bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod, Gadus morhua
Authors: BRADBURY IAN R. , HUBERT SOPHIE , HIGGINS BRENT , BOWMAN SHAREN , PATERSON IAN G. , SNELGROVE PAUL V. R. , MORRIS COREY J. , GREGORY ROBERT S. , HARDIE DAVID C. , BORZA TUDOR , BENTZEN PAUL 
Published: February 2011

AbstractThe increasing use of single nucleotide polymorphisms (SNPs) in studies of nonmodel organisms accentuates the need to evaluate the influence of ascertainment bias on accurate ecological or evolutionary inference. Using a panel of 1641 expressed sequence tag–derived SNPs developed for northwest Atlantic cod (Gadus morhua), we examined the influence of ascertainment bias and its potential impact on assignment of individuals to populations ranging widely in origin. We hypothesized that reductions in assignment success would be associated with lower diversity in geographical regions outside the location of ascertainment. Individuals were genotyped from 13 locations spanning much of the contemporary range of Atlantic cod. Diversity, measured as average sample heterozygosity and number of polymorphic loci, declined (c. 30%) from the western (He = 0.36) to eastern (He = 0.25) Atlantic, consistent with a signal of ascertainment bias. Assignment success was examined separately for pools of loci representing differing degrees of reductions in diversity. SNPs displaying the largest declines in diversity produced the most accurate assignment in the ascertainment region (c. 83%) and the lowest levels of correct assignment outside the ascertainment region (c. 31%). Interestingly, several isolated locations showed no effect of assignment bias and consistently displayed 100% correct assignment. Contrary to expectations, estimates of accurate assignment range‐wide using all loci displayed remarkable similarity despite reductions in diversity. Our results support the use of large SNP panels in assignment studies of high geneflow marine species. However, our evidence of significant reductions in assignment success using some pools of loci suggests that ascertainment bias may influence assignment results and should be evaluated in large‐scale assignment studies.
Outlier SNPs show more genetic structure between two Bay of Fundy metapopulations of Atlantic salmon than do neutral SNPs
Authors: FREAMO HEATHER , O’REILLY PATRICK , BERG PAUL R. , LIEN SIGBJØRN , BOULDING ELIZABETH G. 
Published: February 2011

AbstractAtlantic salmon of Eastern Canada were once of considerable importance to aboriginal, recreational, and commercial fisheries, yet many populations are now in decline, particularly those of the inner Bay of Fundy (iBoF), which were recently listed as endangered. We investigated whether nonneutral SNPs could be used to assign individual Atlantic salmon accurately to either the iBoF or the outer Bay of Fundy (oBoF) metapopulations because this has been difficult with existing neutral markers. We first searched for markers under diversifying selection by genotyping eight captively bred Bay of Fundy (BoF) populations for 320 SNP loci with the Sequenom MassARRAY™ system and then analysed the data set with four different FST outlier detection programs. Three outlier loci were identified by both BayesFST and BayeScan whereas seven outlier loci, including the three previously mentioned, were identified by both Fdist and Arlequin. A subset of 14 nonneutral SNPs was more accurate (85% accuracy) than a subset of 67 neutral SNPs (75% accuracy) at assigning individual salmon back to their metapopulation. We then chose a subset of nine outlier SNP markers and used them to inexpensively genotype archived DNA samples from seven wild BoF populations using Invader™ chemistry. Hierarchical AMOVA of these independent wild samples corroborated our previous findings of significant genetic differentiation between iBoF and oBoF salmon metapopulations. Our research shows that identifying and using outlier loci is an important step towards achieving the goal of consistently and accurately distinguishing iBoF from oBoF Atlantic salmon, which will aid in their conservation.
An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population
Authors: HAUSER LORENZ , BAIRD MELISSA , HILBORN RAY , SEEB LISA W. , SEEB JAMES E. 
Published: February 2011

