bluuebunny/crossref_metadata_2025_split huggingface dataset:
HLA and cytokine gene polymorphisms in biliary atresia
Authors: Donaldson Peter T. , Clare Michael , Constantini Patrizia K. , Hadzic Nedim , Mieli‐Vergani Giorginia , Howard Edward , Kelley Dympna 
Published: December 2004

Abstract:Background/aims:Extrahepatic biliary atresia remains one of the major hepatic causes of death in early childhood. Though a number of hypotheses have been developed to account for this disease, its aetiopathogenesis is poorly understood. One possibility is that this is an immune mediated disease which occurs following either toxic or infectious insult in a genetically susceptible host. Earlier studies suggested weak HLA associations but these remain unconfirmed. More recently studies of viral and autoimmune liver disease have begun to investigate non‐MHC immunoregulatory gene polymorphisms.Methods:In the present study we used molecular genotyping to investigate selected HLA A, B, DRB1, DQA1, DQB1 and DPB1 alleles as well as polymorphisms in the interleukin‐1 gene family, interleukin‐10 promoter sequence and tumour necrosis factor alpha promoter genes in 101 children referred for surgical assessment with extra hepatic biliary atresia. Genotyping data were compared with those of 134 racially and geographically matched healthy adult health care workers.Results and conclusions:Overall there were no statistically significant differences in the distribution of any of the genes tested comparing patients and controls. These data suggest that biliary atresia is not an HLA‐associated disease and that polymorphisms in both the interleukin‐1 and interleukin‐10 genes are not risk factors for this disease.
Monitoring woodland deer populations in the UK: an imprecise science
Authors: SMART JAMES C. R. , WARD ALASTAIR I. , WHITE PIRAN C. L. 
Published: December 2004

ABSTRACT 1. The need to assess population size and change is central to any population monitoring programme. A range of monitoring techniques is available for deer, but few studies have addressed the performance of these techniques in terms of their accuracy and their power to detect population changes reliably. This study compares the performance of three commonly used techniques to monitor woodland deer populations in terms of their accuracy, precision and statistical power using field data and simulation modelling. 2. Faecal Standing Crop (FSC) was found to provide the most accurate estimates at all deer densities studied, but was outperformed by distance sampling using thermal imaging in terms of precision and statistical power. Faecal Accumulation Rate (FAR) performed worst in terms of precision and statistical power, and was inferior in terms of accuracy to FSC. The accuracy of FAR and distance sampling using thermal imaging was similar. 3. Annual surveying is not the best use of resources, since 10% per annum increases or decreases in a population could not be detected by any of the techniques within a 3‐year time period. Even with the best technique under the most favourable conditions of deer density simulated in this study, a population change could only be detected reliably once the population had increased by 33% or decreased by 27%. In the least favourable conditions, the respective figures were a 380% increase or extinction. 4. All the techniques studied are relatively poor at detecting population change, so their use in practical deer management needs to be treated with caution. The consequences of relying on similar techniques to detect population change for rare species could be severe.
Monitoring cetaceans in European waters
Authors: EVANS PETER G. H. , HAMMOND PHILIP S. 
Published: December 2004

