bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bulking generated considerable bias in detection of amplified fragment length polymorphism variations in oat, fringed brome and smooth bromegrass
Authors: Fu Y. B. , Whitwill S. , Ferdinandez Y. S. N. , Coulman B. E. , Richards K. W. 
Published: December 2004

AbstractAmplified fragment length polymorphism (AFLP) variations in bulk and plant‐by‐plant (PBP) samples of five oat (Avena sativa L.) accessions, one fringed brome (Bromus ciliatus L.) accession and two smooth bromegrass (B. inermis Leyss.) accessions were compared. The proportions of AFLP bands detected in PBP, but lost in bulk, samples of oat, fringed brome, and smooth bromegrass ranged from 19 to 31%, 40 to 44%, and 22 to 33% of the total bands scored, respectively. These lost bands had occurred at frequencies ranging from 0.1 to 1 in the PBP samples. These findings demonstrate bulking can generate substantial bias in detection of AFLP variations.
Eight microsatellite markers for the neotropical tree Luehea seemannii (Tiliaceae)
Authors: Jones F. A. , Poelchau M. F. , Bouck A. C. , Hubbell S. P. 
Published: December 2004

AbstractWe isolated eight polymorphic microsatellites from the neotropical tree Luehea seemannii for gene flow and genetic structure studies. We used a streptavidin subtractive enrichment technique to develop a library of CA/GT repeats. Eight loci were screened for diversity from 96 individuals from Barro Colorado Island (BCI) and neighbouring Gigante peninsula in Panama. Luehea seemannii shows moderate levels of genetic diversity within these two populations. Allelic richness ranged from four to nine alleles and averaged 6.44 alleles per locus. Average expected heterozygosity was 0.65 on BCI and 0.60 on Gigante. Results are compared to microsatellite data from another wind‐dispersed gap colonizing species common in Panama.
Bi‐parentally inherited species‐specific markers identify hybridization between rainbow trout and cutthroat trout subspecies
Authors: Ostberg Carl O. , Rodriguez Russell J. 
Published: December 2004

AbstractEight polymerase chain reaction primer sets amplifying bi‐parentally inherited species‐specific markers were developed that differentiate between rainbow trout (Oncorhynchus mykiss) and various cutthroat trout (O. clarki) subspecies. The primers were tested within known F1 and first generation hybrid backcrosses and were shown to amplify codominantly within hybrids. Heterozygous individuals also amplified a slower migrating band that was a heteroduplex, caused by the annealing of polymerase chain reaction products from both species. These primer sets have numerous advantages for native cutthroat trout conservation including statistical genetic analyses of known crosses and simple hybrid identification.
Characterization of microsatellite loci in Spartina species (Poaceae)
Authors: Blum Michael J. , Sloop Christina M. , Ayres Debra R. , Strong Donald R. 
Published: December 2004

AbstractThe cordgrasses in the genus Spartina have become model organisms for studying biological invasions from both ecological and genetic perspectives. Here we characterize 11 disomic loci in Spartina alterniflora that show promise for population studies and for studying hybridization events between S. alterniflora and S. foliosa. Comparisons among invasive and native S. alterniflora populations showed that levels of allelic variation are lower in invasive populations. In addition, nearly all loci that amplified in S. foliosa populations and in a swarm of S. alterniflora×foliosa hybrids were polymorphic. We also found that several loci amplified successfully in other Spartina species.
Microsatellite loci from the northern house mosquito (Culex pipiens), a principal vector of West Nile virus in North America
Authors: Keyghobadi Nusha , Matrone Michael A. , Ebel Gregory D. , Kramer Laura D. , Fonseca Dina M. 
Published: December 2004

AbstractMicrosatellites were isolated and characterized in the northern house mosquito, Culex pipiens, a widespread pest species and important vector of diseases such as West Nile virus. An enrichment protocol yielded 150 positive clones. We designed primers to amplify 17 unique (GT)n microsatellites, eight of which amplified cleanly and were polymorphic. A survey of 29 individuals showed that these loci are highly variable with the number of alleles ranging from seven to 19 and expected heterozygosity ranging from 0.66 to 0.93. These markers will be useful for studies of population structure and intraspecific variation in epidemiological characteristics of Cx. pipiens.
Microsatellites for use in Nothofagus cunninghamii (Nothofagaceae) and related species
Authors: Jones Rebecca C. , Vaillancourt René E. , Jordan Gregory J. 
Published: December 2004

