bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vertical structure in stratified wakes with high initial Froude number
Authors: SPEDDING G. R. 
Published: November 2006

Initially turbulent bluff body wakes decay in the presence of a stable background density
gradient to form chains of comparatively stable and long-lived vortex structures,
most of the late-time properties of which have been shown to be independent of the
initial generating Froude number (for a sphere of diameter, D, moving at speed, U,
F = 2U/ND, where N is the buoyancy frequency).
Results of experiments with vertical interrogation planes are described, where any anticipated F-dependence might be
most evident, as the competing effects of horizontal inertial forcing and the restoring
buoyancy force can be measured directly by simultaneous measurement of horizontal
and vertical velocity components. Experiments were conducted at sufficiently large
values of Re [ges ] 3 × 103 and F [ges ] 4 that
turbulence can occur over many scales in the near wake, and the scaling properties might then extrapolate
to ocean engineering applications.When F [ges ] 4, the fluid motions in the intermediate, non-equilibrium régime always
occur in coherent patches whose vertical extent is smaller than the total wake height.
The patches of vorticity have longer horizontal than vertical coherence lengths, and
may be termed layers, even though they are far from uniform in the horizontal. The
degree to which the complex vertical structure is later dominated by the mean wake
defect depends strongly on F.The total wake height, LV, depends on the initial
value of F so that LV/D ∼ F0.6.
LV is established early and remains almost unchanged
up to Nt ≈ 30. At later times,
the non-equilibrium wake exchanges potential with kinetic energy and re-adjusts
according to local dynamical constraints, so that, within each layer, the quasi-two-dimensional
flow proceeds without any further dependence on, or memory of, the
initial value of F. The flow is everywhere stable to overturning Kelvin–Helmholtz
instabilities and local length and velocity scales evolve so that the local horizontal
and vertical Froude numbers, FH, FV,
are both of order 0.1.Although Osmidov-length arguments for vertical scale selection appear to be physically
appropriate, they do not correctly predict the measured F-dependence in either
LV, or in the layer height, lV.
Thus the physical mechanism responsible remains
elusive, as the alternative laminar instability mechanisms are not presented with the
appropriate, scale-free initial conditions over the parameter range in which they have
been shown to operate.Ultimately, the measurements support the application of low FH
and FV scaling
theories to the late wake flow. The preceding non-equilibrium stage, when the vertical
structure of the late wake is determined, does not yield so readily to assumptions
involving the smallness of the vertical velocity component.
Do true elevation gravity–capillary solitary
waves exist? A numerical investigation
Authors: CHAMPNEYS A. R. , VANDEN-BROECK J.-M. , LORD G. J. 
Published: November 2006

This paper extends the numerical results of Hunter & Vanden-Broeck (1983) and
Vanden-Broeck (1991) which were concerned with studies of solitary waves on the
surface of fluids of finite depth under the action of gravity and surface tension. The
aim of this paper is to answer the question of whether small-amplitude elevation
solitary waves exist. Several analytical results have proved that bifurcating from
Froude number F = 1, for Bond number τ between 0 and 1/3, there are families
of ‘generalized’ solitary waves with periodic tails whose minimum amplitude is an
exponentially small function of F−1. An open problem (which, for τ sufficiently close
to 1/3, was recently proved by Sun 1999 to be false) is whether this amplitude can
ever be zero, which would give a truly localized solitary wave.The problem is first addressed in terms of model equations taking the form of
generalized fifth-order KdV equations, where it is demonstrated that if such a
zero-tail-amplitude solution occurs, it does so along codimension-one lines in the parameter
plane. Moreover, along solution paths of generalized solitary waves a topological
distinction is found between cases where the tail does vanish and those where it does
not. This motivates a new set of numerical results for the full problem, formulated
using a boundary integral method, namely to probe the size of the tail amplitude as
τ varies for fixed F > 1. The strong conclusion from the numerical results is that true
solitary waves of elevation do not exist for the steady gravity–capillary water wave
problem, at least for 9/50 < τ < 1=3. This finding confirms and explains previous
asymptotic results by Yang & Akylas.
Hippocampal 1H MRS in patients with bipolar disorder taking valproate versus valproate plus quetiapine
Authors: ATMACA MURAD , YILDIRIM HANEFI , OZDEMIR HUSEYIN , OGUR ERKIN , TEZCAN ERTAN 
Published: November 2006