AbstractBecause of their high variability, microsatellites are still considered the marker of choice for studies on parentage and kinship in wild populations. Nevertheless, single nucleotide polymorphisms (SNPs) are becoming increasing popular in many areas of molecular ecology, owing to their high‐throughput, easy transferability between laboratories and low genotyping error. An ongoing discussion concerns the relative power of SNPs compared to microsatellites—that is, how many SNP loci are needed to replace a panel of microsatellites? Here, we evaluate the assignment power of 80 SNPs (HE = 0.30, 80 independent alleles) and 11 microsatellites (HE = 0.85, 192 independent alleles) in a wild population of about 400 sockeye salmon with two commonly used software packages (Cervus3, Colony2) and, for SNPs only, a newly developed software (SNPPIT). Assignment success was higher for SNPs than for microsatellites, especially for parent pairs, irrespective of the method used. Colony2 assigned a larger proportion of offspring to at least one parent than the other methods, although Cervus and SNPPIT detected more parent pairs. Identification of full‐sib groups without parental information from relatedness measures was possible using both marker systems, although explicit reconstruction of such groups in Colony2 was impossible for SNPs because of computation time. Our results confirm the applicability of SNPs for parentage analyses and refute the predictability of assignment success from the number of independent alleles.
Next‐generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
Authors: HOHENLOHE PAUL A. , AMISH STEPHEN J. , CATCHEN JULIAN M. , ALLENDORF FRED W. , LUIKART GORDON 
Published: February 2011

AbstractThe increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to introgression. We used restriction‐site‐associated DNA sequencing to identify a dense set of candidate SNP loci with fixed allelic differences between introduced rainbow trout (Oncorhynchus mykiss) and native westslope cutthroat trout (Oncorhynchus clarkii lewisi). We distinguished candidate SNPs from homeologs (paralogs resulting from whole‐genome duplication) by detecting excessively high observed heterozygosity and deviations from Hardy–Weinberg proportions. We identified 2923 candidate species‐specific SNPs from a single Illumina sequencing lane containing 24 barcode‐labelled individuals. Published sequence data and ongoing genome sequencing of rainbow trout will allow physical mapping of SNP loci for genome‐wide scans and will also provide flanking sequence for design of qPCR‐based TaqMan®assays for high‐throughput, low‐cost hybrid identification using a subset of 50–100 loci. This study demonstrates that it is now feasible to identify thousands of informative SNPs in nonmodel species quickly and at reasonable cost, even if no prior genomic information is available.
Sperm whale population structure in the eastern and central North Pacific inferred by the use of single‐nucleotide polymorphisms, microsatellites and mitochondrial DNA
Authors: MESNICK SARAH L. , TAYLOR BARBARA L. , ARCHER FREDERICK I. , MARTIEN KAREN K. , TREVIÑO SERGIO ESCORZA , HANCOCK‐HANSER BRITTANY L. , MORENO MEDINA SANDRA CAROLINA , PEASE VICTORIA L. , ROBERTSON KELLY M. , STRALEY JANICE M. , BAIRD ROBIN W. , CALAMBOKIDIS JOHN , SCHORR GREGORY S. , WADE PAUL , BURKANOV VLADIMIR , LUNSFORD CHRIS R. , RENDELL LUKE , MORIN PHILLIP A. 
Published: February 2011

AbstractWe use mitochondrial DNA (mtDNA) (400 bp), six microsatellites and 36 single‐nucleotide polymorphisms (SNPs), 20 of which were linked, to investigate population structure of sperm whales (Physeter macrocephalus) in the eastern and central North Pacific. SNP markers, reproducible across technologies and laboratories, are ideal for long‐term studies of globally distributed species such as sperm whales, a species of conservation concern because of both historical and contemporary impacts. We estimate genetic differentiation among three strata in the temperate to tropical waters where females are found: California Current, Hawai`i and the eastern tropical Pacific. We then consider how males on sub‐Arctic foraging grounds assign to these strata. The California Current stratum was differentiated from both the other strata (P < 0.05) for mtDNA, microsatellites and SNPs, suggesting that the region supports a demographically independent population and providing the first indication that males may exhibit reproductive philopatry. Comparisons between the Hawai`i stratum and the eastern tropical Pacific stratum are not conclusive at this time. Comparisons with Alaska males were statistically significant, or nearly so, from all three strata and individuals showed mixed assignment to, and few exclusions from, the three potential source strata, suggesting widespread origin of males on sub‐Arctic feeding grounds. We show that SNPs have sufficient power to detect population structure even when genetic differentiation is low. There is a need for better analytical methods for SNPs, especially when linked SNPs are used, but SNPs appear to be a valuable marker for long‐term studies of globally dispersed and highly mobile species.
The vitreomacular interface in retinal vein occlusion
Authors: Bertelmann Thomas , Kičová Nadia , Messerschmidt‐Roth Anke , Irle Sebastian , Sekundo Walter , Mennel Stefan 
Published: February 2011