ABSTRACT1. Monitoring spatial and temporal patterns in cetacean abundance involves a variety of approaches depending upon the target species and the resources available. As a first step, the collection of incidental sightings or strandings information aids the construction of a species list and a rough measure of status and seasonal variation in abundance. These often make use of networks of volunteer observers although the wide variation in abilities and experience means that special attention must be paid to training and to data quality control. More robust monitoring of numbers requires quantification of effort and some correction for factors that influence detectability, such as sea state.2. The presence of cetaceans may be recorded visually, or indirectly by acoustics. Each has advantages and disadvantages, and their applicability may vary between species. The use of fixed stations tends to allow sustained monitoring at relatively low cost but coverage is limited to the immediate vicinity. For more extensive coverage, mobile platforms are necessary. Platforms of opportunity such as ferries, whale‐watching boats, etc. are often used to survey areas at low cost. These may allow repeat observations to be made over time, but with no control over where the vessel goes, it is typically not possible to sample wide areas, thus limiting abundance estimation.3. Line transect surveys using dedicated platforms allow representative coverage of areas from which abundance estimates can be made (either using indices or absolute measures derived from density estimation). Assumptions relating to detectability and responsiveness need to be addressed and various methods (such as two‐platform surveys) have been developed to accommodate these.4. For some cetacean species, mark‐recapture methods can be applied using photo‐identification of recognizable individuals. Again, a number of assumptions are made, particularly relating to recognizability, representativeness of sampling and capture probabilities. Capturing, on film, as many animals in the population as possible helps to reduce the problem of heterogeneity of capture probabilities. Mark‐recapture methods require at least two sampling occasions. If multiple sampling is employed, either open or closed population models can be used.5. Measuring population change represents a particular challenge for mobile animals such as cetaceans. Changes in ranging patterns may have a large impact on abundance estimates unless very large areas are adequately covered. Power analysis is a useful method to indicate the ability of the data to detect a trend of a given magnitude. Increasingly, spatial modelling using GLMs and GAMs is being used to provide a better understanding of the biotic and hydrographic factors influencing cetacean distribution.
Methods of monitoring red foxesVulpes vulpesand badgersMeles meles: are field signs the answer?
Authors: SADLIER LINDA M. J. , WEBBON CHARLOTTE C. , BAKER PHILIP J. , HARRIS STEPHEN 
Published: December 2004

ABSTRACT1. A national monitoring scheme for recording the abundance of foxes and badgers in Britain would have to utilize a technique or techniques that could detect a wide range of animal densities in structurally different habitats. Furthermore, the likely reliance on volunteers for data collection means that these techniques must be easily applied by people with different levles of field expertise.2. Direct methods that rely on counts of the animals themselves (e.g. capture‐mark‐recapture, radio‐tracking, spotlight counts) are generally unsuitable because of cost, manpower and licensing requirements, are not readily applied to all habitats and cannot easily be used by volunteers. However, density estimates derived from capture‐mark‐recapture and radio‐tracking methods are likely to represent the benchmark against which other estimates of abundance are measured.3. The number of foxes killed per unit area is currently collated by non‐governmental organisations for some patterns of land use, e.g. game estates. No such data are available for badgers, as this species is legally protected in Britain. However, the applicability of hunting statistics for monitoring fox abundance is limited by differences in culling effort, the non‐independence of different culling practices applied in the same region, possible future changes in the legal status of different culling methods and changes in the ratio of land where foxes are and are not culled.4. Indirect methods that rely on counts of the signs of the animals (e.g. droppings, breeding refugia) are less expensive than direct methods, can be applied to the range of habitats found in Britain and can easily be used by volunteers. To date, indirect methods have been utilised to derive estimates of relative animal density or the density of social groups. However, the major factor currently limiting the use of indirect methods is that their relationship with absolute animal density has not been validated. The preliminary results of two projects quantifying the use of field signs as a measure of absolute fox and badger abundance suggest that indirect methods could be applicable for monitoring changes in fox and badger numbers at a national scale.
Human cytomegalovirus and Epstein‐Barr virus type 1 in periodontal abscesses
Authors: Saygun I , Yapar M , Özdemir A , Kubar A , Slots J 
Published: December 2004

