structure and its association with environment and geography in four coniferous species in the Italian mountains.
Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex
Authors: O'Neill Eric M. , Schwartz Rachel , Bullock C. Thomas , Williams Joshua S. , Shaffer H. Bradley , Aguilar‐Miguel X. , Parra‐Olea Gabriela , Weisrock David W. 
Published: October 2012

AbstractModern analytical methods for population genetics and phylogenetics are expected to provide more accurate results when data from multiple genome‐wide loci are analysed. We present the results of an initial application of parallel tagged sequencing (PTS) on a next‐generation platform to sequence thousands of barcoded PCR amplicons generated from 95 nuclear loci and 93 individuals sampled across the range of the tiger salamander (Ambystoma tigrinum) species complex. To manage the bioinformatic processing of this large data set (344 330 reads), we developed a pipeline that sorts PTS data by barcode and locus, identifies high‐quality variable nucleotides and yields phased haplotype sequences for each individual at each locus. Our sequencing and bioinformatic strategy resulted in a genome‐wide data set with relatively low levels of missing data and a wide range of nucleotide variation. structure analyses of these data in a genotypic format resulted in strongly supported assignments for the majority of individuals into nine geographically defined genetic clusters. Species tree analyses of the most variable loci using a multi‐species coalescent model resulted in strong support for most branches in the species tree; however, analyses including more than 50 loci produced parameter sampling trends that indicated a lack of convergence on the posterior distribution. Overall, these results demonstrate the potential for amplicon‐based PTS to rapidly generate large‐scale data for population genetic and phylogenetic‐based research.
Microsatellite length variation in candidate genes correlates with habitat in the gilthead sea bream Sparus aurata
Authors: Chaoui Lamya , Gagnaire Pierre‐Alexandre , Guinand Bruno , Quignard Jean‐Pierre , Tsigenopoulos Costas , Kara M. Hichem , Bonhomme François 
Published: October 2012

AbstractThe genetic basis and evolutionary implications of local adaptation in high gene flow marine organisms are still poorly understood. In several Mediterranean fish species, alternative migration patterns exist between individuals entering coastal lagoons that offer favourable conditions for growth and those staying in the sea where environmental conditions are less subject to rapid and stressful change. Whether these coexisting strategies are phenotypically plastic or include a role for local adaptation through differential survival needs to be determined. Here, we explore the genetic basis of alternate habitat use in western Mediterranean populations of the gilthead sea bream (Sparus aurata). Samples from lagoonal and open‐sea habitats were typed for three candidate gene microsatellite loci, seven anonymous microsatellites and 44 amplified fragment length polymorphism markers to test for genotype–environment associations. While anonymous markers globally indicated high levels of gene flow across geographic locations and habitats, non‐neutral differentiation patterns correlated with habitat type were found at two candidate microsatellite loci located in the promoter region of the growth hormone and prolactin genes. Further analysis of these two genes revealed that a mechanism based on habitat choice alone could not explain the distribution of genotype frequencies at a regional scale, thus implying a role for differential survival between habitats. We also found an association between allele size and habitat type, which, in the light of previous studies, suggests that polymorphisms in the proximal promoter region could influence gene expression by modulating transcription factor binding, thus providing a potential explanatory link between genotype and growth phenotype in nature.