Background. No study to date has examined the effects of mood stabilizer alone and the combination of mood stabilizer and atypical antipsychotic, quetiapine, on hippocampal neurochemical markers of bipolar disordered patients concurrently. We therefore undertook a proton magnetic resonance spectroscopy (1H MRS) study of drug-free patients with bipolar disorder (drug-free group), patients undergoing valproate treatment (valproate group), patients administered valproate+quetiapine (valprote+quetiapine group) and healthy controls, focusing on the in vivo neuroanatomy of the hippocampus.Method. Thirty patients from the Firat University School of Medicine Department of Psychiatry and 10 healthy controls gave written informed consent to participate in the study. The patients and controls underwent proton magnetic resonance spectroscopic imaging (1H MRSI), and measures of N-acetylaspartate (NAA), choline-containing compounds (CHO), and creatine+phosphocreatine (CRE) in hippocampal regions were obtained.Results. The drug-free patients had significantly lower NAA/CRE and NAA/CHO ratios compared with the valproate and valproate+quetiapine groups and the healthy controls. The lower NAA/CRE and NAA/CHO ratios remained statistically significant even after covarying for age or whole brain volume compared with the valproate and valproate+quetiapine groups and healthy controls. In post hoc comparisons, a significant difference was found between the valproate+quetiapine group and the valproate group only with regard to NAA/CHO.Conclusion. Our findings suggest that valproate has a neuroprotective effect. In post hoc comparisons, a significant difference was found between the valproate+quetiapine and the valproate group with regard to NAA/CHO, indicating that the addition of quetiapine further increases the level of NAA and provides an additional neuroprotective effect.
The genetic relationship between neuroticism and autonomic function in female twins
Authors: RIESE HARRIËTTE , ROSMALEN JUDITH G. M. , ORMEL JOHAN , VAN ROON ARIE M. , OLDEHINKEL ALBERTINE J. , RIJSDIJK FRÜHLING V. 
Published: November 2006

Background. Neuroticism is widely used as an explanatory concept in etiological research of psychopathology. In order to clarify what neuroticism actually represents, we investigated the genetic association between neuroticism and cardiovascular measures.Method. In 125 female twin pairs (18–30 years), electrocardiogram and continuous finger blood pressure were assessed during two rest and two mental stress conditions. Mean values for baroreflex sensitivity (BRS), heart rate variability (HRV) and inter-beat interval (IBI) were calculated for each condition. Neuroticism was assessed by multiple questionnaires. Multivariate genetic model-fitting analyses were used to investigate the genetic correlation between latent neuroticism and the cardiovascular autonomic nervous system (ANS) measures.Results. Neuroticism was negatively correlated to BRS and HRV. Neuroticism was not correlated to IBI. For BRS, this phenotypical relation was entirely determined by shared genetic influences. For HRV, the genetic contribution to the phenotypical correlation was not significant, but the proportions of explained covariance showed a trend of more genetic than environmental influences on the phenotypical relationship.Conclusions. High neuroticism is associated with a deregulated ANS. Pleiotropic genetic effects may be partly responsible for this effect.
A new scale to assess the therapeutic relationship in community mental health care: STAR
Authors: McGUIRE-SNIECKUS REBECCA , McCABE ROSEMARIE , CATTY JOCELYN , HANSSON LARS , PRIEBE STEFAN 
Published: November 2006