Objectives:  Recent studies have linked herpesviruses to severe types of periodontal disease, but no information exists on their relationship to periodontal abscesses. The present study determined the presence of human cytomegalovirus (HCMV) and Epstein‐Barr virus type 1 (EBV‐1) in periodontal abscesses and the effect of treatment on the subgingival occurrence of these viruses.Material and methods:  Eighteen adults with periodontal abscesses participated in the study. Subgingival samples were collected from each patient with sterile curettes from an abscess‐affected site and a healthy control site. HCMV and EBV‐1 were identifed by polymerase chain reaction at the time of the abscess and at 4 months after surgical and systemic doxycycline therapy.Results:  HCMV was detected in 66.7% of periodontal abscess sites and in 5.6% of healthy sites (P = 0.002). EBV‐1 occurred in 72.2% of abscess sites but not in any healthy site (P < 0.001). HCMV and EBV‐1 co‐infection was identified in 55.6% of the abscess sites. Posttreatment, HCMV and EBV‐1 were not found in any study site.Conclusions:  HCMV and EBV‐1 genomes are commonly found in periodontal abscesses. These data favor a model in which a herpesvirus infection of the periodontium impairs the host defense and serves as a platform for the entrance of bacterial pathogens into gingival tissue with subsequent risk of abscess development.
How mitochondrial DNA diversity can help to understand the dynamics of wild‐cultivated complexes. The case ofMedicago sativain Spain
Authors: Muller M. H. , Prosperi J. M. , Santoni S. , Ronfort J. 
Published: December 2004

AbstractIn order to clarify the relationships (genetic exchange and shared ancestry) between natural and cultivated populations of alfalfa (Medicago sativaL.) in Spain, we investigated the patterns of mitochondrial DNA variation (characterized through restriction fragment length polymorphism) for 248 individuals in seven natural and six cultivated populations of this species. Mitochondrial variation was evidenced in both natural and cultivated populations ofM. sativa. Among the seven mitotypes idengified in the species, two were specific of the natural populations, a result attesting the fact that the Spanish wild form ofM. sativais an original genetic pool compared to the cultivated one. Other mitotypes were observed in both natural and cultivated populations, suggesting the occurrence of gene flow through seeds from cultivated towards natural populations. Comparisons with previously gathered nuclear and phenotypic data give insights into the different evolutionary forces acting on the different kinds of Spanish natural populations examined so far.
A hybrid zone between hydrothermal vent mussels (Bivalvia: Mytilidae) from the Mid‐Atlantic Ridge
Authors: O’Mullan G. D. , Maas P. A. Y. , Lutz R. A. , Vrijenhoek R. C. 
Published: December 2004

AbstractThis study provides the first example of a hybrid zone between animal taxa distributed along the mid‐ocean ridge system. We examined the distribution and genetic structure of deep‐sea hydrothermal vent mussels (Bivalvia: Mytilidae) along a 2888‐km portion of the Mid‐Atlantic Ridge between 37°50′ N and 14°45′ N latitude. Mitochondrial DNA (mtDNA), allozymes and multivariate–morphometric evidence discriminated between individuals of a northern species,Bathymodiolus azoricus,and a southern species,B. puteoserpentis,that were separated by an intermediate ridge segment almost devoid of mussels. A small sample of mussels from Broken Spur, a vent locality along this intermediate zone, revealed a mixed population with gene frequencies and morphology that were broadly intermediate to those of the northern and southern species. Multilocus clines in mtDNA and allozyme frequencies were centred over the intermediate zone. We consider intrinsic and extrinsic processes that might limit genetic exchange across this hybrid zone.
MHC class II beta sequence diversity in the deer mouse (Peromyscus maniculatus): implications for models of balancing selection
Authors: Richman A. D. , Herrera L. G. , Nash D. 
Published: December 2004

AbstractWe studied population polymorphism at a major histocompatibility complex (MHC) class II beta gene in the deer mouse (Peromyscusmaniculatus). We found that: (i) a single population ofP. maniculatushas significantly higher levels of DNA and protein sequence diversity than worldwide samples from homologous genes in other taxa, including humans and mice; and (ii) the genealogy of allelic sequences inP. maniculatusdeviates significantly from theoretical expectation under a model of symmetric balancing selection, in that alleles are relatively more divergent than expected. We suggest that the observation of high levels of pairwise allelic sequence divergence and deviation of the genealogy from theoretical expectation inP. maniculatustogether provide support for a divergent allele advantage model for the maintenance of MHC polymorphism.
Source population of dispersing rock‐wallabies (Petrogale lateralis) idengified by assignment tests on multilocus genotypic data
Authors: Eldridge M. D. B. , Kinnear J. E. , Onus M. L. 
Published: December 2004

