bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity of oral bacteria to 254 nm ultraviolet light
Authors: Metzger Z. , Dotan M. , Better H. , Abramovitz I. 
Published: November 2006

AbstractAim  To explore the sensitivity of bacteria commonly found in root canals to 254 nm ultraviolet (UV) light, either as individual cells or as participants of a bacterial multilayer.Methodology  The sensitivity of oral bacteria, as individual cells, to UV light was tested by subjecting plates streaked with bacteria to 254 nm UV, at a fluence of 1–20 mJ cm−2. An experimental model was designed to produce a bacterial multilayer and to study absorption of UV light by bacteria in an outer layer and its effect on the elimination of bacteria in the inner layer.Results  Direct exposure to relatively low doses of UV light (2–7 mJ cm−2) effectively eliminated all bacterial strains tested. Furthermore, an Enterococcus faecalis strain, partially resistant to a 24 h exposure to calcium hydroxide, was effectively eliminated within several seconds of exposure to UV light (P < 0.001). UV was absorbed by a multilayer of bacteria. When 4 bacterial cells μm−2 were present in the light path, the UV light dose had to be increased by a factor of ×10 to achieve 100% elimination of the bacteria in an inner layer.Conclusions  The application of UV light to eliminate endodontic pathogens may be possible. Nevertheless, its absorbance by outer layers of bacteria should be considered and the UV light dose adapted accordingly.
Male serum Chlamydia trachomatis IgA and IgG, but not heat shock protein 60 IgG, correlates with negatively affected semen characteristics and lower pregnancy rates in the infertile couple
Authors: Idahl A. , Abramsson L. , Kumlin U. , Liljeqvist J. A. , Olofsson J. I. 
Published: November 2006

SummaryBackground:  The objective of this study was to evaluate whether serum Chlamydia trachomatis immunoglobulin‐A (IgA), IgM and C. trachomatis heat shock protein 60 (CHSP60) IgG are of additional value to C. trachomatis IgG regarding the impact on fecundity in infertile couples, and to relate C. trachomatis serum antibodies to semen characteristics, diagnoses and pregnancy outcome.Methods:  A total of 226 infertile couples, previously tested for C. trachomatis IgG, were tested for C. trachomatis IgA, IgM and CHSP60 IgG, and semen samples from all men were analysed.Results:  Chlamydia trachomatis serum IgA in men (but not in women) correlated with reduced chances of achieving pregnancy [p = 0.021, relative risk (RR) =0.65, 95% confidence interval (CI) 0.42–1.005] and in combination with C. trachomatis IgG the chance was further reduced (p =0.001, RR = 0.35, 95% CI 0.15–0.84). Chlamydia trachomatis serum IgA was also significantly correlated with reduced motility of the spermatozoa (−8.7%, p = 0.023), increased number of dead spermatozoa (+10.5%, p = 0.014) and higher prevalence of leucocytes in semen (+122%, p = 0.005), and in combination with C. trachomatis IgG positivity, there was also a decrease in sperm concentration (−35%, p = 0.033), the number of progressive spermatozoa (−14.8%, p = 0.029) and a rise in the teratozoospermia index (+4.4%, p = 0.010). CHSP60 IgG correlated with reduced motility (−5.6%, p = 0.033), and in the women to tubal factor infertility (p = 0.033), but no correlations of C. trachomatis serum IgM or CHSP60 IgG with pregnancy rates were found.Conclusions:  Chlamydia trachomatis serum IgA in the male partner of the infertile couple has an additive value to IgG in predicting pregnancy chances, and serum IgA and IgG are associated with subtle negative changes in semen characteristics.
Lack of phylogeographic structure in three widespread Australian birds reinforces emerging challenges in Australian historical biogeography
Authors: Joseph Leo , Wilke Thomas 
Published: November 2006