Abstract.Purpose:  To evaluate the posterior vitreous adhesion status in patients with a history of central or branch retinal vein occlusion and to compare the results with the natural time‐course of posterior vitreous detachment in healthy age‐related controls.Methods:  A retrospective chart review in terms of the posterior vitreous adhesion status was performed in 132 patients (133 eyes) with a history of a central (CRVO) or branch (BRVO) retinal vein occlusion. All patients underwent vitrectomy. Based on the operation reports, the vitreous adhesion status was classified as attached, partially detached or completely detached. The results were compared to the natural time‐course of posterior vitreous detachment development in healthy age‐related controls.Results:  Eighty‐one eyes met the inclusion and exclusion criteria. Fifty‐two eyes (64%) had a history of CRVO and 29 eyes (36%) a history of BRVO, respectively. In the CRVO group, the posterior vitreous was attached in 47 eyes (90%) and completely detached in five eyes (10%). In the BRVO group, the posterior vitreous was attached in 27 eyes (93%), partially detached in 1 eye (3%) and completely detached in another eye (3%). A subdivision into age classes and a comparison with healthy age‐related controls [data by Weber‐Krause & Eckardt (1997) Ophthalmologe, 94, 619–623] showed in patients between 65 and 69 years of age an attached posterior vitreous cortex in 72% in healthy eyes, in 100% in CRVO (p = 0.109) and in 89% in BRVO (p = 0.440), in patients between 70 and 79 years of age an attached posterior vitreous cortex in 56% in healthy eyes, in 86% in CRVO (p = 0.010) and in 100% in BRVO (p = 0.038) and in patients between 80 and 89 years of age an attached posterior vitreous cortex in 43% in healthy eyes, in 100% in CRVO (p = 0.191) and in 67% in BRVO (p = 0.582) (Fisher’s exact t‐test).Conclusion:  In patients with a history of CRVO or BRVO, the posterior vitreous cortex stays attached more frequently in all age groups in comparison with the healthy age‐related controls.
Favourable outcome after cataract surgery with IOL implantation in uveitis associated with juvenile idiopathic arthritis
Authors: Grajewski Rafael S. , Zurek‐Imhoff Beatrix , Roesel Martin , Heinz Carsten , Heiligenhaus Arnd 
Published: February 2011

Abstract.Purpose:  Management of uveitic cataract in patients with juvenile idiopathic arthritis (JIA) is challenging, and intraocular lens (IOL) implantation is controversial. This study investigated the outcome after minimally invasive surgery with IOL implantation.Methods:  Retrospective analysis after phacoemulsification with in‐the‐bag IOL implantation was performed in 16 patients (17 operations) with ANA‐positive JIA‐associated chronic uveitis. In these patients, 25 G capsulectomy and anterior vitrectomy was performed and they received an intravitreal triamcinolone (TA) injection.Results:  Mean age at uveitis onset was 5 ± 2 years, and surgery was performed at a mean age of 11 ± 2.2 years. Preoperatively, uveitis was inactive in all patients, and visual acuity was logMAR 0.8 ± 0.44; additional uveitis complications were present in all patients, and 15 patients were receiving systemic immunosuppression/biologicals.After surgery (mean follow‐up 26.5 ± 11.7 months), presence of cystoid macular oedema, papilloedema, ocular hypertension/glaucoma and hypotony did not increase compared with baseline. There was no significant worsening of AC inflammation (by cell numbers and laser flare values). IOL deposits persisted in four patients, and synechiae developed in eight. The visual acuity was improved (≥2 lines) in all patients (mean logMAR 0.3 ± 0.24). Retrolental membrane formation was not noted. Secondary capsular opacification was observed in seven patients, requiring Nd:YAG capsulotomy in five of them.Conclusions:  Phacoemulsification and in‐the‐bag IOL implantation may improve visual outcome in JIA‐associated uveitis with minimally invasive surgical technique and intravitreal TA injection. Well‐controlled uveitis with appropriate use of topical steroids and systemic immunosuppression or biologicals appears as a perioperative requirement.
Normal tension glaucoma and Alzheimer disease: comorbidity?
Authors: Bach‐Holm Daniella , Kessing Svend Vedel , Mogensen Ulla , Forman Julie Lyng , Andersen Per Kragh , Kessing Lars Vedel 
Published: February 2011