AbstractThe ability to confidently idengify or exclude a population as the source of an individual has numerous powerful applications in molecular ecology. Several alternative assignment methods have recently been developed and are yet to be fully evaluated with empirical data. In this study we tested the efficacy of different assignment methods by using a translocated rock‐wallaby (Petrogale lateralis) population, of known provenance. Specimens from the translocated population (n = 43), its known source population (n = 30) and four other nearby populations (n = 19–32) were genotyped for 11 polymorphic microsatellite loci. The results idengified Bayesian clustering, frequency and Bayesian methods as the most consistent and accurate, correctly assigning 93–100% of individuals up to a significance threshold of P = 0.01. Performance was variable among the distance‐based methods, with the Cavalli‐Sforza and Edwards chord distance performing best, whereas Goldstein et al.’s (δµ)2 consistently performed poorly. Using Bayesian clustering, frequency and Bayesian methods we then attempted to determine the source of rock‐wallabies which have recently recolonized an outcrop (Gardners) 8 km from the nearest rock‐wallaby population. Results indicate that the population at Gardners originated via a recent dispersal event from the eastern end of Mt. Caroline. This is only the second published record of dispersal by rock‐wallabies between habitat patches and is the longest movement recorded to date. Molecular techniques and methods of analysis are now available to allow detailed studies of dispersal in rock‐wallabies and should also be possible for many other taxa.
Prey specialization may influence patterns of gene flow in wolves of the Canadian Northwest
Authors: Carmichael L. E. , Nagy J. A. , Larter N. C. , Strobeck C. 
Published: December 2004

AbstractThis study characterizes population genetic structure among grey wolves (Canis lupus) in northwestern Canada, and discusses potential physical and biological determinants of this structure. Four hundred and ninety‐one grey wolves, from nine regions in the Yukon, Northwest Territories and British Columbia, were genotyped using nine microsatellite loci. Results indicate that wolf gene flow is reduced significantly across the Mackenzie River, most likely due to the north–south migration patterns of the barren‐ground caribou herds that flank it. Furthermore, although Banks and Victoria Island wolves are genetically similar, they are distinct from mainland wolf populations across the Amundsen Gulf. However, low‐level island–mainland wolf migration may occur in conjunction with the movements of the Dolphin‐Union caribou herd. Whereas previous authors have examined isolation‐by‐distance in wolves, this study is the first to demonstrate correlations between genetic structure of wolf populations and the presence of topographical barriers between them. Perhaps most interesting is the possibility that these barriers reflect prey specialization by wolves in different regions.
Social and genetic characteristics of geographically isolated populations in the antFormica cinerea
Authors: Goropashnaya A. V. , Seppä P. , Pamilo P. 
Published: December 2004

AbstractThe antFormica cinereain northern Europe has geographically isolated populations that were examined using five microsatellite loci. The populations differ widely regarding the social organization of colonies. Based on genetic relatedness (r) among worker nest mates, the populations were classified as M type with monogynous (single queen) colonies (r > 0.59), as P type with polygynous colonial networks (r < 0.1), or as intermediate with weakly polygynous colonies (0.16 < r < 0.47). The social types showed weak geographical clustering, but the overall distribution indicated that the shift between the social types has occurred several times. The geographically isolated populations had slightly reduced levels of genetic diversity compared to populations from areas where the species is abundant and continuously distributed. Many of the isolated populations consisted of monogynous or weakly polygynous colonies, making their effective population sizes small, and some of them also showed weak bottleneck effects. The overall level of microsatellite diversity within populations was relatively high and differentiation among populations low, indicating recent connections. Isolation of populations may thus be a new phenomenon resulting from reduction of suitable habitats. At the local level, we obtained limited support from a group of nearby subpopulations in southern Finland to the hypothesis that the P type is connected to restricted dispersal. Other P type populations did not, however, show similar elevated levels of differentiation.
Leprosy: dental and periodontal status of the anterior maxilla in 76 patients
Authors: Núñez‐Martí JM , Bagán JV , Scully C , Peñarrocha M 
Published: December 2004