AbstractAims  Building on molecular studies of widespread Australian vertebrates, we tested whether each of three widespread Australian bird species, namely the singing honeyeater, Lichenostomus virescens, spiny‐cheeked honeyeater, Acanthagenys rufogularis (Passeriformes: Meliphagidae), and black‐faced woodswallow, Artamus cinereus (Passeriformes: Artamidae), has undergone a recent (Pleistocene) range expansion across the Australian continent. We related the findings to the presence or absence of geographic variation in each species’ external phenotype and whether historical or non‐historical factors have been involved in generating variation.Methods  A total of 92 specimens of the three species were collected from, as far as possible, the same localities across Australia. They were sampled for mitochondrial DNA (mtDNA) diversity in the 1041 base pairs of the ND2 gene, and these data were analysed with nucleotide diversity statistics, unrooted networks, nested clade analysis, and tests of range expansion or stability.Results  Range expansions could not be rejected in any of the species in our study. Each had low, geographically unstructured nucleotide diversity. Patterns of geographic variation in the singing honeyeater's and, to a lesser extent, the black‐faced woodswallow's external phenotypes are not correlated with mtDNA diversity in ND2.Main conclusions  Our study adds to the increasing number of data sets suggesting the apparent prevalence of Pleistocene population expansions in widespread Australian birds. Furthermore, it shows that observable geographic structure may evolve very quickly, in response either to environmental gradients or to historical factors that operated too recently to be detected by ND2 sequences (e.g. in the singing honeyeater). Conversely, we have shown that a species that has had a recent population expansion need not necessarily be geographically invariant. To understand fully the interplay between vicariance and dispersal in the history of widespread Australian arid‐zone birds, or between the historical and non‐historical origins of their differentiation, carefully conducted case‐by‐case molecular studies will be necessary. Only then will biogeographical patterns and the processes that led to them emerge. Study of the historical biogeography and the more recent population history of Australian arid‐zone birds has reached a point where mtDNA‐based studies, while still informative and contributing to a growing data base of such work, should be complemented with data from multiple, rapidly evolving nuclear loci.
Tree line population monitoring of Pinus sylvestris in the Swedish Scandes, 1973–2005: implications for tree line theory and climate change ecology
Authors: KULLMAN LEIF 
Published: November 2006

Summary

Demographic trends of Pinus sylvestris L. (Scots pine) tree line populations are reported for a 32‐year monitoring period (1973–2005). Functional and projective aspects of tree line performance were analysed by relating temporal variability and change of vital population parameters, such as natality/mortality, vigour, injuries, height growth and seed viability to contemporary variations in air and soil temperatures.
The size of the entire sampled population increased by 50% during the 32‐year observation period and thereby pine has become a more prominent element on the landscape. This reverses a natural multicentennial or even millennial trend of tree line decline and recession.
Contrasting population trends were recorded for the subperiods 1973–87 and 1988–2005, viz. decline and increase, respectively. Mean summer temperatures (JJA) did not change perceivably over and between these intervals, although some exceptionally warm summers from 1997 onwards have contributed to population expansion by increased seed viability and seedling emergence. Winter temperatures (DJF) decreased significantly over the first subperiod and were consistently higher during the second, which has significantly lowered the mortality rates.
A functional link to winter temperature conditions was particularly stressed by the aetiology of individual plant vigour, injuries and final mortality. Classical symptoms of winter desiccation correlated significantly with low winter temperatures. This negative impact occurred with a high frequency during the decline phase and virtually ceased during the expansion phase from 1988 onwards, when winter air and root zone temperatures were raised to a consistently higher level.
Winter and summer temperatures in the air and soil, as well as positive feedback mechanisms and nonlinear responses, must be taken into account in the search for global or regional mechanical explanations for the tree line phenomenon. This insight helps to generate realistic tree line models for a high‐CO2 world, when winter warming is usually predicted to be particularly large.
Hierarchical patterns of symbiotic orchid germination linked to adult proximity and environmental gradients
Authors: DIEZ JEFFREY M. 
Published: November 2006