Background. No instrument has been developed specifically for assessing the clinician–patient therapeutic relationship (TR) in community psychiatry. This study aimed to develop a measure of the TR with clinician and patient versions using psychometric principles for test construction.Method. A four-stage prospective study was undertaken, comprising qualitative semi-structured interviews about TRs with clinicians and patients and their assessment of nine established scales for their applicability to community care, administering an amalgamated scale of more than 100 items, followed by Principal Components Analysis (PCA) of these ratings for preliminary scale construction, test–retest reliability of the scale and administering the scale in a new sample to confirm its factorial structure. The sample consisted of patients with severe mental illness and a designated key worker in the care of 17 community mental health teams in England and Sweden.Results. New items not covered by established scales were identified, including clinician helpfulness in accessing services, patient aggression and family interference. The new patient (STAR-P) and clinician scales (STAR-C) each have 12 items comprising three subscales: positive collaboration and positive clinician input in both versions, non-supportive clinician input in the patient version, and emotional difficulties in the clinician version. Test–retest reliability was r=0·76 for STAR-P and r=0·68 for STAR-C. The factorial structure of the new scale was confirmed with a good fit.Conclusions. STAR is a specifically developed, brief scale to assess TRs in community psychiatry with good psychometric properties and is suitable for use in research and routine care.
Changes in ascertainment of Hib and its influence on the estimation of disease incidence in the United Kingdom
Authors: LADHANI S. , SLACK M. P. , HEATH P. T. , RAMSAY M. E. 
Published: November 2006

SUMMARYEnhanced surveillance for Hib infection, initially covering Wales and five English regions, began in 1990 and in 1995 was extended to the whole of England and Wales. To determine whether changes in the ascertainment ofHaemophilus influenzaemay have affected estimates of Hib disease incidence, data from January 1990 to December 2003 were analysed. A total of 8887 and 4020 (45%) cases ofH. influenzaeand Hib respectively were reported. The proportion of isolates that were serotyped increased over time, and therefore reported incidence may have underestimated the true incidence in the early years of the study. Adjusting for this under-ascertainment, the incidence in children aged <5 years declined from a peak of 28·3/100 000 in 1991 to 0·97/100 000 in 1998 and increased to 3·8/100 000 in 2003. Following the implementation of universal vaccination a dramatic decline in the true incidence of invasive Hib disease occurred. The observation of the subsequent resurgence was real but the highest incidence reached was 85% below the corrected incidence in the pre-vaccine era. Continued high-quality surveillance is needed in order to accurately monitor and detect changes in disease incidence.
Odds ratio based multifactor-dimensionality reduction method for detecting gene–gene interactions
Authors: Chung Yujin , Lee Seung Yeoun , Elston Robert C. , Park Taesung 
Published: November 2006

AbstractMotivation: The identification and characterization of genes that increase the susceptibility to common complex multifactorial diseases is a challenging task in genetic association studies. The multifactor dimensionality reduction (MDR) method has been proposed and implemented by Ritchie et al. (2001) to identify the combinations of multilocus genotypes and discrete environmental factors that are associated with a particular disease. However, the original MDR method classifies the combination of multilocus genotypes into high-risk and low-risk groups in an ad hoc manner based on a simple comparison of the ratios of the number of cases and controls. Hence, the MDR approach is prone to false positive and negative errors when the ratio of the number of cases and controls in a combination of genotypes is similar to that in the entire data, or when both the number of cases and controls is small. Hence, we propose the odds ratio based multifactor dimensionality reduction (OR MDR) method that uses the odds ratio as a new quantitative measure of disease risk.Results: While the original MDR method provides a simple binary measure of risk, the OR MDR method provides not only the odds ratio as a quantitative measure of risk but also the ordering of the multilocus combinations from the highest risk to lowest risk groups. Furthermore, the OR MDR method provides a confidence interval for the odds ratio for each multilocus combination, which is extremely informative in judging its importance as a risk factor. The proposed OR MDR method is illustrated using the dataset obtained from the CDC Chronic Fatigue Syndrome Research Group.Availability: The program written in R is available.Contact: tspark@snu.ac.kr
Modular organization of protein interaction networks
Authors: Luo Feng , Yang Yunfeng , Chen Chin-Fu , Chang Roger , Zhou Jizhong , Scheuermann Richard H. 
Published: November 2006