Abstract.Purpose:  To investigate whether normal tension glaucoma (NTG) is associated with increased risk of developing dementia/Alzheimer disease (AD).Methods:  A total of 69 patients with NTG were identified in the case note files in the Glaucoma Clinic, University Hospital of Copenhagen (Rigshospitalet), Denmark from 1980 to 2001. The rate of a subsequent diagnosis of dementia as recorded in nationwide health care registers from 1980 to 2005 was estimated and compared with the rate for the general population [standard mortality rate (SMR) = observed number of cases of dementia/expected number of cases of dementia].Results:  The 69 patients had a median age of 64 years (quartiles 57 and 73) at the time of the diagnosis, and the average follow‐up period was 12.7 years. The SMRdementia was 0.20 (95% CI 0.01–1.11). No patient developed AD.Conclusion:  Normal tension glaucoma was not associated with an increased risk of developing dementia/AD.
Regional economic levels and adverse events linked to intrauterine devices
Authors: Zhan Gao , Ling Li , Ying Li , You‐ping Li , Jin Wen , Li Wang 
Published: February 2011

Abstract Objective To explore the relationship between macro‐economic indicators and incidences of adverse events linked to intrauterine devices (IUDs). Methods Data on IUD‐associated adverse events were collected from a cohort study conducted between September 2005 and December 2006. Regional economic data were from the 2006 National Economic and Social Development Statistical Bulletins and Statistical Yearbooks of various regions. A total of 20,220 IUD users in 236 towns in Jiangsu, Shanghai, Guangdong, Anhui, Sichuan, and Chongqing provinces in China were included in this study. Linear correlation and regression analyses were used to analyze the relationships between regional income and total incidences of adverse events, incidences of mild adverse events, and incidences of severe adverse events. Results Incidences of total adverse events and mild adverse events were positively correlated with regional economic level (rs= 0.336, p < 0.05; rs= 0.272, p < 0.05), while incidences of severe adverse events were not correlated with regional economic level. Conclusions The positive relationship between regional economic level and reported IUD‐associated mild adverse events likely reflects income‐related disparities in women seeking care and receiving treatment for mild adverse events. This points to a need to improve both public health education and the quality of health services, particularly in poorer areas.
Theoretical and experimental approaches to the deposition and clearance of ultrafine carcinogens in the human respiratory tract
Authors: Sturm Robert 
Published: February 2011

AbstractIntroduction:  Although inhaled ultrafine particles (UFPs) represent serious lung burdens and are thus responsible for a remarkable number of respiratory diseases (including cancer), only limited information on their deposition and clearance in the lung compartments is available. The study presented here tries to overcome this deficit by using a detailed theoretical approach to UFP behavior in the lungs.Methods:  The deposition model used in this context is based upon a stochastic lung geometry and the generation of single‐particle trajectories in the tracheobronchial tree according to the random walk algorithm. Simulation of UFP clearance is conducted with the help of a multi‐compartment model that considers cellular/non‐cellular sites of temporary particle storage as separate compartments.Results:  As predicted by the models and confirmed by experimental findings, deposition of UFPs by Brownian motion takes place in both the upper and lower compartments of the respiratory tract. Alveolar accumulation of particulate mass increases proportionally with the inhalative flow rate. Clearance of UFPs is chiefly dominated by slow mechanisms with respective half‐times ranging from several days to months.Discussion:  Modeling of UFP behavior in the respiratory tract represents an appropriate tool for forthcoming medical studies on this particle class, but it needs to be subjected to further refinements.