Summary

The recruitment stage can be critical in determining plant population dynamics, as juveniles encounter a range of abiotic and biotic stressors in the environments where they land after dispersal, and often experience high mortality rates. Although both abiotic and biotic constraints on recruitment are often assumed to operate at multiple scales, these relationships are rarely quantified in ways that enable prediction of recruitment dynamics across environmental gradients.
In plants such as orchids, an important bottleneck on recruitment may arise from an obligate dependence on mycorrhizal fungi in order to reach photosynthetic stage. Very little is known, however, about the factors controlling the distribution of the fungi or how fungal distributions may constrain orchid recruitment and distributions.
In this study, seed introduction experiments were used to test for relationships between symbiotic germination success of an orchid, Goodyera pubescens, and both proximity to adult orchids and soil abiotic conditions. Experiments were linked to ongoing demographic monitoring across a large environmental gradient to place patterns of germination better in the context of longer‐term demographic patterns.
A hierarchical Bayesian statistical framework was used to evaluate explicitly how recruitment varies across scales and how this variation is explained by key abiotic variables. This framework was further utilized to link hypothesis testing to model building, and thereby improve our ability to make predictions across a range of environmental conditions.
At a microsite scale (< 4 m2) strong evidence was found for decreasing germination success further from adult plants. At distances greater than 1 m from adults, increased germination success was associated with higher soil moisture, higher organic content and lower pH, although the strength of these relationships varied regionally. Patterns of symbiotic germination success were also highly correlated with observed recruitment patterns at the population level.
Explicitly linking plant recruitment to underlying abiotic gradients and key biotic interactions using a hierarchical, predictive modelling framework is essential for understanding basic plant population processes and building capacity to make predictions of how species and communities may respond to environmental changes.
Dormancy is associated with decreased adult survival in the burnt orchid, Neotinea ustulata
Authors: SHEFFERSON RICHARD P. , TALI KADRI 
Published: November 2006

Summary

Prolonged dormancy, a condition in which herbaceous perennial plants do not sprout for more than a year, has only been described to any great extent in long‐lived clonal species, particularly in the family Orchidaceae. However, some short‐lived, partly clonal or non‐clonal perennials also experience dormancy, and their shorter life spans and reduced or absent clonality may change the life history costs and benefits of this phenomenon.
We explored the life history context of dormancy in one such plant, Neotinea ustulata. A total of 1013 plants were monitored in five populations across Estonia between 1993 and 2005. Cormack–Jolly–Seber (CJS) and multistate analyses, two statistical methods to estimate demographic parameters in open populations, were conducted to estimate the probabilities of survival, dormancy and state transition among flowering, vegetative and dormant states among the populations.
The best‐fit CJS model suggested that dormancy varied among populations unpredictably, while survival varied in parallel among populations across time. Mean survival was 0.727 ± 0.115 (± SE) and mean dormancy was 0.543 ± 0.129.
Multi‐state analyses suggested that survival varied in parallel with life history state across all populations, with flowering plants surviving almost completely (0.999 ± 0.007) and dormant plants being the least likely to survive (0.684 ± 0.042). Vegetative plants were found to be intermediate (0.793 ± 0.051). All plants were likely to revert to a dormant state (range 0.451 ± 0.085–0.812 ± 0.053).
Dormancy appears to be maladaptive in N. ustulata, although we suggest that it may still be adaptive as a bet‐hedging trait if it results in substantially lower variability in survival and fitness over the long term. We suggest that conservation measures aimed at preserving populations of dormancy‐prone plants be linked to censuses focusing on detecting and estimating dormancy levels because high levels of dormancy indicate a low annual survival.
An ecologist's guide to ecogenomics
Authors: OUBORG N. J. , VRIEZEN W. H. 
Published: November 2006