AbstractMotivation: Accumulating evidence suggests that biological systems are composed of interacting, separable, functional modules. Identifying these modules is essential to understand the organization of biological systems.Result: In this paper, we present a framework to identify modules within biological networks. In this approach, the concept of degree is extended from the single vertex to the sub-graph, and a formal definition of module in a network is used. A new agglomerative algorithm was developed to identify modules from the network by combining the new module definition with the relative edge order generated by the Girvan-Newman (G-N) algorithm. A JAVA program, MoNet, was developed to implement the algorithm. Applying MoNet to the yeast core protein interaction network from the database of interacting proteins (DIP) identified 86 simple modules with sizes larger than three proteins. The modules obtained are significantly enriched in proteins with related biological process Gene Ontology terms. A comparison between the MoNet modules and modules defined by Radicchi et al. (2004) indicates that MoNet modules show stronger co-clustering of related genes and are more robust to ties in betweenness values. Further, the MoNet output retains the adjacent relationships between modules and allows the construction of an interaction web of modules providing insight regarding the relationships between different functional modules. Thus, MoNet provides an objective approach to understand the organization and interactions of biological processes in cellular systems.Availability: MoNet is available upon request from the authors.Contact: luofeng@cs.clemson.eduSupplementary information: Supplementary Data are available at Bioinformatics online.
Biodiversity of an interface zone of a nutrient‐deficient lake (Nabugabo) in Uganda: macrophytes
Authors: Kateyo Eliezer M. 
Published: November 2006

AbstractLake Nabugabo was a big bay of Lake Victoria before being separated from the latter by a sand bar about 4000 years ago. Whereas conductivity of Lake Victoria is 100 μScm−1 that of Nabugabo has been less than 30 μ cm−2 since the Cambridge Scientific Expedition, 1962. Dissolved calcium carbonate is below detectable levels although nitrate and phosphate are not significantly different from those of Lake Victoria. However, the total cations and anions are five times more in Lake Victoria than Nabugabo. Along the eastern, southern and south‐western margins of the lake is an emergent swamp composed of different types of plants. In most places, Miscanthidium violaceum forms a floating platform of matted roots and rhizomes which border the open lake; it is associated with Sphagnum, a type of moss which normally grows in acidic and low‐temperature conditions at very high altitudes and latitudes. Because of the presence of this moss, the Nabugabo swamps are sometimes called ‘Sphagnum swamps’. Vossia cuspidata (hippo grass) is yet another emergent swamp plant in Lake Nabugabo, occurring in a number of isolated narrow mats stretching from a few metres to 0.5 km or longer along the edge of the emergent swamp. These floating mats are firmly anchored to the Micanthidium platform. Cyperus latifolia is another emergent‐floating plant in Lake Nabugabo firmly anchored on to the Miscanthidium platform. Cyperus latifolia and V. cuspidata tend to grow side by side but in completely sheltered bays the former plant grows alone. Cyperus papyrus L. occurs in very few patches within the emergent swamp. In the interface zone along the emergent swamp, there are a number of euhydrophyte plant species: Nymphaea caerulea is the most dominant and widespread euhydrophyte species except in the eastern tip of the lake where it is replaced by Nymphaea lotus; interspersed among these lilies is Ceratophyllum demersum in certain bays which could either be water inlets or out‐flows; Utricularia andNymphoides indica are associated with monospecific stand of N. caerulea in the south‐western end of the zone.
Combined clinical, thyroid ultrasound and cytological features help to predict thyroid malignancy in follicular and Hϋrthle cell thyroid lesions: results from a series of 505 consecutive patients
Authors: Rago T. , Di Coscio G. , Basolo F. , Scutari M. , Elisei R. , Berti P. , Miccoli P. , Romani R. , Faviana P. , Pinchera A. , Vitti P. 
Published: November 2006

SummaryObjective  The cytological patterns of follicular and Hϋrthle cell nodules are included among the indeterminate results of fine‐needle aspiration cytology, because distinction between benign and malignant lesion can only be made on histological criteria. The diagnostic value of atypia at cytology, clinical parameters and echographic patterns were examined to establish the risk of malignancy in 505 patients with follicular and Hϋrthle cell thyroid nodules at cytology.Design and patients  The study included 505 consecutive patients who had undergone thyroidectomy from the period 2002–2005.Results  Histological diagnosis of malignancy was carried out in 125 of 505 (25%) patients, the follicular variant of papillary carcinoma being the most frequent histotype. Only atypia at cytology (P < 0·0001) and spot microcalcifications at ultrasound (P = 0·009) were predictive of malignancy. Male gender, normal thyroid volume, single nodularity, nodule hypoechogenicity, size and blurred margins were associated with malignancy, although not significantly. An arbitrary clinical score allowed the identification of patients with high (41%, 110 patients) and low (16%, 242 patients) risk of malignancy. Combining the clinical score with the presence of atypia at cytology we could identify 30 patients (6%) in whom the risk of malignancy was as high as 63%.Conclusions  Twenty‐five per cent of patients with a cytological result of follicular and Hϋrthle cell thyroid lesion had a final diagnosis of malignancy. Only atypia at cytology and spot microcalcifications at thyroid ultrasound were significantly associated with malignancy. Other clinical parameters and thyroid ultrasound patterns can be used to set up a clinical score useful for predicting the individual risk of malignancy before surgery.
Serum thyroglobulin concentrations predict disease‐free remission and death in differentiated thyroid carcinoma
Authors: Heemstra Karen A. , Liu Ying Y. , Stokkel Marcel , Kievit Job , Corssmit Eleonora , Pereira Alberto M. , Romijn Johannes A. , Smit Johannes W. A. 
Published: November 2006