Abstract Nothofagus cunninghamii (myrtle) has a widespread distribution through the temperate rainforest of southeastern Australia with some disjunct populations existing in putative glacial refugia. Polymorphic nuclear markers are required to resolve the biogeographical history of the species and will also be useful for conservation and forestry applications in this and other species of Nothofagus. Fourteen polymorphic microsatellite loci were isolated from N. cunninghamii, with four to 10 alleles amplified in 15 individuals tested. Transferability to other species of Nothofagus was successful, with six loci transferring to all eight other species tested.
Isolation and characterization of polymorphic microsatellite loci from the Dungeness crab Cancer magister
Authors: Toonen Robert J. , Locke Melissa , Grosberg Rick 
Published: December 2004

AbstractThe Dungeness crab, Cancer magister, is the focus of one of the most intensely harvested fisheries in North America. Given its economic importance, there is considerable interest in assessing the degree and spatial pattern of genetic structure in C. magister. To that end, we developed a series of 17 hypervariable microsatellite loci. Six of these 17 loci could be amplified in a single multiplex PCR reaction. Using dye‐labelled primers all six loci can be coamplified and scored simultaneously on an automated sequencer. The ability to multiplex multiple loci greatly increases the ease and speed of genotyping for this species.
Polymorphic microsatellite loci in the mosquito Aedes polynesiensis
Authors: Behbahani A. , Dutton T. J. , Raju A. K. , Townson H. , Sinkins S. P. 
Published: December 2004

AbstractThe Aedes scutellaris complex of mosquitoes contains the most important vectors of lymphatic filariasis in the South Pacific region, particularly Aedes polynesiensis. Six microsatellite loci were isolated and characterized from this species; all were polymorphic and appear to be useful markers for population studies. Five of the primer pairs also amplified homologous products from three other species in the A. scutellaris group and from the important dengue vector Aedes albopictus.
Microsatellite multiplexes for high‐throughput genotyping of French grunts (Haemulon flavolineatum, Pisces: Haemulidae) and their utility in other grunt species
Authors: Williams D. A. , Purcell J. , Cowen R. K. , Hughes C. R. 
Published: December 2004

AbstractGrunts of the genus Haemulon are abundant in the western Atlantic and are an important component of regional fisheries. Management efforts for these and other Caribbean reef fish require an understanding of population structure and the extent of dispersal among populations. We characterized 11 polymorphic microsatellite loci for French grunts (Haemulon flavolineatum) and grouped them into three PCR multiplexes to facilitate high‐throughput genotyping. These loci will be useful for population genetic studies of French grunts. Cross‐species amplifications suggest these loci are also suitable for population genetic studies of H. aurolineatum, H. plumieri, and H. sciurus.
Microsatellite loci for the greater horseshoe bat, Rhinolophus ferrumequinum (Rhinolophidae, Chiroptera) and their cross‐utility in 17 other bat species
Authors: Dawson Deborah A. , Rossiter Stephen J. , Jones Gareth , Faulkes Christopher G. 
Published: December 2004

AbstractWe have isolated 14 polymorphic greater horseshoe bat, Rhinolophus ferrumequinum microsatellite loci. The number of alleles varied from two to 12 in 58 individuals. These loci will be used to assign paternity in order to characterize patterns of breeding and reproductive success in a wild R. ferrumequinum population. Loci were also tested in 17 other bat species. Twelve loci cross‐amplified in other species and three loci were polymorphic in all eight Rhinolophus species tested.
Isolation by distance, based on microsatellite data, tested with spatial autocorrelation (spaida) and assignment test (spassign)
Authors: Pálsson Snæbjörn 
Published: December 2004