Summary

Currently, plant ecologists are increasingly adopting approaches and techniques from molecular biology. The new field of ecogenomics aims at understanding the mechanistic basis for adaptation and phenotypic variation by using genomic techniques to investigate the mechanistic and evolutionary basis of species interactions, and focuses on identifying the genes affected by evolution.
While the entire toolbox of genomics is only available for model species such as Arabidopsis thaliana, we describe the options open to ecologists interested in pursuing an ecogenomics research program on ecologically relevant traits or phenomena in non‐model species, for which part of the genomic toolbox may be currently unavailable. In these non‐model species, a viable ecogenomics research program is possible with relatively modest effort.
Four challenges to further development of ecogenomics are described and discussed: (i) the ecogenomic study of non‐model species; (ii) reconciliation of experimental languages of ecology and evolutionary biology with molecular biology; (iii) development of specific ecogenomic data analysis tool; and (iv) adoption of a multidisciplinary cooperative research culture.
An important task for ecologists is to provide the necessary ecological input (the ‘eco’ part) to ecogenomics.
A novel method for evaluation of improved survival trend for common cancer: early detection or improvement of medical care
Authors: Chie Wei‐Chu , Chang Yi‐Hsin , Chen Hsiu‐Hsi 
Published: November 2006

AbstractRationale, aims and objectives  The improvement of survival with time for cancers has been observed worldwide. However, whether and to what extent such an improvement is attributed to early detection or the advance in medical technology is barely addressed.Method  We developed a novel graphic method to calculate attributable proportions related to two factors. This graphic method was first to calculate adjusted survival curve by the application of direct standardized epidemiological method to tumour staging. The crude survival curve was then compared with the adjusted survival curve.Results  Cumulative survival curves of two time epochs, 1989–1993 (period 1) and 1994–1998 (period 2), on six common cancers collected from cancer registry of National Taiwan University between 1989 and 1998, were compared. The attributable proportions due to early detection and medical care were 77% and 23% for breast cancer, 50% and 50% for cervical cancer, 52% and 48% for colorectal cancer, 76% and 24% for gastric cancer, 66% and 34% for liver cancer, and 30% and 70% for prostate cancer respectively.Conclusion  Distinguishing between early detection from advance in medical care associated with the improvement of survival trend using our graphic method has a significant implication for secondary and tertiary prevention of common cancers.
Stakeholder perspectives on new ways of delivering unscheduled health care: the role of ownership and organizational identity
Authors: Haddow Gill , O’Donnell Catherine A. , Heaney David 
Published: November 2006

AbstractRationale, aims and objectives  To explore stakeholder perspectives of the implementation of a new, national integrated nurse‐led telephone advice and consultation service [National Health Service 24 (NHS 24)], comparing the views of stakeholders from different health care organizations.Methods  Semi‐structured interviews with 26 stakeholders including partner organizations located in primary and secondary unscheduled care settings [general practitioner (GP) out‐of‐hours cooperative; accident and emergency department; national ambulance service, members of NHS 24 and national policy makers. Attendance at key meetings, documentary review and email implementation diaries provided a contextual history of events with which interview data could be compared.Results  The contextual history of events highlighted a fast‐paced implementation process, with little time for reflection. Key areas of partner concern were increasing workload, the clinical safety of nurse triage and the lack of communication across the organizations. Concerns were most apparent within the GP out‐of‐hours cooperative, leading to calls for the dissolution of the partnership. Accident and emergency and ambulance service responses were more conciliatory, suggesting that such problems were to be expected within the developmental phase of a new organization. Further exploration of these responses highlighted the sense of ownership within the GP cooperative, with GPs having both financial and philosophical ownership of the cooperative. This was not apparent within the other two partner organizations, in particular the ambulance service, which operated on a regional model very similar to that of NHS 24.Conclusions  As the delivery of unscheduled primary health care crosses professional boundaries and locations, different organizations and professional groups must develop new ways of partnership working, developing trust and confidence in each other. The results of this study highlight, for the first time, the key importance of understanding the professional ownership and identity of individual organizations, in order to facilitate the most effective mechanisms to enable that partnership working.
The usefulness and feasibility of a reflexivity method to improve clinical handover
Authors: Broekhuis Manda , Veldkamp Carla 
Published: November 2006