SummaryObjective  Most studies on the diagnostic value of serum thyroglobulin (Tg) concentrations in differentiated thyroid carcinoma (DTC) use fixed cut‐off levels in heterogeneous groups of patients with respect to initial therapy and do not provide prognostic data. The objective was to investigate the prognostic values of serum Tg for disease‐free remission and death, measured at fixed time‐points after initial therapy using receiver operator characteristic (ROC) curve analyses.Design  Single‐centre observational study with 366 consecutive patients with DTC, who had all been treated according to the same protocol for initial therapy and follow‐up.Methods  Tg concentrations were measured at five fixed time‐points after initial surgery. Tg cut‐off values with the highest accuracy were calculated with ROC analyses.Results  During the 8·3 ± 4·6 years of follow‐up, 84% of the patients were cured. Pre‐ablative Tg levels were an independent prognostic indicator for disease‐free remission (Tg cut‐off value 27·5 µg/l, positive predictive value 98%). The highest diagnostic accuracies of serum Tg for tumour presence were found during TSH‐stimulated Tg measurements, 6 months after initial therapy (Tg cut‐off value 10 µg/l; sensitivity 100%, specificity 93%). DTC‐related mortality was 14%. TSH‐stimulated Tg levels before ablation and 6 months after initial therapy were independent prognostic indicators for death.Conclusion  Optimal institutional Tg cut‐off levels for diagnosis and prognosis should be defined using ROC analyses for each condition and time‐point. Tg measurements 6 months after initial therapy during TSH stimulation had an excellent diagnostic value. Tg levels are independent prognostic indicators for disease‐free remission and death. Using this strategy, high‐risk patient groups can be selected based on Tg levels, in addition to conventionally used prognostic indicators.
Anuran abundance and persistence in agricultural landscapes during a climatic extreme
Authors: PIHA HENNA , LUOTO MISKA , PIHA MARKUS , MERILÄ JUHA 
Published: November 2006

AbstractClimate change in concert with habitat loss and degradation are major threats to global biodiversity. As part of climate change, the occurrence of extreme climatic events is expected to increase. Agricultural intensification has led to the increased homogeneity of agricultural habitats and declines in farmland species diversity. We investigated the abundance of common frogRana temporariapopulations in boreal farmlands in relation to multiple scales of landscape structure during years 2002–2003, and the effect of habitat structure onR. temporariapopulation persistence during a severe drought. On average, 113 and 24 egg clutches were observed per site in years 2002 and 2003, respectively. This dramatic decline was synchronized over the entire study area (ca. 320 km2), with some local variations. Population persistence was higher in sites where ground water levels decreased less but it was also positively correlated with the heterogeneity of the adjacent landscape. Under normal weather conditions, local habitat characteristics had a dominating role onR. temporariapopulation abundance, as it was positively correlated with the amount of ditches and ponds within the study sites. After the drought, however, population abundance was related to landscape and regional level factors. The results indicate that landscape homogenization can have negative effects on population persistence during climate change. They also show that the scale at which landscape characteristics affect populations can be strongly dependent of processes functioning at large scales, such as weather. In summary, heterogeneous landscapes may lower the risk of regional amphibian population declines under extreme weather perturbations and serve as sources of recovery in postdisturbance recovery phases. Thus, maintaining such areas should be promoted in long‐term biodiversity conservation.