Abstract spassign and spaida are two small programs useful to detect isolate by distance of microsatellite loci. The programs are written in C and are available for Linux and Windows system at http://www.hi.is/~snaebj/programs.html. spaida calculates two estimates of spatial autocorrelation, Moran's I and Geary's c, first by assuming the infinite allele model, and second by assuming a stepwise mutational model. spassign calculates the assignment probabilities of an individuals genotype to the location where it was sampled and compares probabilities of assignment to other locations. Genetic distances among regions based on the overall differences in likelihoods are calculated.
Development and characterization of microsatellite markers for Fagus crenata Blume
Authors: Asuka Y. , Tani N. , Tsumura Y. , Tomaru N. 
Published: December 2004

AbstractMicrosatellite markers can yield high‐resolution genetic profiles for individual identification, and for parentage analysis, when evaluating gene dispersal in populations. Fagus crenata is an important dominant species in the cool temperate forests in Japan, and although many studies on the species have been conducted the patterns of gene dispersal via pollen and seeds are poorly understood. In order to be better informed about gene dispersal in Fagus crenata, we have developed 16 new microsatellite loci from an enriched library of genomic DNA. These 16 loci were highly variable, with 3–40 alleles per locus and an expected heterozygosity value of 0.11–0.98.
Cross‐species amplification of microsatellite loci in aphids: assessment and application
Authors: Wilson Alex C. C. , Massonnet Blandine , Simon Jean‐Christophe , Prunier‐Leterme Nathalie , Dolatti Lotfali , Llewellyn Kate S. , Figueroa Christian C. , Ramirez Claudio C. , Blackman Roger L. , Estoup Arnaud , Sunnucks Paul 
Published: December 2004

AbstractDespite the relative ease of isolating microsatellites, their development still requires substantial inputs of time, money and expertise. For this reason there is considerable interest in using existing microsatellites on species from which markers were not cloned. We tested cross‐species amplification of 48 existing aphid loci in species of the following genera: Aphidinae: Aphidini: Aphis and Rhopalosiphum; Aphidinae: Macrosiphini: Acyrthosiphum, Brevicoryne, Diuraphis, Illinoia, Macrosiphoniella, Macrosiphum, Metopeurum, Metapolophium, Myzus, Phorodon, Sitobion and Uroleucon and Neuquenaphidinae: Neuquenaphis. Our results show cross‐species application of known microsatellite loci is a highly promising source of codominant markers for population genetic and evolutionary studies in aphids.
The UWCDot colour vision test and low vision
Authors: Hovis Jeffery K. , Leat Susan J. , Epp Karen 
Published: December 2004

AbstractPurpose: Previous studies have shown that colour vision defects are common in the low vision population even when properly designed tests are used. However, there are very few clinical tests available that are suitable for this group of patients. One of the more common is the Jumbo D‐15 (JD15). Although this test uses caps more suitable for the reduced acuity, it requires the patient to have some knowledge of colour order and sufficient dexterity to manipulate the caps. We compared the JD15 with the University of Waterloo Colored Dot test (UWCDot), which has neither of these requirements, to determine whether the UWCDot test could be used as a substitute for the JD15.Methods: The colour vision of 40 consecutive low vision patients was evaluated with both tests. Acuities ranged from 6/6 to 6/1600 with a median value of 6/30.Results:  All subjects could perform both tests. The κ coefficient of agreement between tests was high at 0.85 when any major crossing was a failure on the JD15 and any mistake was a failure on the UWCDot. Classification of the type of defect was also reasonable when the defect was relatively severe.Conclusions: The UWCDot can be used as a substitute for the JD15 in the low vision clinic. Both tests identify individuals with moderate‐to‐severe deficiencies, but the UWCDot does not require any manual dexterity and it does not require knowledge of colour‐order.
Evaluating anxiety in patients attending optometric practice
Authors: Margrain Tom H. , Greenland Katy , Anderson Jane 
Published: December 2004