AbstractObjective  The evaluation of the usefulness and feasibility of the reflexivity method (RM), which encourages dialogue and reflections between doctors, and enables change.Methods  On the basis of literature research into effective medical professional learning and reflection, essential elements that stimulate reflection and learning were distinguished and converted into the basic elements of a method developed for this purpose, the RM. The method is used as a tool to stimulate reflection processes, which, in turn, will enable change. It was used 20 times in a large university medical centre in the Netherlands. Clinical handovers were the subject of reflection. The evaluation of the usefulness and feasibility of the RM is based on analysing the improvements realized by using the method, and a questionnaire to measure the experiences of the users of the method.Results  Each of the 17 departments evaluated received 10 recommendations on average. Fifty‐eight per cent of these were realized after 6–9 months, and 18% were in the working‐out phase. Improvements in the structure, rules and protocols concerning handovers were realized as well as in the atmosphere. The users of the method evaluated the method overall positively: they appreciated the created context for reflection, that is, having a dialogue with a colleague working at the same hierarchical level, the non‐normative character of the method and the ‘doctor‐ownership’ of the method. They also reported an effect on their handling and thinking regarding handovers.Conclusions  The RM seems to be a useful and feasible method to stimulate the doctors’ reflection processes, resulting in implemented improvements.
In situ hybridization and RT‐PCR detection of Macrobrachium rosenbergii nodavirus in giant freshwater prawn, Macrobrachium rosenbergii (de Man), in Taiwan
Authors: Hsieh C‐Y , Wu Z‐B , Tung M‐C , Tu C , Lo S‐P , Chang T‐C , Chang C‐D , Chen S‐C , Hsieh Y‐C , Tsai S‐S 
Published: November 2006

AbstractBetween January and March 2006, suspected outbreaks of white tail disease were observed in post‐larvae and juveniles of Macrobrachium rosenbergii in hatcheries and nursery ponds at Kaohsiung and Pingtung Counties in southern Taiwan. Pathognomonic lesions showed the presence of large oval and/or irregular basophilic, cytoplasmic inclusion bodies in the infected muscles and hepatopancreas. Reverse transcriptase polymerase chain reaction (RT‐PCR) assay and in situ hybridization (ISH) revealed evidence of M. rosenbergii nodavirus (MrNV) infection but did not detect extra small virus. Phylogenetic analysis indicated that there were very high identities between nucleotide sequences among six strains obtained in this study (99.5–100%), moderate identities with Caribbean and Indian strains (98.2–98.6%), but slightly lower identity with a Chinese strain (95.2%). This is the first confirmation of MrNV in giant freshwater prawns, using an RT‐PCR and ISH, in Taiwan.
Characterization of Lancefield group C Streptococcus dysgalactiae isolated from farmed fish
Authors: Nomoto R , Unose N , Shimahara Y , Nakamura A , Hirae T , Maebuchi K , Harada S , Misawa N , Itami T , Kagawa H , Yoshida T 
Published: November 2006

AbstractA Lancefield group C streptococcal (GCS) infection caused by Streptococcus dysgalactiae that is characterized by severe necrotic lesions of the caudal peduncle has been an increasing cause of mortality in farmed fish such as amberjack, Seriola dumerili, and yellowtail, Seriola quinqueradiata, in the southern part of Kyushu, Japan. In this study, enzymatic profiles of GCS strains from fish and mammals were investigated using the API ZYM system, and genotypic characterization of GCS strains was performed using biased sinusoidal field gel electrophoresis (BSFGE). The partial sequence of the 16S‐23S rDNA intergenic spacer region of the GCS strain isolates from fish and mammals was also compared. The API ZYM test indicated that it is difficult to differentiate isolates of S. dysgalactiae from fish and animals based on enzymological variations. In the BSFGE analysis, the macrorestriction profiles, which were obtained using SmaI or ApaI as a restriction enzyme, revealed variations between the fish and animal isolates. The partial sequence of the 16S‐23S rDNA intergenic spacer region of all the tested fish isolates differed from all mammalian isolates in one or two nucleotides. The possibility of a clonal expansion of S. dysgalactiae strains in farmed fish was also suggested by the BSFGE profiles of fish isolates.