As outlined by this study, alveolar deposition of UFPs, correlating with a noticeable risk of malignant transformations and cancer development, is determined by a number of factors, including effective particle size and velocity of particle transport in the conducting airways.
With the help of appropriately validated models, respective predictions on the pulmonary burdens of UFP after short‐term or long‐term exposure can be made. In the case of subjects suffering from bronchial and/or alveolar UFP overloads, respective clearance approaches may be applied to simulate particle removal scenarios.
Insulin Resistance Selectively Alters Cell‐Surface Glucose Transporters but not their Total Protein Expression in Equine Skeletal Muscle
Authors: Waller A.P. , Burns T.A. , Mudge M.C. , Belknap J.K. , Lacombe V.A. 
Published: February 2011

Background: Insulin resistance (IR) has been widely recognized in humans, and more recently in horses, but its underlying mechanisms are still not well understood. The translocation of glucose transporter 4 (GLUT4) to the cell surface is the limiting step for glucose uptake in insulin‐sensitive tissues. Although the downstream signaling pathways regulating GLUT translocation are not well defined, AS160 recently has emerged as a potential key component. In addition, the role of GLUT12, one of the most recently identified insulin‐sensitive GLUTs, during IR is unknown.Hypothesis/Objectives: We hypothesized that cell‐surface GLUT will be decreased in muscle by an AS160‐dependent pathway in horses with IR.Animals: Insulin‐sensitive (IS) or IR mares (n = 5/group).Methods: Muscle biopsies were performed in mares classified as IS or IR based on results of an insulin‐modified frequently sampled IV glucose tolerance test. By an exofacial bis‐mannose photolabeled method, we specifically quantified active cell‐surface GLUT4 and GLUT12 transporters. Total GLUT4 and GLUT12 and AS160 protein expression were measured by Western blots.Results: IR decreased basal cell‐surface GLUT4 expression (P= .027), but not GLUT12, by an AS160‐independent pathway, without affecting total GLUT4 and GLUT12 content. Cell‐surface GLUT4 was not further enhanced by insulin stimulation in either group.Conclusions and Clinical Importance: IR induced defects in the skeletal muscle glucose transport pathway by decreasing active cell‐surface GLUT4.
Increase in Minimal Residual Disease in Peripheral Blood before Clinical Relapse in Dogs with Lymphoma that Achieved Complete Remission after Chemotherapy
Authors: Sato M. , Yamazaki J. , Goto‐Koshino Y. , Takahashi M. , Fujino Y. , Ohno K. , Tsujimoto H. 
Published: February 2011

Background: We developed previously a minimal residual disease (MRD) monitoring system in dogs with lymphoma by exploring a highly sensitive real‐time PCR system.Objectives: To identify the change in MRD before clinical relapse in dogs with lymphoma that achieved complete remission after chemotherapy.Animals: Twenty dogs with multicentric high‐grade B‐cell lymphoma.Methods: MRD levels in peripheral blood mononuclear cells (PBMCs) were measured by real‐time PCR amplifying the rearranged immunoglobulin heavy chain gene. MRD measurement and clinical assessment were performed every 2–4 weeks for 28–601 days after completion of chemotherapy. An increase in MRD was defined as an increase by more than 0.5, calculated by log10[copy number of MRD per 105 PBMCs], based on the uncertainty level observed in a canine lymphoma cell line.Results: During the follow‐up period, 15 dogs relapsed in 28–320 days (median, 120 days) after completion of chemotherapy. An increase in MRD was detected 2 weeks or more before relapse in 14 of the 15 dogs, but an increase in MRD before relapse could not be detected in the remaining 1 dog. The time from increased MRD to clinical relapse was 0–63 days (median, 42 days). In contrast, no increase in MRD was detected in 5 dogs that did not experience clinical relapse.Conclusion and Clinical Importance: An increase in MRD can be detected before clinical relapse in dogs with lymphoma. Application of early reinduction therapy based on an increase in MRD before clinical relapse may improve treatment outcome in canine lymphoma.