AbstractAlthough anxiety is a well‐established obstacle to the delivery of effective health care, there have been no attempts to measure it in the optometric consulting room. In this paper, we introduce physiological and psychological techniques that may be used to evaluate anxiety and arousal in the consulting room and present data from a small group of patients attending for a routine eye examination. Specifically, arousal was assessed before, during, and after the examination by measuring skin conductance in five patients. Anxiety was evaluated using the State–Trait Anxiety Inventory. Our data confirm the ability of these techniques to quantify arousal and anxiety in the optometric consulting room and reveal a previously unknown but important facet of the eye examination. We conclude that these techniques are suitable for use in further experimental work and may be used to identify factors capable of reducing anxiety in the optometric consulting room.
AlamarBlue bioassay for cellular investigation of UV‐induced crystalline lens damage
Authors: Oriowo Olanrewaju M. 
Published: December 2004

AbstractPurpose: The use of the alamarBlue fluorescence dye for cellular study of UV‐induced photodamage in cultured ocular lenses was examined by comparing the results from the fluorometric assay to lens optical quality using a scanning laser system to measure the focal lengths of the lenses following UVB treatment.Methods: Excised porcine lenses were cultured in M199 supplemented with 1% antibiotics and 4% porcine serum. After 1 week of pre‐incubation at 37°C, baseline measurements were taken. Treated lenses were irradiated with a range of UVB radiant exposures from 0.019 to 0.076 J cm−2. The lenses were maintained for a further 4 weeks, with measurements carried out every 48 h in the first 9 days post‐UVB treatment and then once each week. At each measurement session, treated and control lenses were transferred into a 24‐well plate, one lens per well containing the assay. The lenses were incubated for 50 min, after which fluorescence readings were taken with a plate reader.Results: Analyses showed significant (p < 0.05) inhibition of lens metabolic activity and optical function in the 0.038 and 0.076 J cm−2 UVB treated lenses. Lenses treated with 0.019 J cm−2 UVB did not exhibit any photodamage.Conclusions: These results suggest that the alamarBlue assay is useful for the in vitro study of UV‐induced lens damage. The decrease in the capacity of treated lenses to reduce alamarBlue over time confirms that UVB photo‐oxidation can cause diminution of viable lens epithelial and fibre cells. The results also suggest that the energy threshold for broadband UVB induced cataractogenesis in vitro ranges between 0.019 and 0.038 J cm−2.
The effect of axial length on ocular blood flow assessment in anisometropes
Authors: Lam Andrew K. C. , Chan Suk‐tak , Chan Ben , Chan Henry 
Published: December 2004

AbstractBackground: Pulsatile ocular blood flow (POBF) assessment measures the choroidal circulation and therefore provides data with diagnostic value in certain ocular diseases, such as glaucoma. The technique assumes a constant pressure–volume relationship. The current study investigated the effect of axial length on POBF from subjects with axial anisometropia. Ocular blood supply in the ophthalmic artery was also determined using colour Doppler ultrasonography.Methods: Thirty‐one normal, anisometropic subjects were recruited, whose ages ranged from 20 to 34 years. They had axial anisometropia (expressed by spherical equivalent) of at least 2 D. After Goldmann tonometry, the POBF of each eye was measured in a supine posture by one examiner, followed by a measurement of the blood flow velocity in the ophthalmic artery using colour Doppler ultrasonography in the same posture by another examiner. There was a 10 min rest between the two techniques. All the measurements were made at around the same time to eliminate any effect from diurnal variation.Results: The mean anisometropia (expressed by spherical equivalent) was 3.89 ± 1.96 D and the mean inter‐ocular axial length difference was 1.49 ± 1.00 mm. The anisometropia and axial length were significantly different between the two eyes (paired t‐tests: p < 0.001). However, the intra‐ocular pressure was similar between the two eyes (paired t‐test: p = 0.41). The POBF was significantly lower in the eye with the longer axial length (459.3 μL min−1) than the fellow eye (590.8 μL min−1), paired t‐test: p < 0.001. The pulse amplitude was also significantly lower in the eye with the longer axial length (1.61 mmHg) than the fellow eye (1.89 mmHg), paired t‐test: p < 0.001. However, the blood flow velocity from colour Doppler ultrasonography did not demonstrate any significant difference between the two eyes (paired t‐test: p > 0.05).Conclusions: The POBF and pulse amplitude were found to be reduced in the eye with the longer axial length but colour Doppler ultrasonography did not show any significant difference. This suggests that a new pressure–volume relation should be considered in deriving POBF. Practitioners should measure the axial length in POBF assessment.
Optical performance in eyes wearing two multifocal contact lens designs
Authors: Pujol J. , Gispets J. , Arjona M. 
Published: December 2004