Objective:  To evaluate the presence of oral disease, as assessed by dental and periodontal indices, in the anterior maxilla of a group of 76 patients with leprosy, compared with a group of matched control subjects.Materials and Methods:  The study included 76 patients with leprosy (age range 40–82 years; 39 males), resident in the sanatorium of San Francisco de Borja de Fontilles (Alicante, Spain). Clinical examination was carried out to evaluate the decayed missing and filled index, and the periodontal status in the anterior maxilla, using the Löe–Silness dental plaque index, mean periodontal probing depth and the average periodontal attachment loss.Results:  In the leprosy patients, a large proportion of maxillary incisors and canines were missing. The mean plaque index in leprosy was 2.35 ± 0.7, with a probing depth of 2.96 ± 0.8, and an average attachment loss of 4.18 ± 1.3, indices all statistically greater than in controls. There were no differences detected in the oral indices measured according to the presence or absence of facial destruction or the type of leprosy.Conclusions:  Patients with leprosy show a tendency to poor dental and periodontal health, unrelated to the presence of facial destruction or the type of leprosy.
Xanthomonas citri: breaking the surface
Authors: Brunings Asha M. , Gabriel Dean W. 
Published: December 2004

SUMMARYTaxonomy: Bacteria; Proteobacteria, Gammaproteobacteria; Xanthomonadales; Xanthomonadaceae, Xanthomonas.Microbiological properties: Gram‐negative, obligately aerobic, straight rods, motile by a single polar flagellum, yellow pigment.Related species: X. campestris
,
X. axonopodis
,
X. oryzae
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X. albilineans . Host range: Affects Rutaceous plants, primarily Citrus spp., Fortunella spp., and Poncirus spp., world‐wide. Quarantined pathogen in many countries. Economically important hosts are cultivated orange, grapefruit, lime, lemon, pomelo and citrus rootstock. Disease symptoms: On leaves, first appearance is as oily looking, 2–10 mm, similarly sized, circular spots, usually on the abaxial surface. On leaves, stems, thorns and fruit, circular lesions become raised and blister‐like, growing into white or yellow spongy pustules. These pustules then darken and thicken into a light tan to brown corky canker, which is rough to the touch. On stems, pustules may coalesce to split the epidermis along the stem length, and occasionally girdling of young stems may occur. Older lesions on leaves and fruit tend to have more elevated margins and are at times surrounded by a yellow chlorotic halo (that may disappear) and a sunken centre. Sunken craters are especially noticeable on fruit, but the lesions do not penetrate far into the rind. Defoliation and premature abscission of affected fruit occurs on heavily infected trees. Useful websites: <http://www.biotech.ufl.edu/PlantContainment/canker.htm>; <http://cancer.lbi.ic.unicamp.br/xanthomonas/>
Molecular determinants of the transmission of plant viruses by nematodes
Authors: Macfarlane Stuart A. 
Published: December 2004

SUMMARYUnderstanding the mechanisms of transmission of plant viruses is an important part of devising effective and sustainable strategies to protect crop plants against plant virus diseases. There are many difficulties associated with the study of virus transmission by nematodes, particularly as these vector organisms live below ground in the soil feeding on plant roots and cannot be maintained in pure culture. Nevertheless, with recent advances in molecular cloning techniques many details of the transmission process have begun to be revealed, especially with regard to the virus proteins that are required for successful transmission.