AbstractThe optical performance of eyes wearing soft multifocal contact lenses was studied using the double‐pass technique. Retinal image quality was measured in a group of six eyes wearing two different designs of multifocal lenses: an aspheric design and a spheric multicurve design. Measurements were performed for far, intermediate and near vision conditions and with two different pupil diameters: 3 and 5 mm. The results show that the best optical performance is obtained for far vision conditions when no lens is worn. For near vision conditions, the optical performance when the lens is worn is, in general, better than when no lens is worn. When the lens is worn, the optical performance for far and intermediate vision conditions is similar for the aspherical design, but it decreases for near vision conditions. For the spherical multicurve design, the optical performance obtained for far vision conditions is similar to that obtained for intermediate vision conditions for low values of object vergence, but decreases when the object vergence is high and therefore also for near vision. In general, the differences in optical performance are greater for small pupil diameters (3 vs 5 mm). The general trends of the results obtained by computing the modulation transfer function of the contact lens–eye system can also be shown qualitatively by means of double‐pass images or quantitatively by computing the Imax/Imed of the image.
The S‐cone electroretinogram: a comparison of techniques, normative data and age‐related variation
Authors: Chiti Zohreh , North Rachel V. , Mortlock Katharine E. , Drasdo Neville 
Published: December 2004

AbstractThe blue sensitive mechanism in human colour vision is highly susceptible to damage in ocular disease. There is a need for objective methods to assess this and several methods of recording the blue cone (S‐cone) electroretinogram (ERG) have been described. We therefore compared a silent substitution technique (SST) and a selective adaptation technique (SAT) using a novel combination of optical filters, on 24 normal subjects. The age‐related variation in the S‐cone ERG was also investigated in a further 73 normal subjects. S‐cone ERGs elicited by SAT were of higher amplitude, (p < 0.001) with smaller coefficients of variation than those elicited with SST. The SST method has already been shown to be highly sensitive in primary open angle glaucoma and, unlike SAT, has no significant age related variation. However, the results of this study suggest that the new, SAT method may prove to be more convenient and effective in clinical practice, provided that age norms are applied.
A comparison of manual and automated methods of measuring conjunctival vessel widths from photographic and digital images
Authors: Owen Christopher G. , Ellis Timothy J. , Woodward E. Geoffrey 
Published: December 2004

AbstractWe investigated the application of a fully automated computer algorithm for identifying vessels of the conjunctiva from their scleral surround, and compared measures of vessel width with established methods. Vessel widths at 101 locations (ranging from 20 to 140 μm), from 12 patients, were measured from film and digital images, using a variety of methods, and compared. Widths were measured manually, by semi‐automated methods using grey level (densitometric) profiles taken from digital images, and by automated techniques set at different operating levels. Good intra‐session repeatibility was obtained using the automated method with an operating sigma value of 3 pixels (16 μm) (mean difference 0.5 μm, 95% CI −8.5 to 9.4 μm) and manual calliper measurements from digitally created photographic slides (mean difference 0.4 μm, −9.3 to 10.1 μm). For comparison with other measures of width, the latter was used as the gold standard. Widths measured from film were slightly larger than those measured directly from digital images, although this effect was small (5 μm) for most vessels. Overall widths measured using the automated method, with a sigma value of 3 pixels, agreed best with the gold standard (inter‐method repeatibility; mean difference 1.4 μm, −32.5 to 35.2 μm) although the automated method overestimated small widths (<40 μm) and underestimated larger vessel widths (>40 μm). Automated detection of vessels of the conjunctiva from digital images avoids manual and operator involved measures which are time consuming, and which preclude large patient studies. The resulting data may help in monitoring the vascular response of the conjunctiva to surgical or pharmacological intervention, and in describing vascular changes in response to ocular or systemic disease. The application of this algorithm to the study of retinal vessels is yet to be realised.